Note: Descriptions are shown in the official language in which they were submitted.
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
TITLE
PLANTS WITH ALTERED ROOT ARCHITECTURE,
RELATED CONSTRUCTS AND METHODS INVOLVING GENES ENCODING
REP2 POLYPEPTIDES AND HOMOLOGS THEREOF
CROSS REFERENCE TO RELATED APPLICATIONS
This application claims the benefit of U.S. Provisional Application No.
61/083,288 filed July 24, 2008, the entire contents of which is herein
incorporated by
reference.
FIELD OF THE INVENTION
The field of invention relates to plant breeding and genetics and, in
particular,
relates to recombinant DNA constructs useful in plants for altering root
architecture.
BACKGROUND OF THE INVENTION
Water and nutrient availability limit plant growth in all but a very few
natural
ecosystems. They limit yield in most agricultural ecosystems. Plant roots
serve
important functions such as water and nutrient uptake, anchorage of the plants
in
the soil and the establishment of biotic interactions at the rhizosphere.
Elucidation
of the genetic regulation of plant root development and function is therefore
the
subject of considerable interest in agriculture and ecology.
The root system originates from a primary root that develops during
embryogenesis. The primary root produces secondary roots, which in turn
produce
tertiary roots. All secondary, tertiary, quaternary and further roots are
referred to as
lateral roots. Many plants, including maize, can also produce shoot borne
roots,
from consecutive under-ground nodes (crown roots) or above-ground nodes (brace
roots). Three major processes affect the overall architecture of the root
system.
First, cell division at the primary root meristem enables indeterminate growth
by
adding new cells to the root. Second, lateral root formation increases the
exploratory capacity of the root system. Third, root-hair formation increases
the
total surface of primary and lateral roots (Lopez-Bucio et al., Current
Opinion in
Plant Biology (2003) 6:280-287). In maize mutants have been isolated that are
missing only a subset of root types. In Arabidopsis, mutations in root
patterning
genes such as SHORTROOT and SCARECROW, which show developmental
defects in primary and lateral roots, have been identified (J.E. Malamy,
Plant, Cell
1
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
and Environment (2005) 28: 67-77).
A number of maize mutants affected specifically in root development have
been identified (Hochholdinger et al 2004, Annals of Botany 93:359-368). The
recessive mutants rtcs and rt1 forms no, or fewer, crown and brace roots,
while the
primary and lateral roots are not affected. In the recessive mutants des21,
lateral
seminal roots and root hairs are absent. Root hairs are lacking in the
recessive
mutant rthl-3. The mutants lrt1 and rum1 are affected before lateral root
initiation
and mutants slr1 and slr2 are impaired in lateral root elongation. Intrinsic
response
pathways that determine root system architecture include hormones, cell cycle
regulators and regulatory genes. Water stress and nutrient availability belong
to
the environmental response pathways that determine root system architecture.
U.S. Application No. 2005-57473 filed February 14, 2005 (U.S.Patent
Publication No. 2005/223429 Al published October 6, 2005) concerns the use of
Arabidopsis cytokinin oxidase genes to alter cytokinin levels in plants and
stimulate
root growth.
U.S. Patent No. 6,344,601 (issued February 5, 2002) concerns the under- or
overexpression of profilin in a plant cell to alter plant growth habit, e.g. a
reduced
root and root hair system, delay in the onset of flowering.
W02004/US16432 (filed May 21, 2004 (W02004/106531 published
December 9, 2004) concerns the use of methods to manipulate the growth rate
and/or yield and/or architecture by over expression of cis-prenyltransferase.
U.S. Application No. 2004/489500 filed September 30, 2004 (U.S.Patent
Publication No. 2005/059154 Al published March 13, 2005) concerns methods to
modify cell number, architecture and yield using over expression of the
transcription
factor E2F in plants.
Activation tagging can be utilized to identify genes with the ability to
affect a
trait. This approach has been used in the model plant species Arabidopsis
thaliana
(Weigel et al., 2000, Plant Physiol. 122:1003-1013).
Insertions of transcriptional enhancer elements can dominantly activate
and/or elevate the expression of nearby endogenous genes.
SUMMARY OF THE INVENTION
The present invention includes:
In one embodiment, a plant comprising in its genome a recombinant DNA
2
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
construct comprising a polynucleotide operably linked to at least one
regulatory
element, wherein said polynucleotide encodes a polypeptide having an amino
acid
sequence of at least 50% sequence identity, based on the Clustal V method of
alignment, when compared to SEQ ID NO: 15, 17, 19, 21, 23, 25, 27, 29, 31, 33,
35,
37, 39, 41, or 42 and wherein said plant exhibits altered root architecture
when
compared to a control plant not comprising said recombinant DNA construct.
In another embodiment, a plant comprising in its genome a recombinant DNA
construct comprising a polynucleotide operably linked to at least one
regulatory
element, wherein said polynucleotide encodes a polypeptide having an amino
acid
sequence of at least 50% sequence identity, based on the Clustal V method of
alignment, when compared to SEQ ID NO: 15, 17, 19, 21, 23, 25, 27, 29, 31, 33,
35,
37, 39, 41, or 42 and wherein said plant exhibits an alteration of at least
one
agronomic characteristic when compared to a control plant not comprising said
recombinant DNA construct. Optionally, the plant exhibits said alteration of
at least
one agronomic characteristic when compared, under varying environmental
conditions, wherein said varying environmental conditions is at least one
selected
from drought, nitrogen, or disease, to said control plant not comprising said
recombinant DNA construct.
In another embodiment, the present invention includes any of the plants of
the present invention wherein the plant is a maize plant or a soybean plant.
In another embodiment, a method of altering root architecture in a plant,
comprising: (a) introducing into a regenerable plant cell a recombinant DNA
construct comprising a polynucleotide operably linked to at least one
regulatory
sequence, wherein the polynucleotide encodes a polypeptide having an amino
acid
sequence of at least 50% sequence identity, based on the Clustal V method of
alignment, when compared to SEQ ID NO: 15, 17, 19, 21, 23, 25, 27, 29, 31, 33,
35,
37, 39, 41, or 42; (b) regenerating a transgenic plant from the regenerable
plant cell
after step (a), wherein the transgenic plant comprises in its genome the
recombinant
DNA construct; and, (c) obtaining a progeny plant derived from the transgenic
plant
of step (b), wherein said progeny plant comprises in its genome the
recombinant
DNA construct and exhibits altered root architecture when compared to a
control
plant not comprising the recombinant DNA construct.
In another embodiment, a method of evaluating root architecture in a plant,
3
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
comprising: (a) introducing into a regenerable plant cell a recombinant DNA
construct comprising a polynucleotide operably linked to at least one
regulatory
sequence, wherein the polynucleotide encodes a polypeptide having an amino
acid
sequence of at least 50% sequence identity, based on the Clustal V method of
alignment, when compared to SEQ ID NO: 15, 17, 19, 21, 23, 25, 27, 29, 31, 33,
35,
37, 39, 41, or 42;(b) regenerating a transgenic plant from the regenerable
plant cell
after step (a), wherein the transgenic plant comprises in its genome the
recombinant
DNA construct; (c) obtaining a progeny plant derived from the transgenic
plant,
wherein the progeny plant comprises in its genome the recombinant DNA
construct ;
and (d) evaluating root architecture of the progeny plant compared to a
control plant
not comprising the recombinant DNA construct.
In another embodiment, a method of determining an alteration of at least one
agronomic characteristic in a plant, comprising: (a) introducing into a
regenerable
plant cell a recombinant DNA construct comprising a polynucleotide operably
linked
to at least one regulatory sequence, wherein the polynucleotide encodes a
polypeptide having an amino acid sequence of at least 50% sequence identity,
based on the Clustal V method of alignment, when compared to SEQ ID NO: 15,
17,
19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, or 42 (b) regenerating a
transgenic
plant from the regenerable plant cell after step (a), wherein the transgenic
plant
comprises in its genome the recombinant DNA construct; (c) obtaining a progeny
plant derived from the transgenic plant, wherein the progeny plant comprises
in its
genome the recombinant DNA construct; and (d) determining whether the progeny
plant exhibits an alteration of at least one agronomic characteristic when
compared
to a control plant not comprising the recombinant DNA construct. Optionally,
said
determining step (d) comprises determining whether the transgenic plant
exhibits
said alteration of at least one agronomic characteristic when compared, under
varying environmental conditions, wherein said varying environmental
conditions is
at least one selected from drought, nitrogen, or disease, to said control
plant not
comprising said recombinant DNA construct.
In another embodiment, the present invention includes an isolated
polynucleotide comprising: (a) a nucleic acid sequence encoding a REP2 or REP2-
like polypeptide having an amino acid sequence of at least 80% sequence
identity,
when compared to SEQ ID NO:41, or of at least 85% sequence identity, when
4
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
compared to SEQ ID NO:37 or 39, or of at least 95% sequence identity, when
compared to SEQ ID NO:1 7 or 33 based on the Clustal V method of alignment, or
a
full complement of said nucleic acid sequence, wherein the full complement and
the
nucleotide sequence consist of the same number of nucleotides and are 100%
complementary. The polypeptides may comprise the amino acid sequence of SEQ
ID NO: 17, 33, 37, 39, or 41. The nucleotide sequence may comprise the
nucleotide
sequence of SEQ ID NO: 16, 32, 36, 38, or 40.
In another embodiment, the present invention concerns a recombinant DNA
construct comprising any of the isolated polynucleotides of the present
invention
operably linked to at least one regulatory sequence, a cell, a plant, and a
seed
comprising the recombinant DNA construct.
BRIEF DESCRIPTION OF THE FIGURES AND SEQUENCE LISTINGS
The invention can be more fully understood from the following detailed
description and the accompanying drawings and Sequence Listing which form a
part
of this application.
Figure 1A-1 B show the multiple alignment of the full length amino
acid sequences of the REP2 homologs of SEQ ID Nos: 15, 17, 29, 21, 23, 25, 27,
29, 31, 33, 35, 37, 39, 41 and SEQ ID NOs: 42, 43, 44, 45, 46, and 47.
Residues
that match the Consensus sequence exactly are shaded. The consensus sequence
is shown above each alignment. The consensus residues are determined by a
straight majority.
Figure 2 shows a chart of the percent sequence identity and the divergence
values for each pair of amino acid sequences of the REP2 homologs displayed in
Figures 1A-1 B.
Figure 3 is the growth medium used for semi-hydroponics maize growth in
Example 18.
Figure 4 is a chart setting forth data relating to the effect of different
nitrate
concentrations on the growth and development of Gaspe Bay Flint derived maize
lines in Example 18.
The sequence descriptions and Sequence Listing attached hereto comply
with the rules governing nucleotide and/or amino acid sequence disclosures in
patent applications as set forth in 37 C.F.R. 1.821-1.825.
The Sequence Listing contains the one letter code for nucleotide sequence
5
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
characters and the three letter codes for amino acids as defined in conformity
with
the IUPAC-IUBMB standards described in Nucleic Acids Res. 13:3021-3030 (1985)
and in the Biochemical J. 219 (No. 2):345-373 (1984) which are herein
incorporated
by reference. The symbols and format used for nucleotide and amino acid
sequence data comply with the rules set forth in 37 C.F.R. 1.822.
SEQ ID NO:1 pHSbarENDs2
SEQ ID NO:2 pDONRTM/Zeo
SEQ ID NO:3 pDONRTM221
SEQ ID NO:4 pBC-yellow
SEQ ID NO:5 PHP27840
SEQ ID NO:6 PHP23236
SEQ ID NO:7 PHP10523
SEQ ID NO:8 PHP23235
SEQ ID NO:9 PHP20234
SEQ ID NO:10 PHP28529
SEQ ID NO:11 PHP28408
SEQ ID NO:12 PHP22020
SEQ ID NO:13 PHP29635
Table 1 lists the polypeptides that are described herein, the designation of
the cDNA clones that comprise the nucleic acid fragments encoding polypeptides
representing all or a substantial portion of these polypeptides, and the
corresponding identifier (SEQ ID NO: ) as used in the attached Sequence
listing.
TABLE 1
Root enhancing proteins (REP)
Protein Clone Designation SEQ ID NO: SEQ ID NO:
(Nucleotide) (Amino Acid)
REP2-like cmstl s.pk003.p21 a:fis 14 15
REP2-like my.ctal n.pk0015.b12 16 17
REP2-like cfp2n.pk064.114:fis 18 19
REP2-like cppl c.pk003.123:fis 20 21
REP2-like Idsl c.pk015.17 22 23
6
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
REP2-like dmsl c.pk001.e16:fis 24 25
REP2-like ebb2c.pk008.k7:fis 26 27
REP2-like sgc6c.pk001.f21:fis 28 29
REP2-like ebsl c.pk003.n2l :fis 30 31
REP2-like ecil c.pk007.i2:fis 32 33
REP2-like ecrl c.pkO1 2.d1 3:fis 34 35
REP2-like vpllc.pk007.b20:fis 36 37
REP2-like hsol c.pkO10.g9:fis 38 39
REP2-like srl.pk0078.a4:fis 40 41
SEQ ID NO:42 corresponds to NCBI GI No: 15241137 (At5g19590)
SEQ ID NO:43 corresponds to NCBI GI No: 115463429
SEQ ID NO:44 corresponds to NCBI GI No: 125552383
SEQ ID NO:45 corresponds to NCBI GI No: 115438148
SEQ ID NO:46 corresponds to NCBI GI No: 125533926
SEQ ID NO:47 corresponds to NCBI GI No: 118487434
SEQ ID NO:48 is the nucleotide sequence of the Arabidopsis thaliana
"unknown protein" (REP2) (At5gl9590) (coding for the amino acid sequence
represented in SEQ ID NO:42, NCBI General Identifier No. 15241137).
SEQ ID NO:49 is the nucleotide sequence of the cDNA encoding the
Arabidopsis thaliana "unknown protein" (REP2) amino acid sequence represented
in
SEQ ID NO:42, NCBI General Identifier No. 15241137).
SEQ ID NO:50 is the forward primer used to introduce the attB1 sequence in
Example 4.
SEQ ID NO:51 is the reverse primer used to introduce the attB2 sequence in
Example 4.
SEQ ID NO:52 is the attB1 sequence.
SEQ ID NO:53 is the attB2 sequence.
SEQ ID NO:54 is the forward primer VC062 in Example 5.
SEQ ID NO:55 is the reverse primer VC063 in Example 5.
SEQ ID NO:56 PIIOXS2a-FRT87(ni)m.
SEQ ID NO:57 is the maize NAS2 promoter.
SEQ ID NO:58 is the GOS2 promoter.
7
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
SEQ ID NO:59 is the ubiquitin promoter.
SEQ ID NO:60 is the S2A promoter.
SEQ ID NO:61 is the PINII terminator.
DETAILED DESCRIPTION OF PREFERRED EMBODIMENTS
The disclosure of each reference set forth herein is hereby incorporated by
reference in its entirety.
As used herein and in the appended claims, the singular forms "a", "an", and
"the" include plural reference unless the context clearly dictates otherwise.
Thus,
for example, reference to "a plant" includes a plurality of such plants,
reference to "a
cell" includes one or more cells and equivalents thereof known to those
skilled in the
art, and so forth.
An "Expressed Sequence Tag" ("EST") is a DNA sequence derived from a cDNA
library and therefore is a sequence which has been transcribed. An EST is
typically
obtained by a single sequencing pass of a cDNA insert. The sequence of an
entire
cDNA insert is termed the "Full-Insert Sequence" ("FIS"). A "Contig" sequence
is a
sequence assembled from two or more sequences that can be selected from, but
not limited to, the group consisting of an EST, FIS and PCR sequence. A
sequence
encoding an entire or functional protein is termed a "Complete Gene Sequence"
("CGS") and can be derived from a FIS or a contig.
The term "root architecture" refers to the arrangement of the different parts
that comprise the root. The terms "root architecture", "root structure", "root
system"
or "root system architecture" are used interchangeably herewithin.
In general, the first root of a plant that develops from the embryo is called
the
primary root. In most dicots, the primary root is called the taproot. This
main root
grows downward and gives rise to branch (lateral) roots. In monocots the
primary
root of the plant branches, giving rise to a fibrous root system.
The term "altered root architecture" refers to aspects of alterations of the
different parts that make up the root system at different stages of its
development
compared to a reference or control plant. It is understood that altered root
architecture encompasses alterations in one or more measurable parameters,
including but not limited to, the diameter, length, number, angle or surface
of one or
more of the root system parts, including but not limited to, the primary root,
lateral or
branch root, adventitious root, and root hairs, all of which fall within the
scope of this
8
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
invention. These changes can lead to an overall alteration in the area or
volume
occupied by the root. The reference or control plant does not comprise in its
genome the recombinant DNA construct or heterologous construct.
"Agronomic characteristics" is a measurable parameter including but not
limited to greenness, yield, growth rate, biomass, fresh weight at maturation,
dry
weight at maturation, fruit yield, seed yield, total plant nitrogen content,
fruit nitrogen
content, seed nitrogen content, nitrogen content in a vegetative tissue, total
plant
free amino acid content, fruit free amino acid content, seed free amino acid
content,
free amino acid content in a vegetative tissue, total plant protein content,
fruit
protein content, seed protein content, protein content in a vegetative tissue,
drought
tolerance, nitrogen uptake, root lodging, root mass, stalk lodging, plant
height, ear
length, and harvest index.
The term "V" stage refers to the leaf stages of a corn plant; e.g. V4 = four,
V5=five leaves with visible leaf collars. The leaf collar is the light-colored
collar-like
"band" located at the base of an exposed leaf blade, near the spot where the
leaf
blade comes in contact with the stem of the plant. The leaves are counted
beginning with the lowermost, short, rounded-tip true leaf and ending with the
uppermost leaf with a visible leaf collar
"rep2", recpu3 and "recpu2" are used interchangeably herewithin and refer to
the Arabidopsis thaliana locus, At5g19590 (SEQ ID NO:48). "REP2", RECPU3 and
"RECPU2" are used interchangeably herewithin and refer to the protein (SEQ ID
NO:42) encoded by At5g19590 (SEQ ID NO:48).
"rep2-like" refers to nucleotide homologs from different species, such as corn
and soybean, of the Arabidopsis thaliana "rep2" locus, At5g19590 (SEQ ID
NO:48)
and includes without limitation any of the nucleotide sequences of SEQ ID
NOs:14,
16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, or 40.
"REP2-like" refers to protein homologs from different species, such as corn
and soybean, of the Arabidopsis thaliana "REP2" (SEQ ID NO:42) and includes
without limitation any of the amino acid sequences of SEQ ID NOs:15, 17, 19,
21,
23, 25, 27, 29, 31, 33, 35, 37, 39, or 41.
"Environmental conditions" refer to conditions under which the plant is grown,
such as the availability of water, availability of nutrients (for example
nitrogen), or
the presence of disease.
9
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
"Transgenic" refers to any cell, cell line, callus, tissue, plant part or
plant, the
genome of which has been altered by the presence of a heterologous nucleic
acid,
such as a recombinant DNA construct, including those initial transgenic events
as
well as those created by sexual crosses or asexual propagation from the
initial
transgenic event. The term "transgenic" as used herein does not encompass the
alteration of the genome (chromosomal or extra-chromosomal) by conventional
plant breeding methods or by naturally occurring events such as random cross-
fertilization, non-recombinant viral infection, non-recombinant bacterial
transformation, non-recombinant transposition, or spontaneous mutation.
"Genome" as it applies to plant cells encompasses not only chromosomal
DNA found within the nucleus, but organelle DNA found within subcellular
components (e.g., mitochondrial, plastid) of the cell.
"Plant" includes reference to whole plants, plant organs, plant tissues, seeds
and plant cells and progeny of same. Plant cells include, without limitation,
cells
from seeds, suspension cultures, embryos, meristematic regions, callus tissue,
leaves, roots, shoots, gametophytes, sporophytes, pollen, and microspores.
"Progeny" comprises any subsequent generation of a plant.
"Transgenic" refers to any cell, cell line, callus, tissue, plant part or
plant, the
genome of which has been altered by the presence of a heterologous nucleic
acid,
such as a recombinant DNA construct, including those initial transgenic events
as
well as those created by sexual crosses or asexual propagation from the
initial
transgenic event. The term "transgenic" as used herein does not encompass the
alteration of the genome (chromosomal or extra-chromosomal) by conventional
plant breeding methods or by naturally occurring events such as random cross-
fertilization, non-recombinant viral infection, non-recombinant bacterial
transformation, non-recombinant transposition, or spontaneous mutation.
"Transgenic plant" includes reference to a plant which comprises within its
genome a heterologous polynucleotide. Preferably, the heterologous
polynucleotide
is stably integrated within the genome such that the polynucleotide is passed
on to
successive generations. The heterologous polynucleotide may be integrated into
the genome alone or as part of a recombinant DNA construct.
"Heterologous" with respect to sequence means a sequence that originates
from a foreign species, or, if from the same species, is substantially
modified from
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
its native form in composition and/or genomic locus by deliberate human
intervention.
"Polynucleotide", "nucleic acid sequence", "nucleotide sequence", or "nucleic
acid fragment" are used interchangeably and is a polymer of RNA or DNA that is
single- or double-stranded, optionally containing synthetic, non-natural or
altered
nucleotide bases. Nucleotides (usually found in their 5'-monophosphate form)
are
referred to by their single letter designation as follows: "A" for adenylate
or
deoxyadenylate (for RNA or DNA, respectively), "C" for cytidylate or
deoxycytidylate,
"G" for guanylate or deoxyguanylate, "U" for uridylate, "T" for
deoxythymidylate, "R"
for purines (A or G), "Y" for pyrimidines (C or T), "K" for G or T, "H" for A
or C or T,
"I" for inosine, and "N" for any nucleotide.
"Polypeptide", "peptide", "amino acid sequence" and "protein" are used
interchangeably herein to refer to a polymer of amino acid residues. The terms
apply to amino acid polymers in which one or more amino acid residue is an
artificial
chemical analogue of a corresponding naturally occurring amino acid, as well
as to
naturally occurring amino acid polymers. The terms "polypeptide", "peptide",
"amino
acid sequence", and "protein" are also inclusive of modifications including,
but not
limited to, glycosylation, lipid attachment, sulfation, gamma-carboxylation of
glutamic acid residues, hydroxylation and ADP-ribosylation.
"Messenger RNA (mRNA)" refers to the RNA that is without introns and that
can be translated into protein by the cell.
"cDNA" refers to a DNA that is complementary to and synthesized from a
mRNA template using the enzyme reverse transcriptase. The cDNA can be single-
stranded or converted into the double-stranded form using the Klenow fragment
of
DNA polymerase I.
