# Patent

## Title
Genes encoding wheat starch synthases and uses thereof

## Abstract

The present invention provides isolated nucleic acid molecules encoding wheat starch synthases, and probes and primers derived therefrom, which are useful in the modification of plant starch content and/or composition, and for screening plant lines to determine the presence of natural and/or induced mutations in starch synthase genes which affect starch content and/or composition. More particularly, the isolated nucleic acid molecules of the present invention further provide for the screening-assisted breeding of plants having desirable starch content and/or composition, in addition to providing for the direct genetic manipulation of plant starch content and/or composition.

## Background
This application is a divisional of U.S. Ser. No. 10/018,418, filed May 9, 2002, now U.S. Pat. No. 7,001,771, issued Feb. 21, 2006, which was a §371 national stage of PCT International Application No. PCT/AU00/00385, filed Apr. 28, 2000, claiming priority of Australian Application No. PQ0052/99, filed Apr. 29, 1999, the contents of which are hereby incorporated by reference into this application.


FIELD OF THE INVENTION
The present invention relates generally to isolated nucleic acid molecules encoding wheat starch synthase enzymes and more particularly, to isolate nucleic acid molecules that encode wheat SSII and SSIII enzyme activities. The isolated nucleic acid molecules provide the means for modifying starch content and composition in plants, for example the ratio of amylose:amylopectin in the starch granule of the endosperm during the grain-filling phase of endosperm development. The isolated nucleic acid molecules of the present invention also provide the means for screening plant lines to determine the presence of natural and/or induced mutations in starch synthase genes which affect starch content and/or composition. The isolated nucleic acid molecules of the present invention further provide for the screening-assisted breeding of plants having desirable starch content and/or composition, in addition to providing for the direct genetic manipulation of plant starch content and/or composition.
GENERAL
Bibliographic details of the publications numerically referred to in this specification are collected at the end of the description. Reference herein to any published document is not to be taken as an indication or admission that any such published document is part of the common general knowledge or background information of a skilled worker in the relevant field.
This specification contains nucleotide and amino acid sequence information (SEQ ID NOS:) prepared using the programme PatentIn Version 2.0, presented herein at the end of the specification. Each nucleotide or amino acid sequence is identified in the sequence listing by the numeric indicator <210> followed by the sequence identifier (e.g. <210>1, <210>2, etc.) The length, type of sequence (DNA, protein (PRT), etc) and source organism for each nucleotide or amino acid sequence are indicated by information provided in the numeric indicator fields <211>, <212> and <213>, respectively. Nucleotide and amino acid sequences (SEQ ID NOs:) referred to in the specification are defined by the information provided in numeric indicator field <400> followed by the sequence identifier (eg. SEQ ID NO: 1 is <400>1, etc).
The designation of nucleotide residues referred to herein are those recommended by the IUPAC-IUB Biochemical Nomenclature Commission, wherein A represents Adenine, C represents Cytosine, G represents Guanine, T represents thymine, Y represents a pyrimidine residue, R represents a purine residue, M represents Adenine or Cytosine, K represents Guanine or Thymine, S represents Guanine or Cytosine, W represents Adenine or Thymine, H represents a nucleotide other than Guanine, B represents a nucleotide other than Adenine, V represents a nucleotide other than Thymine, D represents a nucleotide other than Cytosine and N represents any nucleotide residue.
The designations for naturally-occurring amino acid residues referred to herein are set forth in Table I. The designations for a non-limiting set of non-naturally-occurring amino acids is listed in Table 2.
As used herein the term “derived from” shall be taken to indicate that a specified integer may be obtained from a particular source albeit not necessarily directly from that source.
Throughout this specification, unless the context requires otherwise, the word “comprise”, or variations such as “comprises” or “comprising”, will be understood to imply the inclusion of a stated step or element or integer or group of steps or elements or integers but not the exclusion of any other step or element or integer or group of steps or elements or integers.









TABLE 1





Amino Acid
Three-letter Code
One-letter Code







Alanine
Ala
A


Arginine
Arg
R


Asparagine
Asn
N


Aspartic acid
Asp
D


Cysteine
Cys
C


Glutamine
Gln
Q


Glutamic acid
Glu
E


Glycine
Gly
G


Histidine
His
H


Isoleucine
Ile
I


Leucine
Leu
L


Lysine
Lys
K


Methionine
Met
M


Phenylalanine
Phe
F


Proline
Pro
P


Serine
Ser
S


Threonine
Thr
T


Tryptophan
Trp
W


Tyrosine
Tyr
Y


Valine
Val
V


Aspartate/glutamate
Baa
B


Asparagine/glutamine


Any amino acid as above
Xaa
X



















TABLE 2





Non-conventional

Non-conventional



amino acid
Code
amino acid
Code







α-aminobutyric acid
Abu
L-N-methylalanine
Nmala


α-amino-α-methylbutyrate
Mgabu
L-N-methylarginine
Nmarg


aminocyclopropane-
Cpro
L-N-methylasparagine
Nmasn


carboxylate

L-N-methylaspartic acid
Nmasp


aminoisobutyric acid
Aib
L-N-methylcysteine
Nmcys


aminonorbornyl-
Norb
L-N-methylglutamine
Nmgln


carboxylate

L-N-methylglutamic acid
Nmglu


cyclohexylalanine
Chexa
L-N-methylhistidine
Nmhis


cyclopentylalanine
Cpen
L-N-methylisolleucine
Nmile


D-alanine
Dal
L-N-methylleucine
Nmleu


D-arginine
Darg
L-N-methyllysine
Nmlys


D-aspartic acid
Dasp
L-N-methylmethionine
Nmmet


D-cysteine
Dcys
L-N-methylnorleucine
Nmnle


D-glutamine
Dgln
L-N-methylnorvaline
Nmnva


D-glutamic acid
Dglu
L-N-methylornithine
Nmorn


D-histidine
Dhis
L-N-methylphenylalanine
Nmphe


D-isoleucine
Dile
L-N-methylproline
Nmpro


D-leucine
Dleu
L-N-methylserine
Nmser


D-lysine
Dlys
L-N-methylthreonine
Nmthr


D-methionine
Dmet
L-N-methyltryptophan
Nmtrp


D-ornithine
Dorn
L-N-methyltyrosine
Nmtyr


D-phenylalanine
Dphe
L-N-methylvaline
Nmval


D-proline
Dpro
L-N-methylethylglycine
Nmetg


D-serine
Dser
L-N-methyl-t-butylglycine
Nmtbug


D-threonine
Dthr
L-norleucine
Nle


D-tryptophan
Dtrp
L-norvaline
Nva


D-tyrosine
Dtyr
α-methyl-aminoisobutyrate
Maib


D-valine
Dval
α-methyl-γ-aminobutyrate
Mgabu


D-α-methylalanine
Dmala
α-methylcyclohexylalanine
Mchexa


D-α-methylarginine
Dmarg
α-methylcylcopentylalanine
Mcpen


D-α-methylasparagine
Dmasn
α-methyl-α-napthylalanine
Manap


D-α-methylaspartate
Dmasp
α-methylpenicillamine
Mpen


D-α-methylcysteine
Dmcys
N-(4-aminobutyl)glycine
Nglu


D-α-methylglutamine
Dmgln
N-(2-aminoethyl)glycine
Naeg


D-α-methylhistidine
Dmhis
N-(3-aminopropyl)glycine
Norn


D-α-methylisoleucine
Dmile
N-amino-α-methylbutyrate
Nmaabu


D-α-methylleucine
Dmleu
α-napthylalanine
Anap


D-α-methyllysine
Dmlys
N-benzylglycine
Nphe


D-α-methylmethionine
Dmmet
N-(2-carbamylethyl)glycine
Ngln


D-α-methylornithine
Dmorn
N-(carbamylmethyl)glycine
Nasn


D-α-methylphenylalanine
Dmphe
N-(2-carboxyethyl)glycine
Nglu


D-α-methylproline
Dmpro
N-(carboxymethyl)glycine
Nasp


D-α-methylserine
Dmser
N-cyclobutylglycine
Ncbut


D-α-methylthreonine
Dmthr
N-cycloheptylglycine
Nchep


D-α-methyltryptophan
Dmtrp
N-cyclohexylglycine
Nchex


D-α-methyltyrosine
Dmty
N-cyclodecylglycine
Ncdec


D-α-methylvaline
Dmval
N-cylcododecylglycine
Ncdod


D-N-methylalanine
Dnmala
N-cyclooctylglycine
Ncoct


D-N-methylarginine
Dnmarg
N-cyclopropylglycine
Ncpro


D-N-methylasparagine
Dnmasn
N-cycloundecylglycine
Ncund


D-N-methylaspartate
Dnmasp
N-(2,2-diphenylethyl)glycine
Nbhm


D-N-methylcysteine
Dnmcys
N-(3,3-diphenylpropyl)glycine
Nbhe


D-N-methylglutamine
Dnmgln
N-(3-guanidinopropyl)glycine
Narg


D-N-methylglutamate
Dnmglu
N-(1-hydroxyethyl)glycine
Nthr


D-N-methylhistidine
Dnmhis
N-(hydroxyethyl))glycine
Nser


D-N-methylisoleucine
Dnmile
N-(imidazolylethyl))glycine
Nhis


D-N-methylleucine
Dnmleu
N-(3-indolylyethyl)glycine
Nhtrp


D-N-methyllysine
Dnmlys
N-methyl-γ-aminobutyrate
Nmgabu


N-methylcyclohexylalanine
Nmchexa
D-N-methylmethionine
Dnmmet


D-N-methylornithine
Dnmorn
N-methylcyclopentylalanine
Nmcpen


N-methylglycine
Nala
D-N-methylphenylalanine
Dnmphe


N-methylaminoisobutyrate
Nmaib
D-N-methylproline
Dnmpro


N-(1-methylpropyl)glycine
Nile
D-N-methylserine
Dnmser


N-(2-methylpropyl)glycine
Nleu
D-N-methylthreonine
Dnmthr


D-N-methyltryptophan
Dnmtrp
N-(1-methylethyl)glycine
Nval


D-N-methyltyrosine
Dnmtyr
N-methyla-napthylalanine
Nmanap


D-N-methylvaline
Dnmval
N-methylpenicillamine
Nmpen


γ-aminobutyric acid
Gabu
N-(p-hydroxyphenyl)glycine
Nhtyr


L-t-butylglycine
Tbug
N-(thiomethyl)glycine
Ncys


L-ethylglycine
Etg
penicillamine
Pen


L-homophenylalanine
Hphe
L-α-methylalanine
Mala


L-α-methylarginine
Marg
L-α-methylasparagine
Masn


L-α-methylaspartate
Masp
L-α-methyl-t-butylglycine
Mtbug


L-α-methylcysteine
Mcys
L-α-methylethylglycine
Metg


L-α-methylglutamine
Mgln
L-α-methylglutamate
Mglu


L-α-methylhistidine
Mhis
L-α-methylhomophenylalanine
Mhphe


L-α-methylisoleucine
Mile
N-(2-methylthioethyl)glycine
Nmet


L-α-methylleucine
Mleu
L-α-methyllysine
Mlys


L-α-methylmethionine
Mmet
L-α-methylnorleucine
Mnle


L-α-methylnorvaline
Mnva
L-α-methylornithine
Morn


L-α-methylphenylalanine
Mphe
L-α-methylproline
Mpro


L-α-methylserine
Mser
L-α-methylthreonine
Mthr


L-α-methyltryptophan
Mtrp
L-α-methyltyrosine
Mtyr


L-α-methylvaline
Mval
L-α-methylhomophenylalanine
Nmhphe


N-(N-(2,2-diphenylethyl)
Nnbhm
N-(N-(3,3-diphenylpropyl)
Nnbhe


carbamylmethyl)glycine

carbamylmethyl)glycine


1-carboxy-1-(2,2-diphenyl-
Nmbc


ethylamino)cyclopropane









Those skilled in the art will appreciate that the invention described herein is susceptible to variations and modifications other than those specifically described. It is to be understood that the invention includes all such variations and modifications. The invention also includes all of the steps, features, compositions and compounds referred to or indicated in this specification, individually or collectively, and any and all combinations or any two or more of said steps or features.
The present invention is not to be limited in scope by the specific embodiments described herein, which are intended for the purposes of exemplification only. Functionally-equivalent products, compositions and methods are clearly within the scope of the invention, as described herein.
BACKGROUND TO THE INVENTION
The biosynthesis of the starch granule is a complex process which involves the action of an array of isoforms of enzymes involved in the starch biosynthesis. Following the formation of glucose-1-phosphate, the enzyme activities required for the synthesis of granular starch include ADP glucose pyrophosphorylase (EC 2.7.7.27), starch synthases (EC 2.4.1.21), branching enzymes (EC 2.4.1.18) and debranching enzymes (EC 3.2.1.41 and EC 3.2.1.68) (Mouille et al., 1996). Plants contain isozymes of each of these activities, and the definition of these isoforms and their roles has been conducted through investigation of the properties of the suite of soluble enzymes found in the stroma of the plastid, analysis of the proteins entrapped within the matrix of the starch granule, and mutational studies to identify genes and define linkages between individual genes and their specific roles.
Starch synthases extend regions of α-1,4 glucan through the transfer of the glucosyl moiety of ADPglucose to the non-reducing end of a pre-existing α-1,4 glucan. In addition to GBSS, 3 other classes of starch synthase have been identified in plants, SSI (wheat, Li et al., 1999 and GenBank Accession No. U48227; rice, Baba et al., 1993; potato, Genbank Accession No.-Y10416, SSII (pea, Dry et al. 1992; potato, Edwards et al., 1995; maize, Harn et al., 1998 and GenBank Accession No. U66377) and SSIII (potato, Abel et al., 1996; maize, Gao et al., 1998. In the cereals, the most comprehensively studied species is maize, where in addition to GBSS, cDNAs encoding SSI, and SSIIb have been isolated, and both cDNA and genomic clones for dull1 have been characterised (Knight et al., 1998; Harn et al., 1998; Goa et al., 1998). In maize, the product of the du1 gene is known as maize SSII, however this gene is the homologue of potato SSIII.
The proteins within the matrix of the wheat starch granule have been extensively studied (Denyer et al., 1995; Rahman et al., 1995; Takaoka et al., 1997; Yamamori and Endo, 1996) and 60, 75, 85, 100, 104 and 105 kDa protein bands can be visualised following SOS-PAGE. The predominant 60 kDa protein is exclusively granule-bound and is analogous to the ‘waxy’ granule bound starch synthase (GBSS) gene in maize (Rahman et al., 1995). The combination of three null alleles for this enzyme from each of the wheat genomes (Nakamura et al., 1995) results in the amylose-free ‘waxy’ phenotype found in other species The 75 kDa starch synthase I (wSSI) is found in both the granule and the soluble fraction of wheat endosperm (Denyer et al., 1995; Li et al., 1999) and has been assigned to chromosomes 7A, 7B and 7D (Yamamori and Endo, 1996; Li et al., 1999). The 85 kDa band contains a class II branching enzyme and an unidentified polypeptide (Rahman et al., 1995). The 100, 104 and 105 kDa proteins of the wheat starch granule (designated Sgp-B1, Sgp-D1 and Sgp-A1 by Yamamori and Endo, 1996) have been shown to be encoded by a homeologous set of genes on the short arm of chromosome 7B, 7A and 7D respectively (Yamamori and Endo, 1996; Takaoka et al., 1997). Denyer et al. (1995) concluded on the basis of enzyme activity assays that these proteins were also starch synthases. These genes are referred to hereinafter as the “wheat SSII genes”.
While GBSS has been established to be essential for amylose synthesis, the remaining starch synthases are thought to be primarily responsible for the elongation of amylopectin chains, although this does not preclude them from also having non-essential roles in amylose biosynthesis. Differences in kinetic properties between isoforms, and the analysis of mutants lacking various isoforms, suggests that each isoenzyme contributes to the extension of specific subsets of the available non-reducing ends.
SUMMARY OF THE INVENTION
The production of plants that produce improved starches that are modified for particular end-use applications, such as, for example, starches having high or low amylose:amylopectin ratios, requires the availability of genes encoding the various starch synthase isoforms. Because of species-specific codon usages, and variations in the kinetic parameters of the starch synthase isoforms between species, the production of modified starches may require the use of genes derived from particular species.
Furthermore, the screening-assisted breeding of plants having desirable starch content and/or composition requires specific gene sequences to be provided that can be used to distinguish between different homeologous genes encoding the various isoforms of wheat starch synthases, such as, for example, to identify and distinguish between naturally-occurring variant gene sequences. It is a particular object of the present invention to provide gene sequences to facilitate the screening-assisted selection of wheat plants having starch traits which are associated with the presence and/or expression of one or more wheat SSI and/or SSIII genes.
Accordingly, the present invention provides isolated nucleotide sequences encoding the wheat SSII (i.e. wSSII) and wheat SSIII (i.e. wSSIII) isoenzymes, and DNA markers derived therefrom. The present invention further facilitates the production of transformed plants carrying these nucleotide sequences.
More particularly, the present invention provides isolated nucleic acid molecules encoding the 100, 104 and 105 kDa SSII (Sgp-1) polypeptides of the wheat starch granule matrix, as determined using the SDS/PAGE system of Rahman et al. (1995), which polypeptides are equivalent to the 100, 108 and 115 kDa polypeptides described by Yamamori and Endo (1996).
The present invention further provides isolated nucleic acid molecules encoding the soluble dull1-type wheat starch synthase III polypeptide. Analysis of the polypeptides encoded by these nucleic acid molecules reveals several consensus amino acid sequence motifs that are highly conserved in wheat starch synthase isoenzymes, in addition to isoenzyme-specific sequences, which sequences possess utility in isolating related starch synthase-encoding sequences and in assaying plants for their expression of one or more starch synthase isoenzymes.
Accordingly, one aspect of the present invention provides an isolated nucleic acid molecule which comprises a sequence of nucleotides which encodes, or is complementary to a nucleic acid molecule which encodes a wheat starch synthase polypeptide, protein or enzyme molecule or a functional subunit thereof selected from the following:

    
    
        (i) a wheat starch synthase II (wSSII) polypeptide, protein or enzyme or functional subunit thereof which comprises an amino acid sequence which is at least about 85% identical overall to an amino acid sequence set forth in any one of SEQ ID NOS: 2, 4, or 6;
        (ii) a wheat starch synthase III (wSSIII) polypeptide, protein or enzyme or functional subunit thereof which comprises an amino acid sequence which is at least about 85% identical overall to an amino acid sequence set forth in any one of SEQ ID NOS: 8 or 10;
        (iii) a wheat starch synthase polypeptide, protein or enzyme or functional subunit thereof which comprises a conserved amino acid sequence having at least 25% identity to an amino acid sequence selected from the group consisting of:
    
    












(a)
KVGGLGDVVTS;
(SEQ ID NO: 39)



 


(b)
GHTVEVILPKY;
(SEQ ID NO: 40)


 


(c)
HDWSSAPVAWLYKEHY;
(SEQ ID NO: 41)


 


(d)
GILNGIDPDIWDPYTD;
(SEQ ID NO: 42)


 


(e)
DVPIVGIITRLTAQKG;
(SEQ ID NO: 43)


 


(f)
NGQVVLLGSA;
(SEQ ID NO: 44)


 


(g)
AGSDFIIVPSIFEPCGLTQLVAMRYGS;
(SEQ ID NO: 45)


and


 


(h)
TGGLVDTV;
(SEQ ID NO: 46)






    
    
        wherein said wheat starch synthase polypeptide further comprises an amino acid sequence having at least about 85% identity overall to an amino acid sequence set forth in any one of SEQ ID NOS: 2, 4, 6, 8 or 10; and
        (iv) a wheat starch synthase polypeptide, protein or enzyme or functional subunit thereof which comprises a conserved amino acid sequence having at least 25% identity to an amino acid sequence selected from the group consisting of:
    
    














(a)
KTGGLGDVAGA;
(SEQ ID NO: 47)




 



(b)
GHRVMVVVPRY;
(SEQ ID NO: 48)



 



(c)
NDWHTALLPVYLKAYY;
(SEQ ID NO: 49)



 



(d)
GIVNGIDNMEWNPEVD;
(SEQ ID NO: 50)



 



(e)
DVPLLGFIGRLDGQKG;
(SEQ ID NO: 51)



 



(f)
DVQLVMLGTG;
(SEQ ID NO: 52)



 



(g)
AGADALLMPSRF(E/
(SEQ ID NO: 53)




V)PCGLNQLYAMAYGT;



and



 



(h)
VGG(V/L)RDTV;
(SEQ ID NO: 54)






    
    
        wherein said wheat starch synthase polypeptide further comprises an amino acid sequence having at least about 85% identity overall to an amino acid sequence set forth in any one of SEQ ID NOS: 2, 4, 6, 8 or 10.
    