"Mature" protein refers to a post-translationally processed polypeptide; i.e.,
one from which any pre- or pro-peptides present in the primary translation
product
have been removed.
"Precursor" protein refers to the primary product of translation of mRNA;
i.e.,
with pre- and pro-peptides still present. Pre- and pro-peptides may be and are
not
limited to intracellular localization signals.
"Isolated" refers to materials, such as nucleic acid molecules and/or
proteins,
which are substantially free or otherwise removed from components that
normally
11
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
accompany or interact with the materials in a naturally occurring environment.
Isolated polynucleotides may be purified from a host cell in which they
naturally
occur. Conventional nucleic acid purification methods known to skilled
artisans may
be used to obtain isolated polynucleotides. The term also embraces recombinant
polynucleotides and chemically synthesized polynucleotides.
"Recombinant" refers to an artificial combination of two otherwise separated
segments of sequence, e.g., by chemical synthesis or by the manipulation of
isolated segments of nucleic acids by genetic engineering techniques.
"Recombinant" also includes reference to a cell or vector, that has been
modified by
the introduction of a heterologous nucleic acid or a cell derived from a cell
so
modified, but does not encompass the alteration of the cell or vector by
naturally
occurring events (e.g., spontaneous mutation, natural
transformation/transduction/transposition) such as those occurring without
deliberate human intervention.
"Recombinant DNA construct" refers to a combination of nucleic acid
fragments that are not normally found together in nature. Accordingly, a
recombinant DNA construct may comprise regulatory sequences and coding
sequences that are derived from different sources, or regulatory sequences and
coding sequences derived from the same source, but arranged in a manner
different
than that normally found in nature.
The terms "entry clone" and "entry vector" are used interchangeably herein.
"Regulatory sequences" refer to nucleotide sequences located upstream (5'
non-coding sequences), within, or downstream (3' non-coding sequences) of a
coding sequence, and which influence the transcription, RNA processing or
stability,
or translation of the associated coding sequence. Regulatory sequences may
include, but are not limited to, promoters, translation leader sequences,
introns, and
polyadenylation recognition sequences. The terms "regulatory sequence" and
"regulatory element" are used interchangeably herein.
"Promoter" refers to a nucleic acid fragment capable of controlling
transcription of another nucleic acid fragment.
"Promoter functional in a plant" is a promoter capable of controlling
transcription in plant cells whether or not its origin is from a plant cell.
"Tissue-specific promoter" and "tissue-preferred promoter" are used
12
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
interchangeably, and refer to a promoter that is expressed predominantly but
not
necessarily exclusively in one tissue or organ, but that may also be expressed
in
one specific cell.
"Developmentally regulated promoter" refers to a promoter whose activity is
determined by developmental events.
"Operably linked" refers to the association of nucleic acid fragments in a
single fragment so that the function of one is regulated by the other. For
example, a
promoter is operably linked with a nucleic acid fragment when it is capable of
regulating the transcription of that nucleic acid fragment.
"Expression" refers to the production of a functional product. For example,
expression of a nucleic acid fragment may refer to transcription of the
nucleic acid
fragment (e.g., transcription resulting in mRNA or functional RNA) and/or
translation
of mRNA into a precursor or mature protein.
"Phenotype" means the detectable characteristics of a cell or organism.
"Introduced" in the context of inserting a nucleic acid fragment (e.g., a
recombinant DNA construct) into a cell, means "transfection" or
"transformation" or
"transduction" and includes reference to the incorporation of a nucleic acid
fragment
into a eukaryotic or prokaryotic cell where the nucleic acid fragment may be
incorporated into the genome of the cell (e.g., chromosome, plasmid, plastid
or
mitochondrial DNA), converted into an autonomous replicon, or transiently
expressed (e.g., transfected mRNA).
A "transformed cell" is any cell into which a nucleic acid fragment (e.g., a
recombinant DNA construct) has been introduced.
"Transformation" as used herein refers to both stable transformation and
transient transformation.
"Stable transformation" refers to the introduction of a nucleic acid fragment
into a genome of a host organism resulting in genetically stable inheritance.
Once
stably transformed, the nucleic acid fragment is stably integrated in the
genome of
the host organism and any subsequent generation.
"Transient transformation" refers to the introduction of a nucleic acid
fragment
into the nucleus, or DNA-containing organelle, of a host organism resulting in
gene
expression without genetically stable inheritance.
"Allele" is one of several alternative forms of a gene occupying a given locus
13
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
on a chromosome. When the alleles present at a given locus on a pair of
homologous chromosomes in a diploid plant are the same that plant is
homozygous
at that locus. If the alleles present at a given locus on a pair of homologous
chromosomes in a diploid plant differ that plant is heterozygous at that
locus. If a
transgene is present on one of a pair of homologous chromosomes in a diploid
plant
that plant is hemizygous at that locus.
Sequence alignments and percent identity calculations may be determined
using a variety of comparison methods designed to detect homologous sequences
including, but not limited to, the Megalign program of the LASERGENE
bioinformatics computing suite (DNASTAR Inc., Madison, WI). Unless stated
otherwise, multiple alignment of the sequences provided herein were performed
using the Clustal V method of alignment (Higgins and Sharp (1989) CABIOS.
5:151-153) with the default parameters (GAP PENALTY=10, GAP LENGTH
PENALTY=10). Default parameters for pairwise alignments and calculation of
percent identity of protein sequences using the Clustal V method are KTUPLE=1,
GAP PENALTY=3, WINDOW=5 and DIAGONALS SAVED=5. For nucleic acids
these parameters are KTUPLE=2, GAP PENALTY=5, WINDOW=4 and
DIAGONALS SAVED=4. After alignment of the sequences, using the Clustal V
program, it is possible to obtain "percent identity" and "divergence" values
by
viewing the "sequence distances" table on the same program; unless stated
otherwise, percent identities and divergences provided and claimed herein were
calculated in this manner.
Standard recombinant DNA and molecular cloning techniques used herein
are well known in the art and are described more fully in Sambrook, J.,
Fritsch, E.F.
and Maniatis, T. Molecular Cloning: A Laboratory Manual; Cold Spring Harbor
Laboratory Press: Cold Spring Harbor, 1989 (hereinafter "Sambrook").
Turning now to preferred embodiments:
Preferred embodiments include isolated polynucleotides and polypeptides,
recombinant DNA constructs, compositions (such as plants or seeds) comprising
these recombinant DNA constructs, and methods utilizing these recombinant DNA
constructs.
Preferred Isolated Polynucleotides and Polypeptides
The present invention includes the following preferred isolated
14
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
polynucleotides and polypeptides:
An isolated polynucleotide comprising: (i) a nucleic acid sequence encoding a
polypeptide having an amino acid sequence of at least 50%, 51 %, 52%, 53%,
54%,
55%, 56%, 57%, 58%, 59%, 60%, 56%, 62%, 63%, 64%, 65%, 66%, 67%, 68%,
69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%,
83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,
97%, 98%, 99%, or 100% sequence identity, based on the Clustal V method of
alignment, when compared to SEQ ID NO: 15, 17, 19, 21, 23, 25, 27, 29, 31, 33,
35,
37, 39, 41, or 42; or (ii) a full complement of the nucleic acid sequence of
(i). Any of
the foregoing isolated polynucleotides may be utilized in any recombinant DNA
constructs (including suppression DNA constructs) of the present invention.
The
polypeptide is preferably a REP2 or REP2-like protein.
An isolated polypeptide having an amino acid sequence of at least 50%,
51%,52%,53%,54%,55%,56%,57%,58%,59%,60%,56%,62%,63%,64%,
65%,66%,67%,68%,69%,70%,71%,72%,73%,74%,75%,76%,77%,78%,
79%,80%,81%,82%,83%,84%,85%,86%,87%,88%,89%,90%,91%,92%,
93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity, based on the
Clustal V method of alignment, when compared to SEQ ID NO: 15, 17, 19, 21, 23,
25, 27, 29, 31, 33, 35, 37, 39, 41, or 42. The polypeptide is preferably a
REP2 or
REP2-like protein.
An isolated polynucleotide comprising (i) a nucleic acid sequence of at least
50%,51%,52%,53%,54%,55%,56%,57%,58%,59%,60%,56%,62%,63%,
64%,65%,66%,67%,68%,69%,70%,71%,72%,73%,74%,75%,76%,77%,
78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91 %,
92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity, based on
the Clustal V method of alignment, when compared to SEQ ID NO: 14, 16, 18, 20,
22, 24, 26, 28, 30, 32, 34, 36, 38, 40, or 49, or (ii) a full complement of
the nucleic
acid sequence of (i). Any of the foregoing isolated polynucleotides may be
utilized
in any recombinant DNA constructs (including suppression DNA constructs) of
the
present invention. The isolated polynucleotide encodes a REP2 or REP2-like
protein.
Preferred Recombinant DNA Constructs and Suppression DNA Constructs.
In one aspect, the present invention includes recombinant DNA constructs
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
(including suppression DNA constructs).
In one preferred embodiment, a recombinant DNA construct comprises a
polynucleotide operably linked to at least one regulatory sequence (e.g., a
promoter
functional in a plant), wherein the polynucleotide comprises (i) a nucleic
acid
sequence encoding an amino acid sequence of at least 50%, 51 %, 52%, 53%, 54%,
55%, 56%, 57%, 58%, 59%, 60%, 56%, 62%, 63%, 64%, 65%, 66%, 67%, 68%,
69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%,
83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,
97%, 98%, 99%, or 100% sequence identity, based on the Clustal V method of
alignment, when compared to SEQ ID NO: 15, 17, 19, 21, 23, 25, 27, 29, 31, 33,
35,
37, 39, 41, or 42, or(ii) a full complement of the nucleic acid sequence of
(i).
In another preferred embodiment, a recombinant DNA construct comprises a
polynucleotide operably linked to at least one regulatory sequence (e.g., a
promoter
functional in a plant), wherein said polynucleotide comprises (i) a nucleic
acid
sequence of at least 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%,
56%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%,
75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%,
89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence
identity, based on the Clustal V method of alignment, when compared to SEQ ID
NO: 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, or 49 or (ii) a
full
complement of the nucleic acid sequence of (i).
Figs. 1A -1 B show the multiple alignment of the amino acid sequences of
SEQ ID NOs: 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, and 41 and SEQ
ID
NOs:42, 43, 44, 45, 46, and 47. The multiple alignment of the sequences was
performed using the Megalign program of the LASERGENE bioinformatics
computing suite (DNASTAR Inc., Madison, WI); in particular, using the Clustal
V
method of alignment (Higgins and Sharp (1989) CABIOS. 5:151-153) with the
multiple alignment default parameters of GAP PENALTY=1 0 and GAP LENGTH
PENALTY=10, and the pairwise alignment default parameters of KTUPLE=1, GAP
PENALTY=3, WINDOW=5 and DIAGONALS SAVED=5.
FIG. 2 shows the percent sequence identity and the divergence values for
each pair of amino acids sequences displayed in Figs. 1A-1 B.
In another preferred embodiment, a recombinant DNA construct comprises a
16
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
polynucleotide operably linked to at least one regulatory sequence (e.g., a
promoter
functional in a plant), wherein said polynucleotide encodes a REP2 or REP2-
like
protein.
In another aspect, the present invention includes suppression DNA
constructs.
A suppression DNA construct preferably comprises at least one regulatory
sequence (preferably a promoter functional in a plant) operably linked to (a)
all or
part of (i) a nucleic acid sequence encoding a polypeptide having an amino
acid
sequence of at least 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%,
56%,62%,63%,64%,65%,66%,67%,68%,69%,70%,71%,72%,73%,74%,
75%,76%,77%,78%,79%,80%,81%,82%,83%,84%,85%,86%,87%,88%,
89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence
identity, based on the Clustal V method of alignment, when compared to SEQ ID
NO: 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, or 42 or (ii) a
full
complement of the nucleic acid sequence of (a)(i); or (b) a region derived
from all or
part of a sense strand or antisense strand of a target gene of interest, said
region
having a nucleic acid sequence of at least 50%, 51 %, 52%, 53%, 54%, 55%, 56%,
57%,58%,59%,60%,56%,62%,63%,64%,65%,66%,67%,68%,69%,70%,
71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%,
85%,86%,87%,88%,89%,90%,91%,92%,93%,94%,95%,96%,97%,98%,
99%, or 100% sequence identity, based on the Clustal V method of alignment,
when
compared to said all or part of a sense strand or antisense strand from which
said
region is derived, and wherein said target gene of interest encodes a REP2 or
REP2-like protein; or (c) all or part of (i) a nucleic acid sequence of at
least 50%,
51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 56%, 62%, 63%, 64%,
65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%,
79%,80%,81%,82%,83%,84%,85%,86%,87%,88%,89%,90%,91%,92%,
93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity, based on the
Clustal V method of alignment, when compared to SEQ ID NO: 14, 16, 18, 20, 22,
24, 26, 28, 30, 32, 34, 36, 38, 40, or 49, or (ii) a full complement of the
nucleic acid
sequence of (c)(i). The suppression DNA construct preferably comprises a
cosuppression construct, antisense construct, viral-suppression construct,
hairpin
suppression construct, stem-loop suppression construct, double-stranded RNA-
17
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
producing construct, RNAi construct, or small RNA construct (e.g., an sRNA
construct or an miRNA construct).
It is understood, as those skilled in the art will appreciate, that the
invention
encompasses more than the specific exemplary sequences. Alterations in a
nucleic
acid fragment which result in the production of a chemically equivalent amino
acid at
a given site, but do not affect the functional properties of the encoded
polypeptide,
are well known in the art. For example, a codon for the amino acid alanine, a
hydrophobic amino acid, may be substituted by a codon encoding another less
hydrophobic residue, such as glycine, or a more hydrophobic residue, such as
valine, leucine, or isoleucine. Similarly, changes which result in
substitution of one
negatively charged residue for another, such as aspartic acid for glutamic
acid, or
one positively charged residue for another, such as lysine for arginine, can
also be
expected to produce a functionally equivalent product. Nucleotide changes
which
result in alteration of the N-terminal and C-terminal portions of the
polypeptide
molecule would also not be expected to alter the activity of the polypeptide.
Each of
the proposed modifications is well within the routine skill in the art, as is
determination of retention of biological activity of the encoded products.
"Suppression DNA construct" is a recombinant DNA construct which when
transformed or stably integrated into the genome of the plant, results in
"silencing" of
a target gene in the plant. The target gene may be endogenous or transgenic to
the
plant. "Silencing," as used herein with respect to the target gene, refers
generally to
the suppression of levels of mRNA or protein/enzyme expressed by the target
gene,
and/or the level of the enzyme activity or protein functionality. The term
"suppression" includes lower, reduce, decline, decrease, inhibit, eliminate or
prevent. "Silencing" or "gene silencing" does not specify mechanism and is
inclusive, and not limited to, anti-sense, cosuppression, viral-suppression,
hairpin
suppression, stem-loop suppression, RNAi-based approaches, and small RNA-
based approaches.
A suppression DNA construct may comprise a region derived from a target
gene of interest and may comprise all or part of the nucleic acid sequence of
the
sense strand (or antisense strand) of the target gene of interest. Depending
upon
the approach to be utilized, the region may be 100% identical or less than
100%
identical (e.g., at least 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%,
18
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
60%, 56%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%,
74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%,
88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% identical) to all
or part of the sense strand (or antisense strand) of the gene of interest.
Suppression DNA constructs are well-known in the art, are readily
constructed once the target gene of interest is selected, and include, without
limitation, cosuppression constructs, antisense constructs, viral-suppression
constructs, hairpin suppression constructs, stem-loop suppression constructs,
double-stranded RNA-producing constructs, and more generally, RNAi (RNA
interference) constructs and small RNA constructs such as sRNA (short
interfering
RNA) constructs and miRNA (microRNA) constructs.
"Antisense inhibition" refers to the production of antisense RNA transcripts
capable of suppressing the expression of the target protein.
"Antisense RNA" refers to an RNA transcript that is complementary to all or
part of a
target primary transcript or mRNA and that blocks the expression of a target
isolated
nucleic acid fragment (U.S. Patent No. 5,107,065). The complementarity of an
antisense RNA may be with any part of the specific gene transcript, i.e., at
the 5'
non-coding sequence, 3' non-coding sequence, introns, or the coding sequence.
"Cosuppression" refers to the production of sense RNA transcripts capable of
suppressing the expression of the target protein. "Sense" RNA refers to RNA
transcript that includes the mRNA and can be translated into protein within a
cell or
in vitro. Cosuppression constructs in plants have been previously designed by
focusing on overexpression of a nucleic acid sequence having homology to a
native
mRNA, in the sense orientation, which results in the reduction of all RNA
having
homology to the overexpressed sequence (see Vaucheret et al. (1998) Plant J.
16:651-659; and Gura (2000) Nature 404:804-808).
Another variation describes the use of plant viral sequences to direct the
suppression of proximal mRNA encoding sequences (PCT Publication WO
98/36083 published on August 20, 1998).
Previously described is the use of "hairpin" structures that incorporate all,
or
part, of an mRNA encoding sequence in a complementary orientation that results
in
a potential "stem-loop" structure for the expressed RNA (PCT Publication WO
99/53050 published on October 21, 1999). In this case the stem is formed by
19
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
polynucleotides corresponding to the gene of interest inserted in either sense
or
anti-sense orientation with respect to the promoter and the loop is formed by
some
polynucleotides of the gene of interest, which do not have a complement in the
construct. This increases the frequency of cosuppression or silencing in the
recovered transgenic plants. For review of hairpin suppression see Wesley,
S.V. et
al. (2003) Methods in Molecular Biology, Plant Functional Genomics: Methods
and
Protocols 236:273-286.
A construct where the stem is formed by at least 30 nucleotides from a gene
to be suppressed and the loop is formed by a random nucleotide sequence has
also
effectively been used for suppression (PCT Publication No. WO 99/61632
published
on December 2, 1999).
The use of poly-T and poly-A sequences to generate the stem in the stem-
loop structure has also been described (PCT Publication No. WO 02/00894
published January 3, 2002).
Yet another variation includes using synthetic repeats to promote formation of
a stem in the stem-loop structure. Transgenic organisms prepared with such
recombinant DNA fragments have been shown to have reduced levels of the
protein
encoded by the nucleotide fragment forming the loop as described in PCT
Publication No. WO 02/00904, published 03 January 2002.
RNA interference refers to the process of sequence-specific post-
transcriptional gene silencing in animals mediated by short interfering RNAs
(siRNAs) (Fire et al., Nature 391:806 1998). The corresponding process in
plants is
commonly referred to as post-transcriptional gene silencing (PTGS) or RNA
silencing and is also referred to as quelling in fungi. The process of post-
transcriptional gene silencing is thought to be an evolutionarily-conserved
cellular
defense mechanism used to prevent the expression of foreign genes and is
commonly shared by diverse flora and phyla (Fire et al., Trends Genet. 15:358
1999). Such protection from foreign gene expression may have evolved in
response to the production of double-stranded RNAs (dsRNAs) derived from viral
infection or from the random integration of transposon elements into a host
genome
via a cellular response that specifically destroys homologous single-stranded
RNA
of viral genomic RNA. The presence of dsRNA in cells triggers the RNAi
response
through a mechanism that has yet to be fully characterized.
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
The presence of long dsRNAs in cells stimulates the activity of a
ribonuclease III enzyme referred to as dicer. Dicer is involved in the
processing of
the dsRNA into short pieces of dsRNA known as short interfering RNAs (siRNAs)
(Berstein et al., Nature 409:363 2001). Short interfering RNAs derived from
dicer
activity are typically about 21 to about 23 nucleotides in length and comprise
about
19 base pair duplexes (Elbashir et al., Genes Dev. 15:188 2001). Dicer has
also
been implicated in the excision of 21- and 22-nucleotide small temporal RNAs
(stRNAs) from precursor RNA of conserved structure that are implicated in
translational control (Hutvagner et al., 2001, Science 293:834). The RNAi
response
also features an endonuclease complex, commonly referred to as an RNA-induced
silencing complex (RISC), which mediates cleavage of single-stranded RNA
having
sequence complementarity to the antisense strand of the sRNA duplex. Cleavage
of the target RNA takes place in the middle of the region complementary to the
antisense strand of the sRNA duplex (Elbashir et al., Genes Dev. 15:188 2001).
In
addition, RNA interference can also involve small RNA (e.g., miRNA) mediated
gene silencing, presumably through cellular mechanisms that regulate chromatin
structure and thereby prevent transcription of target gene sequences (see,
e.g.,
Allshire, Science 297:1818-1819 2002; Volpe et al., Science 297:1833-1837
2002;
Jenuwein, Science 297:2215-2218 2002; and Hall et al., Science 297:2232-2237
2002). As such, miRNA molecules of the invention can be used to mediate gene
silencing via interaction with RNA transcripts or alternately by interaction
with
particular gene sequences, wherein such interaction results in gene silencing
either
at the transcriptional or post-transcriptional level.
RNAi has been studied in a variety of systems. Fire et al. (Nature 391:806
1998) were the first to observe RNAi in C. elegans. Manny and Goetz (Nature
Cell
Biol. 2:70 1999) describe RNAi mediated by dsRNA in mouse embryos. Hammond
et al. (Nature 404:293 2000) describe RNAi in Drosophila cells transfected
with
dsRNA. Elbashir et al., (Nature 411:494 2001) describe RNAi induced by
introduction of duplexes of synthetic 21 -nucleotide RNAs in cultured
mammalian
cells including human embryonic kidney and HeLa cells.
Small RNAs play an important role in controlling gene expression. Regulation
of many developmental processes, including flowering, is controlled by small
RNAs.
It is now possible to engineer changes in gene expression of plant genes by
using
21
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
transgenic constructs which produce small RNAs in the plant.
Small RNAs appear to function by base-pairing to complementary RNA or
DNA target sequences. When bound to RNA, small RNAs trigger either RNA
cleavage or translational inhibition of the target sequence. When bound to DNA
target sequences, it is thought that small RNAs can mediate DNA methylation of
the
target sequence. The consequence of these events, regardless of the specific
mechanism, is that gene expression is inhibited.
It is thought that sequence complementarity between small RNAs and their
RNA targets helps to determine which mechanism, RNA cleavage or translational
inhibition, is employed. It is believed that siRNAs, which are perfectly
complementary with their targets, work by RNA cleavage. Some miRNAs have
perfect or near-perfect complementarity with their targets, and RNA cleavage
has
been demonstrated for at least a few of these miRNAs. Other miRNAs have
several
mismatches with their targets, and apparently inhibit their targets at the
translational
level. Again, without being held to a particular theory on the mechanism of
action, a
general rule is emerging that perfect or near-perfect complementarity causes
RNA
cleavage, whereas translational inhibition is favored when the miRNA/target
duplex
contains many mismatches. The apparent exception to this is microRNA 172
(miR172) in plants. One of the targets of miR172 is APETALA2 (AP2), and
although
miR172 shares near-perfect complementarity with AP2 it appears to cause
translational inhibition of AP2 rather than RNA cleavage.
MicroRNAs (miRNAs) are noncoding RNAs of about 19 to about 24
nucleotides (nt) in length that have been identified in both animals and
plants
(Lagos-Quintana et al., Science 294:853-858 2001, Lagos-Quintana et al., Curr.
Biol. 12:735-739 2002; Lau et al., Science 294:858-862 2001; Lee and Ambros,
Science 294:862-864 2001; Llave et al., Plant Cell 14:1605-1619 2002;
Mourelatos
et al., Genes. Dev. 16:720-728 2002; Park et al., Curr. Biol. 12:1484-1495
2002;
Reinhart et al., Genes. Dev. 16:1616-1626 2002). They are processed from
longer
precursor transcripts that range in size from approximately 70 to 200 nt, and
these
precursor transcripts have the ability to form stable hairpin structures. In
animals,
the enzyme involved in processing miRNA precursors is called Dicer, an RNAse
III-
like protein (Grishok et al., Cell 106:23-34 2001; Hutvagner et al., Science
293:834-
838 2001; Ketting et al., Genes. Dev. 15:2654-2659 2001). Plants also have a
22
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
Dicer-like enzyme, DCL1 (previously named CARPEL FACTORY/SHORT
INTEGUMENTS1/ SUSPENSOR1), and recent evidence indicates that it, like Dicer,
is involved in processing the hairpin precursors to generate mature miRNAs
(Park et
al., Curr. Biol. 12:1484-1495 2002; Reinhart et al., Genes. Dev. 16:1616-1626
2002). Furthermore, it is becoming clear from recent work that at least some
miRNA hairpin precursors originate as longer polyadenylated transcripts, and
several different miRNAs and associated hairpins can be present in a single
transcript (Lagos-Quintana et al., Science 294:853-858 2001; Lee et al., EMBO
J
21:4663-4670 2002). Recent work has also examined the selection of the miRNA
strand from the dsRNA product arising from processing of the hairpin by DICER
(Schwartz, et al. 2003 Cell 115:199-208). It appears that the stability (i.e.
G:C vs.
A:U content, and/or mismatches) of the two ends of the processed dsRNA affects
the strand selection, with the low stability end being easier to unwind by a
helicase
activity. The 5' end strand at the low stability end is incorporated into the
RISC
complex, while the other strand is degraded.
MicroRNAs appear to regulate target genes by binding to complementary
sequences located in the transcripts produced by these genes. In the case of
lin-4
and let-7, the target sites are located in the 3' UTRs of the target mRNAs
(Lee et al.,
Cell 75:843-854 1993; Wightman et al., Cell 75:855-862 1993; Reinhart et al.,
Nature 403:901-906 2000; Slack et al., Mol. Cell 5:659-669 2000), and there
are
several mismatches between the lin-4 and let-7 miRNAs and their target sites.
Binding of the lin-4 or let-7 miRNA appears to cause downregulation of steady-
state
levels of the protein encoded by the target mRNA without affecting the
transcript
itself (Olsen and Ambros, Dev. Biol. 216:671-680 1999). On the other hand,
recent
evidence suggests that miRNAs can in some cases cause specific RNA cleavage of
the target transcript within the target site, and this cleavage step appears
to require
100% complementarity between the miRNA and the target transcript (Hutvagner
and Zamore, Science 297:2056-2060 2002; Llave et al., Plant Cell 14:1605-1619
2002). It seems likely that miRNAs can enter at least two pathways of target
gene
regulation: Protein downregulation when target complementarity is <100%, and
RNA cleavage when target complementarity is 100%. MicroRNAs entering the RNA
cleavage pathway are analogous to the 21-25 nt short interfering RNAs (siRNAs)
generated during RNA interference (RNAi) in animals and posttranscriptional
gene
23
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
silencing (PTGS) in plants (Hamilton and Baulcombe 1999; Hammond et al., 2000;
Zamore et al., 2000; Elbashir et al., 2001), and likely are incorporated into
an RNA-
induced silencing complex (RISC) that is similar or identical to that seen for
RNAi.
Identifying the targets of miRNAs with bioinformatics has not been successful
in animals, and this is probably due to the fact that animal miRNAs have a low
degree of complementarity with their targets. On the other hand, bioinformatic
approaches have been successfully used to predict targets for plant miRNAs
(Llave
et al., Plant Cell 14:1605-1619 2002; Park et al., Curr. Biol. 12:1484-1495
2002;
Rhoades et al., Cell 110:513-520 2002), and thus it appears that plant miRNAs
have
higher overall complementarity with their putative targets than do animal
miRNAs.
Most of these predicted target transcripts of plant miRNAs encode members of
transcription factor families implicated in plant developmental patterning or
cell
differentiation.
A recombinant DNA construct (including a suppression DNA construct) of the
present invention preferably comprises at least one regulatory sequence.
A preferred regulatory sequence is a promoter.
A number of promoters can be used in recombinant DNA constructs (and
suppression DNA constructs) of the present invention. The promoters can be
selected based on the desired outcome, and may include constitutive, tissue-
specific, cell specific, inducible, or other promoters for expression in the
host
organism.
High level, constitutive expression of the candidate gene under control of the
35S or UBI promoter may have pleiotropic effects, although Candidate gene
efficacy
may be estimated when driven by a constitutive promoter.
Use of tissue-specific and/or stress-specific expression may eliminate
undesirable effects but retain the ability to alter root architecture. This
effect has
been observed in Arabidopsis (Kasuga et al. (1999) Nature Biotechnol. 17:287-
291).
Suitable constitutive promoters for use in a plant host cell include, for
example, the core promoter of the Rsyn7 promoter and other constitutive
promoters
disclosed in WO 99/43838 and U.S. Patent No. 6,072,050; the core CaMV 35S
promoter (Odell et al., Nature 313:810-812 (1985)); rice actin (McElroy et
al., Plant
Cell 2:163-171 (1990)); ubiquitin (UBI) (Christensen et al., Plant Mol. Biol.
12:619-
632 (1989) and Christensen et al., Plant Mol. Biol. 18:675-689 (1992)); pEMU
(Last
24
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
et al., Theor. Appl. Genet. 81:581-588 (1991)); MAS (Velten et al., EMBO J.
3:2723-
2730 (1984)); ALS promoter (U.S. Patent No. 5,659,026), the maize GOS2
promoter
(W00020571 A2, published April 1, 2000) and the like. Other constitutive
promoters
include, for example, those discussed in U.S. Patent Nos. 5,608,149;
5,608,144;
5,604,121; 5,569,597; 5,466,785; 5,399,680; 5,268,463; 5,608,142; and
6,177,611.
In choosing a promoter to use in the methods of the invention, it may be
desirable to use a tissue-specific or developmentally regulated promoter.
A preferred tissue-specific or developmentally regulated promoter is a DNA
sequence which regulates the expression of a DNA sequence selectively in the
cells/tissues of a plant critical to tassel development, seed set, or both,
and limits
the expression of such a DNA sequence to the period of tassel development or
seed
maturation in the plant. Any identifiable promoter may be used in the methods
of
the present invention which causes the desired temporal and spatial
expression.
Promoters which are seed or embryo specific and may be useful in the
invention include soybean Kunitz trysin inhibitor (Kti3, Jofuku and Goldberg,
Plant
Cell 1:1079-1093 (1989)), patatin (potato tubers) (Rocha-Sosa, M., et al.
(1989)
EMBO J. 8:23-29), convicilin, vicilin, and legumin (pea cotyledons) (Rerie,
W.G., et
al. (1991) Mol. Gen. Genet. 259:149-157; Newbigin, E.J., et al. (1990) Planta
180:461-470; Higgins, T.J.V., et al. (1988) Plant. Mol. Biol. 11:683-695),
zein (maize
endosperm) (Schemthaner, J.P., et al. (1988) EMBO J. 7:1249-1255), phaseolin
(bean cotyledon) (Segupta-Gopalan, C., et al. (1985) Proc. NatI. Acad. Sci.
U.S.A.
82:3320-3324), phytohemagglutinin (bean cotyledon) (Voelker, T. et al. (1987)
EMBO J. 6:3571-3577), B-conglycinin and glycinin (soybean cotyledon) (Chen, Z-
L,
et al. (1988) EMBO J. 7:297- 302), glutelin (rice endosperm), hordein (barley
endosperm) (Marris, C., et al. (1988) Plant Mol. Biol. 10:359-366), glutenin
and
gliadin (wheat endosperm) (Colot, V., et al. (1987) EMBO J. 6:3559-3564), and
sporamin (sweet potato tuberous root) (Hattori, T., et al. (1990) Plant Mol.
Biol.
14:595-604). Promoters of seed-specific genes operably linked to heterologous
coding regions in chimeric gene constructions maintain their temporal and
spatial
expression pattern in transgenic plants. Such examples include Arabidopsis
thaliana 2S seed storage protein gene promoter to express enkephalin peptides
in
Arabidopsis and Brassica napus seeds (Vanderkerckhove et al., Bio/Technology
7:L929-932 (1989)), bean lectin and bean beta-phaseolin promoters to express
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
luciferase (Riggs et al., Plant Sci. 63:47-57 (1989)), and wheat glutenin
promoters to
express chloramphenicol acetyl transferase (Colot et al., EMBO J 6:3559- 3564
(1987)).
Inducible promoters selectively express an operably linked DNA sequence in
response to the presence of an endogenous or exogenous stimulus, for example
by
chemical compounds (chemical inducers) or in response to environmental,
hormonal, chemical, and/or developmental signals. Inducible or regulated
promoters include, for example, promoters regulated by light, heat, stress,
flooding
or drought, phytohormones, wounding, or chemicals such as ethanol, jasmonate,
salicylic acid, or safeners.
Preferred promoters include the following: 1) the stress-inducible RD29A
promoter (Kasuga et al. (1999) Nature Biotechnol. 17:287-91); 2) the barley
promoter, B22E; expression of B22E is specific to the pedicel in developing
maize
kernels ("Primary Structure of a Novel Barley Gene Differentially Expressed in
Immature Aleurone Layers". Klemsdal, S.S. et al., Mol. Gen. Genet. 228(1/2):9-
16
(1991)); and 3) maize promoter, Zag2 ("Identification and molecular
characterization
of ZAG1, the maize homolog of the Arabidopsis floral homeotic gene AGAMOUS",
Schmidt, R.J. et al., Plant Cell 5(7):729-737 (1993))."Structural
characterization,
chromosomal localization and phylogenetic evaluation of two pairs of AGAMOUS-
like MADS-box genes from maize", Theissen et al., Gene 156(2): 155-166 (1995);
NCBI GenBank Accession No. X80206)). Zag2 transcripts can be detected 5 days
prior to pollination to 7 to 8 days after pollination (DAP), and directs
expression in
the carpel of developing female inflorescences and Ciml which is specific to
the
nucleus of developing maize kernels. Ciml transcript is detected 4 to 5 days
before
pollination to 6 to 8 DAP. Other useful promoters include any promoter which
can
be derived from a gene whose expression is maternally associated with
developing
female florets.
Additional preferred promoters for regulating the expression of the nucleotide
sequences of the present invention in plants are vascular element specific or
stalk-
preferrred promoters. Such stalk-preferred promoters include the alfalfa S2A
promoter (GenBank Accession No. EF030816; Abrahams et al., Plant Mol. Biol.
27:513-528 (1995)) and S2B promoter (GenBank Accession No. EF030817) and the
like, herein incorporated by reference.
26
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
Promoters may be derived in their entirety from a native gene, or be
composed of different elements derived from different promoters found in
nature, or
even comprise synthetic DNA segments. It is understood by those skilled in the
art
that different promoters may direct the expression of a gene in different
tissues or
cell types, or at different stages of development, or in response to different
environmental conditions. It is further recognized that since in most cases
the exact
boundaries of regulatory sequences have not been completely defined, DNA
fragments of some variation may have identical promoter activity. Promoters
that
cause a gene to be expressed in most cell types at most times are commonly
referred to as "constitutive promoters". New promoters of various types useful
in
plant cells are constantly being discovered; numerous examples may be found in
the compilation by Okamuro, J. K., and Goldberg, R. B., Biochemistry of Plants
15:1-82 (1989). (Put this with the other constitutive promoter description.)
Preferred promoters may include: RIP2, mLIP15, ZmCOR1, Rab17, CaMV
35S, RD29A, B22E, Zag2, SAM synthetase, ubiquitin (SEQ ID NO:59), CaMV 19S,
nos, Adh, sucrose synthase, R-allele, root cell promoter, the vascular tissue
specific
promoters S2A (Genbank accession number EF030816; SEQ ID NO:60) and S2B
(Genbank accession number EF030817) and the constitutive promoter GOS2 (SEQ
ID NO:58) from Zea mays. Other preferred promoters include root preferred
promoters, such as the maize NAS2 promoter (SEQ ID NO:57), the maize Cyclo
promoter (US 2006/0156439, published July 13, 2006), the maize ROOTMET2
promoter (WO05063998, published July 14, 2005), the CR1 BIO promoter
(WO06055487, published May 26, 2006), the CRWAQ81 (WO05035770, published
April 21, 2005) and the maize ZRP2.47 promoter (NCBI accession number: U38790,
gi: 1063664).
A "substantial portion" of a nucleotide sequence comprises a nucleotide
sequence that is sufficient to afford putative identification of the promoter
that the
nucleotide sequence comprises. Nucleotide sequences can be evaluated either
manually, by one skilled in the art, or using computer-based sequence
comparison
and identification tools that employ algorithms such as BLAST (Basic Local
Alignment Search Tool; Altschul et al. (1993) J. Mol. Biol. 215:403-410). In
general,
a sequence of thirty or more contiguous nucleotides is necessary in order to
putatively identify a promoter nucleic acid sequence as homologous to a known
27
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
promoter. The skilled artisan, having the benefit of the sequences as reported
herein, may now use all or a substantial portion of the disclosed sequences
for
purposes known to those skilled in this art. Accordingly, the instant
invention
comprises the complete sequences as reported in the accompanying Sequence
Listing, as well as substantial portions of those sequences as defined above.
Recombinant DNA constructs (and suppression DNA constructs) of the
present invention may also include other regulatory sequences, including but
not
limited to, translation leader sequences, introns, and polyadenylation
recognition
sequences. In another preferred embodiment of the present invention, a
recombinant DNA construct of the present invention further comprises an
enhancer
or silencer.
An intron sequence can be added to the 5' untranslated region or the coding
sequence of the partial coding sequence to increase the amount of the mature
message that accumulates in the cytosol. Inclusion of a spliceable intron in
the
transcription unit in both plant and animal expression constructs has been
shown to
increase gene expression at both the mRNA and protein levels up to 1000-fold.
Buchman and Berg, Mol. Cell Biol. 8:4395-4405 (1988); Callis et al., Genes
Dev.
1:1183-1200 (1987). Such intron enhancement of gene expression is typically
greatest when placed near the 5' end of the transcription unit. Use of maize
introns
Adhl-S intron 1, 2, and 6, the Bronze-1 intron are known in the art. See
generally,
The Maize Handbook, Chapter 116, Freeling and Walbot, Eds., Springer, New York
(1994).
If polypeptide expression is desired, it is generally desirable to include a
polyadenylation region at the 3'-end of a polynucleotide coding region. The
polyadenylation region can be derived from the natural gene, from a variety of
other
plant genes, or from T-DNA. The 3' end sequence to be added can be derived
from,
for example, the nopaline synthase or octopine synthase genes, or
alternatively
from another plant gene, or less preferably from any other eukaryotic gene.
A translation leader sequence is a DNA sequence located between the
promoter sequence of a gene and the coding sequence. The translation leader
sequence is present in the fully processed mRNA upstream of the translation
start
sequence. The translation leader sequence may affect processing of the primary
transcript to mRNA, mRNA stability or translation efficiency. Examples of
translation
28
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
leader sequences have been described (Turner, R. and Foster, G. D. Molecular
Biotechnology 3:225 (1995)).
In another preferred embodiment of the present invention, a recombinant
DNA construct of the present invention further comprises an enhancer or
silencer.
Any plant can be selected for the identification of regulatory sequences and
genes to be used in creating recombinant DNA constructs and suppression DNA
constructs of the present invention. Examples of suitable plant targets for
the
isolation of genes and regulatory sequences would include but are not limited
to
alfalfa, apple, apricot, Arabidopsis, artichoke, arugula, asparagus, avocado,
banana,
barley, beans, beet, blackberry, blueberry, broccoli, brussels sprouts,
cabbage,
canola, cantaloupe, carrot, cassava, castorbean, cauliflower, celery, cherry,
chicory,
cilantro, citrus, clementines, clover, coconut, coffee, corn, cotton,
cranberry,
cucumber, Douglas fir, eggplant, endive, escarole, eucalyptus, fennel, figs,
garlic,
gourd, grape, grapefruit, honey dew, jicama, kiwifruit, lettuce, leeks, lemon,
lime,
Loblolly pine, linseed, mango, melon, mushroom, nectarine, nut, oat, oil palm,
oil
seed rape, okra, olive, onion, orange, an ornamental plant, palm, papaya,
parsley,
parsnip, pea, peach, peanut, pear, pepper, persimmon, pine, pineapple,
plantain,
plum, pomegranate, poplar, potato, pumpkin, quince, radiata pine, radicchio,
radish,
rapeseed, raspberry, rice, rye, sorghum, Southern pine, soybean, spinach,
squash,
strawberry, sugarbeet, sugarcane, sunflower, sweet potato, sweetgum,
tangerine,
tea, tobacco, tomato, triticale, turf, turnip, a vine, watermelon, wheat,
yams, and
zucchini. Particularly preferred plants for the identification of regulatory
sequences
are Arabidopsis, corn, wheat, soybean, and cotton.
Preferred Compositions
A preferred composition of the present invention is a plant comprising in its
genome any of the recombinant DNA constructs (including any of the suppression
DNA constructs) of the present invention (such as those preferred constructs
discussed above). Preferred compositions also include any progeny of the
plant,
and any seed obtained from the plant or its progeny, wherein the progeny or
seed
comprises within its genome the recombinant DNA construct (or suppression DNA
construct). Progeny includes subsequent generations obtained by self-
pollination or
out-crossing of a plant. Progeny also includes hybrids and inbreds.
Preferably, in hybrid seed propagated crops, mature transgenic plants can be
29
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
self-pollinated to produce a homozygous inbred plant. The inbred plant
produces
seed containing the newly introduced recombinant DNA construct (or suppression
DNA construct). These seeds can be grown to produce plants that would exhibit
altered root (or plant) architecture, or used in a breeding program to produce
hybrid
seed, which can be grown to produce plants that would exhibit altered root (or
plant) architecture. Preferably, the seeds are maize.
Preferably, the plant is a monocotyledonous or dicotyledonous plant, more
preferably, a maize or soybean plant, even more preferably a maize plant, such
as a
maize hybrid plant or a maize inbred plant. The plant may also be sunflower,
sorghum, canola, wheat, alfalfa, cotton, rice, barley or millet.
Preferably, the recombinant DNA construct is stably integrated into the
genome of the plant.
Particularly preferred embodiments include but are not limited to the
following
preferred embodiments:
1. A plant (preferably a maize or soybean plant) comprising in its genome
a recombinant DNA construct comprising a polynucleotide operably linked to at
least
one regulatory sequence, wherein said polynucleotide encodes a polypeptide
having an amino acid sequence of at least 50%, 51 %, 52%, 53%, 54%, 55%, 56%,
57%, 58%, 59%, 60%, 56%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%,
71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%,
85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,
99%, or 100% sequence identity, based on the Clustal V method of alignment,
when compared to SEQ ID NO: 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37,
39, 41,
or 42 and wherein said plant exhibits an altered root architecture when
compared to
a control plant not comprising said recombinant DNA construct. Preferably, the
plant further exhibits an alteration of at least one agronomic characteristic
when
compared to the control plant.
2. A plant (preferably a maize or soybean plant) comprising in its
genome:
a recombinant DNA construct comprising:
(a) a polynucleotide operably linked to at least one regulatory element,
wherein said polynucleotide encodes a polypeptide having an amino acid
sequence
of at least 50% sequence identity, based on the Clustal V method of alignment,
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
when compared to SEQ ID NO: 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37,
39, 41,
or 42, or
(b) a suppression DNA construct comprising at least one regulatory
element operably linked to:
(i) all or part of: (A) a nucleic acid sequence encoding a
polypeptide having an amino acid sequence of at least 50% sequence identity,
based on the Clustal V method of alignment, when compared to SEQ ID NO: 15,
17,
19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, or 42 or (B) a full complement
of the
nucleic acid sequence of (b)(i)(A); or
(ii) a region derived from all or part of a sense strand or antisense
strand of a target gene of interest, said region having a nucleic acid
sequence of at
least 50% sequence identity, based on the Clustal V method of alignment, when
compared to said all or part of a sense strand or antisense strand from which
said
region is derived, and wherein said target gene of interest encodes a REP2 or
REP2-like polypeptide, and wherein said plant exhibits an alteration of at
least one
agronomic characteristic when compared to a control plant not comprising said
recombinant DNA construct.
3. A plant (preferably a maize or soybean plant) comprising in its genome
a recombinant DNA construct comprising a polynucleotide operably linked to at
least
one regulatory sequence, wherein said polynucleotide encodes a REP2 or REP2-
like protein, and wherein said plant exhibits an altered root architecture
when
compared to a control plant not comprising said recombinant DNA construct.
Preferably, the plant further exhibits an alteration of at least one agronomic
characteristic.
Preferably, the REP2 protein is from Arabidopsis thaliana, Zea mays, Glycine
max, Glycine tabacina, Glycine soja or Glycine tomentella.
4. A plant (preferably a maize or soybean plant) comprising in its genome
a suppression DNA construct comprising at least one regulatory element
operably
linked to a region derived from all or part of a sense strand or antisense
strand of a
target gene of interest, said region having a nucleic acid sequence of at
least 50%,
51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 56%, 62%, 63%, 64%,
65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%,
79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%,
31
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity, based on the
Clustal V method of alignment, when compared to said all or part of a sense
strand
or antisense strand from which said region is derived, and wherein said target
gene
of interest encodes a REP2 or REP2-like protein, and wherein said plant
exhibits an
alteration of at least one agronomic characteristic when compared to a control
plant
not comprising said recombinant DNA construct.