    


In a preferred embodiment, the isolated nucleic acid molecule encodes a starch synthase polypeptide, protein or enzyme having at least about 90% amino acid sequence identity to any one of SEQ ID NOS: 2, 4, 6, 8 or 10, more preferably having at least about 95% or about 97% or about 99% identity to any one of said amino acid sequences.
In an alternative embodiment, the isolated nucleic acid molecule of the present invention encodes a wheat starch synthase polypeptide which comprises one or more amino acid sequences selected from the group consisting of:










(a)
GHTVEVILPKY;
(SEQ ID NO: 40)



 


(b)
HDWSSAPVAWLYKEHY;
(SEQ ID NO: 41)


 


(c)
DVPIVGIITRLTAQKG;
(SEQ ID NO: 43)


 


(d)
NGQVVLLGSA;
(SEQ ID NO: 44)


 


(e)
AGSDFIIVPSIFEPCGLTQLVAMRYGS;
(SEQ ID NO: 45)


 


(f)
TGGLVDTV;
(SEQ ID NO: 46)


 


(g)
GIVNGIDNMEWNPEVD;
(SEQ ID NO: 50)


and


 


(h)
AGADALLMPSRF(E/
(SEQ ID NO: 53)



V)PCGLNQLYAMAYGT.






in an alternative embodiment, the present invention provides an isolated nucleic acid molecule which encodes a wheat starch synthase polypeptide, protein or enzyme molecule or a functional subunit thereof, wherein said nucleic acid molecule comprises a nucleotide sequence having at least about 85% nucleotide sequence identity to any one of SEQ ID NOS: 1, 3, 5, 7, 9, 11-16, 37 or 38 or a complementary nucleotide sequence thereto.

In a preferred embodiment, the isolated nucleic acid molecule comprises the nucleotide sequence set forth in any one of SEQ ID NOS: 1, 3, 5, 7, 9, 11-16, 37 or 38, or is at least about 90% identical, more preferably at least about 95% or 97% or 99% identical to all or a protein-encoding part thereof.
In an alternative embodiment, the present invention provides an isolated nucleic acid molecule which encodes a wheat starch synthase polypeptide, protein or enzyme molecule or a functional subunit thereof, wherein said nucleic acid molecule comprises a nucleotide sequence that is capable of hybridising under at least moderate stringency hybridisation conditions to at least about 30 contiguous nucleotides derived from any one of SEQ ID NOS: 1, 3, 5, 7, 9, 11-16, 37 or 38, or a complementary nucleotide sequence thereto.
A second aspect of the present invention provides a method of isolating a nucleic acid molecule that encodes a starch synthase polypeptide, protein or enzyme described supra, said method comprising:

    
    
        (i) hybridising a probe or primer comprising at least about 15 contiguous nucleotides in length derived from any one of SEQ ID NOS: 1, 3, 5, 7, 9, 11-16, 37 or 38, or a complementary nucleotide sequence thereto to single-stranded or double-stranded mRNA, cDNA or genomic DNA; and
        (ii) detecting the hybridised mRNA, cDNA or genomic DNA using a detecting means.
    
    


Preferably, the detecting means is a reporter molecule covalently attached to the probe or primer molecule or alternatively, a polymerase chain reaction format. Accordingly, the present invention clearly extends to the use of the nucleic acid molecules provided herein to isolate related starch synthase-encoding sequences using standard hybridisation and/or polymerase chain reaction techniques.
A third aspect of the invention provides an isolated probe or primer comprising at least about 15 contiguous nucleotides in length derived from any one of SEQ ID NOS: 1, 3, 5, 7, 9, 11-16, 37 or 38, or a complementary nucleotide sequence thereto.
Preferably, the probe or primer comprises a nucleotide sequence set forth in any one of SEQ ID NOS: 25 to 34.
A fourth aspect of the present invention is directed to an isolated or recombinant starch synthase polypeptide, protein or enzyme, preferably substantially free of conspecific or non-specific proteins, which comprises an amino acid sequence selected from the following:

    
    
        (i) a wheat starch synthase II (wSSII) polypeptide, protein or enzyme or functional subunit thereof which comprises an amino acid sequence which is at least about 85% identical overall to an amino acid sequence set forth in any one of SEQ ID NOS: 2, 4, or 6;
        (ii) a wheat starch synthase III (wSSIII) polypeptide, protein or enzyme or functional subunit thereof which comprises an amino acid sequence which is at least about 85% identical overall to an amino acid sequence set forth in any one of SEQ ID NOS: 8 or 10;
        (iii) a wheat starch synthase polypeptide, protein or enzyme or functional subunit thereof which comprises a conserved amino acid sequence having at least 25% identity to an amino acid sequence selected from the group consisting of:
    
    












(a)
KVGGLGDVVTS;
(SEQ ID NO: 39)



 


(b)
GHTVEVILPKY;
(SEQ ID NO: 40)


 


(c)
HDWSSAPVAWLYKEHY;
(SEQ ID NO: 41)


 


(d)
GILNGIDPDIWDPYTD;
(SEQ ID NO: 42)


 


(e)
DVPIVGIITRLTAQKG;
(SEQ ID NO: 43)


 


(f)
NGQVVLLGSA;
(SEQ ID NO: 44)


 


(g)
AGSDFIIVPSIFEPCGLTQLVAMRYGS;
(SEQ ID NO: 45)


and


 


(h)
TGGLVDTV
(SEQ ID NO: 46)






    
    
        wherein said wheat starch synthase polypeptide further comprises an amino acid sequence having at least about 85% identity overall to an amino acid sequence set forth in any one of SEQ ID NOS:2, 4, 6, 8 or 10; and
        iv) a wheat starch synthase polypeptide, protein or enzyme or functional subunit thereof which comprises a conserved amino acid sequence having at least 25% identity to an amino acid sequence selected from the group consisting of:
    
    














(a)
KTGGLGDVAGA;
(SEQ ID NO: 47)




 



(b)
GHRVMVVVPRY;
(SEQ ID NO: 48)



 



(c)
NDWHTALLPVYLKAYY;
(SEQ ID NO: 49)



 



(d)
GIVNGIDNMEWNPEVD;
(SEQ ID NO: 50)



 



(e)
DVPLLGFIGRLDGQKG;
(SEQ ID NO: 51)



 



(f)
DVQLVMLGTG;
(SEQ ID NO: 52)



 



(g)
AGADALLMPSRF(E/
(SEQ ID NO: 53)




V)PCGLNQLYAMAYGT;



and



 



(h)
VGG(V/L)RDTV.
(SEQ ID NO: 54)






    
    
        wherein said wheat starch synthase polypeptide further comprises an amino acid sequence having at least about 85% identity overall to an amino acid sequence set forth in any one of SEQ ID NOS: 2, 4, 6, 8 or 10.
    
    


The present invention clearly encompasses the mature protein region of a wheat starch synthase polypeptide which is obtained by removal of the N-terminal transit peptide sequence.
A further aspect of the invention provides a method of assaying for the presence or absence of a starch synthase isoenzyme or the copy number of a gene encoding same in a plant, comprising contacting a biological sample derived from said plant with an isolated nucleic acid molecule derived from any one of SEQ ID NOS 1, 3, 5, 7, 9, 11-16, 37 or 38, or any one of SEQ ID NOS: 25 to 34, or a complementary nucleotide sequence thereto for a time and under conditions sufficient for hybridisation to occur and then detecting said hybridisation using a detection means.
The detection means according to this aspect of the invention is any nucleic acid based hybridisation or amplification reaction.
A further aspect of the present invention utilises the above-mentioned assay method in the breeding and/or selection of plants which express or do not express particular starch synthase isoenzymes or alternatively, which express a particular starch synthase isoenzyme at a particular level in one or more plant tissues. This aspect clearly extends to the selection of transformed plant material which contains one or more of the isolated nucleic acid molecules of the present invention.
A further aspect of the present invention provides a method of modifying the starch content and/or starch composition of one or more tissues or organs of a plant, comprising expressing therein a sense molecule, antisense molecule, ribozyme molecule, co-suppression molecule, or gene-targeting molecule having at least about 85% nucleotide sequence identity to any one of any one of SEQ ID NOS: 1, 3, 5, 7, 9, 11-16, 37 or 38, or a complementary nucleotide sequence thereto for a time and under conditions sufficient for the enzyme activity of one or more starch synthase isoenzymes to be modified. This aspect of the invention clearly extends to the introduction of the sense molecule, antisense molecule, ribozyme molecule, co-suppression molecule, or gene-targeting molecule to isolated plant cells, tissues or organs or organelles by cell fusion or transgenic means and the regeneration of intact plants therefrom.
A further aspect of the present invention provides an isolated promoter that is operable in the endosperm of a monocotyledonous plant cell, tissue or organ, and preferably in the endosperm of a monocotyledonous plant cell, tissue or organ. For example, the HMG promoter from wheat, or the maize zein gene promoter are particularly preferred, as is the promoter derived from a starch synthase gene of the present invention, such as a promoter that is linked in vivo to any one of SEQ ID NOS 1, 3, 5, 7, 9, 11-16, 37 or 38, or a complementary nucleotide sequence thereto.
A still further aspect of the present invention contemplates a transgenic plant comprising an introduced sense molecule, antisense molecule, ribozyme molecule, co-suppression molecule, or gene-targeting molecule having at least about 85% nucleotide sequence identity to any one of any one of SEQ ID NOS: 1, 3, 5, 7, 9, 11-16, 37 or 38, or a complementary nucleotide sequence thereto or a genetic construct comprising same, and to plant propagules, cells, tissues, organs or plant parts derived from said transgenic plant that also carry the introduced molecule(s).



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 is a copy of a photographic representation showing the distribution of wheat endosperm starch synthases between the starch granule and soluble fractions. Lane 1, SOS-PAGE of wheat endosperm starch granule proteins revealed by silver staining; lanes 2-7, immunoblot of wheat endosperm soluble phase and starch granule proteins separated by SDS-PAGE from various developmental stages and probed with an anti-(wheat wSSII peptide) monoclonal antibody. Lanes 2-4 contain proteins from the soluble fraction of wheat endosperm at 15 days post anthesis (Lane 2); 20 days post anthesis (Lane 3); and at 25 days post anthesis (Lane 4). Lanes 5-7 contain proteins from the starch granule of wheat endosperm at 15 days post anthesis (Lane 5); 20 days post anthesis (Lane 6); and at 25 days post anthesis (Lane 7).
FIG. 2 (Figure panel 2A-2O) is a copy of a schematic representation comparing the nucleotide sequences of cDNA clones designated wSSIIA (SEQ ID NO:3), wSSIIB (SEQ ID NO:1) and wSSIID (SEQ ID NO:5), encoding the starch synthase II polypeptides from wheat, using the PILEUP programme of Devereaux et al. (1984).
FIG. 3 (Figure panels 3A-3G) is a copy of a schematic representation comparing the deduced amino acid sequences of starch synthase II from wheat (wSSIIA (SEQ ID NO:3), wSSIIB (SEQ ID NO:1) and wSSIID (SEQ ID NO:5), maize (maize SSIIa and maize SSIIb; Harn et al., 1998), pea (pea SSII; Dry et al., 1992) and potato (potato SSII; van der Leij et al., 1991) Identical amino acid residues among each of these sequences are indicated below the sequences with “*”. The alignments of maize SSIIa with maize SSIIb, and pea SSII and potato SSII are essentially as described in Harn et al. (1998) and Edwards et al. (1995). All sequences are aligned to position the transit peptide cleavage site below the arrow () between residues 59 and 60 of the wSSIIA sequence. The wSSIIp1 sequence, the sequence of SGP-B1 (peptide3), and of eight conserved regions are annotated and underlined.
FIG. 4 is a copy of a photographic representation of a northern blot showing the expression of wheat wSSII mRNA in wheat plants. Total RNAs were isolated from leaves pre-anthesis florets and endosperm of the wheat cultivar “Gabo”, grown under a photoperiod comprising 16 hours daylength, and at 18° C. during the day, and at 13° C. during the night cycle, and probed with the wSSIIp2 DNA fragment. The source of each RNA is indicated at the top of the Figure as follows: Lane 1, leaf; Lane 2, pre-anthesis florets; Lanes 3-11, endosperm at: 4 days post-anthesis (Lane 3); 6 days post-anthesis (Lane 4); 8 days post-anthesis (Lane 5); 10 days post-anthesis (Lane 6); 12 days post-anthesis (Lane 7); 15 days post-anthesis (Lane 8); 18 days post-anthesis (Lane 9); 21 days post-anthesis (Lane 10); and 25 days post-anthesis (Lane 11).
FIG. 5 is a copy of a photographic representation showing the localization of wheat starch synthase II genes on the wheat genome by PCR, using the primers ssIIc, ssIId and ssIIe in the amplification reaction. The nullisomic-tetrasomic genomic DNA of wheat cv. Chinese Spring was used as template DNA. Lane D, Triticum tauschii; Lane AB, Accession line N7DT7B having no 7D chromosome and four copies of the 7B chromosome; Lane AD, Accession line N7BT7A having no 7B chromosome and four copies of the 7A chromosome; Lane BD. Accession line N7AT7B having no 7A chromosome and four copies of the 7B chromosome; Lane ABD, wheat cv. Chinese Spring. PCR products derived from each cDNA clone are labelled. The results indicate that the cDNA clones, wSSIIB, wSSIIA and wSSIID are derived from the B-, A- and D-genomes of wheat, respectively.
FIG. 6 is a schematic representation showing the organisation of introns (lines) and exons (boxes) in the wheat SSII gene shown in SEQ ID NO: 37. The scale (bases), relative to the nucleotide sequence set forth in SEQ ID NO: 37, is provided at the bottom of the figure.
FIG. 7 (Figure panels 7A-7I) is a schematic representation comparing the deduced amino acid Sequences of the maize (SEQ ID NO:55), potato (SEQ ID NO:56 and wheat SSIII (SEQ ID NO:8) polypeptides.
FIG. 8 is a copy of a photographic representation showing the expression of wheat wSSIII mRNA in wheat. Total RNAs were isolated from the endosperm of the wheat cultivars Wyuna (Panel a) and Gabo (Panel b) leaves pre-anthesis florets and endosperm of the wheat cultivar “Gabo”, grown under a photoperiod comprising 16 hours daylength, and at 18° C. during the day cycle, and at 13° C. during the night cycle, and probed with the wSSIIIp1 DNA fragment derived from wSSIII.B3 cDNA. The source of each RNA is indicated at the top of the Figure as follows: Lane 1, endosperm at: 4 days post-anthesis; Lane 2, endosperm at 6 days post-anthesis; Lane 4, endosperm at 8 days post-anthesis; Lane 4, endosperm at 10 days post-anthesis; Lane 5, endosperm at 12 days post-anthesis; Lane 6, endosperm at 15 days post-anthesis; Lane 7, endosperm at 18 days post-anthesis; Lane 8, endosperm at 21 days post-anthesis; Lane 9, endosperm at 25 days post-anthesis; and Lane 10, endosperm at 31 days post-anthesis (Panel a only). In panel (c), L refers to leaf RNA, and P refers to RNA from pre-anthesis florets derived from the cultivar Gabo.
FIG. 9 (Figure panels 9A-9F) is a schematic representation showing the position of conserved amino acid sequences within four wheat starch synthase proteins. The eight highly-conserved regions between the wheat starch synthase polypeptides are underlined and annotated at the top of each group of amino acid sequences. The sequences included in the alignment are the wheat SSII-A1 and wheat SSIII polypeptides of the present invention; wheat GBSS (wGBSS; SEQ ID NO:57 Yan et al., 1999; wheat SSI (wSS1; SEQ ID NO:58 Li et al., 1999; wheat SSII (wSS2; SEQ ID NO:4); ans wheat SSIII (wSS3; SEQ ID NO:8).
FIG. 10 is a schematic representation showing the relationships between the primary amino acid sequences of starch synthases (SS) and glycogen synthase of E. coli (GS). The dendrogram was generated by the program PILEUP (Devereaux et al., 1984). The amino acid sequences used for the analysis are those of the wheat SSIIA, wheat SSIIB, wheat SSIID, and wheat SSIII polypeptides of the present invention compared to the deduced amino acid sequences of wheat GBSS (Clark et al., 1991), wheat SSI (Li et al., 1999), rice GBSS (Okagaki, 1992), rice SSI (Baba et al., 1993), maize GBSS (Kloesgen et al., 1986), maize SSI (Knight et al., 1998), maize SSIIa and maize SSIIb (Harn et al., 1998), maize SSIII (Gao et al., 1998), pea GBSS (Dry et al., 1992), pea SSII (Dry et al., 1992), potato GBSS (van der Leij et al., 1991), potato SSI (Genbank accession number: STSTASYNT), potato SSII (Edwards et al., 1995), potato SSIII (Abel et al., 1996), and E. coli glycogen synthase (GS) (Kumar et al., 1986). Five groups of enzymes included in the alignment are granule-bound starch synthase (GBSS), starch synthase-I (SSI), starch synthase-II (SSII), starch synthase-III (SSIII) and glycogen synthase (GS).
FIG. 11 is a schematic representation showing the position of conserved regions within cereal starch synthase genes. Comparisons of cereal starch synthases were made based on their deduced amino acid sequences and 8 conserved regions identified. Conserved regions are shown in bold and transit peptides (where defined) in grey. The sequences included in the alignment are the wheat SSII-A1 and wheat SSIII polypeptides of the present invention; wheat GBSS (Ainsworth et al., 1993); wheat SSI (Li et al., 1999); maize SSIIa (Harn et al., 1998); and maize dull-1 (Gao et al., 1998).
FIG. 12 is a copy of a schematic representation of a gene map showing the alignment of fragments 1 to 6 of the genomic SSIII gene (lower line) with the corresponding SSIII cDNA clone (upper line). Raised regions in the genomic clone fragments (lower line) represent protein-encoding regions of the gene.
FIG. 13 is a schematic representation showing the organisation of introns (lines) and exons (boxes) in the wheat SSIII gene shown in SEQ ID NO: 38. The scale (bases), relative to the nucleotide sequence set forth in SEQ ID NO: 38, is provided at the bottom of the figure.



DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS
One aspect of the present invention provides an isolated nucleic acid molecule which comprises a sequence of nucleotides which encodes, or is complementary to a nucleic acid molecule which encodes a wheat starch synthase polypeptide, protein or enzyme molecule or a functional subunit thereof selected from the following:

    
    
        (i) a wheat starch synthase II (wSSII) polypeptide, protein or enzyme or functional subunit thereof which comprises an amino acid sequence set forth in any one of SEQ ID NOS: 2, 4, or 6; and
        (ii) a wheat starch synthase III (wSSIII) polypeptide, protein or enzyme or functional subunit thereof which comprises an amino acid sequence set forth in any one of SEQ ID NOS: 8 or 10.
    
    


Alternatively or in addition, the isolated nucleic acid molecule of the present invention encodes a wheat starch synthase II (wSSII) polypeptide, protein or enzyme or functional subunit thereof and comprises a nucleotide sequence set forth in any one of SEQ ID NOS: 1, 3, 5, or 37.
Alternatively or in addition, the isolated nucleic acid molecule of the present invention encodes a wheat starch synthase III (wSSIII) polypeptide, protein or enzyme or functional subunit thereof and comprises a nucleotide sequence set forth in any one of SEQ ID NOS: 7, 9, or 38.
As used herein, the term “starch synthase” shall be taken to refer to any enzymatically-active peptide, polypeptide, oligopeptide, polypeptide, protein or enzyme molecule that is at least capable of transferring a glucosyl moiety from ADP-glucose to an α-1,4-glucan molecule, or a peptide, polypeptide, oligopeptide or polypeptide fragment of such an enzymatically-active molecule.
The term “wheat starch synthase” refers to a starch synthase derived from hexaploid wheat or barley or a progenitor species, or a relative thereto such as the diploid Triticum tauschii or other diploid, tetraploid, aneuploid, polyploid, nullisomic, or a wheat/barley addition line, amongst others, the only requirement that the genomic DNA is at least about 80% identical to the genome of a wheat plant as determined by standard DNA melting curve analyses.
The term “starch synthase II” or “wSSII” or similar term shall be taken to refer to a starch synthase as hereinbefore defined that is detectable in the starch granule of a plant seed endosperm and possesses one or more properties selected from the group consisting of:
(i) it is immunologically cross-reactive with the wheat starch granule proteins designated Sgp-B1 and/or Sgp-D1 and/or Sgp-A1, having estimated molecular weights of about 85 kDa to about 115 kDa;

    
    
        (ii) it is encoded by one of a homeologous set of genes localised on wheat chromosomes 7B or 7A or 7D;
        (iii) it is encoded by a nucleotide sequence that comprises at least about 15 nucleotides in length derived from any one or more of SEQ ID NOS: 1, 3, 5, or 37 or a complementary nucleotide sequence thereto;
        (iv) it is encoded by a nucleotide sequence that is at least about 85% identical to one or more of the nucleotide sequences set forth in SEQ ID NOS: 1, 3, 5, or 37, or a complementary nucleotide sequence thereto;
        (v) it comprises an amino acid sequence having at least about 85% identity to one or more of SEQ ID NOS: 2 or 4 or 6;
        (vi) it comprises at least about 5 contiguous amino acids, preferably at least about 10 contiguous amino acids, more preferably at least about 15 contiguous amino acids, even more preferably at least about 20 contiguous amino acids and still even more preferably at least about 25-50 contiguous amino acids of the amino acid sequences set forth in SEQ ID NOS: 2 or 4 or 6;
        (vii) it which comprises a conserved amino acid sequence having at least 25% identity to an amino acid sequence selected from a group consisting of:
    
    












(a)
KVGGLGDVVTS;
(SEQ ID NO: 39)



 


(b)
GHTVEVILPKY;
(SEQ ID NO: 40)


 


(c)
HDWSSAPVAWLYKEHY;
(SEQ ID NO: 41)


 


(d)
GILNGIDPDIWDPYTD;
(SEQ ID NO: 42)


 


(e)
DVPIVGIITRLTAQKG;
(SEQ ID NO: 43)


 


(f)
NGQVVLLGSA;
(SEQ ID NO: 44)


 


(g)
AGSDFIIVPSIFEPCGLTQLVAMRYGS;
(SEQ ID NO: 45)


and


 


(h)
TGGLVDTV.
(SEQ ID NO: 46)






    
    
        in addition to any one or more of (i) to (vi); and
        (viii) it which comprises a conserved amino acid sequence having at least 25% identity to an amino acid sequence selected from the group consisting of:
    
    














(a)
KTGGLGDVAGA;
(SEQ ID NO: 47)




 



(b)
GHRVMVVVPRY;
(SEQ ID NO: 48)



 



(c)
NDWHTALLPVYLKAYY;
(SEQ ID NO: 49)



 



(d)
GIVNGIDNMEWNPEVD;
(SEQ ID NO: 50)



 



(e)
DVPLLGFIGRLDGQKG;
(SEQ ID NO: 51)



 



(f)
DVQLVMLGTG;
(SEQ ID NO: 52)



 



(g)
AGADALLMPSRF(E/
(SEQ ID NO: 53)




V)PCGLNQLYAMAYGT;



and



 



(h)
VGG(V/L)RDTV,
(SEQ ID NO: 54)






    
    
        in addition to any one or more of (i) to (vi).
    
    


The term “starch synthase III” or “wSSIII” or similar term shall be taken to refer to a starch synthase as hereinbefore defined that possesses one or more properties selected from the group consisting of:

    
    
        (i) it is encoded by a nucleotide sequence that comprises at least about 15 nucleotides in length derived from any one or more of SEQ ID NOS: 7, 9, 11-16, or 38, or a complementary nucleotide sequence thereto;
        (ii) it is encoded by a nucleotide sequence that is at least about 85% identical to one or more of the nucleotide sequences set forth in SEQ ID NOS: 7, 9, 11-16, or 38, or a complementary nucleotide sequence thereto; and
        (iii) it comprises an amino acid sequence having at least about 85% identity to one or more of SEQ ID NOS: 8 or 10;
        (iv) it comprises at least about 5 contiguous amino acids, preferably at least about 10 contiguous amino acids, more preferably at least about 15 contiguous amino acids, even more preferably at least about 20 contiguous amino acids and still even more preferably at least about 25-50 contiguous amino acids of the amino acid sequences set forth in SEQ ID NOS: 8 or 10;
        (v) which comprises a conserved amino acid sequence having at least 25% identity to an amino acid sequence selected from the group consisting of:
    
    












(a)
KVGGLGDVVTS;
(SEQ ID NO: 39)



 


(b)
GHTVEVILPKY;
(SEQ ID NO: 40)


 


(c)
HDWSSAPVAWLYKEHY;
(SEQ ID NO: 41)


 


(d)
GILNGIDPDIWDPYTD;
(SEQ ID NO: 42)


 


(e)
DVPIVGIITRLTAQKG;
(SEQ ID NO: 43)


 


(f)
NGQVVLLGSA;
(SEQ ID NO: 44)


 


(g)
AGSDFIIVPSIFEPCGLTQLVAMRYGS;
(SEQ ID NO: 45)


and


 


(h)
TGGLVDTV
(SEQ ID NO: 46)






    
    
        in addition to any one or more of (i) to (iv); and
        (vi) it which comprises a conserved amino acid sequence having at least 25% identity to an amino acid sequence selected from the group consisting of:
    
    














(a)
KTGGLGDVAGA;
(SEQ ID NO: 47)




 



(b)
GHRVMVVVPRY;
(SEQ ID NO: 48)



 



(c)
NDWHTALLPVYLKAYY;
(SEQ ID NO: 49)



 



(d)
GIVNGIDNMEWNPEVD;
(SEQ ID NO: 50)



 



(e)
DVPLLGFIGRLDGQKG;
(SEQ ID NO: 51)



 



(f)
DVQLVMLGTG;
(SEQ ID NO: 52)



 



(g)
AGADALLMPSRF(E/
(SEQ ID NO: 53)




V)PCGLNQLYAMAYGT;



and



 



(h)
VGG(V/L)RDTV,
(SEQ ID NO: 54)






    
    
        in addition to any one or more of (I) to (iv).
    
    


In a more preferred embodiment, the WSSII or WSSIII polypeptide encoded by the nucleic acid molecule of the present invention will comprise a substantial contiguous region of any one of SEQ ID NOS: 2, 4, 6, 8 or 10 or 17 sufficient to possess the biological activity of a starch synthase polypeptide.
For the purposes of nomenclature, the nucleotide sequence set forth in SEQ ID NO: 1 relates to the cDNA molecule encoding the WSSII (i.e. Sgp-B1) polypeptide of wheat. The amino acid sequence of the corresponding polypeptide is set forth herein as SEQ ID NO:2. The nucleotide sequence set forth in SEQ ID NO: 3 relates to the cDNA molecule encoding the WSSII (i.e. Sgp-A1) polypeptide of wheat. The amino acid sequence of the corresponding polypeptide is set forth herein as SEQ ID NO:4.
The nucleotide sequence set forth in SEQ ID NO: 5 relates to the cDNA molecule encoding the WSSII (i.e. Sgp-D1) polypeptide of wheat. The amino acid sequence of the corresponding polypeptide is set forth herein as SEQ ID NO:6. The nucleotide sequences set forth in SEQ ID NOs: 7 and 9 relate, respectively, to full-length and partial cDNA molecules encoding the WSSIII polypeptide of wheat. The amino acid sequences of the corresponding polypeptides are set forth herein as SEQ ID NOS: 8 and 10, respectively. The nucleotide sequences set forth in SEQ ID NOs: 11 to 16 relates to fragments of the genomic gene encoding the WSSIII polypeptide of wheat, significant protein-encoding regions of which are described by reference to Table 4 and FIG. 11. The nucleotide sequence set forth in SEQ ID NO: 37 relates to the WSSII genomic gene of Triticum tauschii, corresponding to the WSSII gene of the D-genome of wheat, which encodes the WSSII polypeptide. The nucleotide sequence set forth in SEQ ID NO: 38 relates to the wheat WSSIII genomic gene.
Preferably, the isolated nucleic acid molecule of the present invention comprises a sequence of nucleotides which encodes, or is complementary to a nucleic acid molecule which encodes a wheat starch synthase polypeptide, protein or enzyme molecule or a functional subunit thereof which comprises an amino acid sequence which is at least about 85% identical overall to an amino acid sequence set forth in any one of SEQ ID NOS: 2, 4, 6, 8 or 10 and more preferably, which additionally comprises which comprises one or more amino acid sequences selected from the group consisting of:










(a)
KVGGLGDVVTS;
(SEQ ID NO: 39)



 


(b)
GHTVEVILPKY;
(SEQ ID NO: 40)


 


(c)
HDWSSAPVAWLYKEHY;
(SEQ ID NO: 41)


 


(d)
GILNGIDPDIWDPYTD;
(SEQ ID NO: 42)


 


(e)
DVPIVGIITRLTAQKG;
(SEQ ID NO: 43)


 


(f)
NGQVVLLGSA;
(SEQ ID NO: 44)


 


(g)
AGSDFIIVPSIFEPCGLTQLVAMRYGS;
(SEQ ID NO: 45)


 


(h)
TGGLVDTV;
(SEQ ID NO: 46)


 


(i)
KTGGLGDVAGA;
(SEQ ID NO: 47)


 


(j)
GHRVMVVVPRY;
(SEQ ID NO: 48)


 


(k)
NDWHTALLPVYLKAYY;
(SEQ ID NO: 49)


 


(l)
GIVNGIDNMEWNPEVD;
(SEQ ID NO: 50)


 


(m)
DVPLLGFIGRLDGQKG;
(SEQ ID NO: 51)


 


(n)
DVQLVMLGTG;
(SEQ ID NO: 52)


 


(o)
AGADALLMPSRF(E/
(SEQ ID NO: 53)



V)PCGLNQLYAMAYGT;


and


 


(p)
VGG(V/L)RDTV.
(SEQ ID NO: 54)






The present invention clearly extends to homologues, analogues and derivatives of the wheat starch synthase II and III genes exemplified by the nucleotide sequences set forth herein as SEQ ID NOs: 1, 3, 5, 7, 9, 11-16, 37 or 38.
Preferred starch synthase genes may be derived from a naturally-occurring starch synthase gene by standard recombinant techniques. Generally, a starch synthase gene may be subjected to mutagenesis to produce single or multiple nucleotide substitutions, deletions and/or additions. Nucleotide insertional derivatives of the starch synthase gene of the present invention include 5′ and 3′ terminal fusions as well as intra-sequence insertions of single or multiple nucleotides. Insertional nucleotide sequence variants are those in which one or more nucleotides are introduced into a predetermined site in the nucleotide sequence although random insertion is also possible with suitable screening of the resulting product. Deletional variants are characterised by the removal of one or more nucleotides from the sequence. Substitutional nucleotide variants are those in which at least one nucleotide in the sequence has been removed and a different nucleotide inserted in its place. Such a substitution may be “silent” in that the substitution does not change the amino acid defined by the codon. Alternatively, substituents are designed to alter one amino acid for another similar acting amino acid, or amino acid of like charge, polarity, or hydrophobicity.
For the present purpose, “homologues” of a nucleotide sequence shall be taken to refer to an isolated nucleic acid molecule which is substantially the same as the nucleic acid molecule of the present invention or its complementary nucleotide sequence, notwithstanding the occurrence within said sequence, of one or more nucleotide substitutions, insertions, deletions, or rearrangements.
“Analogues” of a nucleotide sequence set forth herein shall be taken to refer to an isolated nucleic acid molecule which is substantially the same as a nucleic acid molecule of the present invention or its complementary nucleotide sequence, notwithstanding the occurrence of any non-nucleotide constituents not normally present in said isolated nucleic acid molecule, for example carbohydrates, radiochemicals including radionucleotides, reporter molecules such as, but not limited to DIG, alkaline phosphatase or horseradish peroxidase, amongst others.
“Derivatives” of a nucleotide sequence set forth herein shall be taken to refer to any isolated nucleic acid molecule which contains significant sequence similarity to said sequence or a part thereof. Generally, the nucleotide sequence of the present invention may be subjected to mutagenesis to produce single or multiple nucleotide substitutions, deletions and/or insertions. Nucleotide insertional derivatives of the nucleotide sequence of the present invention include 5′ and 3′ terminal fusions as well as intra-sequence insertions of single or multiple nucleotides or nucleotide analogues. Insertional nucleotide sequence variants are those in which one or more nucleotides or nucleotide analogues are introduced into a predetermined site in the nucleotide sequence of said sequence, although random insertion is also possible with suitable screening of the resulting product being performed. Deletional variants are characterised by the removal of one or more nucleotides from the nucleotide sequence. Substitutional nucleotide variants are those in which at least one nucleotide in the sequence has been removed and a different nucleotide or nucleotide analogue inserted in its place.
The present invention extends to the isolated nucleic acid molecule when integrated into the genome of a cell as an addition to the endogenous cellular complement of starch synthase genes, irrespective of whether or not the introduced nucleotide sequence is translatable or non-translatable to produce a polypeptide. The present invention clearly contemplates the introduction of additional copies of starch synthase genes into plants, particularly wheat plants, in the antisense orientation to reduce the expression of particular wheat starch synthase genes. As will be known to those skilled in the art, such antisense genes are non-translatable, notwithstanding that they can be expressed to produce antisense mRNA molecules.
The said integrated nucleic acid molecule may, or may not, contain promoter sequences to regulate expression of the subject genetic sequence.
Accordingly, the present invention clearly encompasses preferred homologues, analogues and derivatives that comprise a sequence of nucleotides which encodes, or is complementary to a nucleic acid molecule which encodes a wheat starch synthase polypeptide, protein or enzyme molecule or a functional subunit thereof selected from the following:

    
    
        (i) a wheat starch synthase II (wSSII) polypeptide, protein or enzyme or functional subunit thereof which comprises an amino acid sequence which is at least about 85% identical overall to an amino acid sequence set forth in any one of SEQ ID NOS: 2, 4, or 6;
        (ii) a wheat starch synthase III (wSSIII) polypeptide, protein or enzyme or functional subunit thereof which comprises an amino acid sequence which is at least about 85% identical overall to an amino acid sequence set forth in any one of SEQ ID NOS: 8 or 10;
        (iii) a wheat starch synthase polypeptide, protein or enzyme or functional subunit thereof which comprises a conserved amino acid sequence having at least 25% identity to an amino acid sequence selected from the group consisting of:
    
    












(a)
KVGGLGDVVTS;
(SEQ ID NO: 39)



 


(b)
GHTVEVILPKY;
(SEQ ID NO: 40)


 


(c)
HDWSSAPVAWLYKEHY;
(SEQ ID NO: 41)


 


(d)
GILNGIDPDIWDPYTD;
(SEQ ID NO: 42)


 


(e)
DVPIVGIITRLTAQKG;
(SEQ ID NO: 43)


 


(f)
NGQVVLLGSA;
(SEQ ID NO: 44)


 


(g)
AGSDFIIVPSIFEPCGLTQLVAMRYGS;
(SEQ ID NO: 45)


and


 


(h)
TGGLVDTV
(SEQ ID NO: 46)






    
    
        and wherein said wheat starch synthase polypeptide further comprises an amino acid sequence having at least about 85% identity overall to an amino acid sequence set forth in any one of SEQ ID NOS:2, 4, 6, 8 or 10; and
        (iv) a wheat starch synthase polypeptide, protein or enzyme or functional subunit thereof which comprises a conserved amino acid sequence having at least 25% identity to an amino acid sequence selected from the group consisting of:
    
    














(a)
KTGGLGDVAGA;
(SEQ ID NO: 47)




 



(b)
GHRVMVVVPRY;
(SEQ ID NO: 48)



 



(c)
NDWHTALLPVYLKAYY;
(SEQ ID NO: 49)



 



(d)
GIVNGIDNMEWNPEVD;
(SEQ ID NO: 50)



 



(e)
DVPLLGFIGRLDGQKG;
(SEQ ID NO: 51)



 



(f)
DVQLVMLGTG;
(SEQ ID NO: 52)



 



(g)
AGADALLMPSRF(E/
(SEQ ID NO: 53)




V)PCGLNQLYAMAYGT;



and



 



(h)
VGG(V/L)RDTV,
(SEQ ID NO: 54)






    
    
        and wherein said wheat starch synthase polypeptide further comprises an amino acid sequence having at least about 85% identity overall to an amino acid sequence set forth in any one of SEQ ID NOS:2, 4, 6, 8 or 10.
    