5. A plant (preferably a maize or soybean plant) comprising in its genome
a suppression DNA construct comprising at least one regulatory element
operably
linked to all or part of (a) a nucleic acid sequence encoding a polypeptide
having an
amino acid sequence of at least 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%,
59%, 60%, 56%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%,
73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%,
87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%
sequence identity, based on the Clustal V method of alignment, when compared
to
SEQ ID NO: 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, or 42, or
(b) a full
complement of the nucleic acid sequence of (a), and wherein said plant
exhibits an
alteration of at least one agronomic characteristic when compared to a control
plant
not comprising said recombinant DNA construct.
6. Any progeny of the above plants in preferred embodiments 1-5, any
seeds of the above plants in preferred embodiments 1-5, any seeds of progeny
of
the above plants in preferred embodiments 1-5, and cells from any of the above
plants in preferred embodiments 1-5 and progeny thereof.
In any of the foregoing preferred embodiments 1-6 or any other embodiments
of the present invention, the recombinant DNA construct (or suppression DNA
construct) preferably comprises at least a promoter that is functional in a
plant as a
preferred regulatory sequence.
In any of the foregoing preferred embodiments 1-6 or any other embodiments
of the present invention, the alteration of at least one agronomic
characteristic is
either an increase or decrease, preferably an increase.
In any of the foregoing preferred embodiments 1-6 or any other embodiments
of the present invention, the at least one agronomic characteristic is
preferably
selected from the group consisting of greenness, yield, growth rate, biomass,
fresh
weight at maturation, dry weight at maturation, fruit yield, seed yield, total
plant
32
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
nitrogen content, fruit nitrogen content, seed nitrogen content, nitrogen
content in a
vegetative tissue, total plant free amino acid content, fruit free amino acid
content,
seed free amino acid content, free amino acid content in a vegetative tissue,
total
plant protein content, fruit protein content, seed protein content, protein
content in a
vegetative tissue, drought tolerance, nitrogen uptake, root mass, root
lodging, stalk
lodging, plant height, ear length and harvest index. Yield, greenness, biomass
and
root lodging are particularly preferred agronomic characteristics for
alteration
(preferably an increase).
In any of the foregoing preferred embodiments 1-6 or any other embodiments
of the present invention, the plant preferably exhibits the alteration of at
least one
agronomic characteristic irrespective of the environmental conditions, for
example,
water and nutrient availability, when compared to a control plant.
One of ordinary skill in the art is familiar with protocols for determining
alteration in plant root architecture. For example, transgenic maize plants
can be
assayed for changes in root architecture at seedling stage, flowering time or
maturity. Alterations in root architecture can be determined by counting the
nodal
root numbers of the top 3 or 4 nodes of the greenhouse grown plants or the
width of
the root band. "Root band" refers to the width of the mat of roots at the
bottom of a
pot at plant maturity. Other measures of alterations in root architecture
include, but
are not limited to, the number of lateral roots, average root diameter of
nodal roots,
average root diameter of lateral roots, number and length of root hairs. The
extent
of lateral root branching (e.g. lateral root number, lateral root length) can
be
determined by sub-sampling a complete root system, imaging with a flat-bed
scanner or a digital camera and analyzing with WinRHIZOTM software (Regent
Instruments Inc.).
Data taken on root phenotype are subjected to statistical analysis, normally a
t-test
to compare the transgenic roots with that of non-transgenic sibling plants.
One-way
ANOVA may also be used in cases where multiple events and/or constructs are
involved in the analysis.
The Examples below describe some representative protocols and techniques
for detecting alterations in root architecture.
One can also evaluate alterations in root architecture by the ability of the
plant to increase yield in field testing when compared, under the same
conditions, to
33
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
a control or reference plant.
One can also evaluate alterations in root architecture by the ability of the
plant to maintain substantial yield (preferably at least 75%, 76%, 77%, 78%,
79%,
80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%,
94%, 95%, 96%, 97%, 98%, 99%, or 100% yield) in field testing under stress
conditions (e.g., nutrient over-abundance or limitation, water over-abundance
or
limitation, presence of disease), when compared to the yield of a control or
reference plant under non-stressed conditions.
Alterations in root architecture can also be measured by determining the
resistance to root lodging of the transgenic plants compared to reference or
control
plants.
One of ordinary skill in the art would readily recognize a suitable control or
reference plant to be utilized when assessing or measuring an agronomic
characteristic or phenotype of a transgenic plant in any embodiment of the
present
invention in which a control or reference plant is utilized (e.g.,
compositions or
methods as described herein). For example, by way of non-limiting
illustrations:
1. Progeny of a transformed plant which is hemizygous with respect to a
recombinant DNA construct (or suppression DNA construct), such that the
progeny
are segregating into plants either comprising or not comprising the
recombinant
DNA construct (or suppression DNA construct): the progeny comprising the
recombinant DNA construct (or suppression DNA construct) would be typically
measured relative to the progeny not comprising the recombinant DNA construct
(or
suppression DNA construct) (i.e., the progeny not comprising the recombinant
DNA
construct (or suppression DNA construct) is the control or reference plant).
2. Introgression of a recombinant DNA construct (or suppression DNA
construct) into an inbred line, such as in maize, or into a variety, such as
in
soybean: the introgressed line would typically be measured relative to the
parent
inbred or variety line (i.e., the parent inbred or variety line is the control
or reference
plant).
3. Two hybrid lines, where the first hybrid line is produced from two
parent inbred lines, and the second hybrid line is produced from the same two
parent inbred lines except that one of the parent inbred lines contains a
recombinant
DNA construct (or suppression DNA construct): the second hybrid line would
34
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
typically be measured relative to the first hybrid line (i.e., the parent
inbred or variety
line is the control or reference plant).
4. A plant comprising a recombinant DNA construct (or suppression DNA
construct): the plant may be assessed or measured relative to a control plant
not
comprising the recombinant DNA construct (or suppression DNA construct) but
otherwise having a comparable genetic background to the plant (e.g., sharing
at
least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence
identity of nuclear genetic material compared to the plant comprising the
recombinant DNA construct (or suppression DNA construct). There are many
laboratory-based techniques available for the analysis, comparison and
characterization of plant genetic backgrounds; among these are Isozyme
Electrophoresis, Restriction Fragment Length Polymorphisms (RFLPs), Randomly
Amplified Polymorphic DNAs (RAPDs), Arbitrarily Primed Polymerase Chain
Reaction (AP-PCR), DNA Amplification Fingerprinting (DAF), Sequence
Characterized Amplified Regions (SCARs), Amplified Fragment Length
Polymorphisms (AFLP s), and Simple Sequence Repeats (SSRs) which are also
referred to as Microsatellites.
Furthermore, one of ordinary skill in the art would readily recognize that a
suitable control or reference plant to be utilized when assessing or measuring
an
agronomic characteristic or phenotype of a transgenic plant would not include
a
plant that had been previously selected, via mutagenesis or transformation,
for the
desired agronomic characteristic or phenotype.
Preferred Methods
Preferred methods include but are not limited to methods for altering root
architecture in a plant, methods for evaluating alteration of root
architecture in a
plant, methods for altering an agronomic characteristic in a plant, methods
for
determining an alteration of an agronomic characteristic in a plant, and
methods for
producing seed. Preferably, the plant is a monocotyledonous or dicotyledonous
plant, more preferably, a maize or soybean plant, even more preferably a maize
plant. The plant may also be sunflower, sorghum, canola, wheat, alfalfa,
cotton,
rice, barley or millet. The seed is preferably a maize or soybean seed, more
preferably a maize seed, and even more preferably, a maize hybrid seed or
maize
inbred seed.
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
Particularly preferred methods include but are not limited to the following:
A method of altering root architecture of a plant, comprising: (a) introducing
into a regenerable plant cell a recombinant DNA construct comprising a
polynucleotide operably linked to at least one regulatory sequence (preferably
a
promoter functional in a plant), wherein the polynucleotide encodes a
polypeptide
having an amino acid sequence of at least 50%, 51 %, 52%, 53%, 54%, 55%, 56%,
57%, 58%, 59%, 60%, 56%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%,
71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%,
85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,
99%, or 100% sequence identity, based on the Clustal V method of alignment,
when
compared to SEQ ID NO: 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41,
or
42; and (b) regenerating a transgenic plant from the regenerable plant cell
after step
(a), wherein the transgenic plant comprises in its genome the recombinant DNA
construct and exhibits altered root architecture when compared to a control
plant not
comprising the recombinant DNA construct. The method may further comprise (c)
obtaining a progeny plant derived from the transgenic plant, wherein said
progeny
plant comprises in its genome the recombinant DNA construct and exhibits
altered
root architecture when compared to a control plant not comprising the
recombinant
DNA construct.
A method of altering root architecture in a plant, comprising: (a) introducing
into a regenerable plant cell a suppression DNA construct comprising at least
one
regulatory sequence (preferably a promoter functional in a plant) operably
linked to:
(i) all or part of: (A) a nucleic acid sequence encoding a polypeptide
having an amino acid sequence of at least 50%, 51 %, 52%, 53%, 54%, 55%, 56%,
57%, 58%, 59%, 60%, 56%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%,
71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%,
85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,
99%, or 100% sequence identity, based on the Clustal V method of alignment,
when
compared to SEQ ID NO: 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41,
or 42
or (B) a full complement of the nucleic acid sequence of (a)(i)(A); or
(ii) a region derived from all or part of a sense strand or antisense strand
of a target gene of interest, said region having a nucleic acid sequence of at
least
50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 56%, 62%, 63%,
36
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%,
78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91 %,
92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity, based on
the Clustal V method of alignment, when compared to said all or part of a
sense
strand or antisense strand from which said region is derived, and wherein said
target gene of interest encodes a REP2 or REP2-like polypeptide; and
(b) regenerating a transgenic plant from the regenerable plant cell after step
(a), wherein the transgenic plant comprises in its genome the recombinant DNA
construct and exhibits an altered root architecture when compared to a control
plant
not comprising the suppression DNA construct. The method may further comprise
(c) obtaining a progeny plant derived from the transgenic plant, wherein said
progeny plant comprises in its genome the recombinant DNA construct and
exhibits
altered root architrecture when compared to a control plant not comprising the
suppression DNA construct.
A method of evaluating altered root architecture in a plant, comprising (a)
introducing into a regenerable plant cell a recombinant DNA construct
comprising a
polynucleotide operably linked to at least on regulatory sequence (preferably
a
promoter functional in a plant), wherein the polynucleotide encodes a
polypeptide
having an amino acid sequence of at least 50%, 51 %, 52%, 53%, 54%, 55%, 56%,
57%, 58%, 59%, 60%, 56%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%,
71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%,
85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,
99%, or 100% sequence identity, based on the Clustal V method of alignment,
when
compared to SEQ ID NO: 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41,
or 42
(b) regenerating a transgenic plant from the regenerable plant cell after step
(a),
wherein the transgenic plant comprises in its genome the recombinant DNA
construct; and (c) evaluating root architecture of the transgenic plant
compared to a
control plant not comprising the recombinant DNA construct. The method may
further comprise (d) obtaining a progeny plant derived from the transgenic
plant,
wherein the progeny plant comprises in its genome the recombinant DNA
construct;
and (e) evaluating root architecture of the progeny plant compared to a
control plant
not comprising the recombinant DNA construct.
A method of evaluating altered root architecture in a plant, comprising (a)
37
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
introducing into a regenerable plant cell a suppression DNA construct
comprising at
least one regulatory sequence (preferably a promoter functional in a plant)
operably
linked to:
(i) all or part of: (A) a nucleic acid sequence encoding a polypeptide
having an amino acid sequence of at least 50%, 51 %, 52%, 53%, 54%, 55%, 56%,
57%, 58%, 59%, 60%, 56%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%,
71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%,
85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,
99%, or 100% sequence identity, based on the Clustal V method of alignment,
when
compared to SEQ ID NO: 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41,
or
42, or (B) a full complement of the nucleic acid sequence of (a)(i)(A); or
(ii) a region
derived from all or part of a sense strand or antisense strand of a target
gene of
interest, said region having a nucleic acid sequence of at least 50%, 51 %,
52%,
53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 56%, 62%, 63%, 64%, 65%, 66%,
67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%,
81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%, 96%, 97%, 98%, 99%, or 100% sequence identity, based on the Clustal V
method of alignment, when compared to said all or part of a sense strand or
antisense strand from which said region is derived, and wherein said target
gene of
interest encodes a REP2 or REP2-like polypeptide; and
(b) regenerating a transgenic plant from the regenerable plant cell after step
(a), wherein the transgenic plant comprises in its genome the suppression DNA
construct; and (c) evaluating the transgenic plant for altered root
architecture
compared to a control plant not comprising the suppression DNA construct. The
method may further comprise (d) obtaining a progeny plant derived from the
transgenic plant, wherein the progeny plant comprises in its genome the
suppression DNA construct; and (e) evaluating the progeny plant for altered
root
architecture compared to a control plant not comprising the suppression DNA
construct.
A method of evaluating altered root architecture in a plant, comprising (a)
introducing into a regenerable plant cell a recombinant DNA construct
comprising a
polynucleotide operably linked to at least one regulatory sequence (preferably
a
promoter functional in a plant), wherein said polynucleotide encodes a
polypeptide
38
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
having an amino acid sequence of at least 50%, 51 %, 52%, 53%, 54%, 55%, 56%,
57%, 58%, 59%, 60%, 56%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%,
71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%,
85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,
99%, or 100% sequence identity, based on the Clustal V method of alignment,
when
compared to SEQ ID NO: 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41,
or 42
(b) regenerating a transgenic plant from the regenerable plant cell after step
(a),
wherein the transgenic plant comprises in its genome the recombinant DNA
construct; (c) obtaining a progeny plant derived from said transgenic plant,
wherein
the progeny plant comprises in its genome the recombinant DNA construct; and
(d)
evaluating the progeny plant for altered root architecture compared to a
control plant
not comprising the recombinant DNA construct.
A method of evaluating root architecture in a plant, comprising:
(a) introducing into a regenerable plant cell a suppression DNA construct
comprising
at least one regulatory element operably linked to: (i) all or part of: (A) a
nucleic acid
sequence encoding a polypeptide having an amino acid sequence of at least 50%,
51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 56%, 62%, 63%, 64%,
65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%,
79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%,
93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity, based on the
Clustal V method of alignment, when compared to SEQ ID NO: 15, 17, 19, 21, 23,
25, 27, 29, 31, 33, 35, 37, 39, 41, or 42, or (B) a full complement of the
nucleic acid
sequence of (a)(i)(A); or (ii) a region derived from all or part of a sense
strand or
antisense strand of a target gene of interest, said region having a nucleic
acid
sequence of at least 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%,
56%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%,
75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%,
89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence
identity, based on the Clustal V method of alignment, when compared to said
all or
part of a sense strand or antisense strand from which said region is derived,
and
wherein said target gene of interest encodes a REP2 or REP2-like polypeptide;
(b)
regenerating a transgenic plant from the regenerable plant cell after step
(a),
wherein the transgenic plant comprises in its genome the suppression DNA
39
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
construct;
(c) obtaining a progeny plant derived from the transgenic plant, wherein the
progeny
plant comprises in its genome the suppression DNA construct; and (d)
evaluating
root architecture of the progeny plant compared to a control plant not
comprising the
suppression DNA construct.
A method of determining an alteration of an agronomic characteristic in a
plant, comprising (a) introducing into a regenerable plant cell a recombinant
DNA
construct comprising a polynucleotide operably linked to at least on
regulatory
sequence (preferably a promoter functional in a plant), wherein said
polynucleotide
encodes a polypeptide having an amino acid sequence of at least 50%, 51 %,
52%,
53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 56%, 62%, 63%, 64%, 65%, 66%,
67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%,
81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%, 96%, 97%, 98%, 99%, or 100% sequence identity, based on the Clustal V
method of alignment, when compared to SEQ ID NO: 15, 17, 19, 21, 23, 25, 27,
29,
31, 33, 35, 37, 39, 41, or 42 (b) regenerating a transgenic plant from the
regenerable plant cell after step (a), wherein the transgenic plant comprises
in its
genome said recombinant DNA construct; and (c) determining whether the
transgenic plant exhibits an alteration of at least one agronomic
characteristic when
compared to a control plant not comprising the recombinant DNA construct. The
method may further comprise (d) obtaining a progeny plant derived from the
transgenic plant, wherein the progeny plant comprises in its genome the
recombinant DNA construct; and (e) determining whether the progeny plant
exhibits
an alteration of at least one agronomic characteristic when compared to a
control
plant not comprising the recombinant DNA construct.
A method of determining an alteration of an agronomic characteristic in a
plant, comprising (a) introducing into a regenerable plant cell a suppression
DNA
construct comprising at least one regulatory sequence (preferably a promoter
functional in a plant) operably linked to all or part of (i) a nucleic acid
sequence
encoding a polypeptide having an amino acid sequence of at least 50%, 51 %,
52%,
53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 56%, 62%, 63%, 64%, 65%, 66%,
67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%,
81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
95%, 96%, 97%, 98%, 99%, or 100% sequence identity, based on the Clustal V
method of alignment, when compared to SEQ ID NO: 15, 17, 19, 21, 23, 25, 27,
29,
31, 33, 35, 37, 39, 41, or 42 or (ii) a full complement of the nucleic acid
sequence of
(i); (b) regenerating a transgenic plant from the regenerable plant cell after
step (a),
wherein the transgenic plant comprises in its genome the suppression DNA
construct; and (c) determining whether the transgenic plant exhibits an
alteration in
at least one agronomic characteristic when compared to a control plant not
comprising the suppression DNA construct. The method may further comprise (d)
obtaining a progeny plant derived from the transgenic plant, wherein the
progeny
plant comprises in its genome the suppression DNA construct; and (e)
determining
whether the progeny plant exhibits an alteration in at least one agronomic
characteristic when compared to a control plant not comprising the suppression
DNA construct.
A method of determining an alteration of an agronomic characteristic in a
plant, comprising (a) introducing into a regenerable plant cell a recombinant
DNA
construct comprising a polynucleotide operably linked to at least one
regulatory
sequence (preferably a promoter functional in a plant), wherein said
polynucleotide
encodes a polypeptide having an amino acid sequence of at least 50%, 51 %,
52%,
53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 56%, 62%, 63%, 64%, 65%, 66%,
67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%,
81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%, 96%, 97%, 98%, 99%, or 100% sequence identity, based on the Clustal V
method of alignment, when compared to SEQ ID NO: 15, 17, 19, 21, 23, 25, 27,
29,
31, 33, 35, 37, 39, 41, or 42 (b) regenerating a transgenic plant from the
regenerable plant cell after step (a), wherein the transgenic plant comprises
in its
genome said recombinant DNA construct; (c) obtaining a progeny plant derived
from
said transgenic plant, wherein the progeny plant comprises in its genome the
recombinant DNA construct; and (d) determining whether the progeny plant
exhibits
an alteration of at least one agronomic characteristic when compared to a
control
plant not comprising the recombinant DNA construct. The method of determining
an
alteration of an agronomic characteristic in a plant may further comprise
determining
whether the transgenic plant exhibits an alteration of at least one agronomic
characteristic when compared, under varying environmental conditions, to a
control
41
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
plant not comprising the recombinant DNA construct.
A method of determining an alteration of an agronomic characteristic in a
plant, comprising (a) introducing into a regenerable plant cell a suppression
DNA
construct comprising at least one regulatory sequence (preferably a promoter
functional in a plant) operably linked to all or part of (i) a nucleic acid
sequence
encoding a polypeptide having an amino acid sequence of at least 50%, 51 %,
52%,
53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 56%, 62%, 63%, 64%, 65%, 66%,
67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%,
81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%, 96%, 97%, 98%, 99%, or 100% sequence identity, based on the Clustal V
method of alignment, when compared to SEQ ID NO: 15, 17, 19, 21, 23, 25, 27,
29,
31, 33, 35, 37, 39, 41, or 42 or (ii) a full complement of the nucleic acid
sequence of
(i);
(b) regenerating a transgenic plant from the regenerable plant cell after step
(a), wherein the transgenic plant comprises in its genome the suppression DNA
construct; (c) obtaining a progeny plant derived from said transgenic plant,
wherein
the progeny plant comprises in its genome the suppression DNA construct; and
(d)
determining whether the progeny plant exhibits an alteration in at least one
agronomic characteristic when compared to a control plant not comprising the
recombinant DNA construct.
A method of determining an alteration of an agronomic characteristic in a
plant, comprising: (a) introducing into a regenerable plant cell a suppression
DNA
construct comprising at least one regulatory element operably linked to a
region
derived from all or part of a sense strand or antisense strand of a target
gene of
interest, said region having a nucleic acid sequence of at least 50%, 51 %,
52%,
53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 56%, 62%, 63%, 64%, 65%, 66%,
67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%,
81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%, 96%, 97%, 98%, 99%, or 100% sequence identity, based on the Clustal V
method of alignment, when compared to said all or part of a sense strand or
antisense strand from which said region is derived, and wherein said target
gene of
interest encodes a REP2 or REP2-like polypeptide; (b) regenerating a
transgenic
plant from the regenerable plant cell after step (a), wherein the transgenic
plant
42
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
comprises in its genome the suppression DNA construct; and (c) determining
whether the transgenic plant exhibits an alteration of at least one agronomic
characteristic when compared-to a control plant not comprising the suppression
DNA construct. The method may further comprise: (d) obtaining a progeny plant
derived from the transgenic plant, wherein the progeny plant comprises in its
genome the suppression DNA construct; and (e) determining whether the progeny
plant exhibits an alteration of at least one agronomic characteristic when
compared
to a control plant not comprising the suppression DNA construct.
A method of determining an alteration of an agronomic characteristic in a
plant, comprising: (a) introducing into a regenerable plant cell a suppression
DNA
construct comprising at least one regulatory element operably linked to a
region
derived from all or part of a sense strand or antisense strand of a target
gene of
interest, said region having a nucleic acid sequence of at least 50%, 51 %,
52%,
53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 56%, 62%, 63%, 64%, 65%, 66%,
67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%,
81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%, 96%, 97%, 98%, 99%, or 100% sequence identity, based on the Clustal V
method of alignment, when compared to said all or part of a sense strand or
antisense strand from which said region is derived, and wherein said target
gene of
interest encodes a REP2 or REP2-like polypeptide; (b) regenerating a
transgenic
plant from the regenerable plant cell after step (a), wherein the transgenic
plant
comprises in its genome the suppression DNA construct; (c) obtaining a progeny
plant derived from the transgenic plant, wherein the progeny plant comprises
in its
genome the suppression DNA construct; and (d) determining whether the progeny
plant exhibits an alteration of at least one agronomic characteristic when
compared
to a control plant not comprising the suppression DNA construct.
A method of producing seed (preferably seed that can be sold as a product
offering with altered root architecture) comprising any of the preceding
preferred
methods, and further comprising obtaining seeds from said progeny plant,
wherein
said seeds comprise in their genome said recombinant DNA construct (or
suppression DNA construct).
In any of the foregoing preferred methods or any other embodiments of
methods of the present invention, the step of determining an alteration of an
43
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
agronomic characteristic in a transgenic plant, if applicable, may preferably
comprise determining whether the transgenic plant exhibits an alteration of at
least
one agronomic characteristic when compared, under varying environmental
conditions, to a control plant not comprising the recombinant DNA construct.
In any of the foregoing preferred methods or any other embodiments of
methods of the present invention, the step of determining an alteration of an
agronomic characteristic in a progeny plant, if applicable, may preferably
comprise
determining whether the progeny plant exhibits an alteration of at least one
agronomic characteristic when compared, under varying environmental
conditions,
to a control plant not comprising the recombinant DNA construct.
In any of the preceding preferred methods or any other embodiments of
methods of the present invention, in said introducing step said regenerable
plant cell
preferably comprises a callus cell (preferably embryogenic), a gametic cell, a
meristematic cell, or a cell of an immature embryo. The regenerable plant
cells are
preferably from an inbred maize plant.
In any of the preceding preferred methods or any other embodiments of
methods of the present invention, said regenerating step preferably comprises:
(i)
culturing said transformed plant cells in a media comprising an embryogenic
promoting hormone until callus organization is observed; (ii) transferring
said
transformed plant cells of step (i) to a first media which includes a tissue
organization promoting hormone; and (iii) subculturing said transformed plant
cells
after step (ii) onto a second media, to allow for shoot elongation, root
development
or both.
In any of the preceding preferred methods or any other embodiments of
methods of the present invention, alternatives exist for introducing into a
regenerable plant cell a recombinant DNA construct comprising a polynucleotide
operably linked to at least one regulatory sequence. For example, one may
introduce into a regenerable plant cell a regulatory sequence (such as one or
more
enhancers, preferably as part of a transposable element), and then screen for
an
event in which the regulatory sequence is operably linked to an endogenous
gene
encoding a polypeptide of the instant invention.
The introduction of recombinant DNA constructs of the present invention into
plants may be carried out by any suitable technique, including but not limited
to
44
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
direct DNA uptake, chemical treatment, electroporation, microinjection, cell
fusion,
infection, vector mediated DNA transfer, bombardment, or Agrobacterium
mediated
transformation.
In any of the preceding preferred methods or any other embodiments of
methods of the present invention, the at least one agronomic characteristic is
preferably selected from the group consisting of greenness, yield, growth
rate,
biomass, fresh weight at maturation, dry weight at maturation, fruit yield,
seed yield,
total plant nitrogen content, fruit nitrogen content, seed nitrogen content,
nitrogen
content in a vegetative tissue, total plant free amino acid content, fruit
free amino
acid content, seed free amino acid content, free amino acid content in a
vegetative
tissue, total plant protein content, fruit protein content, seed protein
content, protein
content in a vegetative tissue, drought tolerance, nitrogen uptake, root mass,
root
lodging, stalk lodging, plant height, ear length, stalk lodging and harvest
index.
Yield, greenness, biomass and root lodging are particularly preferred
agronomic
characteristics for alteration (preferably an increase).
In any of the preceding preferred methods or any other embodiments of methods
of
the present invention, the plant preferably exhibits the alteration of at
least one
agronomic characteristic irrespective of the environmental conditions when
compared to a control.
The introduction of recombinant DNA constructs of the present invention into
plants may be carried out by any suitable technique, including but not limited
to
direct DNA uptake, chemical treatment, electroporation, microinjection, cell
fusion,
infection, vector mediated DNA transfer, bombardment, or Agrobacterium
mediated
transformation.
Preferred techniques are set forth below in the Examples below for
transformation of maize plant cells and soybean plant cells.
Other preferred methods for transforming dicots, primarily by use of
Agrobacterium tumefaciens, and obtaining transgenic plants include those
published
for cotton (U.S. Patent No. 5,004,863, U.S. Patent No. 5,159,135, U.S. Patent
No.
5,518, 908); soybean (U.S. Patent No. 5,569,834, U.S. Patent No. 5,416,011,
McCabe et. al., Bio/Technology 6:923 (1988), Christou et al., Plant Physiol.
87:671
674 (1988)); Brassica (U.S. Patent No. 5,463,174); peanut (Cheng et al., Plant
Cell
Rep. 15:653 657 (1996), McKently et al., Plant Cell Rep. 14:699 703 (1995));
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
papaya; and pea (Grant et al., Plant Cell Rep. 15:254 258, (1995)).
Transformation of monocotyledons using electroporation, particle
bombardment, and Agrobacterium have also been reported and are included as
preferred methods, for example, transformation and plant regeneration as
achieved
in asparagus (Bytebier et al., Proc. Natl. Acad. Sci. U.S.A. 84:5354, (1987));
barley
(Wan and Lemaux, Plant Physiol. 104:37 (1994)); Zea mays (Rhodes et al.,
Science
240:204 (1988), Gordon-Kamm et al., Plant Cell 2:603 618 (1990), Fromm et al.,
Bio/Technology 8:833 (1990), Koziel et al., Bio/Technology 11:194, (1993),
Armstrong et al., Crop Science 35:550-557 (1995)); oat (Somers et al.,
Bio/Technology 10:1589 (1992)); orchard grass (Horn et al., Plant Cell Rep.
7:469
(1988)); rice (Toriyama et al., Theor. Appl. Genet. 205:34, (1986); Part et
al., Plant
Mol. Biol. 32:1135 1148, (1996); Abedinia et al., Aust. J. Plant Physiol.
24:133 141
(1997); Zhang and Wu, Theor. Appl. Genet. 76:835 (1988); Zhang et al., Plant
Cell
Rep. 7:379, (1988); Battraw and Hall, Plant Sci. 86:191 202 (1992); Christou
et al.,
Bio/Technology 9:957 (1991)); rye (De la Pena et al., Nature 325:274 (1987));
sugarcane (Bower and Birch, Plant J. 2:409 (1992)); tall fescue (Wang et al.,
Bio/Technology 10:691 (1992)), and wheat (Vasil et al., Bio/Technology 10:667
(1992); U.S. Patent No. 5,631,152).
There are a variety of methods for the regeneration of plants from plant
tissue. The particular method of regeneration will depend on the starting
plant
tissue and the particular plant species to be regenerated.
The regeneration, development, and cultivation of plants from single plant
protoplast transformants or from various transformed explants is well known in
the
art (Weissbach and Weissbach, In: Methods for Plant Molecular Biology, (Eds.),
Academic Press, Inc. San Diego, CA, (1988)). This regeneration and growth
process typically includes the steps of selection of transformed cells,
culturing those
individualized cells through the usual stages of embryonic development through
the
rooted plantlet stage. Transgenic embryos and seeds are similarly regenerated.
The resulting transgenic rooted shoots are thereafter planted in an
appropriate plant
growth medium such as soil.
The development or regeneration of plants containing the foreign, exogenous
isolated nucleic acid fragment that encodes a protein of interest is well
known in the
art. Preferably, the regenerated plants are self-pollinated to provide
homozygous
46
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
transgenic plants. Otherwise, pollen obtained from the regenerated plants is
crossed to seed-grown plants of agronomically important lines. Conversely,
pollen
from plants of these important lines is used to pollinate regenerated plants.
A
transgenic plant of the present invention containing a desired polypeptide is
cultivated using methods well known to one skilled in the art.
EXAMPLES
The present invention is further illustrated in the following Examples, in
which
parts and percentages are by weight and degrees are Celsius, unless otherwise
stated. It should be understood that these Examples, while indicating
preferred
embodiments of the invention, are given by way of illustration only. From the
above
discussion and these Examples, one skilled in the art can ascertain the
essential
characteristics of this invention, and without departing from the spirit and
scope
thereof, can make various changes and modifications of the invention to adapt
it to
various usages and conditions. Thus, various modifications of the invention in
addition to those shown and described herein will be apparent to those skilled
in the
art from the foregoing description. Such modifications are also intended to
fall
within the scope of the appended claims.
EXAMPLE 1
Creation of an Arabidopsis Population with Activation-Tapped Genes
A 18.5kb T-DNA based binary construct was created, pHSbarENDs2 (SEQ
ID NO:1;) containing four multimerized enhancer elements derived from the
Cauliflower Mosaic Virus 35S promoter, corresponding to sequences -341 to -64,
as
defined by Odell et al. (1985) Nature 313:810-812. The construct also contains
vector sequences (pUC9) to allow plasmid rescue, transposon sequences (Ds) to
remobilize the T-DNA, and the bar gene to allow for glufosinate selection of
transgenic plants. Only the 10.8kb segment from the right border (RB) to left
border
(LB) inclusive will be transferred into the host plant genome. Since the
enhancer
elements are located near the RB, they can induce cis-activation of genomic
loci
following T-DNA integration.
The pHSbarENDs2 construct was transformed into Agrobacterium
tumefaciens strain C58, grown in LB at 25 C to OD600 -1Ø Cells were then
pelleted by centrifugation and resuspended in an equal volume of 5%
sucrose/0.05% Silwet L-77 (OSI Specialties, Inc). At early bolting, soil grown
47
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
Arabidopsis thaliana ecotype Col-0 were top watered with the Agrobacterium
suspension. A week later, the same plants were top watered again with the same
Agrobacterium strain in sucrose/Silwet. The plants were then allowed to set
seed
as normal. The resulting T, seed were sown on soil, and transgenic seedlings
were
selected by spraying with glufosinate (Finale ; AgrEvo; Bayer Environmental
Science). T2 seed was collected from approximately 35,000 individual
glufosinate
resistant T, plants. T2 plants were grown and equal volumes of T3 seed from 96
separate T2 lines were pooled. This constituted 360 sub-populations.
A total of 100,000 glufosinate resistant T, seedlings were selected. T2 seeds
from each line were kept separate.
EXAMPLE 2
Screens to Identify Lines with Altered Root Architecture
Activation-tagged Arabidopsis seedlings, grown under non-limiting nitrogen
conditions, were analyzed for altered root system architecture when compared
to
control seedlings during early development from the population described in
Example 1.
From each of 96,000 separate T1 activation-tagged lines, ten T2 seeds were
sterilized with chlorine gas and planted on petri plates containing the
following
medium: 0.5x N-Free Hoagland's, 60 mM KNO3, 0.1 % sucrose, 1 mM MES and 1 %
PhytagelTM. Typically 10 plates were placed in a rack. Plates were kept for
three
days at 4 C to stratify seeds and then held vertically for 11 days at 22 C
light and
20 C dark. Photoperiod was 16 h; 8 h dark, average light intensity was -180
pmol/m2/s. Racks (typically holding 10 plates each) were rotated daily within
each
shelf. At day 14, plates were evaluated for seedling status, whole plate
digital
images were taken, and analyzed for root area. Plates were arbitrarily divided
in 10
horizontal areas. The root area in each of 10 horizontal zones on the plate
was
expressed as a percentage of the total area. Only areas in zones 3 to 9 were
used
to calculate the total root area of the line. Rootbot image analysis tool
(proprietary)
was developed by ICORIA to assess root area. Total root area was expressed in
mm2.
Lines with enhanced root growth characteristics were expected to lie at the
upper extreme of the root area distributions. A sliding window approach was
used
to estimate the variance in root area for a given rack with the assumption
that there
48
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
could be up to two outliers in the rack. Environmental variations in various
factors
including growth media, temperature, and humidity can cause significant
variation in
root growth, especially between sow dates. Therefore the lines were grouped by
sow date and shelf for the data analysis. The racks in a particular sow
date/shelf
group were then sorted by mean root area. Root area distributions for sliding
windows were performed by combining data for a rack, r;, with data from the
rack
with the next lowest, (r;_1, and the next highest mean root area, r;+1. The
variance of
the combined distribution was then analyzed to identify outliers in r; using a
Grubbs-
type approach (Barnett et al., Outliers in Statistical Data, John Wiley &
Sons, 3rd
edition (1994).
Lines with significant enhanced root growth as determined by the method
outlined above, were designated as Phase 1 hits. Phase 1 hits were re-screened
in
duplicate under the same assay conditions. When either or both of the Phase 2
replicates showed a significant difference from the mean, the line was then
considered a validated root architecture lineThose lines that were again found
to be
outliers in at least one plate in Phase 2 were subjected to a phase 3
screening
performed both in house, to validate the results obtained in phase 1 and phase
2.
The results were validated in phase 3 using both the Rootboot image analysis
(as
described above) and WinRHIZO 'as described below. The confirmation was
performed in the same fashion as in the first round of screening. T2 seeds
were
sterilized using 50% household bleach .01 % triton X-100 solution and plated
onto
the same plate medium as described in the first round of screening at a
density of
10 seeds/plate. Plates were kept for three days at 4 C to stratify seeds, and
grown
in the same temperature and photoperiod as the first experiment with the light
intensity -160 pmol/m2/s. Plates were placed vertically into the eight center
positions of a 10 plate rack with the first and last position holding blank
plates. The
racks and the plates within a rack were rotated every other day. Two sets of
pictures were taken for each plate. The first set taking place at day 14 - 16
when
the primary roots for most lines had reached the bottom of the plate, the
second set
of pictures two days later after more lateral roots had developed. The latter
set of
picture was usually used for data analysis. These seedlings grown on vertical
plates were analyzed for root growth with the software WinRHIZO (Regent
Instruments Inc), an image analysis system specifically designed for root
49
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
measurement. WinRHIZO uses the contrast in pixels to distinguish the light
root
from the darker background. To identify the maximum amount of roots without
picking up background, the pixel classification was 150 - 170 and the filter
feature
was used to remove objects that have a length/width ratio less then 10Ø The
area
on the plates analyzed was from the edge of the plant's leaves to about 1 cm
from
the bottom of the plate. The exact same WinRHIZO settings and area of
analysis
were used to analyze all plates within a batch. The total root length score
given by
WinRHIZO for a plate was divided by the number of plants that had germinated
and had grown halfway down the plate. Three plates for every line were grown
and
their scores were averaged. This average was then compared to the average of
three plates containing wild type seeds that were grown at the same time.
Arabidopsis activation tagged lines re-confirmed by having a higher value of
root growth compared to wild type were then used for the molecular
identification of
the DNA flanking the T-DNA insertion.
EXAMPLE 3
Identification of Activation-Tagged Genes
Genes flanking the T-DNA insert in lines with altered root architecture are
identified using one, or both, of the following two standard procedures: (1)
thermal
asymmetric interlaced (TAIL) PCR (Liu et al., (1995), Plant J. 8:457-63); and
(2)
SAIFF PCR (Siebert et al., (1995) Nucleic Acids Res. 23:1087-1088). In lines
with
complex multimerized T-DNA inserts, TAIL PCR and SAIFF PCR may both prove
insufficient to identify candidate genes. In these cases, other procedures,
including
inverse PCR, plasmid rescue and/or genomic library construction, can be
employed.
A successful result is one where a single TAIL or SAIFF PCR fragment
contains a T-DNA border sequence and Arabidopsis genomic sequence.
Once a tag of genomic sequence flanking a T-DNA insert is obtained,
candidate genes are identified by alignment to publicly available Arabidopsis
genome sequence.
Specifically, the annotated gene nearest the 35S enhancer elements/T-DNA
RB are candidates for genes that are activated.
To verify that an identified gene is truly near a T-DNA and to rule out the
possibility that the TAIL/SAIFF fragment is a chimeric cloning artifact, a
diagnostic
PCR on genomic DNA is done with one oligo in the T-DNA and one oligo specific
for
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
the candidate gene. Genomic DNA samples that give a PCR product are
interpreted as representing a T-DNA insertion. This analysis also verifies a
situation
in which more than one insertion event occurs in the same line, e.g., if
multiple
differing genomic fragments are identified in TAIL and/or SAIFF PCR analyses.
EXAMPLE 4
Identification of Activation Jagged reg2 Gene
One line displaying altered root architecture was further analyzed. DNA from
the line was extracted and the T-DNA insertion was found by ligation mediated
PCR
(Siebert et al., (1995) Nucleic Acids Res. 23:1087-1088) using primers within
the
LeftBorder of the T-DNA. Once a tag of genomic sequence flanking a T-DNA
insert
was obtained, the candidate gene was identified by sequence alignment to the
completed Arabidopsis genome. One of the insertion sites identified from line
126515 was identified as a chimeric insertion; Left Border T-DNA sequence was
determined to be at both ends of the T-DNA insertion. It was still possible
that the
enhancer elements located near the Right Border of the T-DNA are close enough
to
have an effect on the nearby candidate gene. In this case the location of the
Right
Border was assumed to be present at the insertion site, and the two genes that
flank
the insertion site were chosen as candidates. In the case of line 126515, one
of the
genes nearest the 35S enhancers of the chimeric insertion was At5g19590 (SEQ
ID
NO:48; NCBI GI NO:15241137 ; Arabidopsis thaliana unknown protein), encoding
the REP2 protein (SEQ ID NO:42).
EXAMPLE 5
Validation of a Candidate Arabidopsis Gene (AT5G19590)
via Transformation into Arabidopsis
The candidate gene AT5G19590 was transformed into Arabidopsis and
overexpressed under the 35S promoter. If the same or similar phenotype was
observed in the transgenic line as in the parent activation-tagged line, then
the
candidate gene was considered to be a validated "lead gene" in Arabidopsis.
The
Arabidopsis AT5G19590 gene was directly tested for its ability to enhance Root
Architecture in Arabidopsis.
The Arabidopsis AT5G1 9590 cDNA was PCR amplified with oligos that
introduce the attB1 sequence (SEQ ID NO:52), a consensus start sequence
(CAACA) upstream of the ATG start codon and the first 24 nucleotides of the
protein
51
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
coding-region of the AT5G1 9590 cDNA (SEQ ID NO:49) and the attB2 sequence
(SEQ ID NO:53) and the last 21 nucleotides of the protein-coding region
including
the stop codon of said cDNA. Using Invitrogen TM Gateway technology a
MultiSite
Gateway BP Recombination Reaction was performed with pDONRTM/Zeo
(Invitrogen T"', SEQ ID NO:2). This process removes the bacteria lethal ccdB
gene,
as well as the chloramphenicol resistance gene (CAM) from pDONRTM/Zeo and
directionally clones the PCR product with flanking attB1 (SEQ ID NO:52) and
attB2
(SEQ ID NO:53) sites creating entry clone PHP34600.
A 16.8-kb T-DNA based binary vector, called pBC-yellow (SEQ ID NO:4),
was constructed with the 1.3-kb 35S promoter immediately upstream of the
InvitrogenTM Gateway C1 conversion insert containing the ccdB gene and the
chloramphenicol resistance gene (CAM) flanked by attR1 and attR2 sequences.
The vector also contains a YFP marker under the control of the Rd29a promoter
for
the selection of transformed seeds.
Using Invitrogen TM Gateway technology a MultiSite Gateway LR
Recombination Reaction was performed on the entry clone containing the
directionally cloned PCR product and pBC-yellow. This allowed rapid and
directional cloning of the AT5G1 9590 gene behind the 35S promoter in pBC-
yellow.
The 35Spromoter::AT5G19590 expression construct was introduced into
wild-type Arabidopsis ecotype Col-0, using the same Agrobacterium-mediated
transformation procedure described in Example 1.
Transgenic T1 seeds were selected by the presence of the fluorescent YFP
marker. Fluorescent seeds were subjected to the Root Architecture Assay
following
the procedure described in Example 2. Transgenic T1 seeds were re-screened
using 6 plates per construct. Two plates per rack containing non-transformed
Columbia seed discarded from fluorescent seed sorting served as a control.
Six plates per construct were analyzed statistically and a trend was detected
between the number of plants growing on a plate and their average WinRHIZO
score. WinRHIZO scores were normalized for this trend and the root score
corresponding to the construct was divided by the wild-type root score.
52
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
EXAMPLE 6
Preparation of cDNA Libraries:
Isolation and Sequencing of cDNA Clones
cDNA libraries may be prepared by any one of many methods available. For
example, the cDNAs may be introduced into plasmid vectors by first preparing
the
cDNA libraries in Uni-ZAPTM XR vectors according to the manufacturer's
protocol
(Stratagene Cloning Systems, La Jolla, CA). The Uni-ZAPTM XR libraries are
converted into plasmid libraries according to the protocol provided by
Stratagene.
Upon conversion, cDNA inserts will be contained in the plasmid vector
pBluescript.
In addition, the cDNAs may be introduced directly into precut Bluescript II
SK(+)
vectors (Stratagene) using T4 DNA ligase (New England Biolabs), followed by
transfection into DH10B cells according to the manufacturer's protocol (GIBCO
BRL
Products). Once the cDNA inserts are in plasmid vectors, plasmid DNAs are
prepared from randomly picked bacterial colonies containing recombinant
pBluescript plasmids, or the insert cDNA sequences are amplified via
polymerase
chain reaction using primers specific for vector sequences flanking the
inserted
cDNA sequences. Amplified insert DNAs or plasmid DNAs are sequenced in dye-
primer sequencing reactions to generate partial cDNA sequences (expressed
sequence tags or "ESTs"; see Adams et al., (1991) Science 252:1651-1656). The
resulting ESTs are analyzed using a Perkin Elmer Model 377 fluorescent
sequencer.
Full-insert sequence (FIS) data is generated utilizing a modified
transposition
protocol. Clones identified for FIS are recovered from archived glycerol
stocks as
single colonies, and plasmid DNAs are isolated via alkaline lysis. Isolated
DNA
templates are reacted with vector primed M13 forward and reverse
oligonucleotides
in a PCR-based sequencing reaction and loaded onto automated sequencers.
Confirmation of clone identification is performed by sequence alignment to the
original EST sequence from which the FIS request is made.
Confirmed templates are transposed via the Primer Island transposition kit (PE
Applied Biosystems, Foster City, CA) which is based upon the Saccharomyces
cerevisiae Tyl transposable element (Devine and Boeke (1994) Nucleic Acids
Res.