    


Preferably, the isolated nucleic acid molecule encodes a starch synthase polypeptide, protein or enzyme that comprises two, more preferably three, more preferably four, more preferably five, more preferably six, more preferably seven and even more preferably eight of the conserved amino acid motifs listed supra. Even more preferably, the said amino acid motifs are located in a relative configuration such as that shown for the wheat SSII or wheat SSIII polypeptides described herein.
In a preferred embodiment, the isolated nucleic acid molecule encodes a starch synthase polypeptide, protein or enzyme having at least about 90% amino acid sequence identity to any one of SEQ ID NOS: 2, 4, 6, 8 or 10, more preferably having at least about 95% or about 97% or about 99% identity to any one of said amino acid sequences.
In an alternative embodiment, the present invention provides an isolated nucleic acid molecule which encodes a wheat starch synthase polypeptide, protein or enzyme molecule or a functional subunit thereof, wherein said nucleic acid molecule comprises a nucleotide sequence having at least about 85% nucleotide sequence identity to any one of SEQ ID NOS: 1, 3, 5, 7, 9, 11-16, 37, or 38, or a degenerate nucleotide sequence thereto or a complementary nucleotide sequence thereto.
By “degenerate nucleotide sequence” is meant a nucleotide sequence that encodes a substantially identical amino acid sequence as a stated nucleotide sequence.
In a preferred embodiment, the isolated nucleic acid molecule comprises the nucleotide sequence set forth in any one of SEQ ID NOS: 1, 3, 5, 7, 9, 11-16, 37, or 38, or is at least about 90% identical, more preferably at least about 95% or 97% or 99% identical to all or a protein-encoding part thereof.
In an alternative embodiment, preferred homologues, analogues and derivatives of the nucleic acid molecule of the present invention encodes a wheat starch synthase polypeptide, protein or enzyme molecule or a functional subunit thereof and comprises a nucleotide sequence that is capable of hybridising under at least moderate stringency hybridisation conditions to at least about 30 contiguous nucleotides derived from any one of SEQ ID NOS: 1, 3, 5, 7, 9, 11-16, 37, or 38, or a complementary nucleotide sequence thereto.
For the purposes of defining the level of stringency, a low stringency is defined herein as being a hybridisation and/or a wash carried out in 6×SSC buffer, 0.1% (w/v) SDS at 28° C. Generally, the stringency is increased by reducing the concentration of SSC buffer, and/or increasing the concentration of SDS and/or increasing the temperature of the hybridisation and/or wash. A moderate stringency comprises a hybridisation and/or a wash carried out in 0.2×SSC-2×SSC buffer, 0.1% (w/v) SDS at 42° C. to 65° C., while a high stringency comprises a hybridisation and/or a wash carried out in 0.1×SSC-0.2×SSC buffer, 0.1% (w/v) SDS at a temperature of at least 55° C. Conditions for hybridisations and washes are well understood by one normally skilled in the art. For the purposes of further clarification only, reference to the parameters affecting hybridisation between nucleic acid molecules is found in pages 2.10.8 to 2.10.16. of Ausubel et al., (1987), which is herein incorporated by reference.
Those skilled in the art will be aware of procedures for the isolation of further wheat starch synthase genes to those specifically described herein or homologues, analogues or derivatives of said genes, for example further cDNA sequences and genomic gene equivalents, when provided with one or more of the nucleotide sequences set forth in SEQ ID NOs: 1, 3, 5, 7, 9, 11-16, 37, or 38. In particular, amplifications and/or hybridisations may be performed using one or more nucleic acid primers or hybridisation probes comprising at least 10 contiguous nucleotides and preferably at least about 20 contiguous nucleotides or 50 contiguous nucleotides derived from the nucleotide sequences set forth herein, to isolate cDNA clones, mRNA molecules, genomic clones from a genomic library (in particular genomic clones containing the entire 5′ upstream region of the gene including the promoter sequence, and the entire coding region and 3′-untranslated sequences), and/or synthetic oligonucleotide molecules, amongst others. The present invention clearly extends to such related sequences.
Accordingly, a second aspect of the present invention provides a method of isolating a nucleic acid molecule that encodes a starch synthase polypeptide, protein or enzyme said method comprising:

    
    
        (i) hybridising a probe or primer comprising at least about 15 contiguous nucleotides in length derived from any one of SEQ ID NOS 1, 3, 5, 7, 9, 11-16, 37, or 38, or a complementary nucleotide sequence thereto to single-stranded or double-stranded mRNA, cDNA or genomic DNA; and
        (ii) detecting the hybridised mRNA, cDNA or genomic DNA using a detecting means.
    
    


Preferably, the detecting means is a reporter molecule covalently attached to the probe or primer molecule or alternatively, a polymerase chain reaction format.
An alternative method contemplated in the present invention involves hybridising two nucleic acid “primer molecules” to a nucleic acid “template molecule” which comprises a related starch synthase gene or related starch synthase genetic sequence or a functional part thereof, wherein the first of said primers comprises contiguous nucleotides derived from any one or more of SEQ ID NOS: 1, 3, 5, 7, 9, 11-16, 37, or 38, and the second of said primers comprises contiguous nucleotides complementary to any one or more of SEQ ID NOS: 1, 3, 5, 7, 9, 11-16, 37, or 38. Specific nucleic acid molecule copies of the template molecule are amplified enzymatically in a polymerase chain reaction, a technique that is well known to one skilled in the art.
In a preferred embodiment, each nucleic acid primer molecule is at least 10 nucleotides in length, more preferably at least 20 nucleotides in length, even more preferably at least 30 nucleotides in length, still more preferably at least 40 nucleotides in length and even still more preferably at least 50 nucleotides in length.
Furthermore, the nucleic acid primer molecules consists of a combination of any of the nucleotides adenine, cytidine, guanine, thymidine, or inosine, or functional analogues or derivatives thereof which are at least capable of being incorporated into a polynucleotide molecule without having an inhibitory effect on the hybridisation of said primer to the template molecule in the environment in which it is used.
Furthermore, one or both of the nucleic acid primer molecules may be contained in an aqueous mixture of other nucleic acid primer molecules, for example a mixture of degenerate primer sequences which vary from each other by one or more nucleotide substitutions or deletions. Alternatively, one or both of the nucleic acid primer molecules may be in a substantially pure form.
The nucleic acid template molecule may be in a recombinant form, in a virus particle, bacteriophage particle, yeast cell, animal cell, or a plant cell. Preferably, the nucleic acid template molecule is derived from a plant cell, tissue or organ, in particular a cell, tissue or organ derived from a wheat or barley plant or a progenitor species, or a relative thereto such as the diploid Triticum tauschii or other diploid, tetraploid, aneuploid, polyploid, nullisomic, or a wheat/barley addition line, amongst others.
Those skilled in the art will be aware that there are many known variations of the basic polymerase chain reaction procedure, which may be employed to isolate a related starch synthase gene or related starch synthase genetic sequence when provided with the nucleotide sequences set forth herein. Such variations are discussed, for example, in McPherson et al (1991). The present invention extends to the use of all such variations in the isolation of related starch synthase genes or related starch synthase genetic sequences using the nucleotide sequences embodied by the present invention.
As exemplified herein, the present inventors have isolated several wheat starch synthase genes using both hybridisation and polymerase chain reaction approaches, employing novel probes and primer sequences to do so.
Accordingly, a third aspect of the invention provides an isolated probe or primer comprising at least about 15 contiguous nucleotides in length derived from any one of SEQ ID NOS: 1, 3, 5, 7, 9, 11-16, 37, or 38, or a complementary nucleotide sequence thereto.
Preferably, the probe or primer comprises a nucleotide sequence set forth in any one of SEQ ID NOS: 25 to 34.
The isolated nucleic acid molecule of the present invention may be introduced into and expressed in any cell, for example a plant cell, fungal cell, insect coil, animal cell, yeast cell or bacterial cell. Those skilled in the art will be aware of any modifications which are required to the codon usage or promoter sequences or other regulatory sequences, in order for expression to occur in such cells.
A further aspect of the invention provides a method of assaying for the presence or absence of a starch synthase isoenzyme or the copy number of a gene encoding same in a plant, comprising contacting a biological sample derived from said plant with an isolated nucleic acid molecule derived from any one of SEQ ID NOS 1, 3, 5, 7, 9, 11-16, 37, or 38, or any one of SEQ ID NOS: 25 to 34, or a complementary nucleotide sequence thereto for a time and under conditions sufficient for hybridisation to occur and then detecting said hybridisation using a detection means.
The detection means according to this aspect of the invention is any nucleic acid based hybridisation or amplification reaction.
The hexaploid nature of wheat prevents the straightforward identification of starch synthase allelic variants by hybridisation using the complete starch synthase-encoding sequence, because the similarities between the various alleles generally results in significant cross-hybridisation. Accordingly, sequence-specific hybridisation probes are required to distinguish between the various alleles. Similarly, wherein PCR is used to amplify specific allelic variants of a starch synthase gene, one or more sequence-specific amplification primers are generally required. As will be apparent from the amino acid sequence comparisons provided herein, such as in FIGS. 3 and 13, non-conserved regions of particular wheat starch synthase polypeptides are particularly useful for the design of probes and primers that are capable of distinguishing between one or more starch synthase polypeptide isoenzyme or allelic variant. The present invention clearly contemplates the design of such probes and primers based upon the sequence comparisons provided herein.
In the performance of this embodiment of the present invention, the present inventors particularly contemplate the identification of wheat starch synthase null alleles or alternatively, mutations wherein specific amino acids are inserted or deleted or substituted, compared to one or more of the wheat SSII or SSIII alleles disclosed herein. Such null alleles and other allelic variants are readily identifiable using PCR screening which employs amplification primers based upon the nucleotide and amino acid sequences disclosed herein for SSII and/or SSIII. Once identified, the various mutations can be stacked or pyramided into one or more new wheat lines, such as by introgression and/or standard plant breeding and/or recombinant approaches (eg. transformation, transfection, etc) thereby producing a novel germplasm which exhibits altered starch properties compared to existing lines. DNA markers based upon the nucleotide and amino acid sequences disclosed herein for SSII and/or SSIII can be employed to monitor the stacking of genes into the new lines and to correlate the presence of particular genes with starch phenotypes of said lines.
In this regard, a significant advantage conferred by the present invention is the design of new DNA markers that reveal polymorphisms such as, for example, length polymorphisms, restriction site polymorphisms, and single nucleotide polymorphisms, amongst others, between wheat starch synthases and, in particular, between wheat GBSS and/or SSI and/or SSI and/or SSIII, or between allelic variants of one or more of said starch synthases, that can be used to identify the three genomes of hexaploid wheats (i.e., the A, B and D genomes).
Preferably, such DNA markers are derived from the intron region of a starch synthase gene disclosed herein, more preferably the wheat SSII and/or the wheat SSIII gene. Those skilled in the art will be aware that such regions generally have a higher degree of variation than in the protein-encoding regions and, as a consequence, are particularly useful in identifying specific allelic variants of a particular gene, such as allelic variants contained in any one of the three wheat genomes, or alternatively or in addition, for the purpose of distinguishing between wheat GBSS, SSI, SSII or SSIII genes.
A further approach contemplated by the present inventors is the design of unique isoenzyme-specific and/or allele-specific peptides based upon the amino acid sequence disclosed herein as SEQ ID NOS: 25 and/or SEQ ID NO: 4 and/or SEQ ID NO: 6 and/or SEQ ID NO: 8 and/or SEQ ID NO: 10, which peptides are then used to produce polyclonal or monoclonal antibodies by conventional means. Alternatively, the genes encoding these polypeptides or unique peptide regions thereof can be introduced in an expressible format into an appropriate prokaryotic or eukaryotic expression system, where they can be expressed to produce the isoenzyme-specific and/or allele-specific peptides for antibody production. Such antibodies may also be used as markers for the purpose of both identifying parental lines and germplasms and monitoring the stacking of genes in new lines, using conventional immunoassays such as, for example, ELISA and western blotting.
A further aspect of the present invention utilises the above-mentioned nucleic acid based assay method in the breeding and/or selection of plants which express or do not express particular starch synthase isoenzymes or alternatively, which express a particular starch synthase isoenzyme at a particular level in one or more plant tissues. This aspect clearly extends to the selection of transformed plant material which contains one or more of the isolated nucleic acid molecules of the present invention.
Yet another aspect of the present invention provides for the expression of the nucleic acid molecule of the present invention in a suitable host (e.g. a prokaryote or eukaryote) to produce full length or non-full length recombinant starch synthase gene products.
Hereinafter the term “starch synthase gene product” shall be taken to refer to a recombinant product of a starch synthase gene of the present invention.
Preferably, the recombinant starch synthase gene product comprises an amino acid sequence having the catalytic activity of a starch synthase polypeptide or a functional mutant, derivative part, fragment, or analogue thereof.
In a particularly preferred embodiment of the invention, the recombinant starch synthase gene product is selected from the following:

    
    
        (i) a wheat starch synthase II (wSSII) polypeptide, protein or enzyme or functional subunit thereof which comprises an amino acid sequence which is at least about 85% identical overall to an amino acid sequence set forth in any one of SEQ ID NOS: 2, 4, or 6;
        (ii) a wheat starch synthase III (wSSIII) polypeptide, protein or enzyme or functional subunit thereof which comprises an amino acid sequence which is at least about 85% identical overall to an amino acid sequence set forth in any one of SEQ ID NOS: 8 or 10; and
        (iii) a wheat starch synthase polypeptide, protein or enzyme or functional subunit thereof which comprises a conserved amino acid sequence having at least 25% identity to an amino acid sequence selected from the group consisting of:
    
    












(a)
KVGGLGDVVTS;
(SEQ ID NO: 39)



 


(b)
GHTVEVILPKY;
(SEQ ID NO: 40)


 


(c)
HDWSSAPVAWLYKEHY;
(SEQ ID NO: 41)


 


(d)
GILNGIDPDIWDPYTD;
(SEQ ID NO: 42)


 


(e)
DVPIVGIITRLTAQKG;
(SEQ ID NO: 43)


 


(f)
NGQVVLLGSA;
(SEQ ID NO: 44)


 


(g)
AGSDFIIVPSIFEPCGLTQLVAMRYGS;
(SEQ ID NO: 45)


 


(h)
TGGLVDTV;
(SEQ ID NO: 46)






    
    
        
        
            (i) a wheat starch synthase ii (wSSII) polypeptide, protein or enzyme or functional subunit thereof which comprises an amino acid sequence which is at least about 85% identical overall to an amino acid sequence set forth in any one of SEQ ID NOS:2, 4 or 6;
        
        
        (ii) a wheat starch synthase III (wSSIII) polypeptide, protein or enzyme or functional subunit thereof which comprises an amino acid sequence which is at least about 85% identical overall to an amino acid sequence set forth in any one of SEQ ID NOS: 8 or 10;
        (iii) a wheat starch synthase polypeptide, protein or enzyme or functional subunit thereof which comprises a conserved amino acid sequence having at least 25% identity to an amino acid sequence selected from the group consisting of:
    
    












(a)
KVGGLGDVVTS;
(SEQ ID NO: 39)



 


(b)
GHTVEVILPKY;
(SEQ ID NO: 40)


 


(c)
HDWSSAPVAWLYKEHY;
(SEQ ID NO: 41)


 


(d)
GILNGIDPDIWDPYTD;
(SEQ ID NO: 42)


 


(e)
DVPIVGIITRLTAQKG;
(SEQ ID NO: 43)


 


(f)
NGQVVLLGSA;
(SEQ ID NO: 44)


 


(g)
AGSDFIIVPSIFEPCGLTQLVAMRYGS;
(SEQ ID NO: 45)


and


 


(h)
TGGLVDTV;
(SEQ ID NO: 46)


 


(i)
KTGGLGDVAGA;
(SEQ ID NO: 47)


 


(j)
GHRVMVVVPRY;
(SEQ ID NO: 48)


 


(k)
NDWHTALLPVYLKAYY;
(SEQ ID NO: 49)


 


(l)
GIVNGIDNMEWNPEVD;
(SEQ ID NO: 50)


 


(m)
DVPLLGFIGRLDGQKG;
(SEQ ID NO: 51)


 


(n)
DVQLVMLGTG;
(SEQ ID NO: 52)


 


(o)
AGADALLMPSRF(E/
(SEQ ID NO: 53)



V)PCGLNQLYAMAYGT;


and


 


(p)
VGG(V/L)RDTV.
(SEQ ID NO: 54)