22:3765-3772). The in vitro transposition system places unique binding sites
randomly throughout a population of large DNA molecules. The transposed DNA is
53
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
then used to transform DH10B electro-competent cells (Gibco BRL/Life
Technologies, Rockville, MD) via electroporation. The transposable element
contains an additional selectable marker (named DHFR; Fling and Richards
(1983)
Nucleic Acids Res. 11:5147-5158), allowing for dual selection on agar plates
of only
those subclones containing the integrated transposon. Multiple subclones are
randomly selected from each transposition reaction, plasmid DNAs are prepared
via
alkaline lysis, and templates are sequenced (ABI Prism dye-terminator
ReadyReaction mix) outward from the transposition event site, utilizing unique
primers specific to the binding sites within the transposon.
Sequence data is collected (ABI Prism Collections) and assembled using
Phred and Phrap (Ewing et al. (1998) Genome Res. 8:175-185; Ewing and Green
(1998) Genome Res. 8:186-194). Phred is a public domain software program which
re-reads the ABI sequence data, re-calls the bases, assigns quality values,
and
writes the base calls and quality values into editable output files. The Phrap
sequence assembly program uses these quality values to increase the accuracy
of
the assembled sequence contigs. Assemblies are viewed by the Consed sequence
editor (Gordon et al. (1998) Genome Res. 8:195-202).
In some of the clones the cDNA fragment corresponds to a portion of the
3'-terminus of the gene and does not cover the entire open reading frame. In
order
to obtain the upstream information one of two different protocols are used.
The first
of these methods results in the production of a fragment of DNA containing a
portion
of the desired gene sequence while the second method results in the production
of
a fragment containing the entire open reading frame. Both of these methods use
two rounds of PCR amplification to obtain fragments from one or more
libraries.
The libraries some times are chosen based on previous knowledge that the
specific
gene should be found in a certain tissue and some times are randomly-chosen.
Reactions to obtain the same gene may be performed on several libraries in
parallel
or on a pool of libraries. Library pools are normally prepared using from 3 to
5
different libraries and normalized to a uniform dilution. In the first round
of
amplification both methods use a vector-specific (forward) primer
corresponding to a
portion of the vector located at the 5'-terminus of the clone coupled with a
gene-specific (reverse) primer. The first method uses a sequence that is
complementary to a portion of the already known gene sequence while the second
54
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
method uses a gene-specific primer complementary to a portion of the
3'-untranslated region (also referred to as UTR). In the second round of
amplification a nested set of primers is used for both methods. The resulting
DNA
fragment is ligated into a pBluescript vector using a commercial kit and
following the
manufacturer's protocol. This kit is selected from many available from several
vendors including InvitrogenTM (Carlsbad, CA), Promega Biotech (Madison, WI),
and
Gibco-BRL (Gaithersburg, MD). The plasmid DNA is isolated by alkaline lysis
method and submitted for sequencing and assembly using Phred/Phrap, as above.
EXAMPLE 7
Identification of cDNA Clones
cDNA clones encoding REP2-like polypeptides can be identified by
conducting BLAST (Basic Local Alignment Search Tool; Altschul et al. (1993) J.
Mol. Biol. 215:403-410; see also the explanation of the BLAST algorithm on the
world wide web site for the National Center for Biotechnology Information at
the
National Library of Medicine of the National Institutes of Health) searches
for
similarity to amino acid sequences contained in the BLAST "nr" database
(comprising all non-redundant GenBank CDS translations, sequences derived from
the 3-dimensional structure Brookhaven Protein Data Bank, the last major
release
of the SWISS-PROT protein sequence database, EMBL, and DDBJ databases).
The DNA sequences from clones can be translated in all reading frames and
compared for similarity to all publicly available protein sequences contained
in the
"nr" database using the BLASTX algorithm (Gish and States (1993) Nat. Genet.
3:266-272) provided by the NCBI. The polypeptides encoded by the cDNA
sequences can be analyzed for similarity to all publicly available amino acid
sequences contained in the "nr" database using the BLASTP algorithm provided
by
the National Center for Biotechnology Information (NCBI). For convenience, the
P-value (probability) or the E-value (expectation) of observing a match of a
cDNA-
encoded sequence to a sequence contained in the searched databases merely by
chance as calculated by BLAST are reported herein as "pLog" values, which
represent the negative of the logarithm of the reported P-value or E-value.
Accordingly, the greater the pLog value, the greater the likelihood that the
cDNA-
encoded sequence and the BLAST "hit" represent homologous proteins.
ESTs sequences can be compared to the Genbank database as described
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
above. ESTs that contain sequences more 5- or 3-prime can be found by using
the
BLASTn algorithm (Altschul et al (1997) Nucleic Acids Res. 25:3389-3402.)
against
the Du Pont proprietary database comparing nucleotide sequences that share
common or overlapping regions of sequence homology. Where common or
overlapping sequences exist between two or more nucleic acid fragments, the
sequences can be assembled into a single contiguous nucleotide sequence, thus
extending the original fragment in either the 5 or 3 prime direction. Once the
most
5-prime EST is identified, its complete sequence can be determined by Full
Insert
Sequencing as described above. Homologous genes belonging to different species
can be found by comparing the amino acid sequence of a known gene (from either
a
proprietary source or a public database) against an EST database using the
tBLASTn algorithm. The tBLASTn algorithm searches an amino acid query against
a nucleotide database that is translated in all 6 reading frames. This search
allows
for differences in nucleotide codon usage between different species, and for
codon
degeneracy.
EXAMPLE 8
Characterization of cDNA Clones Encoding
REP2-like Polypeptides
cDNA libraries representing mRNAs from various tissues of Canna edulis
(Canna), Momordica charantia (balsam pear), Brassica (mustard), Cyamopsis
tetragonoloba (guar), Zea mays (maize), Oryza sativa (rice), Glycine max
(soybean), Helianthus annuus (sunflower) and Triticum aestivum (wheat) were
prepared and cDNAs encoding REP2 polypeptides were identified. The
characteristics of the libraries are described below.
56
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
TABLE 3
cDNA Libraries from Canna, Balsam Pear, Mustard, Guar, Maize, Rice,
Soybean, Sunflower and Wheat
. . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . ................................
. . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Library Tissue Clone
___________________________
_______________________________________________________________________________
________________________________________________________
____________________________________________________________
Maize, stalk meristem. Identify genes that are
crost1 s.pk003.p21 a:fi
crostl s expressed in the meristematic region within an
s
internode.
my Myriad project submissions my.ctal n.pk0015.b12
Maize Silk pollinated and unpollinated, pooled,
cfp2n cfp2n.pk064.114:fis
Full-length enriched, normalized
Pericarp library from 21 DAP is needed for
identifying novel cellwall related genes (eg.
cpplc xylan synthase) that are specifically expressed cppl c.pk003.123:fis
during the rapid accumulation of arabinoxylan in
this tissue.
African daisy (Dimorphotheca sinuata)
dmsl c dmsl c.pk001.el 6
developing seeds.
Immature buds of Canola Rf gene knock out
ebb2c mutant line, 02SM5. Isolation of genes involved ebb2c.pkOO8.k7
in CMS restoration.
ebs1 c Sugarbeet,shoot and phloem specific genes ebsl c.pk003.n21
Chyrsobalanus icaco (coco plum) developing
seeds that accumulate large amounts of keto
ecilc eci1 c.pk007.i2
fatty acids and fatty acids with conjugated
double bonds.
Ginger (Curcuma zedoaria. aka shoti starch)
ecr1 c ecr1 c.pk012.d 13
developing rhizomes
hsol c oxalate oxidase-transgenic suflower plants hsol c.pk010.g9
Guar (Cyamopsis tetragonoloba) seeds
Ids1 c Ids1 c.pk015.17
harvested at 15 DAF
Soybean (Glycine max L., Wye) germinating
sgc6c sgc6c.pk001.f21
cotyledon (all yellow; 16-26 DAG).
sr1 Soybean Root srl.pk0078.a4
57
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
vpl l c Grape (Vitis sp.) In vitro plantlets vpl l c.pk007.b20
African daisy (Dimorphotheca sinuata)
dms1 c dms1 c.pk001.e16:fis
developing seeds.
Immature buds of Canola Rf gene knock out
ebb2c mutant line, 02SM5. Isolation of genes involved ebb2c.pkOO8.k7:fis
in CMS restoration.
Soybean (Glycine max L., Wye) germinating
sgc6c sgc6c.pk001.f21:fis
cotyledon (all yellow; 16-26 DAG).
ebsl c Sugarbeet,shoot and phloem specific genes ebsl c.pk003.n2l :fis
Chyrsobalanus icaco (coco plum) developing
seeds that accumulate large amounts of keto
ecilc ecil c.pk007.i2:fis
fatty acids and fatty acids with conjugated
double bonds.
Ginger (Curcuma zedoaria. aka shoti starch)
ecr1 c ecrl c.pk012.d13:fis
developing rhizomes
vpl l c Grape (Vitis sp.) In vitro plantlets vpl l c.pk007.b20:fis
oxalate oxidase-
hsolc oxalate oxidase-transgenic sunflower plants transgenic sunflower
plants
srl Soybean Root srl.pk0078.a4:fis
The BLASTX search using the EST sequences from clones listed in Table 1
revealed similarity of the polypeptides encoded by the cDNAs to REP2-like
polypeptides from Oryza sativa (GI No. 115463429, 125552383, 115438148, and
125533926 corresponding to SEQ ID NO's :43, 44, 45, and 46, respectively) and
to
Polpulus trichocarpa (GI No. 118487434 corresponding to SEQ ID NO:47). Shown
in Table 4 are the BLAST results for individual ESTs ("EST"), the sequences of
the
entire cDNA inserts comprising the indicated cDNA clones ("FIS"), the
sequences of
contigs assembled from two or more EST, FIS or PCR sequences ("Contig"), or
sequences encoding an entire or functional protein derived from a FIS or a
contig
("CGS"):
58
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
TABLE 4
BLAST Results and Percent Identity for Sequences Encoding Polypeptides
Homologous to REP2-like Polypeptides
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . .
. . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ..
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . .
Sequence Statu NCBI GI No. BLAST % identity
s pLog
Score
crostl s.pk003.p2l a:fis CGS 115463429 (Rice) 51 59.5
SEQ ID NO:14 (SEQ ID NO:61)
my.ctal n.pk0015.b12 CGS 125552383 (Rice) 42 55.3
SEQ ID NO:16 (SEQ ID NO:61)
cfp2n.pk064.114:fis CGS 115438148 (Rice) 49 76.3
SEQ ID NO:18 (SEQ ID NO:62)
cppl c.pk003.123:fis CGS 125533926 (Rice) 43 58.0
SEQ ID NO:20 SEQ ID NO:61
Idsl c.pkO15.17 EST 118487434 49 60.7
SEQ ID NO:22
dmsl c.pk001.e16:fis CGS 118487434 51 68.7
SEQ ID NO:24 SEQ ID NO:61
ebb2c.pkOO8.k7:fis CGS 15241137 56 82.0
SEQ ID NO:26 SEQ ID NO:66
sgc6c.pk001.f21:fis CGS 118487434 50 60.7
SEQ ID NO:28 SEQ ID NO:61
ebsl c.pk003.n21:fis CGS 118487434 44 59.3
SEQ ID NO:30 SEQ ID NO:64
ecil c.pk007.i2:fis CGS 118487434 53 71.3
SEQ ID NO:32 SEQ ID NO:66
ecrlc.pk012.d13:fis:fis CGS 15241137 41 52.7
SEQ ID NO:34 SEQ ID NO:64
vpl l c.pk007.b20:fis CGS 118487434 48 63.3
SEQ ID NO:36 SEQ ID NO:62
hsol c.pkO10.g9:fis CGS 118487434 46 64.7
SEQ ID NO:38 SEQ ID NO:61
59
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
srl.pk0078.a4:fis CGS 118487434 51 61.3
SEQ ID NO:40 SEQ ID NO:62
Figures 1A-1 B present an alignment of the amino acid sequences set forth in
SEQ ID NOs: 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, and 42 and
the
amino acid sequences of the REP2 polypeptides from Oryza sativa (GI No.
115463429, 125552383, 115438148, and 125533926 corresponding to SEQ ID
NO's :43, 44, 45, and 46, respectively) and to Polpulus trichocarpa (GI No.
118487434 corresponding to SEQ ID NO:47). Figure 2 presents the percent
sequence identities and divergence values for each sequence pair presented in
Figures 1A-1 B.
Sequence alignments and percent identity calculations were performed using
the Megalign program of the LASERGENE bioinformatics computing suite
(DNASTAR Inc., Madison, WI). Multiple alignment of the sequences was performed
using the Clustal method of alignment (Higgins and Sharp (1989) CABIOS.
5:151-153) with the default parameters (GAP PENALTY=10, GAP LENGTH
PENALTY=10). Default parameters for pairwise alignments using the Clustal
method were KTUPLE 1, GAP PENALTY=3, WINDOW=5 and DIAGONALS
SAVED=5.
Sequence alignments and BLAST scores and probabilities indicate that the
nucleic acid fragments comprising the instant cDNA clones encode REP2-like
polypeptides.
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
TABLE 5
BLAST Results for Sequences Encoding Polypeptides Homologous to REP2
Polypeptides
Sequence Status Reference Blast %
pLog identity
Score
crostl s. k003. 21 a:fis CGS SEQ ID NO: 186191 in 83 97.1
SEQ ID NO:14 U52004214272-A1
my.ctal n.pk0015.b12 CGS SEQ ID NO: 326948 in 42 92.2
SEQ ID NO:16 U52004214272-A1
cfp2n.pk064.114:fis CGS SEQ ID NO: 191053 in 54 98.7
SEQ ID NO:18 U52004214272-A1
cppl c.pk003.123:fis FIS SEQ ID NO: 311140 in 71 100.0
SEQ ID NO:20 U52004214272-A1.
Idslc.pk015.17 CGS SEQ ID NO:6482 in 68 100
SEQ ID NO:22 US2007277269
dmslc.pk001.e16:fis CGS SEQ ID NO:62116 in 46 97.8
SEQ ID NO:24 US2007061916
ebb2c.pkOO8.k7:fis CGS SEQ ID NO:6992 in 57 100
SEQ ID NO:26 US2006107345-Al
sgc6c.pk001.f21:fis EST SEQ ID NO:6482 in 85 95.6
SEQ ID NO:28 US2007277269
61
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
Sequence Status Reference Blast %
pLog identity
Score
ebsl c. k003.n21:fis CGS SEQ ID NO:62116 in 45 97.3
SEQ ID NO:30 US2007061916
ecilc.pk007.i2:fis CGS SEQ ID NO:62116 in 51 91.3
SEQ ID NO:32 US2007061916
ecrlc.pk012.d13:fis:fis CGS SEQ ID NO: 62116 in 40 96.9
SEQ ID NO:34 US2007061916
vpll c.pk007.b20:fis CGS SEQ ID NO:62116 in 49 79.8
SEQ ID NO:36 US2007061916
hsolc.pk010.g9:fis EST SEQ ID NO:62116 in 43 83.1
SEQ ID NO:38 US2007061916
srl.pk0078.a4:fis EST SEQ ID NO:175578 in 85 71.3
SEQ ID NO:40 U52004031072-A1
EXAMPLE 9
Preparation of a Plant Expression Vector
Containing a Homolog of the Arabidopsis Lead Gene (AT5G1 9590)
Sequences homologous to the lead rep2 gene can be identified using
sequence comparison algorithms such as BLAST (Basic Local Alignment Search
Tool; Altschul et al., J. Mol. Biol. 215:403-410 (1993); see also the
explanation of
the BLAST algorithm on the world wide web site for the National Center for
Biotechnology Information at the National Library of Medicine of the National
Institutes of Health). Homologous rep2-like sequences, such as the ones
described
in Example 8, can be PCR-amplified by either of the following methods.
Method 1 (RNA-based): If the 5' and 3' sequence information for the protein-
coding region of a REP2 homolog is available, gene-specific primers can be
designed as outlined in Example 5. RT-PCR can be used with plant RNA to obtain
a nucleic acid fragment containing the REP2 protein-coding region flanked by
attB1
(SEQ ID NO:52) and attB2 (SEQ ID NO:53) sequences. The primer may contain a
consensus Kozak sequence (CAACA) upstream of the start codon.
62
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
Method 2 (DNA-based): Alternatively, if a cDNA clone is available for a gene
encoding a REP2 polypeptide homolog, the entire cDNA insert (containing 5' and
3'
non-coding regions) can be PCR amplified. Forward and reverse primers can be
designed that contain either the attB1 sequence and vector-specific sequence
that
precedes the cDNA insert or the attB2 sequence and vector-specific sequence
that
follows the cDNA insert, respectively. For a cDNA insert cloned into the
vector
pBluescript SK+, the forward primer VC062 (SEQ ID NO:54) and the reverse
primer
VC063 (SEQ ID NO:55) can be used.
Methods 1 and 2 can be modified according to procedures known by one
skilled in the art. For example, the primers of method 1 may contain
restriction sites
instead of attB1 and attB2 sites, for subsequent cloning of the PCR product
into a
vector containing attB1 and attB2 sites. Additionally, method 2 can involve
amplification from a cDNA clone, a lambda clone, a BAC clone or genomic DNA.
A PCR product obtained by either method above can be combined with the
Gateway donor vector, such as pDONRTM/Zeo (InvitrogenTM'; SEQ ID NO:2) or
pDONRTM221 (InvitrogenTM, SEQ ID NO:3) using a BP Recombination Reaction.
This process removes the bacteria lethal ccdB gene, as well as the
chloramphenicol
resistance gene (CAM) from pDONRTM221 and directionally clones the PCR product
with flanking attB1 and attB2 sites to create an entry clone. Using the
InvitrogenTM
Gateway ClonaseTM technology, the homologous rep2-like gene from the entry
clone can then be transferred to a suitable destination vector to obtain a
plant
expression vector for use with Arabidopsis, corn and soy, such as pBC-Yellow
(SEQ
ID NO:4), PHP27840 (SEQ ID NO:5) or PHP23236 (SEQ ID NO:6), to obtain a plant
expression vector for use with Arabidopsis, soybean and corn, respectively.
Alternatively a MultiSite Gateway LR recombination reaction between
multiple entry clones and a suitable destination vector can be performed to
create
an expression vector. An Example of this procedure is outlined in Example 14A,
describing the construction of maize expression vectors for transformation of
maize
lines.
EXAMPLE 10
Preparation of Soybean Expression Vectors and Transformation of Soybean with
Validated Arabidopsis Lead Genes and homologs thereof
Soybean plants can be transformed to overexpress the validated Arabidopsis
63
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
gene (AT5G19590) and the corresponding homologs from various species in order
to examine the resulting phenotype.
The entry clones described in Example 5 and 9 can be used to directionally
clone each gene into PHP27840 vector (SEQ ID NO:5) such that expression of the
gene is under control of the SCP1 promoter.
Soybean embryos may then be transformed with the expression vector
comprising sequences encoding the instant polypeptides.
To induce somatic embryos, cotyledons, 3-5 mm in length dissected from
surface sterilized, immature seeds of the soybean cultivar A2872, can be
cultured in
the light or dark at 26 C on an appropriate agar medium for 6-10 weeks.
Somatic
embryos, which produce secondary embryos, are then excised and placed into a
suitable liquid medium. After repeated selection for clusters of somatic
embryos
which multiply as early, globular staged embryos, the suspensions are
maintained
as described below.
Soybean embryogenic suspension cultures can be maintained in 35mL liquid
media on a rotary shaker, 150 rpm, at 26 C with florescent lights on a 16:8
hour
day/night schedule. Cultures are subcultured every two weeks by inoculating
approximately 35 mg of tissue into 35 mL of liquid medium.
Soybean embryogenic suspension cultures may then be transformed by the method
of particle gun bombardment (Klein et al. (1987) Nature (London) 327:70-73,
U.S.
Patent No. 4,945,050). A DuPont BiolisticTM PDS1000/HE instrument (helium
retrofit) can be used for these transformations.
A selectable marker gene which can be used to facilitate soybean
transformation is a chimeric gene composed of the 35S promoter from
cauliflower
mosaic virus (Odell et al. (1985) Nature 313:810-812), the hygromycin
phosphotransferase gene from plasmid pJR225 (from E. coli; Gritz et al. (1983)
Gene 25:179-188) and the 3' region of the nopaline synthase gene from the T-
DNA
of the Ti plasmid of Agrobacterium tumefaciens. Another selectable marker gene
which can be used to facilitate soybean transformation is an herbicide-
resistant
acetolactate synthase (ALS) gene from soybean or Arabidopsis. ALS is the first
common enzyme in the biosynthesis of the branched-chain amino acids valine,
leucine and isoleucine. Mutations in ALS have been identified that convey
resistance to some or all of three classes of inhibitors of ALS (US Patent No.
64
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
5,013,659; the entire contents of which are herein incorporated by reference).
Expression of the herbicide-resistant ALS gene can be under the control of a
SAM
synthetase promoter (U.S. Patent Application No. US-2003-0226166-A1; the
entire
contents of which are herein incorporated by reference).
To 50 pL of a 60 mg/mL 1 pm gold particle suspension is added (in order): 5
pL DNA (1 pg/pL), 20 pL spermidine (0.1 M), and 50 pL CaCl2 (2.5 M). The
particle
preparation is then agitated for three minutes, spun in a microfuge for 10
seconds
and the supernatant removed. The DNA-coated particles are then washed once in
400 pL 70% ethanol and resuspended in 40 pL of anhydrous ethanol. The
DNA/particle suspension can be sonicated three times for one second each. Five
pL of the DNA-coated gold particles are then loaded on each macro carrier
disk.
Approximately 300-400 mg of a two-week-old suspension culture is placed in
an empty 60x1 5 mm petri dish and the residual liquid removed from the tissue
with a
pipette. For each transformation experiment, approximately 5-10 plates of
tissue
are normally bombarded. Membrane rupture pressure is set at 1100 psi and the
chamber is evacuated to a vacuum of 28 inches mercury. The tissue is placed
approximately 3.5 inches away from the retaining screen and bombarded three
times. Following bombardment, the tissue can be divided in half and placed
back
into liquid and cultured as described above.
Five to seven days post bombardment, the liquid media may be exchanged
with fresh media, and eleven to twelve days post bombardment with fresh media
containing 50 mg/mL hygromycin. This selective media can be refreshed weekly.
Seven to eight weeks post bombardment, green, transformed tissue may be
observed growing from untransformed, necrotic embryogenic clusters. Isolated
green tissue is removed and inoculated into individual flasks to generate new,
clonally propagated, transformed embryogenic suspension cultures. Each new
line
may be treated as an independent transformation event. These suspensions can
then be subcultured and maintained as clusters of immature embryos or
regenerated into whole plants by maturation and germination of individual
somatic
embryos.