Accordingly, the present invention clearly extends to homologues, analogues and derivatives of the amino acid sequences set forth herein as SEQ ID NOS: 2, 4, 6, 8 and 10.
In the present context, “homologues” of an amino acid sequence refer to those polypeptides, enzymes or proteins which have a similar catalytic activity to the amino acid sequences described herein, notwithstanding any amino acid substitutions, additions or deletions thereto. A homologue may be isolated or derived from the same or another plant species as the species from which the polypeptides of the invention are derived.
“Analogues” encompass polypeptides of the invention notwithstanding the occurrence of any non-naturally occurring amino acid analogues therein.
“Derivatives” include modified peptides in which ligands are attached to one or more of the amino acid residues contained therein, such as carbohydrates, enzymes, proteins, polypeptides or reporter molecules such as radionuclides or fluorescent compounds. Glycosylated, fluorescent, acylated or alkylated forms of the subject peptides are particularly contemplated by the present invention. Additionally, derivatives of an amino acid sequence described herein which comprises fragments or parts of the subject amino acid sequences are within the scope of the invention, as are homopolymers or heteropolymers comprising two or more copies of the subject polypeptides. Procedures for derivatizing peptides are well-known in the art.
Substitutions encompass amino acid alterations in which an amino acid is replaced with a different naturally-occurring or a non-conventional amino acid residue. Such substitutions may be classified as “conservative”, in which an amino acid residue contained in a starch synthase gene product is replaced with another naturally-occurring amino acid of similar character, for example GlyAla, ValIleLeu, AspGlu, LysArg, AsnGln or PheTrpTyr.
Substitutions encompassed by the present invention may also be “non-conservative”, in which an amino acid residue which is present in a starch synthase gene product described herein is substituted with an amino acid with different properties, such as a naturally-occurring amino acid from a different group (eg. substituted a charged or hydrophobic amino acid with alanine), or alternatively, in which a naturally-occurring amino acid is substituted with a non-conventional amino acid.
Non-conventional amino acids encompassed by the invention include, but are not limited to those listed in Table 2.
Amino acid substitutions are typically of single residues, but may be of multiple residues, either clustered or dispersed.
Amino acid deletions will usually be of the order of about 1-10 amino acid residues, while insertions may be of any length. Deletions and insertions may be made to the N-terminus, the C-terminus or be internal deletions or insertions. Generally, insertions within the amino acid sequence will be smaller than amino- or carboxy-terminal fusions and of the order of 1-4 amino acid residues.
A homologue, analogue or derivative of a starch synthase gene product as referred to herein may readily be made using peptide synthetic techniques well-known in the art, such as solid phase peptide synthesis and the like, or by recombinant DNA manipulations. Techniques for making substituent mutations at pre-determined sites using recombinant DNA technology, for example by M13 mutagenesis, are also well-known. The manipulation of nucleic acid molecules to produce variant peptides, polypeptides or proteins which manifest as substitutions, insertions or deletions are well-known in the art.
The starch synthase gene products described herein may be derivatized further by the inclusion or attachment thereto of a protective group which prevents, inhibits or slows proteolytic or cellular degradative processes. Such derivatization may be useful where the half-life of the subject polypeptide is required to be extended, for example to increase the amount of starch produced in the endosperm or alternatively, to increase the amount of protein produced in a bacterial or eukaryotic expression system. Examples of chemical groups suitable for this purpose include, but are not limited to, any of the non-conventional amino acid residues listed in Table 2, in particular a D-stereoisomer or a methylated form of a naturally-occurring amino acid listed in Table 1. Additional chemical groups which are useful for this purpose are selected from the list comprising aryl or heterocyclic N-acyl substituents, polyalkylene oxide moieties, desulphatohirudin muteins, alpha-muteins, alpha-aminophosphonic acids, water-soluble polymer groups such as polyethylene glycol attached to sugar residues using hydrazone or oxime groups, benzodiazepine dione derivatives, glycosyl groups such as beta-glycosylamine or a derivative thereof, isocyanate conjugated to a polyol functional group or polyoxyethylene polyol capped with diisocyanate, amongst others. Similarly, a starch synthase gene product or a homologue, analogue or derivative thereof may be cross-linked or fused to itself or to a protease inhibitor peptide, to reduce susceptibility of said molecule to proteolysis.
In a particularly preferred embodiment, the percentage similarity to in any one of SEQ ID NOS: 2, 4, 6, 8 or 10 is at least about 90%, more preferably at least about 95%, even more preferably at least about 97% and even more preferably at least about 98%, or about 99% or 100%.
In a related embodiment, the present invention provides a “sequencably pure” form of the amino acid sequence described herein. “Sequencably pure” is hereinbefore described as substantially homogeneous to facilitate amino acid determination.
In a further related embodiment, the present invention provides a “substantially homogeneous” form of the subject amino acid sequence, wherein the term “substantially homogeneous” is hereinbefore defined as being in a form suitable for interaction with an immunologically interactive molecule. Preferably, the polypeptide is at least 20% homogeneous, more preferably at least 50% homogeneous, still more preferably at least 75% homogeneous and yet still more preferably at least about 95-100% homogenous; in terms of activity per microgram of total protein in the protein preparation.
To produce the recombinant polypeptide of the present invention, the coding region of a starch synthase gene described herein or a functional homologue, analogue or derivative thereof is placed operably in connection with a promoter sequence in the sense orientation, such that a starch synthase gene product is capable of being expressed under the control of said promoter sequence.
In the present context, the term “in operable connection with” means that expression of the isolated nucleotide sequence is under the control of the promoter sequence with which it is connected, regardless of the relative physical distance of the sequences from each other or their relative orientation with respect to each other.
Reference herein to a “promoter” is to be taken in its broadest context and includes the transcriptional regulatory sequences of a classical genomic gene, including the TATA box which is required for accurate transcription initiation, with or without a CCAAT box sequence and additional regulatory elements (i.e. upstream activating sequences, enhancers and silencers) which alter gene expression in response to developmental and/or external stimuli, or in a tissue-specific manner. A promoter is usually, but not necessarily, positioned upstream or 5′, of a structural gene, the expression of which it regulates. Furthermore, the regulatory elements comprising a promoter are usually positioned within 2 kb of the start site of transcription of the gene.
In the present context, the term “promoter” is also used to describe a synthetic or fusion molecule, or derivative which confers, activates or enhances expression of a structural gene or other nucleic acid molecule, particularly in a plant cell and more preferably in a wheat plant or other monocotyledonous plant cell, tissue or organ. Preferred promoters may contain additional copies of one or more specific regulatory elements, to further enhance expression and/or to alter the spatial expression and/or temporal expression. For example, regulatory elements which confer copper inducibility may be placed adjacent to a heterologous promoter sequence, thereby conferring copper inducibility on the expression of said molecule.
Those skilled in the art will be aware that in order to obtain optimum expression of the starch synthase gene of the present invention, it is necessary to position said gene in an appropriate configuration such that expression is controlled by the promoter sequence. Promoters are generally positioned 5′ (upstream) to the genes that they control. In the construction of heterologous promoter/structural gene combinations it is generally preferred to position the promoter at a distance from the gene transcription start site that is approximately the same as the distance between that promoter and the gene it controls in its natural setting, i.e., the gene from which the promoter is derived. As is known in the art, some variation in this distance can be accommodated without loss of promoter function. Similarly, the preferred positioning of a regulatory sequence element with respect to a heterologous gene to be placed under its control is defined by the positioning of the element in its natural setting, i.e., the genes from which it is derived. Again, as is known in the art, some variation in this distance can also occur.
Examples of promoters suitable for expressing the starch synthase gene of the present invention include viral, fungal, bacterial, animal and plant derived promoters capable of functioning in prokaryotic or eukaryotic cells. Preferred promoters are those capable of regulating the expression of the subject starch synthase genes in plants cells, fungal cells, insect cells, yeast cells, animal cells or bacterial cells, amongst others. Particularly preferred promoters are capable of regulating expression of the subject nucleic acid molecules in monocotyledonous plant cells. The promoter may regulate the expression of the said molecule constitutively, or differentially with respect to the tissue in which expression occurs or, with respect to the developmental stage at which expression occurs, or in response to external stimuli such as physiological stresses, or plant pathogens, or metal ions, amongst others.
Accordingly, strong constitutive promoters are particularly preferred for the purposes of the present invention.
Examples of preferred promoters include the bacteriophage T7 promoter, bacteriophage T3 promoter, SP6 promoter, lac operator-promoter, tac promoter, SV40 late promoter, SV40 early promoter, RSV-LTR promoter, CMV IE promoter, CaMV 35S promoter, SCSV promoter, SCBV promoter and the like.
Particularly preferred promoters operable in plant cells include, for example the CaMV 35S promoter, and the SCBV promoter. Those skilled in the art will readily be aware of additional promoter sequences other than those specifically described.
In a particularly preferred embodiment, the promoter may be derived from a genomic starch synthase gene. Preferably, the promoter sequence comprises nucleotide sequences that are linked in vivo to nucleotide sequences set forth in any one of SEQ ID NOs: 1, 3, 5, 7, 9, 11-16, 37, or 38. By “linked in vivo” means that the promoter is present in its native state in the genome of a wheat plant where it controls expression of the starch synthase gene of the present invention.
Conveniently, genetic constructs are employed to facilitate expression of a starch synthase genetic sequence of the present invention or a functional derivative, part, homologue, or analogue thereof. To produce a genetic construct, the starch synthase gene of the invention is inserted into a suitable vector or episome molecule, such as a bacteriophage vector, viral vector or a plasmid, cosmid or artificial chromosome vector which is capable of being maintained and/or replicated and/or expressed in the host cell, tissue or organ into which it is subsequently introduced. The said genetic construct comprises the subject nucleic acid molecule placed operably under the control of a promoter sequence and optionally, a terminator sequence.
The term “terminator” refers to a DNA sequence at the end of a transcriptional unit which signals termination of transcription. Terminators are 3′-non-translated DNA sequences containing a polyadenylation signal, which facilitates the addition of polyadenylate sequences to the 3′-end of a primary transcript. Terminators active in bacteria, yeasts, animal cells and plant cells are known and described in the literature. They may be isolated from bacteria, fungi, viruses, animals and/or plants.
Examples of terminators particularly suitable for use in expressing the nucleic acid molecule of the present invention in plant cells include the nopaline synthase (NOS) gene terminator of Agrobacterium tumefaciens, the terminator of the Cauliflower mosaic virus (CaMV) 35S gene, and the zein gene terminator from Zea mays. 
Genetic constructs will generally further comprise one or more origins of replication and/or selectable marker gene sequences.
The origin of replication can be functional in a bacterial cell and comprise, for example, the pUC or the ColE1 origin. Alternatively, the origin of replication is operable in a eukaryotic cell, tissue and more preferably comprises the 2 micron (2 μm) origin of replication or the SV40 origin of replication.
As used herein, the term “selectable marker gene” includes any gene which confers a phenotype on a cell in which it is expressed to facilitate the identification and/or selection of cells which are transfected or transformed with a genetic construct of the invention or a derivative thereof.
Suitable selectable marker genes contemplated herein include the ampicillin-resistance gene (Ampr), tetracycline-resistance gene (Tcr), bacterial kanamycin-resistance gene (Kanr), is the zeocin resistance gene (Zeocin is a drug of bleomycin family which is trademark of InVitrogen Corporation), the AURI-C gene which confers resistance to the antibiotic aureobasidin A, phosphinothricin-resistance gene, neomycin phosphotransferase gene (nptII), hygromycin-resistance gene, β-glucuronidase (GUS) gene, chloramphenicol acetyltransferase (CAT) gene, green fluorescent protein-encoding gene or the luciferase gene, amongst others. Those skilled in the art will be aware of other selectable marker genes useful in the performance of the present invention and the subject invention is not limited by the nature of the selectable marker gene.
Usually, an origin of replication or a selectable marker gene suitable for use in bacteria is physically-separated from those genetic sequences contained in the genetic construct which are intended to be expressed or transferred to a eukaryotic cell, or integrated into the genome of a eukaryotic cell.
Standard methods can be used to introduce genetic constructs into a cell, tissue or organ for the purposes of modulating gene expression. Particularly preferred methods suited to the introduction of synthetic genes and genetic constructs comprising same to eukaryotic cells include liposome-mediated transfection or transformation, transformation of cells with attenuated virus particles or bacterial cells and standard procedures for the transformation of plant and animal cells, tissues, organs or organisms. Any standard means may be used for their introduction including cell mating, transformation or transfection procedures known to those skilled in the art or described by Ausubel et al. (1992).
In a further embodiment of the present invention, the starch synthase genes of the present invention and genetic constructs comprising same are adapted for integration into the genome of a cell in which it is expressed. Those skilled in the art will be aware that, in order to achieve integration of a genetic sequence or genetic construct into the genome of a host cell, certain additional genetic sequences may be required. In the case of plants, left and right border sequences from the T-DNA of the Agrobacterium tumefaciens Ti plasmid will generally be required.
The invention further contemplates increased starch and/or modified starch composition in transgenic plants expressing the nucleic acid molecule of the invention in the sense orientation such that the activity of one or more starch synthase isoenzymes is increased therein. By increasing the level of one or more starch synthase isoenzymes, the deposition of starch in the amyloplast or chloroplast is increased and/or a modified starch granule structure is produced and/or starch composition is modified and/or the amylose/amylopectin ratio is altered in the plant.
Wherein it is desired to increase the synthesis of a particular starch synthase isoenzyme in a plant cell, the coding region of a starch synthase gene is placed operably behind a promoter, in the sense orientation, such that said starch synthase is expressed under the control of said promoter sequence. In a preferred embodiment, the starch synthase genetic sequence is a starch synthase genomic sequence, cDNA molecule or protein-coding sequence.
Wherein it is desirable to reduce the level of a particular starch synthase isoenzyme in a plant cell, the nucleic acid molecule of the present invention can be expressed in the antisense orientation, as an antisense molecule or a ribozyme molecule, under the control of a suitable promoter.
Alternatively, the nucleic acid molecule of the present invention may also be expressed in the sense orientation, in the form of a co-suppression molecule, to reduce the level of a particular starch synthase isoenzyme in a plant cell. As will be known to those skilled in the art, co-suppression molecules that comprise inverted repeat sequences of a target nucleic acid molecule provide optimum efficiency at reducing expression of said target nucleic acid molecule and, as a consequence, the present invention clearly contemplates the use of inverted repeat sequences of any one or more of the starch synthase genetic sequences exemplified herein, or inverted repeat sequences of a homologue, analogue or derivative of said starch synthase genetic sequences, to reduce the level of a starch synthase isoenzyme in a plant.
The expression of an antisense, ribozyme or co-suppression molecule comprising a starch synthase gene in a cell such as a plant cell, fungal cell, insect cell, animal cell, yeast cell or bacterial cell, may also increase the availability of carbon as a precursor for a secondary metabolite other than starch (e.g. sucrose or cellulose). By targeting the endogenous starch synthase gene, expression is diminished, reduced or otherwise lowered to a level that results in reduced deposition of starch in the amyloplast or chloroplast and/or leads to modified starch granule structure and/or composition and/or altered amylose/amylopectin ratio.
Accordingly, a further aspect of the present invention provides a method of modifying the starch content and/or starch composition of one or more tissues or organs of a plant, comprising expressing therein a sense molecule, antisense molecule, ribozyme molecule, co-suppression molecule, or gene-targeting molecule having at least about 85% nucleotide sequence identity to any one of any one of SEQ ID NOS: 1, 3, 5, 7, 9, 11-16, 37, or 38, or a complementary nucleotide sequence thereto for a time and under conditions sufficient for the enzyme activity of one or more starch synthase isoenzymes to be modified. This aspect of the invention clearly extends to the introduction of the sense molecule, antisense molecule, ribozyme molecule, co-suppression molecule, or gene-targeting molecule to isolated plant cells, tissues or organs or organelles by cell fusion or transgenic means and the regeneration of intact plants therefrom.
Co-suppression is the reduction in expression of an endogenous gene that occurs when one or more copies of said gene, or one or more copies of a substantially similar gene are introduced into the cell, preferably in the form of an inverted repeat structure.
The present inventors have discovered that the genetic sequences disclosed herein are capable of being used to modify the level of starch when expressed, particularly when expressed in plants cells. Accordingly, the present invention clearly extends to the modification of starch biosynthesis in plants, in particular wheat or barley plants or a progenitor plant species, or a relative thereto such as the diploid Triticum tauschii or other diploid, tetraploid, aneuploid, polyploid, nullisomic, or a wheat/barley addition line, amongst others.
In particular, the present invention contemplates decreased starch production and/or modified starch composition in transgenic plants expressing the nucleic acid molecule of the invention in the antisense orientation or alteratively, expressing a ribozyme or co-suppression molecule comprising the nucleic acid sequence of the invention such that the activity of one or more starch synthase isoenzymes is decreased therein.
In the context of the present invention, an antisense molecule is an RNA molecule which is transcribed from the complementary strand of a nuclear gene to that which is normally transcribed to produce a “sense” mRNA molecule capable of being translated into a starch synthase polypeptide. The antisense molecule is therefore complementary to the mRNA transcribed from a sense starch synthase gene or a part thereof. Although not limiting the mode of action of the antisense molecules of the present invention to any specific mechanism, the antisense RNA molecule possesses the capacity to form a double-stranded mRNA by base pairing with the sense mRNA, which may prevent translation of the sense mRNA and subsequent synthesis of a polypeptide gene product.
Ribozymes are synthetic RNA molecules which comprise a hybridising region complementary to two regions, each of at least 5 contiguous nucleotide bases in the target sense mRNA. In addition, ribozymes possess highly specific endoribonuclease activity, which autocatalytically cleaves the target sense mRNA. A complete description of the function of ribozymes is presented by Haseloff and Gerlach (1988) and contained in International Patent Application No. WO89/05852.
The present invention extends to ribozyme which target a sense mRNA encoding a native starch synthase gene product, thereby hybridising to said sense mRNA and cleaving it, such that it is no longer capable of being translated to synthesise a functional polypeptide product.
According to this embodiment, the present invention provides a ribozyme or antisense molecule comprising at least 5 contiguous nucleotide bases derived from any one of SEQ ID NOS: 1, 3, 5, 7, 9, 11-16, 37, or 38, or a complementary nucleotide sequence thereto or a homologue, analogue or derivative thereof, wherein said antisense or ribozyme molecule is able to form a hydrogen-bonded complex with a sense mRNA encoding a starch synthase gene product to reduce translation thereof.
In a preferred embodiment, the antisense or ribozyme molecule comprises at least 10 to 20 contiguous nucleotides derived from any one of SEQ ID NOS: 1, 3, 5, 7, 9, 11-16, 37, or 38, or a complementary nucleotide sequence thereto or a homologue, analogue or derivative thereof. Although the preferred antisense and/or ribozyme molecules hybridise to at least about 10 to 20 nucleotides of the target molecule, the present invention extends to molecules capable of hybridising to at least about 50-100 nucleotide bases in length, or a molecule capable of hybridising to a full-length or substantially full-length mRNA encoded by a starch synthase gene.
Those skilled in the art will be aware of the necessary conditions, if any, for selecting or preparing the antisense or ribozyme molecules of the invention.
It is understood in the art that certain modifications, including nucleotide substitutions amongst others, may be made to the antisense and/or ribozyme molecules of the present invention, without destroying the efficacy of said molecules in inhibiting the expression of a starch synthase gene. It is therefore within the scope of the present invention to include any nucleotide sequence variants, homologues, analogues, or fragments of the said gene encoding same, the only requirement being that said nucleotide sequence variant, when transcribed, produces an antisense and/or ribozyme molecule which is capable of hybridising to a sense mRNA molecule which encodes a starch synthase gene product.
Gene targeting is the replacement of an endogenous gene sequence within a cell by a related DNA sequence to which it hybridises, thereby altering the form and/or function of the endogenous gene and the subsequent phenotype of the cell. According to this embodiment, at least a part of the DNA sequence defined by any one of SEQ ID NOS: 1, 3, 5, 7, 9, 11-16, 37, or 38 may be introduced into target cells containing an endogenous gene that encodes a particular starch synthase isoenzyme, thereby replacing said endogenous gene. According to this embodiment, the polypeptide product of the gene targetting molecule generally encodes a starch synthase isoenzyme that possesses different catalytic activity to the polypeptide product of the endogenous gene, producing in turn modified starch content and/or composition in the target cell.
The present invention extends to genetic constructs designed to facilitate expression of a sense molecule, an antisense molecule, ribozyme molecule, co-suppression molecule, or gene targeting molecule of the present invention. The requirements for expressing such molecules are similar to those for expressing a recombinant polypeptide as described supra.
The present invention further extends to the production and use of starches and proteins produced using the novel genes described herein. Modified starches produced by plants which have been selected using marker-assisted selection, or alternatively, produced by transgenic plants carrying the introduced starch synthase genes, are particularly suitable for use in food products, such as, for example, flour and flour-based products, in particular those products selected from the group consisting of: flour-based sauce; leavened bread; unleavened bread; pasta, noodle; cereal; snack food; cake; and pastry. Modified proteins are also suitable for use in non-food products, such as, for example, those non-food products selected from the group consisting of: films; coatings; adhesives; building materials; and packaging materials.