Enhanced root architecture can be measured in soybean by growing the
plants in soil and wash the roots before analysis of the total root mass with
WinRHIZO .
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
Soybean plants transformed with validated genes can then be assayed to
study agronomic characteristics relative to control or reference plants. For
example,
nitrogen utilization efficacy, yield enhancement and/or stability under
various
environmental conditions (e.g. nitrogen limiting conditions, drought etc.).
EXAMPLE 11
Transformation of Maize with validated Arabidopsis Lead Genes Using Particle
Bombardment
Maize plants can be transformed to overexpress a validated Arabidopsis lead
gene or the corresponding homologs from various species in order to examine
the
resulting phenotype.
The Gateway entry clones described in Example 5 can be used to
directionally clone each gene into a maize transformation vector. Expression
of the
gene in maize can be under control of a constitutive promoter such as the
maize
ubiquitin promoter (Christensen et al., Plant Mol. Biol. 12:619-632 (1989) and
Christensen et al., Plant Mol. Biol. 18:675-689 (1992))
The recombinant DNA construct described above can then be introduced into
maize cells by the following procedure. Immature maize embryos can be
dissected
from developing caryopses derived from crosses of the inbred maize lines H99
and
LH132. The embryos are isolated ten to eleven days after pollination when they
are
1.0 to 1.5 mm long. The embryos are then placed with the axis-side facing down
and in contact with agarose-solidified N6 medium (Chu et al., Sci. Sin. Peking
18:659-668 (1975)). The embryos are kept in the dark at 27 C. Friable
embryogenic callus consisting of undifferentiated masses of cells with somatic
proembryoids and embryoids borne on suspensor structures proliferates from the
scutellum of these immature embryos. The embryogenic callus isolated from the
primary explant can be cultured on N6 medium and sub-cultured on this medium
every two to three weeks.
The plasmid, p35S/Ac (obtained from Dr. Peter Eckes, Hoechst Ag,
Frankfurt, Germany) may be used in transformation experiments in order to
provide
for a selectable marker. This plasmid contains the pat gene (see European
Patent
Publication 0 242 236) which encodes phosphinothricin acetyl transferase
(PAT).
The enzyme PAT confers resistance to herbicidal glutamine synthetase
inhibitors
such as phosphinothricin. The pat gene in p35S/Ac is under the control of the
35S
66
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
promoter from cauliflower mosaic virus (Odell et al., Nature 313:810-812
(1985))
and the 3' region of the nopaline synthase gene from the T-DNA of the Ti
plasmid of
Agrobacterium tumefaciens.
The particle bombardment method (Klein et al., Nature 327:70-73 (1987))
may be used to transfer genes to the callus culture cells. According to this
method,
gold particles (1 pm in diameter) are coated with DNA using the following
technique.
Ten pg of plasmid DNAs are added to 50 pL of a suspension of gold particles
(60
mg per mL). Calcium chloride (50 pL of a 2.5 M solution) and spermidine free
base
(20 pL of a 1.0 M solution) are added to the particles. The suspension is
vortexed
during the addition of these solutions. After ten minutes, the tubes are
briefly
centrifuged (5 sec at 15,000 rpm) and the supernatant removed. The particles
are
resuspended in 200 pL of absolute ethanol, centrifuged again and the
supernatant
removed. The ethanol rinse is performed again and the particles resuspended in
a
final volume of 30 pL of ethanol. An aliquot (5 pL) of the DNA-coated gold
particles
can be placed in the center of a KaptonTM flying disc (Bio-Rad Labs). The
particles
are then accelerated into the maize tissue with a Biolistic PDS-1000/He (Bio-
Rad
Instruments, Hercules CA), using a helium pressure of 1000 psi, a gap distance
of
0.5 cm and a flying distance of 1.0 cm.
For bombardment, the embryogenic tissue is placed on filter paper over
agarose-solidified N6 medium. The tissue is arranged as a thin lawn and covers
a
circular area of about 5 cm in diameter. The petri dish containing the tissue
can be
placed in the chamber of the PDS-1000/He approximately 8 cm from the stopping
screen. The air in the chamber is then evacuated to a vacuum of 28 inches of
Hg.
The macrocarrier is accelerated with a helium shock wave using a rupture
membrane that bursts when the He pressure in the shock tube reaches 1000 psi.
Seven days after bombardment the tissue can be transferred to N6 medium
that contains bialaphos (5 mg per liter) and lacks casein or proline. The
tissue
continues to grow slowly on this medium. After an additional two weeks the
tissue
can be transferred to fresh N6 medium containing bialaphos. After six weeks,
areas
of about 1 cm in diameter of actively growing callus can be identified on some
of the
plates containing the bialaphos-supplemented medium. These calli may continue
to
grow when sub-cultured on the selective medium.
Plants can be regenerated from the transgenic callus by first transferring
67
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
clusters of tissue to N6 medium supplemented with 0.2 mg per liter of 2,4-D.
After
two weeks the tissue can be transferred to regeneration medium (Fromm et al.,
Bio/Technology 8:833-839 (1990)).
Transgenic TO plants can be regenerated and their phenotype determined
following
HTP procedures. T1 seed can be collected.
T1 plants can be grown and analyzed for phenotypic changes. The following
parameters can be quantified using image analysis: plant area, volume, growth
rate
and color analysis can be collected and quantified. Expression constructs that
result in an alteration of root architecture or any one of the agronomic
characteristics
listed above compared to suitable control plants, can be considered evidence
that
the Arabidopsis lead gene functions in maize to alter root architecture or
plant
architecture.
Furthermore, a recombinant DNA construct containing a validated
Arabidopsis gene can be introduced into an maize line either by direct
transformation or introgression from a separately transformed line.
Transgenic plants, either inbred or hybrid, can undergo more vigorous field-
based experiments to study root or plant architecture, yield enhancement
and/or
resistance to root lodging under various environmental conditions (e.g.
variations in
nutrient and water availability).
Subsequent yield analysis can also be done to determine whether plants that
contain the validated Arabidopsis lead gene have an improvement in yield
performance, when compared to the control (or reference) plants that do not
contain
the validated Arabidopsis lead gene. Plants containing the validated
Arabidopsis
lead gene would improved yield relative to the control plants, preferably 50%
less
yield loss under adverse environmental conditions or would have increased
yield
relative to the control plants under varying environmental conditions.
EXAMPLE 12
Electroporation of Agrobacterium tumefaciens LBA4404
Electroporation competent cells (40 pl), such as Agrobacterium tumefaciens
LBA4404 (containing PHP1 0523), are thawn on ice (20-30 min). PHP10523
contains VIR genes for T-DNA transfer, an Agrobacterium low copy number
plasmid
origin of replication, a tetracycline resistance gene, and a cos site for in
vivo DNA
biomolecular recombination. Meanwhile the electroporation cuvette is chilled
on ice.
68
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
The electroporator settings are adjusted to 2.1 kV.
A DNA aliquot (0.5 pL JT (US 7,087,812) parental DNA at a concentration of
0.2 pg -1.0 pg in low salt buffer or twice distilled H2O) is mixed with the
thawn
Agrobacterium cells while still on ice. The mix is transferred to the bottom
of
electroporation cuvette and kept at rest on ice for 1-2 min. The cells are
electroporated (Eppendorf electroporator 2510) by pushing "Pulse" button twice
(ideally achieving a 4.0 msec pulse). Subsequently 0.5 mL 2xYT medium (or
SOCmedium) are added to cuvette and transferred to a 15 mL Falcon tube. The
cells are incubated at 28-30 C, 200-250 rpm for 3 h.
Aliquots of 250 pL are spread onto #30B (YM + 50pg/mL Spectinomycin)
plates and incubated 3 days at 28-30 C. To increase the number of
transformants
one of two optional steps can be performed:
Option 1: overlay plates with 30 pL of 15 mg/mL Rifampicin. LBA4404 has a
chromosomal resistance gene for Rifampicin. This additional selection
eliminates
some contaminating colonies observed when using poorer preparations of LBA4404
competent cells.
Option 2: Perform two replicates of the electroporation to compensate for
poorer
electrocompetent cells.
Identification of transformants:
Four independent colonies are picked and streaked on AB minimal medium
plus 50mg/mL Spectinomycin plates (#12S medium) for isolation of single
colonies.
The plates are incubated at 28 C for 2-3 days.
A single colony for each putative co-integrate is picked and inoculated with 4
mL #60A with 50 mg/L Spectinomycin. The mix is incubated for 24 h at 28 C
with
shaking. Plasmid DNA from 4 mL of culture is isolated using Qiagen Miniprep +
optional PB wash. The DNA is eluted in 30 pL. Aliquots of 2 pL are used to
electroporate 20 pL of DH1 Ob + 20 pL of ddH2O as per above.
Optionally a 15 pL aliquot can be used to transform 75-100 pL of InvitrogenTM-
Library Efficiency DH5a. The cells are spread on LB medium plus 50mg/mL
Spectinomycin plates (#34T medium) and incubated at 37 C overnight.
Three to four independent colonies are picked for each putative co-integrate
and inoculated 4 mL of 2xYT (#60A) with 50 pg/mL Spectinomycin. The cells are
incubated at 37 C overnight with shaking.
69
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
The plasmid DNA is isolated from 4 mL of culture using QlAprep Miniprep
with optional PB wash (elute in 50 pLI) and 8 pL are used for digestion with
Sall
(using JT parent and PHP1 0523 as controls).
Three more digestions using restriction enzymes BamHI, EcoRl, and Hindlll
are performed for 4 plasmids that represent 2 putative co-integrates with
correct Sall
digestion pattern (using parental DNA and PHP1 0523 as controls). Electronic
gels
are recommended for comparison.
Alternatively, for high throughput applications, such as described for Gaspe
Bay Flint Derived Maize Lines (Examples 15-17), instead of evaluating the
resulting
co-integrate vectors by restriction analysis, three colonies can be
simultaneously
used for the infection step as described in Example 13.
EXAMPLE 13
Agrobacterium mediated transformation into maize
Maize plants can be transformed to overexpress a validated Arabidopsis lead
gene or the corresponding homologs from various species in order to examine
the
resulting phenotype.
Agrobacterium-mediated transformation of maize is performed essentially as
described by Zhao et al., in Meth. Mol. Biol. 318:315-323 (2006) (see also
Zhao et
al., Mol. Breed. 8:323-333 (2001) and U.S. Patent No. 5,981,840 issued
November
9, 1999, incorporated herein by reference). The transformation process
involves
bacterium innoculation, co-cultivation, resting, selection and plant
regeneration.
1.Immature Embryo Preparation
Immature embryos are dissected from caryopses and placed in a 2mL microtube
containing 2 mL PHI-A medium.
2.Agrobacterium Infection and Co-Cultivation of Embryos
2.1 Infection Step
PHI-A medium is removed with 1 mL micropipettor and 1 mL Agrobacterium
suspension is added. Tube is gently inverted to mix. The mixture is incubated
for 5
min at room temperature.
2.2 Co-Culture Step
The Agrobacterium suspension is removed from the infection step with a 1
mL micropipettor. Using a sterile spatula the embryos are scraped from the
tube
and transferred to a plate of PHI-B medium in a 100x15 mm Petri dish. The
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
embryos are oriented with the embryonic axis down on the surface of the
medium.
Plates with the embryos are cultured at 200C, in darkness, for 3 days. L-
Cysteine
can be used in the co-cultivation phase. With the standard binary vector, the
co-
cultivation medium supplied with 100-400 mg/L L-cysteine is critical for
recovering
stable transgenic events.
3. Selection of Putative Transgenic Events
To each plate of PHI-D medium in a 100x15 mm Petri dish, 10 embryos are
transferred, maintaining orientation and the dishes are sealed with Parafilm.
The
plates are incubated in darkness at 28 C. Actively growing putative events,
as pale
yellow embryonic tissue are expected to be visible in 6-8 weeks. Embryos that
produce no events may be brown and necrotic, and little friable tissue growth
is
evident. Putative transgenic embryonic tissue is subcultured to fresh PHI-D
plates
at 2-3 week intervals, depending on growth rate. The events are recorded.
4. Regeneration of TO plants
Embryonic tissue propagated on PHI-D medium is subcultured to PHI-E medium
(somatic embryo maturation medium); in 100x25 mm Petri dishes and incubated at
28 C, in darkness, until somatic embryos mature, for about 10-18 days.
Individual,
matured somatic embryos with well-defined scutellum and coleoptile are
transferred
to PHI-F embryo germination medium and incubated at 28 C in the light (about
80
pE from cool white or equivalent fluorescent lamps). In 7-10 days, regenerated
plants, about 10 cm tall, are potted in horticultural mix and hardened-off
using
standard horticultural methods.
Media for Plant Transformation
1. PHI-A: 4g/L CHU basal salts, 1.0 mL/L 1000X Eriksson's vitamin
mix, 0.5mg/L thiamin HCL, 1.5 mg/L 2,4-D, 0.69 g/L L-proline, 68.5
g/L sucrose, 36g/L glucose, pH 5.2. Add 100pM acetosyringone,
filter-sterilized before using.
2. PHI-B: PHI-A without glucose, increased 2,4-D to 2mg/L, reduced
sucrose to 30 g/L and supplemented with 0.85 mg/L silver nitrate
(filter-sterilized), 3.0 g/L gelrite, 100pM acetosyringone (filter-
sterilized), 5.8.
3. PHI-C: PHI-B without gelrite and acetosyringonee, reduced 2,4-D to
1.5 mg/L and supplemented with 8.0 g/L agar, 0.5 g/L Ms-morpholino
71
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
ethane sulfonic acid (MES) buffer, 100mg/L carbenicillin (filter-
sterilized).
4. PHI-D: PHI-C supplemented with 3mg/L bialaphos (filter-sterilized).
5. PHI-E: 4.3 g/L of Murashige and Skoog (MS) salts, (Gibco, BRL
11117-074), 0.5 mg/L nicotinic acid, 0.1 mg/L thiamine HCI, 0.5mg/L
pyridoxine HCI, 2.0 mg/L glycine, 0.1 g/L myo-inositol, 0.5 mg/L
zeatin (Sigma, cat.no. Z-0164), 1 mg/L indole acetic acid (IAA), 26.4
pg/L abscisic acid (ABA), 60 g/L sucrose, 3 mg/L bialaphos (filter-
sterilized), 100 mg/L carbenicillin (fileter-sterilized), 8g/L agar, pH
5.6.
6. PHI-F: PHI-E without zeatin, IAA, ABA; sucrose reduced to 40 g/L;
replacing agar with 1.5 g/L gelrite; pH 5.6.
Plants can be regenerated from the transgenic callus by first transferring
clusters of tissue to N6 medium supplemented with 0.2 mg per liter of 2,4-D.
After
two weeks the tissue can be transferred to regeneration medium (Fromm et al.
(1990) Bio/Technology 8:833-839).
Phenotypic analysis of transgenic TO plants and T1 plants can be performed.
T1 plants can be analyzed for phenotypic changes. Using image analysis T1
plants can be analyzed for phenotypical changes in plant area, volume, growth
rate
and color analysis can be taken at multiple times during growth of the plants.
Alteration in root architecture can be assayed as described in Example 20.
Subsequent analysis of alterations in agronomic characteristics can be done
to determine whether plants containing the validated Arabidopsis lead gene
have an
improvement of at least one agronomic characteristic, when compared to the
control
(or reference) plants that do not contain the validated Arabidopsis lead gene.
The
alterations may also be studied under various environmental conditions.
Expression constructs that result in a significant alteration in root
architecture
will be considered evidence that the Arabidopsis gene functions in maize to
alter
root architecture.
EXAMPLE 14A
Construction of Maize expression vectors with the Arabidopsis Lead Gene
(At5g19590 using Agrobacterium mediated Transformation
Maize expression vectors can be prepared with the Arabidopsis REP2 gene
72
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
(At5g19590) under the control of the NAS2 (SEQ ID NO:57) and GOS 2 (SEQ ID
NO:58 ) promoter. PINII is the terminator (SEQ ID NO:61)
Using Invitrogen TM Gateway technology the entry clone, created as described
in
Example 5, PHP 34600, containing the Arabidopsis REP2 gene (At5gl 9590) can be
used in separate Gateway LR reactions with:
1) the constitutive maize GOS2 promoter entry clone (PHP28408, SEQ ID
NO:1 1) and the Pinll Terminator entry clone (PHP20234, SEQ ID NO:9) into the
destination vector PHP28529 (SEQ ID NO:10). The resulting vector is named
PHP29306.
2) the root maize NAS2 promoter entry clone (PHP22020, SEQ ID NO:12)
and the Pinll Terminator entry clone (PHP20234, SEQ ID NO:9) into the
destination
vector PHP28529 (SEQ ID NO:10). The resulting vector is named PHP29307.
The destination vector PHP28529 added to each of the final vectors (PHP29306
and PHP29307) also an:
1) RD29A promoter::yellow fluorescent protein::Pinll terminator cassette for
Arabidospis seed sorting
2) a Ubiquitin promoter::moPAT/red fluorescent protein fusion::Pinll
terminator
cassette for transformation selection and Z.mays seed sorting.
EXAMPLE 14B
Preparation of a Maize expression constructs containing the Arabidopsis rep2
and
Homologs thereof.
The Arabidopsis rep2 gene and the corresponding homologs from maize and
other species (Table 1) can be transformed into maize lines using the
procedures
outlined in Examples 5A and 14A. Maize expression vectors with Arabidopsis
rep2
gene and the corresponding homologs from maize and other species (Table 1) can
be prepared as outlined in Examples 5A and14A. In addition to the GOS2 or NAS2
promoter, other promoters such as, but not limited to the ubiquitin promoter,
the S2A
and S2B promoter, the maize ROOTMET2 promoter, the maize Cyclo, the CR1 BIO,
the CRWAQ81 and the maize ZRP2.4447 are useful for directing expression of
rep2
and rep2-like genes in maize. Furthermore, a variety of terminators, such as,
but
not limited to the PINII terminator, could be used to achieve expression of
the gene
of interest in maize.
73
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
EXAMPLE 14C
Transformation of Maize Lines with the Arabidopsis Lead Gene (At5Q1 9590) and
corresponding homologs from other species using Agrobacterium mediated
Transformation
The final vectors (vectors for expression in Maize, Example 14A, and B) can be
then
electroporated separately into LBA4404 Agrobacterium containing PHP1 0523 (SEQ
ID NO:7, Komari et al. Plant J 10:165-174 (1996), NCBI GI: 59797027) to create
the
co-integrate vectors for maize transformation. The co-integrate vectors are
formed
by recombination of the final vectors (maize expression vectors) with PHP1
0523,
through the COS recombination sites contained on each vector. The co-integrate
vectors contain in addition to the expression cassettes described in Examples
14A-
C, also genes needed for the Agrobacterium strain and the Agrobacterium
mediated
transformation, JET, TET, TRFA, ORI terminator, CTL, ORI V, VIR C1, VIR C2,
VIR
G, VIR B). Transformation into a maize line can be performed as described in
Example 13.
EXAMPLE15
Preparation of the destination vectors PHP23236 and PHP29635 for
Transformation
of Gaspe Bay Flint derived Maize Lines
Destination vector PHP23236 (SEQ ID NO:6) was obtained by transformation
of Agrobacterium strain LBA4404 containing plasmid PHP10523 (SEQ ID NO:7)
with plasmid PHP23235 (SEQ ID NO:8) and isolation of the resulting co-
integration
product. Destination vector PHP23236, can be used in a recombination reaction
with an entry clone as described in Example 16 to create a maize expression
vector
for transformation of Gaspe Bay Flint derived maize lines. Expression of the
gene
of interest is under control of the ubiquitin promoter (SEQ ID NO:59).
PHP29635 (SEQ ID NO:13) was obtained by transformation of
Agrobacterium strain LBA4404 containing plasmid PHP1 0523 with plasmid
PIIOXS2a-FRT87(ni)m (SEQ ID NO:57) and isolation of the resulting co-
integration
product. Destination vector PHP29635 can be used in a recombination reaction
with an entry clone as described in Example 16 to create a maize expression
vector
for transformation of Gaspe Bay Flint derived maize lines. Expression of the
gene
of interest is under control of the S2A promoter (SEQ ID NO:60).
74
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
EXAMPLE 16
Preparation of Plasmids for Transformation of Gaspe Bay Flint Derived Maize
Lines
Using InvitrogenTM Gateway Recombination technology, entry clones containing
the Arabidopsis rep2 gene (AT5G1 9590) or a maize rep2-like homolog can be
created, as described in Examples 5A and 9 and used to directionally clone
each
gene into destination vector PHP23236 (Example 15) for expression under the
ubiquitin promoter or into destination vector PHP29635 (Example 15) for
expression
under the S2A promoter. Each of the expression vectors are T-DNA binary
vectors
for Agrobacterium-mediated transformation into corn._
Gaspe Bay Flint Derived Maize Lines can be transformed with the expression
constructs as described in Example 17.
EXAMPLE 17
Transformation of Gaspe Bay Flint Derived Maize Lines with Validated
Arabidopsis
Lead Genes and corresponding homologs from other species
Maize plants can be transformed as described in Example 16 to overexpress
the Arabidopsis AT5G19590 gene and the corresponding homologs from other
species, such as the ones listed in Table 1, in order to examine the resulting
phenotype. In addition to the promoters decribed in Example 16 other promoters
such the S2B promoter, the maize ROOTMET2 promoter, the maize Cyclo, the
CR1 BIO, the CRWAQ81 and the maize ZRP2.4447 are useful for directing
expression of rep2 and rep2-like genes in maize. Furthermore, a variety of
terminators, such as, but not limited to the PINII terminator, can be used to
achieve
expression of the gene of interest in Gaspe Bay Flint Derived Maize Lines.
Recipient Plants
Recipient plant cells can be from a uniform maize line having a short life
cycle ("fast cycling"), a reduced size, and high transformation potential.
Typical of
these plant cells for maize are plant cells from any of the publicly available
Gaspe
Bay Flint (GBF) line varieties. One possible candidate plant line variety is
the F1
hybrid of GBF x QTM (Quick Turnaround Maize, a publicly available form of
Gaspe
Bay Flint selected for growth under greenhouse conditions) disclosed in Tomes
et
al. U.S. Patent Application Publication No. 2003/0221212. Transgenic plants
obtained from this line are of such a reduced size that they can be grown in
four
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
inch pots (1/4 the space needed for a normal sized maize plant) and mature in
less
than 2.5 months. (Traditionally 3.5 months is required to obtain transgenic TO
seed
once the transgenic plants are acclimated to the greenhouse.) Another suitable
line
is a double haploid line of GS3 (a highly transformable line) X Gaspe Flint.