Additionally, starch hydrolysates or undegraded starches are both useful in industry and, as a consequence, the present invention is useful in applications relating to the use of both starch hydrolysates and undegraded starches. By “starch hydrolysates” is meant the glucose and glucan components that are obtainable by the enzymatic or chemical degradation of starch in chemical modifications and processes, such as fermentation.
Starch produced by plants expressing the sense, antisense, co-suppression, gene-targetting or ribozyme molecules of the present invention may exhibit modified viscosities and/or gelling properties of its glues when compared to starch derived from wild-type plants. Native starches produced by the performance of the inventive method are useful as an additive in the following: (i) foodstuffs, for the purpose of increasing the viscosity or gelling properties of food; (ii) in non-foodstuffs, such as an adjuvant or additive in the paper and cardboard industries, for retention or as a size filler, or as a solidifying substance or for dehydration, or film coating, amongst others; (iii) in the adhesive industry as pure starch glue, as an additive to synthetic resins and polymer dispersions, or as an extenders for synthetic adhesives; (iv) in the textile and textile care industries to strengthen woven products and reduce burring or to thicken dye pastes; (v) in the building industry, such as a binding agent in the production of gypsum plaster boards, or for the deceleration of the sizing process; (vi) in ground stabilization or for the temporary protection of ground particles against water in artificial earth shifting; (vii) as a wetting agent in plant protectants and fertilizers; (viii) as a binding agent in drugs, pharmaceuticals and medicated foodstuff such as vitamins, etc; (ix) as an additive in coal and briquettes; (xi) as a flocculent in the processing of coal ore and slurries; (xii) as a binding agent in casting processes to increase flow resistance and improve binding strength; and (xiii) to improve the technical and optical quality of rubber and plastic products. Additional applications are not excluded.
A further aspect of the present invention provides an isolated promoter that is operable in the endosperm of a monocotyledonous plant cell, tissue or organ, and preferably in the endosperm of a monocotyledonous plant cell, tissue or organ. According to this embodiment, it is preferred that the promoter is derived from a starch synthase gene of the present invention, such as a promoter that is linked in vivo to any one of SEQ ID NOS: 1, 3, 5, 7, 9, 11-16, 37, or 38, or a complementary nucleotide sequence thereto.
In a particularly preferred embodiment, the promoter comprises a nucleotide sequence derivable from the 5′-upstream region of SEQ ID NO: 11 or SEQ ID NO: 37 or SEQ ID NO: 38, or a complementary nucleotide sequence thereto, an more preferably comprises nucleotides 1 to about 287 of SEQ ID NO: 11, or nucleotides 1 to about 1416 of SEQ ID NO: 37, or nucleotides 1 to about 973 of SEQ ID NO: 38, or a complementary nucleotide sequence thereto. The present invention clearly extends to promoter sequences that comprise further nucleotide sequences in the region upstream of the stated nucleotide sequence that are linked in vivo to said nucleotide sequence in the wheat genome.
In a related embodiment, the promoter sequence of the present invention will further comprise an exon sequence derived from a starch synthase gene, such as, for example, an intron I sequence described herein, or a complementary nucleotide sequence thereto. Those skilled in the art will be aware that the inclusion of such nucleotide sequences may increase the expression of a heterologous structural gene, the expression of which is controlled thereby. Preferred intron I sequences include, for example, nucleotide sequences in the region of about position 1744 to about 1847 of SEQ ID NO: 37, and/or about position 1100 to about position 2056 of SEQ ID NO: 38. Additional sequences comprising intron/exon junction boundary sequences which are readily determined by those skilled in the art are not excluded.
The present invention further extends to the expression of any structural gene operably under the control of the starch synthase promoter sequence exemplified herein or a functional homologue, analogue or derivative of said promoter sequence.
As with other embodiments described herein for expression in cells, a genetic construct may be employed to effect said expression and the present invention clearly extends to said genetic constructs.
The polypeptide encoded by the structural gene component may be a reporter molecule which is encoded by a gene such as the bacterial β-glucuronidase gene or chloramphenicol acetyltransferase gene or alternatively, the firefly luciferase gene. Alternatively, wherein it is desirable to alter carbon partitioning within the endosperm, the polypeptide may be an enzyme of the starch sucrose biosynthetic pathways. Preferably, the promoter sequence is used to regulate the expression of one or more of the starch synthase genes of the present invention or a sense, antisense, ribozyme, co-suppression or gene-targetting molecule comprising or derived from same.
Recombinant DNA molecules carrying the aforesaid nucleic acid molecule of the present invention or a sense, antisense, ribozyme, gene-targetting or co-suppression molecule and/or genetic construct comprising same, may be introduced into plant issue, thereby producing a “transgenic plant”, by various techniques known to those skilled in the art. The technique used for a given plant species or specific type of plant issue depends on the known successful techniques. Means for introducing recombinant DNA into plant tissue include, but are not limited to, transformation (Paszkowski et al., 1984), electroporation (Fromm et al., 1985), or microinjection of the DNA (Crossway et al., 1986), or T-DNA-mediated transfer from Agrobacterium to the plant tissue. Representative T-DNA vector systems are described in the following references: An et al. (1985); Herrera-Estrella et al. (1983a, b); Herrera-Estrella et al. (1985). Once introduced into the plant tissue, the expression of the introduced gene may be assayed in a transient expression system, or it may be determined after selection for stable integration within the plant genome. Techniques are known for the in vitro culture of plant tissue, and in a number of cases, for regeneration into whole plants. Procedures for transferring the introduced gene from the originally transformed plant into commercially useful cultivars are known to those skilled in the art.
In general, plants are regenerated from transformed plant cells or tissues or organs on hormone-containing media and the regenerated plants may take a variety of forms, such as chimeras of transformed cells and non-transformed cells; clonal transformants (e.g., all cells transformed to contain the expression cassette); grafts of transformed and untransformed tissues (e.g., a transformed root stock grafted to an untransformed scion in citrus species). Transformed plants may be propagated by a variety of means, such as by clonal propagation or classical breeding techniques. For example, a first generation (or T1) transformed plants may be selfed to give homozygous second generation (or T2) transformed plants, and the T2 plants further propagated through classical breeding techniques.
Accordingly, a still further aspect of the present invention contemplates a transgenic plant comprising an introduced sense molecule, antisense molecule, ribozyme molecule, co-suppression molecule, or gene-targeting molecule having at least about 85% nucleotide sequence identity to any one of any one of SEQ ID NOS: 1, 3, 5, 7, 9, 11-16, 37, or 38, or a complementary nucleotide sequence thereto or a genetic construct comprising same. The present invention further extends to those plant parts, propagules and progeny of said transgenic plant or derived therefrom, the only requirement being that said propagules and progeny also carry the introduced nucleic acid molecule(s).
The present invention is further described by reference to the following non-limiting examples.
Example 1
Plant Material
Genetic stocks of hexaploid bread wheat Triticum aestivum cv. Chinese Spring with various chromosome additions and deletions were kindly supplied by Dr E. Lagudah (CSIRO Plant Industry. Canberra) and derived from stocks described in Sears and Miller (1985). The hexaploid (Triticum aestivum) wheats cv Gabo and cv Wyuna were grown in controlled growth cabinet conditions (18° C. day and 13° C. night, with a photoperiod of 16 h). Wheat leaves and florets prior to anthesis, and endosperm were collected over the grain filling period, immediately frozen in liquid nitrogen and stored at −80° C. until required.
Example 2
Gel Electrophoresis, Antibodies and Immunoblotting
Monoclonal antibodies against the Sgp-1 proteins, and their use in the immunoblotting of SDS-PAGE gels have been described previously (Rahman et al., 1995).
Example 3
Preparation of Total RNA from Wheat
Total RNA was isolated from the leaf, floret and endosperm tissues of wheat essentially as described by Higgins et al. (1976) or Rahman et al. (1998). RNA was quantified by UV absorption and by separation in 1.4% (w/v) agarose-formaldehyde gels which were then visualised under UV light after staining with ethidium bromide.
Example 4
Construction and Screening of cDNA Libraries
A first cDNA library, an expression cDNA library of wheat endosperm, was constructed from mRNA isolated from wheat cv Chinese Spring. RNA from 5, 7, 9, 11 and 13 days after anthesis was pooled and random primers were used for the first strand of cDNA synthesis. Monoclonal antibodies against 100-105 kDa proteins in wheat starch granules (Rahman et al., 1995) were used for immunoscreening of the expression cDNA library.
A second cDNA library was constructed from the endosperm mRNA of the hexaploid Triticum aestivum cultivar Wyuna, 8-12 days after anthesis, as described by Rahman et al. (1997). This library was screened with a 85-bp cDNA fragment, wSSIIp1, which was obtained by immunoscreening of the expression cDNA library as described above. The wSSIIp1 probe corresponded to nucleotide positions 988 to 1072 of wSSIIB (SEQ ID NO:1) at the hybridisation conditions as described earlier (Rahman et al., 1998).
A third cDNA library was constructed from RNA from the endosperm of the hexaploid Triticum aestivum cultivar Rosella as described by Rahman et al. (1997). This library was screened with a 347-bp cDNA fragment, wSSIIIp1 for the first screening, and a 478-bp cDNA fragment wSSIIIp3 for the second screening using the hybridisation conditions described herein.
Example 5
Construction and Screening of Triticum tauschii Genomic Library
The genomic library used in this study, prepared from Triticum tauschii, var strangulata, (Accession Number CPI 110799), has been described in Rahman et al., (1997). Of all the accessions of T. tauschii surveyed, DNA marker analysis suggests that the genome of CPI 110799 is the most closely related to the D genome of hexaploid wheat (Lagudah et al., 1991).
Hybridisations were carried out in 25% formamide, 6×SSC, 0.1% SDS at 42° C. for 16 hours, then filters were washed 3 times using 2×SSC containing 0.1% SDS at 65° C. for 1 hour per wash.
For the isolation of a genomic wSSII clone, the probe comprised the PCR-derived DNA fragment wSSIIp2 and positive-hybridising plaques were digested using the restriction enzyme BamHI, separated on a 1% agarose gel, transferred to nitrocellulose membrane and hybridised to probe wSSIIp4 comprising nucleotides 1 to 367 of the wSSIIA cDNA clone, using the conditions described by Rahman et al. (1997).
For the isolation of a genomic wSSIII clone, plaques hybridising to the PCR-derived DNA fragment wSSIIIp1 from clone wSSIII.B3 (i.e. nucleotides 3620 to 3966 of SEQ ID NO:7) were selected and re-screened until plaque-purified.
Example 6
DNA Sequencing and Analysis
DNA sequencing was performed using the automated ABI system with dye terminators as described by the manufacturers. DNA sequences were analysed using the GCG suite of programs (Devereaux et al., 1984).
Example 7
DNA and RNA Analysis
DNA was isolated and analysed as previously described (Maniatis et al., 1982; Rahman et al., 1998). Approximately 20 μg of DNA was digested with restriction enzymes BamHI, DraI and EcoRI, separated on a 1% agarose gel and transferred to reinforced nitrocellulose membranes (BioRad) and hybridised with 32P-labelled DNA probe, either wSSIIIp1, corresponding to nucleotides 3620 to 3966 of the wheat SSIII gene, or alternatively, with the entire wSSII cDNA clone. DNA fragment probes were labelled with the Rapid Multiprime DNA Probe Labelling Kit (Promega).
The hybridisation and wash conditions were performed as described in Rahman et al. (1997). For RNA analysis, 10 μg of total RNA was separated in a 1.4% agarose-formaldehyde gel and transferred to a Hybond N+ membrane (Amersham), and hybridised with cDNA probe at 42° C. as previously described by Khandjian et al., (1987) or Rahman et al., (1998). After washing for 30 minutes at 65° C. with 2×SSC, 0.1% SDS; followed by three washes of 40 minutes at 65° C. with 0.2×SSC, 1% SDS, the membranes were visualised by overnight exposure at −80° C. with Kodak MR X-ray film.
Example 8
Expression of Wheat Sgp-1 Polypeptides in the Wheat Endosperm
The development and use of monoclonal antibodies to the Sgp-1 proteins has been described previously (Rahman et al., 1995). These antibodies were used by the present inventors to characterise the expression and localisation of the Sgp-1 proteins.
The proteins found in the matrix of the wheat starch granule are shown in FIG. 1, lane 1. The remaining lanes show an immunoblot of proteins from the soluble phase (FIG. 1; lanes 24) and the starch granule (FIG. 1; lanes 5-7), respectively, following SDS-PAGE. In addition to cross-reactivity with the 100-105 kDa proteins, a weak cross-reaction with a 50 kDa protein in both the granule and the soluble fractions were observed (FIG. 1). The Sgp-1 polypeptides are present in the starch granule throughout endosperm development (FIG. 1; lanes 5-7, also see Rahman et al., 1995). However, as the endosperms matures, there is a reduction in the amount of Sgp-1 protein found in the soluble fraction. Lane 4 shows that by 25 days after anthesis, the level of these proteins in the soluble fraction is substantially reduced. This observation is consistent with previous results from Rahman et al., (1995), who suggested that the Sgp-1 proteins were exclusively granule bound based on studies of granules from endosperm in mid-late stages endosperm development, however, these results suggest that the partitioning of these proteins between the granule and the soluble phase changes during development.
Example 9
Isolation of cDNA Clones Encoding Wheat Starch Synthase II (wSSII) Proteins
Monoclonal antibodies against Sgp-1 polypeptides (Rahman et al., 1995) were used to probe the expression library described in Example 4 (i.e. the first cDNA library). Three immunoreactive plaques were identified and sequenced. One clone, designated wSSIIp1, contained an 85-bp cDNA insert with homology to maize SSIIa (Ham et al., 1998).
DNA from the wSSIIp1 clone was used as a probe in the hybridisation screening of the second cDNA library, prepared from Triticum aestivum cultivar Wyuna endosperm RNA as described in Example 4. Ten hybridising cDNA clones were selected and sequenced. On the basis of the DNA sequences obtained, the 10 cDNA clones can be classified into three groups. Group 1 contains 7 cDNA clones, group 2 contains 2 cDNA clones and group 3 contains 1 cDNA clone.
The longest clone from group 1 (designated wSSIIB) is 2939 bp in length (SEQ ID NO:1) and encodes a 798-amino acid polypeptide in the region from nucleotide position 176 to nucleotide position 2569 (SEQ ID NO:2).
The longest clone from group 2 (designated wSSIIA) is 2842 bp in length (SEQ ID NO:3) and encodes a 799-amino acid polypeptide in the region from nucleotide position 89 to nucleotide position 2485 (SEQ ID NO:4).
The cDNA from group 3 is a partial cDNA clone (designated wSSIID), which is 2107 bp in length (SEQ ID NO:5) and encodes a 597-amino acid polypeptide in the region from nucleotide position 1 to nucleotide position 1791 (SEQ ID NO:6). The encoded polypeptide is approximately a 200 amino acid residues shorter than that of polypeptides encoded by longest clones of group 1 or 2 clones, respectively (FIG. 2).
Comparison of the three cDNA clones, wSSIIB, wSSIIA and wSSIID shows that they share 95.7% to 96.6% identity at the amino acid level, with variation at 44 amino acid positions between the three sequences (FIG. 3). Of the 44 amino acid changes between these sequences, 31 changes occur in the N-terminal region (residues 1 to 300), 10 changes occur in the central region (residues 301 to 729) and 3 changes occur in the C-terminal region (residues 730 to 799). The wSSIIA polypeptide (799 amino acid residues) and wSSIIB polypeptide (798 amino acid residues) sequences differ in length by a single amino acid residue, due to the deletion of Asp-69 from the wSSIIB polypeptide sequence.
A comparison of the nucleotide sequences of the wSSIA, wSSIIB and wSSIID cDNA clones with the nucleotide sequence of the wSSIIp1 cDNA obtained by immunoscreening confirms that the wSSIIp1 sequence is found in each cDNA (FIG. 3). The peptide encoded by the wSSIIp1 cDNA clone corresponds to amino acid residues in the region from residue 272 to residue 298 of the wSSIIA polypeptide, and to amino acid residues in the region from residue 271 to residue 297 of the wSSIIB polypeptide (see FIG. 3). Thus, the peptide epitope encoded by wSSIIp1 that reacts with the anti-Sgp-1 monoclonal antibodies can therefore be localised to this region of the wSSIIA and wSSIIB polypeptides and to the corresponding region of the wSSIID polypeptide.
Notwithstanding that a region having about 63% amino acid sequence identity to the peptide epitope encoded by clone wSSIIp1 is found in the maize SSIIa polypeptide (FIG. 3), the degree of amino acid conservation between maize and wheat sequences in this region of the polypeptide is insufficient for immunological cross-reactivity to occur between these species using the monoclonal antibodies to the wheat Sgp-1 proteins described by Rahman et al. (1995). Additionally, this peptide epitope is not found in granule-bound starch synthases, SSI, or SSIII (data not shown).
The wSSIIB cDNA (SEQ ID NO:1) encodes an amino acid sequence comprising the peptide motif AAGKKDAGID (SEQ ID NO: 18) between residues 60 and 69 of SEQ ID NO:2 (FIG. 3) which, with the exception of the second residue, is identical to the N-terminal of the 100 kDa (AT/LGKKDAGID: SEQ ID NOS:19 and 20) protein (Sgp-B1) from the wheat starch granule (note that the sequence given in Rahman et al., 1995 (AT/LGKKDAL: SEQ ID NOS: 21 and 22) has been revised following further amino acid sequence analysis).
The wSSIIA cDNA clone (SEQ ID NO:3) encodes an amino acid sequence comprising the peptide motif AAGKKDARVDDDAA (SEQ ID NO: 23) at residues 60 to 73 of SEQ ID NO:4, which is about 66% identical to the N-terminal amino acid sequence (i.e. ALGKKDAGIVDGA: SEQ ID NO: 24) of the 104 kDa and 105 kDa starch granule proteins, Sgp-D1 and Sgp-A1 respectively, as determined by sequence analysis of isolated protein (Rahman et al., 1995).
Furthermore, Takaoka et al. (1997) reported the amino acid sequences of 3 polypeptides obtained from sequencing starch granule proteins derived from the Sgp-1 proteins. Peptide 3 described by Takaoka et al. (1997) corresponds to amino acid residues 378 to 387 of the amino acid sequence of the wSSIIA cDNA (SEQ ID NO:4; FIG. 3). Peptides 1 and 2 described by Takaoka et al. (1997) could not be detected in the amino acid sequences of the wSSII cDNA clones of the present invention, however peptide 1 of Takaoka et al. (1997) can be found in the amino acid sequences of SSI from maize, rice, wheat and potato (data not shown).
Denyer et al. (1995) demonstrated that the Sgp-1 proteins possess starch synthase activity and, as a consequence, the wSSIIB, wSSIA and wSSIID cDNA clones encode starch synthase enzymes that are differentially expressed in a developmentally-regulated manner in both the soluble and granule-bound fractions of the endosperm (FIG. 1). Based on the nomenclature suggested by Harn et al. (1998), it is appropriate to describe the Sgp-1 proteins as “starch synthases” rather than “granule-bound starch synthases”.
Example 10
Analysis of Wheat Starch Synthase II mRNA Expression
The mRNA for wheat starch synthase II could be detected in leaves, pre-anthesis florets and endosperm of wheat when total RNAs isolated from these tissue were probed with a PCR probe, wSSIIp2, corresponding to nucleotide positions 1435 to 1835 bp of wSSIIB-cDNA (SEQ ID NO:1; FIG. 4). Unlike wSSI, which could not be detected in wheat leaves derived from plants grown under the same conditions, wSSII genes are highly-expressed in the leaves (FIG. 4, lane 1), and expressed at an intermediate level in pre-anthesis florets (FIG. 4, lane 2), and at much lower levels in developing wheat endosperm cells (FIG. 4, lanes 3-11). In contrast, the maize SSIIa is expressed predominantly in the endosperm, whilst the maize SSIIb is detected mainly in the leaf, albeit at low levels (Harn et al., 1998).
The wSSII mRNA was detectable in the endosperm 6 days after anthesis and mRNA levels increase between 8 and 18 days post-anthesis, after which time levels of mRNA decline.
Southern blotting experiments in wheat demonstrated that the wSSIIp2 probe used detected only a single copy of the SSII gene in each genome (data not shown). Thus, it is unlikely that this probe cross-hybridised with mRNAs encoded by genes other than wSSII.
Example 11
Chromosomal Localization of the Wheat wSSII Genes
I. Amplification of Specific cDNA Regions of Wheat Starch Synthase II using PCR
Two PCR products, wSSIIp2 and wSSIIp3 were amplified from the cDNA clone wSSIIB and used for the northern hybridisation and Southern hybridisaton, respectively.
The primers ssIIa (5′ TGTTGAGGTTCCATGGCACGTTC 3′: SEQ ID NO: 25) and ssIIb (5′ AGTCGTTCTGCCGTATGATGTCG 3′: SEQ ID NO: 26) were used to amplify the cDNA fragment wSSIIp2 (i.e. nucleotide positions 1435 to 1835 of SEQ ID NO:1).
The primers ssIIc (5′ CCAAGTACCAGTGGTGAACGC 3′: SEQ ID NO: 27) and ssIId (5′ CGGTGGGATCCAACGGCCC 3′: SEQ ID NO: 28) were used to amplify the cDNA fragment wSSIIp3 (i.e. nucleotide positions 2556 to 2921 of SEQ ID NO:1).
The amplification reactions were performed using a FTS-1 thermal sequencer (Corbett, Australia) for 1 cycle of 95° C. for 2 minutes; 35 cycles of 95° C. for 30 seconds, 60° C. for 1 minutes, 72° C. for 2 minutes and 1 cycle of 25° C. for 1 minute.
II. PCR and Nucleotide Sequence Analysis of 3′ Sequences of Wheat SSII Genes
Genomic DNA was extracted from wild-type Chinese Spring wheat, and from three nullisomic-tetrasomic lines of chromosome 7 of Chinese Spring wheat, and from Triticum tauschii (var strangulata, accession number CPI 100799), and used as a template for the amplification and nucleotide sequence analysis of wheat SSII genes.
RFLP analysis of BamHI and EcoRI restricted DNA from each wheat or T. Tauschii line was carried out using the wSSIIp3 fragment as a probe. Three hybridising bands were obtained which could be assigned to chromosomes 7A, 7B and 7D, respectively (data not shown). This analysis indicates that there is a single copy of the wSSII gene in each genome in hexaploid wheat, consistent with the findings of Yamamori and Endo (1996) who located the SGP-A1, B1 and D1 proteins to the short arm of chromosome 7.
PCR analysis was used to assign each of the cDNA clones to the individual wheat genomes. A single 365 bp PCR fragment was obtained from nullisomic-tetrasomic genomic DNA of Chinese Spring when primers ssIIc and ssIId were used for the PCR amplification (FIG. 5, right panel). This PCR product is obtained only from lines bearing the B genome. The fragment was cloned and sequenced and shown to be identical to a 365 bp region of the wSSIIB cDNA. An identical fragment is obtained by PCR amplification of the wSSIIB cDNA clone, but not by amplification of the wSSIIA or wSSIID clones, supporting the conclusion that the wSSIIB cDNA is the product of a gene located on chromosome 7 of the B genome of hexaploid wheat.
Two PCR products were also amplified from nullisomic-tetrasomic genomic DNA of Chinese Spring using the primers ssIIe and ssIIe (FIG. 5, left panel). One PCR fragment, approximately 350 bp is only amplified when the A genome is present, and a second 322 bp product is only amplified when the D-genome is present. The 350 and 322 bp PCR products were also cloned and sequenced and shown to be identical to the wSSIIA and wSSIID cDNAs, respectively, supporting the conclusion that the wSSIIA and wSSIID cDNAs are the products of genes located on chromosomes 7A and 7D, respectively.
Example 12
Isolation of Genomic wSSII Clones
Screening of a genomic library from the D-genome donor of wheat, T. tauschii, was performed as described in Example 5, using the PCR-derived DNA fragment wSSIIp2 as a hybridisation probe. A positive-hybridising clone, designated wSSII-8, and comprising a putative T. tauschii homologue of the wSSII gene, was isolated.
Positive-hybridising plaques were digested using the restriction enzyme BamHI, separated on a 1% agarose gel, transferred to nitrocellulose membrane and hybridised to probe wSSIIp4 comprising nucleotides 1 to 367 of the wSSIIA cDNA clone, using the conditions described by Rahman et al. (1997). Clone wSSII-8 also hybridises strongly to the wSSIIp4 probe, confirming its identity as a genomic wSSII gene.
The complete nucleotide sequence of the wSSII gene was determined and is presented herein as SEQ ID NO: 37. The structural features of this gene are present in Table 3. A schematic representation of the intron/exon organisation of this gene is also presented in FIG. 6.