Yet
another suitable line is a transformable elite inbred line carrying a
transgene which
causes early flowering, reduced stature, or both.
Transformation Protocol
Any suitable method may be used to introduce the transgenes into the maize
cells, including but not limited to inoculation type procedures using
Agrobacterium
based vectors as described in Example 9. Transformation may be performed on
immature embryos of the recipient (target) plant.
Precision Growth and Plant Tracking
The event population of transgenic (TO) plants resulting from the transformed
maize embryos is grown in a controlled greenhouse environment using a modified
randomized block design to reduce or eliminate environmental error. A
randomized
block design is a plant layout in which the experimental plants are divided
into
groups (e.g., thirty plants per group), referred to as blocks, and each plant
is
randomly assigned a location with the block.
For a group of thirty plants, twenty-four transformed, experimental plants and
six control plants (plants with a set phenotype) (collectively, a "replicate
group") are
placed in pots which are arranged in an array (a.k.a. a replicate group or
block) on a
table located inside a greenhouse. Each plant, control or experimental, is
randomly
assigned to a location with the block which is mapped to a unique, physical
greenhouse location as well as to the replicate group. Multiple replicate
groups of
thirty plants each may be grown in the same greenhouse in a single experiment.
The layout (arrangement) of the replicate groups should be determined to
minimize
space requirements as well as environmental effects within the greenhouse.
Such a
layout may be referred to as a compressed greenhouse layout.
An alternative to the addition of a specific control group is to identify
those
transgenic plants that do not express the gene of interest. A variety of
techniques
such as RT-PCR can be applied to quantitatively assess the expression level of
the
introduced gene. TO plants that do not express the transgene can be compared
to
those which do.
76
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
Each plant in the event population is identified and tracked throughout the
evaluation process, and the data gathered from that plant is automatically
associated with that plant so that the gathered data can be associated with
the
transgene carried by the plant. For example, each plant container can have a
machine readable label (such as a Universal Product Code (UPC) bar code) which
includes information about the plant identity, which in turn is correlated to
a
greenhouse location so that data obtained from the plant can be automatically
associated with that plant.
Alternatively any efficient, machine readable, plant identification system can
be used, such as two-dimensional matrix codes or even radio frequency
identification tags (RFID) in which the data is received and interpreted by a
radio
frequency receiver/processor. See U.S. Published Patent Application No.
2004/0122592, incorporated herein by reference.
Phenotypic Analysis Using Three-Dimensional Imaging
Each greenhouse plant in the TO event population, including any control
plants, is analyzed for agronomic characteristics of interest, and the
agronomic data
for each plant is recorded or stored in a manner so that it is associated with
the
identifying data (see above) for that plant. Confirmation of a phenotype (gene
effect) can be accomplished in the T1 generation with a similar experimental
design
to that described above.
The TO plants are analyzed at the phenotypic level using quantitative, non-
destructive imaging technology throughout the plant's entire greenhouse life
cycle to
assess the traits of interest. Preferably, a digital imaging analyzer is used
for
automatic multi-dimensional analyzing of total plants. The imaging may be done
inside the greenhouse. Two camera systems, located at the top and side, and an
apparatus to rotate the plant, are used to view and image plants from all
sides.
Images are acquired from the top, front and side of each plant. All three
images
together provide sufficient information to evaluate the biomass, size and
morphology
of each plant.
Due to the change in size of the plants from the time the first leaf appears
from the soil to the time the plants are at the end of their development, the
early
stages of plant development are best documented with a higher magnification
from
the top. This may be accomplished by using a motorized zoom lens system that
is
77
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
fully controlled by the imaging software.
In a single imaging analysis operation, the following events occur: (1) the
plant is conveyed inside the analyzer area, rotated 360 degrees so its machine
readable label can be read, and left at rest until its leaves stop moving; (2)
the side
image is taken and entered into a database; (3) the plant is rotated 90
degrees and
again left at rest until its leaves stop moving, and (4) the plant is
transported out of
the analyzer.
Plants are allowed at least six hours of darkness per twenty four hour period
in order to have a normal day/night cycle.
Imaging Instrumentation
Any suitable imaging instrumentation may be used, including but not limited
to light spectrum digital imaging instrumentation commercially available from
LemnaTec GmbH of Wurselen, Germany. The images are taken and analyzed with
a LemnaTec Scanalyzer HTS LT-0001-2 having a 1/2" IT Progressive Scan IEE
CCD imaging device. The imaging cameras may be equipped with a motor zoom,
motor aperture and motor focus. All camera settings may be made using LemnaTec
software. Preferably, the instrumental variance of the imaging analyzer is
less than
about 5% for major components and less than about 10% for minor components.
Software
The imaging analysis system comprises a LemnaTec HTS Bonit software
program for color and architecture analysis and a server database for storing
data
from about 500,000 analyses, including the analysis dates. The original images
and
the analyzed images are stored together to allow the user to do as much
reanalyzing as desired. The database can be connected to the imaging hardware
for automatic data collection and storage. A variety of commercially available
software systems (e.g. Matlab, others) can be used for quantitative
interpretation of
the imaging data, and any of these software systems can be applied to the
image
data set.
Conveyor System
A conveyor system with a plant rotating device may be used to transport the
plants to the imaging area and rotate them during imaging. For example, up to
four
plants, each with a maximum height of 1.5 m, are loaded onto cars that travel
over
the circulating conveyor system and through the imaging measurement area. In
this
78
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
case the total footprint of the unit (imaging analyzer and conveyor loop) is
about 5 m
x5m.
The conveyor system can be enlarged to accommodate more plants at a
time. The plants are transported along the conveyor loop to the imaging area
and
are analyzed for up to 50 seconds per plant. Three views of the plant are
taken.
The conveyor system, as well as the imaging equipment, should be capable of
being used in greenhouse environmental conditions.
Illumination
Any suitable mode of illumination may be used for the image acquisition. For
example, a top light above a black background can be used. Alternatively, a
combination of top- and backlight using a white background can be used. The
illuminated area should be housed to ensure constant illumination conditions.
The
housing should be longer than the measurement area so that constant light
conditions prevail without requiring the opening and closing or doors.
Alternaively,
the illumination can be varied to cause excitation of either transgene (e.g.,
green
fluorescent protein (GFP), red fluorescent protein (RFP)) or endogenous (e.g.
Chlorophyll) fluorophores.
Biomass Estimation Based on Three-Dimensional Imaging
For best estimation of biomass the plant images should be taken from at
least three axes, preferably the top and two side (sides 1 and 2) views. These
images are then analyzed to separate the plant from the background, pot and
pollen
control bag (if applicable). The volume of the plant can be estimated by the
calculation:
Volume(voxels) = TopArea(pixels) x SidelArea(pixels) x Side2Area(pixels)
In the equation above the units of volume and area are "arbitrary units".
Arbitrary units are entirely sufficient to detect gene effects on plant size
and growth
in this system because what is desired is to detect differences (both positive-
larger
and negative-smaller) from the experimental mean, or control mean. The
arbitrary
units of size (e.g. area) may be trivially converted to physical measurements
by the
addition of a physical reference to the imaging process. For instance, a
physical
reference of known area can be included in both top and side imaging
processes.
79
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
Based on the area of these physical references a conversion factor can be
determined to allow conversion from pixels to a unit of area such as square
centimeters (cm) . The physical reference may or may not be an independent
sample. For instance, the pot, with a known diameter and height, could serve
as an
adequate physical reference.
Color Classification
The imaging technology may also be used to determine plant color and to
assign plant colors to various color classes. The assignment of image colors
to
color classes is an inherent feature of the LemnaTec software. With other
image
analysis software systems color classification may be determined by a variety
of
computational approaches.
For the determination of plant size and growth parameters, a useful
classification scheme is to define a simple color scheme including two or
three
shades of green and, in addition, a color class for chlorosis, necrosis and
bleaching,
should these conditions occur. A background color class which includes non
plant
colors in the image (for example pot and soil colors) is also used and these
pixels
are specifically excluded from the determination of size. The plants are
analyzed
under controlled constant illumination so that any change within one plant
over time,
or between plants or different batches of plants (e.g. seasonal differences)
can be
quantified.
In addition to its usefulness in determining plant size growth, color
classification can be used to assess other yield component traits. For these
other
yield component traits additional color classification schemes may be used.
For
instance, the trait known as "staygreen", which has been associated with
improvements in yield, may be assessed by a color classification that
separates
shades of green from shades of yellow and brown (which are indicative of
senescing
tissues). By applying this color classification to images taken toward the end
of the
TO or T1 plants' life cycle, plants that have increased amounts of green
colors
relative to yellow and brown colors (expressed, for instance, as Green/Yellow
Ratio)
may be identified. Plants with a significant difference in this Green/Yellow
ratio can
be identified as carrying transgenes which impact this important agronomic
trait.
The skilled plant biologist will recognize that other plant colors arise which
can indicate plant health or stress response (for instance anthocyanins), and
that
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
other color classification schemes can provide further measures of gene action
in
traits related to these responses.
Plant Architecture Analysis
Transgenes which modify plant architecture parameters may also be
identified using the present invention, including such parameters as maximum
height and width, internodal distances, angle between leaves and stem, number
of
leaves starting at nodes and leaf length. The LemnaTec system software may be
used to determine plant architecture as follows. The plant is reduced to its
main
geometric architecture in a first imaging step and then, based on this image,
parameterized identification of the different architecture parameters can be
performed. Transgenes that modify any of these architecture parameters either
singly or in combination can be identified by applying the statistical
approaches
previously described.
Pollen Shed Date
Pollen shed date is an important parameter to be analyzed in a transformed
plant, and may be determined by the first appearance on the plant of an active
male
flower. To find the male flower object, the upper end of the stem is
classified by
color to detect yellow or violet anthers. This color classification analysis
is then
used to define an active flower, which in turn can be used to calculate pollen
shed
date.
Alternatively, pollen shed date and other easily visually detected plant
attributes (e.g. pollination date, first silk date) can be recorded by the
personnel
responsible for performing plant care. To maximize data integrity and process
efficiency this data is tracked by utilizing the same barcodes utilized by the
LemnaTec light spectrum digital analyzing device. A computer with a barcode
reader, a palm device, or a notebook PC may be used for ease of data capture
recording time of observation, plant identifier, and the operator who captured
the
data.
Orientation of the Plants
Mature maize plants grown at densities approximating commercial planting
often have a planar architecture. That is, the plant has a clearly discernable
broad
side, and a narrow side. The image of the plant from the broadside is
determined.
To each plant a well defined basic orientation is assigned to obtain the
maximum
81
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
difference between the broadside and edgewise images. The top image is used to
determine the main axis of the plant, and an additional rotating device is
used to
turn the plant to the appropriate orientation prior to starting the main image
acquisition.
EXAMPLE 18
Screening of Gaspe Bay Flint Derived Maize Lines and Hybrids
Under Nitrogen Limiting Conditions
Some transgenic plants will contain two or three doses of Gaspe Flint-3 with
one dose of GS3 (GS3/(Gaspe-3)2X or GS3/(Gaspe-3)3X) and will segregate 1:1
for a dominant transgene. Other transgenic plants will be regular inbreds and
will be
used in top crosses to generate test hybrids. Plants will be planted in
Turface, a
commercial potting medium, and watered four times each day with 1 mM KNO3
growth medium and with 2 mM KNO3, or higher, growth medium (Fig.3). Control
plants grown in 1 mM KNO3 medium will be less green, produce less biomass and
have a smaller ear at anthesis. Gaspe-derived lines will be grown to flowering
stage
whereas regular inbreds and hybrids will be grown to V4 to V5 stages.
Statistics are used to decide if differences seen between treatments are
significantly different. Fig.4 illustrates one method which places letters
after the
values. Those values in the same column that have the same letter (not group
of
letters) following them are not significantly different. Using this method, if
there are
no letters following the values in a column, then there are no significant
differences
between any of the values in that column or, in other words, all the values in
that
column are equal.
Expression of a transgene will result in plants with improved plant growth in
1
mM KNO3 when compared to a transgenic null. Thus biomass and greenness data
will be collected at time of sampling (anthesis for Gaspe and V4-V5 for
others) and
compared to a transgenic null. In addition, total nitrogen in the plants will
be
analyzed in ground tissues. Improvements in growth, greenness, nitrogen
accumulation and ear size at anthesis will be indications of increased
nitrogen use
efficiency.
EXAMPLE 19
Yield Analysis of Maize Lines with Validated Arabidopsis Lead Gene (AT5G19590)
A recombinant DNA construct containing a validated Arabidopsis gene can
82
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
be introduced into a maize line either by direct transformation or
introgression from
a separately transformed line.
Transgenic plants, either inbreds or top cross hybrids, can undergo more
vigorous field-based experiments to study yield enhancement and/or stability
under
various environmental conditions, such as variations in water and nutrient
availability. A standardized yield trial will typically include 4 to 6
replications, and at
least 4 locations. Combine harvest yield data will be collected.
Subsequent yield analysis can be done to determine whether plants that
contain the validated Arabidopsis lead gene have an improvement in yield
performance under various environmental conditions, when compared to the
control
plants, either a construct null or wildtype, that do not contain the validated
Arabidopsis lead gene. Reduction in yield can be measured for both in the case
of
nitrogen or water stress environments. Plants containing the validated
Arabidopsis
lead gene have less yield loss relative to the control plants, preferably 50%
less
yield loss.
EXAMPLE 20
Screening of Gaspe Bay Flint Derived Maize Lines
Under Nitrogen Limiting Conditions
Transgenic plants will contain two or three doses of Gaspe Flint-3 with one
dose of GS3 (GS3/(Gaspe-3)2X or GS3/(Gaspe-3)3X) and will segregate 1:1 for a
dominant transgene. Plants will be planted in Turface, a commercial potting
medium, and watered four times each day with 1 mM KNO3 growth medium and
with 2 mM KNO3, or higher, growth medium (see Fig.3). Control plants grown in
1
mM KNO3 medium will be less green, produce less biomass and have a smaller ear
at anthesis (see Fig.4 for an illustration of sample data).
Statistics are used to decide if differences seen between treatments are
really different. Fig.4 illustrates one method which places letters after the
values.
Those values in the same column that have the same letter (not group of
letters)
following them are not significantly different. Using this method, if there
are no
letters following the values in a column, then there are no significant
differences
between any of the values in that column or, in other words, all the values in
that
column are equal.
Expression of a transgene will result in plants with improved plant growth in
1
83
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
mM KNO3 when compared to a transgenic null. Thus biomass and greenness (as
described in Example 17) will be monitored during growth and compared to a
transgenic null. Improvements in growth, greenness and ear size at anthesis
will be
indications of increased nitrogen tolerance.
EXAMPLE 21
Yield Analysis of Maize Lines with Validated Arabidopsis Lead Gene (AT5G19590)
A recombinant DNA construct containing a validated Arabidopsis gene can
be introduced into a maize line either by direct transformation or
introgression from
a separately transformed line.
Transgenic plants, either inbred or hybrid, can undergo more vigorous field-
based experiments to study yield enhancement and/or stability under various
environmental conditions, such as variations in water and nutrient
availability.
Subsequent yield analysis can be done to determine whether plants that
contain the validated Arabidopsis lead gene have an improvement in yield
performance under various environmental conditions, when compared to the
control
plants that do not contain the validated Arabidopsis lead gene. Reduction in
yield
can be measured for both. Plants containing the validated Arabidopsis lead
gene
have less yield loss relative to the control plants, preferably 50% less yield
loss.
EXAMPLE 22
Assays to Determine Alterations of Root Architecture in Maize
Transgenic maize plants are assayed for changes in root architecture at
seedling
stage, flowering time or maturity. Assays to measure alterations of root
architecture
of maize plants include, but are not limited to the methods outlined below. To
facilitate manual or automated assays of root architecture alterations, corn
plants
can be grown in clear pots.
1) Root mass (dry weights). Plants are grown in Turface, a growth media that
allows easy separation of roots. Oven-dried shoot and root tissues are
weighed and a root/shoot ratio calculated.
2) Levels of lateral root branching. The extent of lateral root branching
(e.g.
lateral root number, lateral root length) is determined by sub-sampling a
complete root system, imaging with a flat-bed scanner or a digital camera
and analyzing with WinRHIZOTM software (Regent Instruments Inc.).
3) Root band width measurements. The root band is the band or mass of roots
84
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
that forms at the bottom of greenhouse pots as the plants mature. The
thickness of the root band is measured in mm at maturity as a rough
estimate of root mass.
4) Nodal root count. The number of crown roots coming off the upper nodes
can be determined after separating the root from the support medium (e.g.
potting mix). In addition the angle of crown roots and/or brace roots can be
measured. Digital analysis of the nodal roots and amount of branching of
nodal roots form another extension to the aforementioned manual method.
All data taken on root phenotype are subjected to statistical analysis,
normally a t-
test to compare the transgenic roots with that of non-transgenic sibling
plants. One-
way ANOVA may also be used in cases where multiple events and/or constructs
are
involved in the analysis.
EXAMPLE 23
Analysis of Roots of Maize Seedlings containing the Arabidopsis rep2 Gene
compared to Roots from Seedlings not containing the rep2 Gene
A maize expression vector, containing the maize UBI promoter and the
Arabidopsis
rep2 (recpu3) gene was prepared as described in Example 14A. Transformation of
maize was achieved via Agrobacterium mediated transformation as described in
example 14C by creating a cointegrate vector (PHP30478) and roots were assayed
using a seedling assay as described in Example 22. All 8 events from construct
PHP30478 (ZM-UBI::AT-RECPU3) were assayed in a greenhouse experiment,
where 9 plants per each event were grown in Turface media to V4 stage. Seeds
were from the T1 generation (from ears collected from TO plants). The control
in the
experiment were plants of the same hybrid maize line, not containing the
recombinant construct, grown to the same stage. Seeds were planted using a
complete random block design. Plants were harvested 19 days after planting,
when
they reached V4 stage. Roots were washed and collected separately from shoots.
All samples were oven-dried before dry weights were taken on an analytical
balance.
As can be seen from Table 6 several events were found to have significant
changes in all of the traits measured , when compared to the control.
T-test analysis was performed to show significant differences between each
transgenic event and the control. The p-values are shown for each trait: root
dry
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
weights, shoot dry weights, and root-to-shoot ratios. Bold face fonts indicate
the
transgenic had a higher value than the control. Those that had a p-value of
less
than 0.1 are indicated with an asterisk (*).
TABLE 6
Comparison of transgenic and control seedlings
EVENT Root Dry Weight Shoot Dry Weight Root/Shoot Ratio
1 NS 0.093 0.041 *
2 0.002* 0.047* 0.003*
3 NS NS 0.037
4 0.073 * NS 0.025 *
5 NS NS 0.047*
6 <0.001* <0.001* NS
7 NS NS NS
8 0.015 0.003 NS
EVENT Total DW Nitrogen/ Dry Total Nitrogen
Weight (m/) (Mg)
1 NS 0.039* NS
2 0.017* NS 0.028*
3 NS <0.001* <0.001*
4 NS NS NS *
5 NS 0.003* 0.076*
6 <0.001* 0.003 0.010*
7 NS NS NS
8 0.004 NS NS
EXAMPLE 24
Yield testing of transgenic hybrids grown under normal and under nitrogen
depleted
conditions in the field.
A field experiment was carried out at two filed sites, one in California (site
1) and
the other in Iowa (site 2), in the 2008 season. Ten (10) transgenic events
carrying
the Arabidopsis REP2 (RECPU3) gene (At5G19590) driven by the maize UBI
promoter, and controls were included in the experiment. The control consisted
of a
non-transgenic bulked null from individual nulls across all 10 events. All of
the
plants were hybrid maize lines generated from a common inbred tester.
Two treatments were applied, consisting of conditions wherein the plants
were either grown under "normal" nitrogen or under nitrogen "depleted"
conditions.
The nitrogen depletion treatment was carried out in a field where soil
nitrogen levels
86
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
had been drawn down by crops grown in previous years without fertilization.
The
experiments were set up as 2-row plots with a density of 32000 plants per
acre.
There were 4 replications in normal nitrogen treatment and 6 replications in
depleted
nitrogen treatment.
At site 1 in the normal treatment, nitrogen fertilizer was applied at a rate
of
2501b per acre. The depleted nitrogen treatment received a 901b per acre
fertilization that led to 13% yield reduction when compared to the normal
nitrogen
treatment. The experiments were planted on April 26-28, 2008 and harvestd by
combine on October 18, 2008.
At site 2 in the normal treatment, nitrogen fertilizer was applied at a rate
of
2601b per acre. The depleted nitrogen treatment received a 60 to 80 lb per
acre
nitrogen fertilization that led to 6% yield reduction when compared to the
normal
nitrogen treatment. The experiments were planted on My 15, 2008 and harvested
by combine on October 18, 2008.
The grain yield data in bushels per acre from the experiments are
summarized as percent increases over the null control, in Table 7. Overall,
there
were 3 events under depleted nitrogen and 7 events under normal nitrogen that
had
significant increase (indicated by an asterix *) in yield over the bulked null
control
(alpha=0.2, 2 tail analysis). Most events tested showed a positive trend in
yield
increase over nulls.
87
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
TABLE 7
Yield tests of transgenic versus control plants under low and normal nitrogen
conditions.
Site Event Yield increase Significance Treatment
over null
1 1 1.38% Low nitrogen
1 2 -1.74% Low nitrogen
1 3 6.26% Low nitrogen
1 4 2.30% Low nitrogen
1 5 6.30% * Low nitrogen
1 6 2.47% Low nitrogen
1 7 1.70% Low nitrogen
1 8 4.85% Low nitrogen
1 9 3.41% Low nitrogen
1 10 -2.00% Low nitrogen
1 1 3.04% Normal nitrogen
1 2 1.87% Normal nitrogen
1 3 5.59% Normal nitrogen
1 4 2.28% Normal nitrogen
1 5 5.16% * Normal nitrogen
1 6 5.63% * Normal nitrogen
1 7 1.11% Normal nitrogen
1 8 0.88% Normal nitrogen
1 9 -1.88% Normal nitrogen
1 10 2.41% Normal nitrogen
2 1 8.87% Normal Nitrogen
2 2 17.09% * Normal Nitrogen
88
CA 02729099 2010-12-22
WO 2010/011907 PCT/US2009/051665
2 3 Not tested Normal Nitrogen
2 4 Not tested Normal Nitrogen
2 5 10.86% * Normal Nitrogen
2 6 10.39% * Normal Nitrogen
2 7 4.02% Normal Nitrogen
2 8 4.17% Normal Nitrogen
2 9 10.29% * Normal Nitrogen
2 10 4.09% Normal Nitrogen
89