TABLE 3







Structural features of the wheat starch synthase II genomic gene









Nucleotide Position




in SEQ ID NO: 37
Feature
Length (bases)












  1–1416
5′-untranscribed region and
1416



promoter sequence


1417–1743
exon 1
327


1480–1482
translation start codon (ATG)
3


1744–1847
intron 1
104


1848–2553
exon 2
706


2554–2641
intron 2
88


2642–2706
exon 3
65


2707–3606
intron 3
900


3607–3684
exon 4
78


3685–3773
intron 4
89


3774–3884
exon 5
111


3885–3981
intron 5
97


3982–4026
exon 6
45


4027–4406
intron 6
380


4407–4580
exon 7
174


4581–7296
intron 7
2716


7297–8547
exon 8
1251


8251–8253
translation stop codon (TGA)
3


8548–9024
3′-untranscribed region
477









Example 13
Cloning of Specific cDNA Regions of Wheat Starch Synthase III using RT-PCR
PCR primers were used to amplify sequences of starch synthase III from wheat endosperm cDNA. The design of PCR primers was based on the sequences of starch synthase III from potato and the du1 starch synthase III gene of maize.
First-strand cDNAs were synthesised from 1 μg of total RNA (derived from endosperm of the cultivar Rosella, 12 days after anthesis) as described by Maniatis et al. (1982), and then used as templates to amplify two specific cDNA regions, wSSIIIp1 and wSSIIIp2, of wheat starch synthase III by PCR.
The primers used to obtain the cDNA clone wSSIIIp1 were as follows:










Primer
(5′ GGAGGTCTTGGTGATGTTGT 3′:;
SEQ ID NO: 29)



wSS3pa


and


 


Primer
(5′ CTTGACCAATCATGGCAATG 3′:.
SEQ ID NO: 30)


wSS3pb






The primers used to obtain the cDNA clone wSSIIIp2 were as follows:









Primer wSS3pc




(5′ CATTGCCATGATTGGTCAAG 3′:;
SEQ ID NO: 31)


and


 


Primer wSS3pd


(5′ ACCACCTGTCCGTTCCGTTGC 3′:.
SEQ ID NO: 32)






The amplified clones wSSIIIp1 and wSSIIIp2 were used as probes to screen the third cDNA library and T. tauschii genomic DNA library as described in Example 4.
A further probe designated wSSIIIp3 was used for screening the third cDNA library, as described in Example 4. Probe wSSIIIp3 was amplified by PCR from a cDNA clone produced from the first screening using the following amplification primers:









Primer wSS3pe




(5′ GCACGGTCTATGAGAACAATGGC 3′:;
SEQ ID NO: 33)


and


 


Primer wSS3pf


(5′ TCTGCATACCACCAATCGCCG 3′:.
SEQ ID NO: 34)






The amplification reactions were performed using a FTS-1 or FTS4000 thermal sequencer (Corbett, Australia) for 1 cycle of 95° C. for 2 minutes; 35 cycles of 95° C. for seconds, 60° C. for 1 minutes, 72° C. for 2 minutes and 1 cycle of 25° C. for 1 minute. Amplified sequences of the expected length were obtained, cloned and sequenced, and shown to contain DNA sequences highly homologous to the maize and potato SSIII genes. PCR fragments were subsequently used to probe a wheat cDNA library by DNA hybridisation and 8 positive clones were obtained, including one 3 kb cDNA. A region from the 5′ end of this cDNA was amplified by PCR and used a probe for a second round of screening the cDNA library, obtaining 8 cDNA clones. Of these, one cDNA was demonstrated to be full length (wSSIII.B3, 5.36 kb insert). The sequence of the 5,346 bp wSSIII.B3 cDNA clone is given in SEQ ID NO:7.
Sequencing of the 8 cDNA clones obtained from the second round screening of the wheat cDNA library revealed that there were at least 2 classes of cDNA encoding SSIII present, possibly being encoded by homeologous genes on different wheat genomes. The sequence of a representative of this second class of cDNA clones, wSSIII.B1, is shown in SEQ ID NO:9. The 3261 bp clone wSSIII.B1 is not full length, however it is similar to nucleotides 1739 to 5346 of the homeologous clone wSSIII.B3 (SEQ ID NO: 7). Clone wSSIII.B1 has an open reading frame between nucleotide positions 1 and 3177.
An open reading frame is found in the cDNA clone wSSIII.B3 (SEQ ID NO:7), in the region between position 29, commencing the ATG start codon, and nucleotide position 4912. The amino acid sequence deduced from this open reading frame is shown in SEQ ID NO:8.
An alignment of the deduced amino acid sequences of SSIII from maize, potato and wheat is shown in FIG. 7. There is about 56.6% identity between the maize SSIII and wheat wSSIII.B3 sequence at the amino acid level.
The C-terminal domain of starch synthases comprise the catalytic domain, and a characteristic amino acid sequence motif KVGGLGDVVTSLSRAVQDLGHNVEV (SEQ ID NO: 35) in maize, or alternatively KVGGLGDVVTSLSRAIQDLGHTVEV (SEQ ID NO: 36) in wheat, marking the first conserved region in the C-terminal domain. This amino acid sequence is present at amino acid residues 1194 to 1218 of SEQ ID NO: 8.
The amino acid identity between maize dull1 and wSSIII.B3 in the N-terminal region (i.e. amino acids 1 to 600 in FIG. 7) is only 32.2%; whilst the amino acid identity in the central region (i.e. amino acids 601 to 1248 in FIG. 7) is 68.4%; and in the C-terminal region (i.e. amino acids 1249 to 1631 in FIG. 7) is 84.6%. Accordingly, the SSIII starch synthases are much more highly conserved between maize and wheat in the region comprising the catalytic domain of the proteins.
Example 14
Analysis of Wheat Starch Synthase III mRNA Expression
FIG. 8 shows the expression of wSSIII mRNA during endosperm development in two wheat varieties grown under defined environmental conditions. The expression of the gene is seen very early in endosperm development in both cultivars, 4 days after anthesis (FIG. 8, panels a and b). Expression in the leaf of the variety Gabo is very weak (FIG. 8, panel c, Lane L) whereas strong expression is seen in pre-anthesis florets (FIG. 8. panel c, Lane P).
Example 15
Amino Acid Sequence Comparisons between Wheat SSII and SSIII Polypeptides
Amino acid sequence comparisons between wheat BSSS, SSI, SSII and SSIII polypeptides reveals eight highly-conserved domains (FIG. 9). The amino acid sequences of these domains are represented in the wheat SSIII amino acid sequence by the following sequence motifs:










(a)
Region 1:





KVGGLGDVVTS;
(SEQ ID NO: 39)


 


(b)
Region 2:



GHTVEVILPKY;
(SEQ ID NO: 40)


 


(c)
Region 3:



HDWSSAPVAWLYKEHY;
(SEQ ID NO: 41)


 


(d)
Region 4:



GILNGIDPDIWDPYTD;
(SEQ ID NO: 42)


 


(e)
Region 5:



DVPIVGIITRLTAQKG;
(SEQ ID NO: 43)


 


(f)
Region 5a:



NGQVVLLGSA;
(SEQ ID NO: 44)


 


(g)
Region 6:



AGSDFIIVPSIFEPCGLTQLVAMRYGS;
(SEQ ID NO: 45)


and


 


(h)
Region 7:



TGGLVDTV.
(SEQ ID NO: 46)






These conserved amino acid sequences are summarised in Table 4. As shown in Table 4 below, there is at least about 25% amino acid sequence identity, preferably at least about 30% amino acid sequence identity, more preferably at least about 35% amino acid sequence identity, more preferably at least about 40% amino acid sequence identity, more preferably at least about 45% amino acid sequence identity, more preferably at least about 50% amino acid sequence identity, more preferably at least about 55% amino acid sequence identity, more preferably at least about 60% amino acid sequence identity, more preferably at least about 65% amino acid sequence identity, more preferably at least about 70% amino acid sequence identity, more preferably at least about 75% amino acid sequence identity, more preferably at least about 80% amino acid sequence identity, more preferably at least about 85% amino acid sequence identity, more preferably at least about 90% amino acid sequence identity and even more preferably at least about 95% amino acid sequence identity between the amino acid sequences of plant starch synthase enzymes, in particular wheat starch synthases.
From the data presented in Table 4, the most conserved regions of the wheat SSII and SSIII polypeptides are a region of 6 or 7 identical amino acids in Region 1 and a region of 8 or 9 identical amino acids in Region 6. The lowest regions of identity are found in regions 3 and 5a.
For each of the amino acid sequences presented in the first column of Table 4, which are specific for wSSIII polypeptides, corresponding signature motifs which are specific for wSSII-A, wSSII-B, and wSSII-D polypeptides can be derived from the alignment, as follows:









Region 1:




KTGGLGDVAGA;
(SEQ ID NO: 47)


 


Region 2:


GHRVMVVVPRY;
(SEQ ID NO: 48)


 


Region 3:


NDWHTALLPVYLKAYY;
(SEQ ID NO: 49)


 


Region 4:


GIVNGIDNMEWNPEVD;
(SEQ ID NO: 50)


 


Region 5:


DVPLLGFIGRLDGQKG;
(SEQ ID NO: 51)


 


Region 5a:


DVQLVMLGTG;
(SEQ ID NO: 52)


 


Region 6:


AGADALLMPSRF(E/V)PCGLNQLYAMAYGT;
(SEQ ID NO: 53)


and


 


Region 7:


VGG(V/L)RDTV.
(SEQ ID NO: 54)






Comparison of the amino acid sequences of all available starch synthases with the deduced amino acid sequences of the three wSSII cDNA clones of the present invention (i.e. wSSIIB, wSSIIA and wSSIID) was conducted using PILEUP analysis (Devereaux et al., 1984) and data are presented herein as a dendrogram (FIG. 10). The sequence of the glycogen synthase of E. coli was also included. Based upon their amino acid similarities, four classes of plant starch synthases can be defined: GBSS, SSI, SSII and SSIII.
Table 5 shows that levels of identity at the amino acid level between the wSSII sequences, as determined using the BESTFIT programme in GCG (Devereaux et al., 1984), and other class II starch synthases range from 70% identity with potato SSII to 85% identity with maize SSIIa. Both wSSIIB and wSSIID showed significantly higher homology to maize SSIIa than wSSIIA. Based upon sequence identities and the function of the Sgp-1 proteins in wheat, the wSSIIB, wSSIIA and wSSID cDNA clones are members of the starch synthase II (SSII) group and are more similar in sequence to maize SSIIa than maize SSIIb.








TABLE 4







Identities between conserved motifs of plant



starch synthases












Number of con-




Number of con-
served residues



served residues
between wheat


Sequence in wSSIII
between wheat
SSII and SSIII


polypeptide
starch synthases
polypeptides





Region 1:
 6/11 residues
 6/11 residues



KVGGLGDVVTS


 


Region 2:
 6/11 residues
 6/11 residues


GHTVEVILPKY


 


Region 3:
 4/16 residues
 5/16 residues


HDWSSAPVAWLYKEHY


 


Region 4:
 7/16 residues
 8/16 residues


GILNGIDPDIWDPYTD


 


Region 5:
 8/16 residues
10/16 residues


DVPIVGIITRLTAQKG


 


Region 5a:
 4/10 residues
 4/10 residues


NGQVVLLGSA


 


Region 6:


AGSDFIIVPSIFEPCGLT
15/27 residues
17/27 residues


QLVAMRYGS


 


Region 7:
 5/9 residues
 5/9 residues


TGGLVDTV




















TABLE 5







wSSII-A
wSSII-B
wSSII-D





















wSSI-A
 100%





wSSII-B
95.9%
 100%



wSSII-D
96.3%
96.7%
 100%



maize SSIIa
76.1%
85.2%
84.7%



maize SSIIb
76.3%
76.7%
75.9%



pea SSII
72.0%
72.2%
71.8%



potato SSII
70.9%
71.1%
70.3%










FIG. 11 shows a schematic representation of an alignment of plant starch synthase sequences, including wheat GBSS, wheat SSI, wheat SSII-A1, maize SSIIa, and maize dull-1 polypeptides, in which the position of the first homologous region, comprising the consensus motif KXGG, is used as the basis of the alignment. The major differences in structure between the classes of genes are found in the length of the N-terminal region between the transit peptide and the first conserved region. At one extreme, the GBSS genes have a very short N-terminal arm, whereas the du1 starch synthase contains a very long N-terminal extension containing several distinct regions. The wSSII genes contain an N-terminal extension which is longer than either GBSS, SSI, or SSIIb, and slightly longer than the maize SSIIa gene.
Example 16
Isolation of Genomic Clones for SSIII
Screening of a genomic library from the D-genome donor of wheat, T. tauschii, identified a number of clones which hybridised to the wSSIII PCR fragment. Positive plaques in the genomic library were selected as those hybridising with a probe that had been generated by PCR (amplifying between nucleotide positions 3620 to 3966) from the SSIII cDNA as template. The primer sequences used were as follows:










wSS3pa
(5′ GGAGGTCTTGGTGATGTTGT 3′:;
SEQ ID NO: 29)



and


 


wSS3pb
(5′ CTTGACCAATCATGGCAATG 3′:.
SEQ ID NO: 30)






Hybridisation was carried out in 25% formamide, 6×SSC, 0.1% SDS at 42° C. for 16 hour, then washed three times with 2×SSC containing 0.1% SDS at 65° C., for 1 hour per wash. shows an example of a plaque lift showing positive and negative hybridisations for plaques containing the T. tauschii homologue of the wSSIII.B3 gene.
DNA was isolated from positive-hybridising λ clones using methods described by Maniatis et al., Briefly, DNA was digested using BamHI or BglI and sub-coned in to the vector pJKKmfm. DNA sequencing was performed using the automated ABI system with dye terminators as described by the manufacturers. DNA sequences were analysed using the GCG suite of programs (Devereaux et al., 1984).
Nucleotide sequences of the genomic SSIII clone from T. tauschii are provided herein as 6 contiguous sequences designated fragments 1 to 6 (SEQ ID NOs: 11 to 16, respectively). Table 6 defines the relative positions of these fragments with respect to the SSIII cDNA and describes the positions of exons. FIG. 11 shows this information schematically.
The complete nucleotide sequence of a wheat SSIII genomic gene is presented herein as SEQ ID NO: 38. The structural features of this gene are presented in Table 7. A schematic representation of the intron/exon organisation of this gene is also presented in FIG. 12.
Example 17
Discussion
Early work on the Sgp-1 starch synthase proteins (Denyer et al., 1995; Rahman et al., 1995) was based on the localisation of these proteins in the wheat starch granule, and no definitive conclusion concerning their presence or absence in soluble extracts of the wheat endosperm was presented.
We have now demonstrated that a monoclonal antibody against the Sgp-1 proteins cross reacts strongly with those starch synthase proteins having apparent molecular weights of 100-105 kDa in soluble extracts, however, the appearance of these proteins in soluble extracts is dependant on the developmental stage of the endosperm material. Whilst the proteins can be detected in the soluble phase in early to mid endosperm development, little or no soluble protein remains in late endosperm development (FIG. 1). This observation accounts for the failure of Rahman et al. (1995) to detect the protein in soluble extracts in a previous report.
Based upon the localisation of the Sgp-1 starch synthase proteins in the wheat endosperm, the following nomenclature is suggested for wheat starch synthase enzymes: wGBSS for the 60 kDa granule bound starch synthase (Wx); wSSI for the 75 kDa starch synthase I (Sgp-3); wSSII for the 100-105 kDa proteins (Sgp-1); and wSSIII for a soluble high molecular starch synthase.
The present invention provides cDNA and genomic clones encoding the wSSII and wSSIII polypeptides and the corresponding genomic clones. Whilst the evidence is compelling that the wSSIIA, wSSIIB and wSSIID cDNAs encode the Sgp-A1, Sgp-B1 and Sgp-D1 proteins of the wheat starch granule, molecular weights calculated from the deduced amino acid sequences of the clones are considerably lower than estimates obtained from SDS-PAGE. The molecular weight of the precursor wSSIIA protein is 87,229 Da, and the mature protein 81,164 Da, yet the estimated molecular weight in our experience is 105 kDa. The assignment of the wSSIIA cDNA to the A-genome of wheat is demonstrated in FIG. 5, and the assignment of the 105 kDa protein to the A-genome in Denyer et al. (1995) and Yamamori and Endo (1996). Similarly, the molecular weight of the wSSIIB protein is 86,790 Da and the mature protein 80,759 Da, yet the molecular weight of the Sgp-B1 protein is estimated to be 100 kDa. No comparison can be made of the wSSIID sequences as a full length cDNA clone was not obtained. The wSSIIA and wSSIIB amino acid sequences differ by just a single amino acid residue, yet there is an apparent difference of 5 kDa in molecular weight when estimated by SDS-PAGE. Several possibilities can be advanced to account for this apparent discrepancy in molecular weights. Firstly, the wSSII proteins may not migrate in SDS-PAGE in accordance with their molecular weight because they retain some conformation under the denaturing conditions used. Secondly, the proteins may be glycosylated. It is also possible that the proteins may be non-covalently linked to starch through a high affinity starch binding site which survives denaturation and SOS-PAGE. Differences between the apparent molecular weights and those calculated from the deduced amino acid sequences will have to be defined in establishing the relationship between the wSSII proteins and proteins encoded by the analogous SSII genes of other species.
The catalytic domain of the starch synthases is found at the C-terminal end of the protein (Gao et al., 1998; Harn et al., 1998). Harn et al. (1998) identified 7 conserved regions among SSIIa, SSIIb, SSI and GBSS sequences. We have identified an additional conserved region (designated region 5a in Table 4 and FIG. 10) comprising the amino acid sequence motif DVQLVMLGTG (SEQ ID NO:52), by a comparison of the wSSII and wSSIII sequences of the present invention with differing isoforms of other plant starch synthase (GBSS, SS1, SSII and SSIID). The conservation of eight peptide regions among the 4 classes of starch synthases is striking, in terms of their sequence homologies and their alignment.
Analysis of the wheat SSII genes shows that there is a motif, PVNGENK (SEQ ID NO:59) which is repeated. The area surrounding the repeated PVNGENK (SEQ ID NO:59) motif is not homologous to maize SSIIa and the insertion of this region is responsible for the difference in length between the wheat SSII and maize SSIIa genes. In pea and potato SSII polypeptides, a PPP motif (FIG. 3; residues 251-253 and 287-289 respectively) has been suggested to mark the end of the N-terminal region and to facilitate the flexibility of an “N-terminal arm”. This motif is not found in either the maize or wheat SSII sequences.
The generation of a wheat line combining null alleles at each of the three wSSII loci, wSSIIA, wSSIIB and wSSIID, has been reported recently by Yamamori (1998). In this triple null line, the large starch granules were reported to be mostly deformed and a novel starch with high blue value was observed when stained with iodine, indicating that wSSII is a key enzyme for the synthesis of starch in wheat. Further analysis of the starch derived from this triple null mutant is in progress.
Mutations in starch synthases are known in three other species. In pea, mutation in SSII gives rise to starch with altered granule morphology and an amylopectin which yields an oligosaccharide distribution with reduced chain length on debranching, compared to the wild type (Craig et al., 1998). A similar mutation in a gene designated SSII is known in Chlamydomonas (the sta-3 mutation) and similar effects on granule morphology and amylopectin structure are observed (Fontaine et al., 1993). In maize, two mutations affecting starch synthases are known. First, the dull1 mutation has been shown to be caused by a lesion within the du1 SSIII-type starch synthase gene (Gao et al., 1998). A second mutation, the sugary-2 mutation yields a starch with reduced amylopectin chain lengths on debranching (this mutation co-segregates with the SSIIa locus (Harn et al., 1998) although direct evidence that the sugary-2 mutation is caused by a lesion in the SSIIa gene is lacking). In the SSII mutants of each of these species, amylose biosynthesis capacity is retained, suggesting different roles in amylose and amylopectin synthesis for the GBSS and SSII genes. Given the conservation in overall organisation of the GBSS and SSII genes (see FIGS. 12 and 13), when an alignment is made based on the KTGGL motif of the first conserved region, this focuses attention on the role(s) of the N-terminal region in defining substrate specificity and the localisation of the proteins as the N-terminal region is the major area of divergence between the 4 classes of starch synthases. However, it is premature to exclude the influence of more subtle mutations in central and C-terminal regions of the gene.
The cloning of the wSSII and wSSIII cDNAs and genomic clones described herein provides useful tools for the further study of the roles of the starch synthases in wheat. Firstly, they provide a source of markers which can be used to recover and combine null or divergent alleles. Secondly, genetic manipulation of wheat by gene suppression or over-expression can be carried out, and the genes may be used for over expression in other species. The promoter regions of these genes are also useful in regulating the expression of starch synthase genes and other heterologous genes in the developing wheat endosperm and in pre-anthesis florets of wheat.







TABLE 6







Summary of the Wheat Starch Synthase III Genomic Sequence










Fragment in genomic
Length




DNA clone
(bp)
Features In SEQ ID NOS: 11 to 16
Corresponding region in cDNA sequence













Fragment 1
728
Translation start codon (nucleotides 287 to 289);
Exon 1.1: nucleotides 1 to 126


(SEQ ID NO: 11)

Exon 1.1 (nucleotides 260 to 385).


Fragment 2
2446
Exon 2.1 (nucleotides 1 to 1938);
Exon 2.1: nucleotides 1008 to 2948;


(SEQ ID NO: 12)

Exon 2.2 (nucleotides 2197 to 2418).
Exon 2.2: nucleotides 2949 to 3171


Fragment 3
1032
Exon 3.1 (nucleotides 310 to 580)
Exon 3.1: nucleotides 3172 to 3440


(SEQ ID NO: 13)


Fragment 4
892
Exon 4.1 (nucleotides 678 to 853)
Exon 4.1: nucleotides 3441 to 3616


(SEQ ID NO: 14)


Fragment 5
871
Partial Exon 5.1 (nucleotides 1 to 29)
Exon 5.1: nucleotides 3908 to 3937 (partial)


(SEQ ID NO: 15)

Exon 5.2 (nucleotides 293 to 463)
Exon 5.2: nucleotides 3938 to 4108




Exon 5.3 (nucleotides 589 to 695)
Exon 5.3: nucleotides 4109 to 4215


Fragment 6
1583
Exon 6.1 (nucleotides 471 to 653);
Exon 6.1: nucleotides 4238 to 4420


(SEQ ID NO: 16)

Exon 6.2 (nucleotides 770 to 902);
Exon 6.2: nucleotides 4421 to 4552




Exon 6.3 (nucleotides 999 to 1110);
Exon 6.3: nucleotides 4553 to 4664




Exon 6.4 (nucleotides 1201 to 1328);
Exon 6.4: nucleotides 4665 to 4793




Partial Exon 6.5 (nucleotides 1408 to 1583);
Exon 6.5: nucleotides 4794 to 4966 (partial)




Translation stop codon (nucleotides 1536 to 1538)
















TABLE 7







Structural features of the wheat starch synthase III genomic gene









Nucleotide Position




in SEQ ID NO: 38
Feature
Length (bases)












 1-973
5′-untranscribed region and
973



promoter sequence


 974-1099
exon 1
126


1001-1003
translation start codon (ATG)
3


1100-2056
intron 1
957


2057-2120
exon 2
64


2121-2588
intron 2
468


2589-5291
exon 3
2703


5292-5549
intron 3
258


5550-5767
exon 4
218


5768-6103
intron 4
336


6104-6374
exon 5
271


6375-7148
intron 5
774


7149-7324
exon 6
176


7325-7438
intron 6
114


7439-7546
exon 7
108


7547-7792
intron 7
246


7793-7902
exon 8
110


7903-8797
intron 8
895


8798-8900
exon 9
103


8901-9164
intron 9
264


9165-9335
exon 10
171


9336-9460
intron 10
125


9461-9589
exon 11
129


9590-9677
intron 11
88


9678-9860
exon 12
183


9861-9977
intron 12
117


 9978-10109
exon 13
132


10110-10205
intron 13
96


10206-10317
exon 14
112


10318-10407
intron 14
90


10408-10536
exon 15
129


10537-10618
intron 15
82


10619-11146
exon 16
128


10744-10746
translation stop codon (TGA)
3


11147-11611
3′-untranscribed region
465









REFERENCES


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## Claims

1. A process for identifying a wheat plant comprising a starch synthase II null allele or a starch synthase II mutant allele, the process comprising
a) contacting a nucleic acid sample of a wheat plant with two nucleic acid primers including at least one sequence-specific amplification primer for a time and under conditions sufficient for a polymerase chain reaction to occur, the first of the primers comprising at least 15 contiguous nucleotides whose sequence is selected from
a nucleotide sequence set forth in SEQ ID NO: 37, and the second of the primers comprising at least 15 contiguous nucleotides whose sequence is complementary to a nucleotide sequence set forth in SEQ ID NO: 37; and

b) determining whether a nucleic acid of the sample is amplified by polymerase chain reaction, so as to thereby identify the wheat plant that comprises the starch synthase II null allele or the starch synthase II mutant allele.

2. The process of claim 1, wherein the identified wheat plant produces starch in its grain having an altered amylose/amylopectin ratio as compared to wild-type wheat starch.

3. The process of claim 1, wherein the identified wheat plant produces starch in its grain having an increased amylose/amylopectin ratio as compared to wild-type wheat starch.

4. The process of claim 1, wherein the identified wheat plant is hexaploid wheat and the null allele or mutant allele is on the A genome.

5. The process of claim 1, wherein the identified wheat plant is hexaploid wheat and the null allele or mutant allele is on the B genome.

6. The process of claim 1, wherein the identified wheat plant is hexaploid wheat and the null allele or mutant allele is on the D genome.

7. The process of claim 1, wherein the identified wheat plant comprises multiple starch synthase II null alleles or mutant alleles.

8. The process of claim 1, wherein the null allele or mutant allele comprises a length polymorphism, restriction site polymorphism or single nucleotide polymorphism.

9. The process of claim 1, wherein the null allele or mutant allele comprises a variation in an intron region of a wheat starch synthase II gene.

10. The process of claim 1, wherein the first or second primer comprises a reporter molecule covalently attached thereto.

11. The process of claim 1, wherein the sequence of contiguous nucleotides is selected from the protein encoding region of the nucleotide sequence set forth in SEQ ID NO: 37.

12. A process of breeding a wheat plant that produces starch in its grain having an increased amylose/amylopectin ratio as compared to wild-type wheat starch, the process comprising
A) obtaining a first wheat plant which was identified to have a starch synthase II null allele or a starch synthase II mutant allele by
a) contacting a nucleic acid sample of a wheat plant with two nucleic acid primers including at least one sequence-specific amplification primer for a time and under conditions sufficient for a polymerase chain reaction to occur, the first of the primers comprising at least 15 contiguous nucleotides whose sequence is selected from
a nucleotide sequence set forth in SEQ ID NO: 37, and the second of the primers comprising at least 15 contiguous nucleotides whose sequence is complementary to a nucleotide sequence set forth in SEQ ID NO: 37; and

b) determining whether a nucleic acid of the sample is amplified by polymerase chain reaction, thereby identifying the first wheat plant with the starch synthase II null allele or the starch synthase II mutant allele;

B) obtaining a second wheat plant; and
C) crossing the first wheat plant with the second wheat plant, thereby breeding the wheat plant that produces wheat starch having increased amylose/amylopectin ratio as compared to wild-type wheat starch.

13. The process of claim 12, wherein the first wheat plant is hexaploid wheat and the null allele or mutant allele is on the A genome.

14. The process of claim 12, wherein the first wheat plant is hexaploid wheat and the null allele or mutant allele is on the B genome.

15. The process of claim 12, wherein the first wheat plant is hexaploid wheat and the null allele or mutant allele is on the D genome.

16. The process of claim 12, wherein the null allele or mutant allele comprises a length polymorphism, restriction site polymorphism or single nucleotide polymorphism.

17. The process of claim 12, wherein the null allele or mutant allele comprises a variation in an intron region of a wheat starch synthase II gene.

18. The process of claim 12, wherein the second wheat plant comprises a starch synthase II null allele or a starch synthase II mutant allele.

19. The process of claim 18, wherein the second wheat plant comprises an endogenous starch synthase II null allele or an endogenous starch synthase II mutant allele.

20. The process of claim 12, wherein the wheat plant that produces starch in its grain having an increased amylose/amylopectin ratio as compared to wild-type wheat starch comprises multiple starch synthase II null alleles or mutant alleles.

21. A process of making a food product comprising obtaining starch from a wheat plant produced by the process of claim 1, and making the food product.

22. A process of making a food product comprising obtaining starch from a wheat plant produced by the process of claim 12, and making the food product.

23. A process of making a non-food product comprising obtaining starch from a wheat plant produced by the process of claim 1, and making the non-food product.

24. A process of making a non-food product comprising obtaining starch from a wheat plant produced by the process of claim 12, and making the non-food product.

25. The process of claim 1, further comprising determining whether the starch synthase II null allele or the starch synthase II mutant allele is on the D genome of the wheat plant.

26. A process of breeding a wheat plant that produces starch in its grain having an increased amylose/amylopectin ratio as compared to wild-type wheat starch, the process comprising
A) obtaining a first wheat plant which was identified to have a starch synthase II null allele or a starch synthase II mutant allele on the D genome by
a) contacting a nucleic acid sample of a wheat plant with two nucleic acid primers including at least one sequence-specific amplification primer for a time and under conditions sufficient for a polymerase chain reaction to occur, the first of the primers comprising at least 15 contiguous nucleotides whose sequence is selected from a nucleotide sequence set forth in SEQ ID NO: 37, and the second of the primers comprising at least 15 contiguous nucleotides whose sequence is complementary to a nucleotide sequence set forth in SEQ ID NO: 37; and
b) determining whether a nucleic acid of the sample is amplified by polymerase chain reaction, and determining whether the starch synthase II null allele or the starch synthase II mutant allele is on the D genome of the wheat plant, thereby identifying the first wheat plant with the starch synthase II null allele or the starch synthase II mutant allele on the D genome;

B) obtaining a second wheat plant; and
C) crossing the first wheat plant with the second wheat plant, thereby breeding the wheat plant that produces wheat starch having increased amylose/amylopectin ratio as compared to wild-type wheat starch.