The wheat (T. aestivum) sucrose synthase 2 gene (TaSus2) active in endosperm development is associated with yield traits

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ORIGINAL PAPER

The wheat (T. aestivum) sucrose synthase 2 gene (TaSus2)active in endosperm development is associatedwith yield traits

Qiyan Jiang & Jian Hou & Chenyang Hao &

Lanfen Wang & Hongmei Ge & Yushen Dong &

Xueyong Zhang

Received: 6 April 2010 /Revised: 4 August 2010 /Accepted: 16 August 2010 /Published online: 4 September 2010# Springer-Verlag 2010

Abstract Sucrose synthase catalyzes the reaction sucrose+UDP→UDP-glucose+fructose, the first step in the conver-sion of sucrose to starch in endosperm. Previous studiesidentified two tissue-specific, yet functionally redundant,sucrose synthase (SUS) genes, Sus1 and Sus2. In the presentstudy, the wheat Sus2 orthologous gene (TaSus2) series wasisolated and mapped on chromosomes 2A, 2B, and 2D. Basedon sequencing in 61 wheat accessions, three single-nucleotidepolymorphisms (SNPs) were detected in TaSus2-2B. Theseformed two haplotypes (Hap-H and Hap-L), but no diversitywas found in either TaSus2-2A or TaSus2-2D. Based on thesequences of the two haplotypes, we developed a co-dominantmarker, TaSus2-2Btgw, which amplified 423 or 381-bpfragments in different wheat accessions. TaSus2-2Btgw waslocated between markers Xbarc102.2 and Xbarc91 onchromosome 2BS in a RIL population from Xiaoyan 54×Jing 411. Association analysis suggested that the twohaplotypes were significantly associated with 1,000 grainweight (TGW) in 89 modern wheat varieties in the Chinesemini-core collection. Mean TGW difference between the two

haplotypes over three cropping seasons was 4.26 g (varyingfrom 3.71 to 4.94 g). Comparative genomics analysis detectedmajor kernel weight QTLs not only in the chromosome regioncontaining TaSus2-2Btgw, but also in the collinear regions ofTaSus2 on rice chromosome 7 and maize chromosome 9. Thepreferred Hap-H haplotype for high TGW underwent verystrong positive selection in Chinese wheat breeding, but not inEurope. The geographic distribution of Hap-H was perhapsdetermined by both latitude and the intensity of selection inwheat breeding.

Keywords Triticum aestivum . Sucrose synthase 2 .

Haplotype . Thousand grain weight

Introduction

Dry weight accumulation and final grain yield of wheat(Triticum aestivum L., AABBDD) involves storage reservesof protein, lipids and carbohydrates. Starch in the endospermis the major form of these reserves and comprises 65% to85% of the final dry weight of the grain (Housley et al. 1981;Dale and Housley 1986; Hurkman et al. 2003). The enzymesucrose synthase (SUS) catalyzes the reaction sucrose+UDP→UDP-glucose+fructose, the first step in the conver-sion of sucrose to starch, and in this respect, controls theflow of carbon into starch biosynthesis. SUS activity isprimarily associated with wheat endosperm development,with highest activities occurring during periods of peakstarch synthesis (Chevalier and Lingle 1983; Kumar andSingh 1980). Plants with suppressed SUS activities producelower starch levels: 62% in maize (Chourey and Nelson1976), 34–63% in potato (Zrenner et al. 1995) and 26% incarrot (Tang and Sturm 1999). SUS activity is positively

Electronic supplementary material The online version of this article(doi:10.1007/s10142-010-0188-x) contains supplementary material,which is available to authorized users.

Q. Jiang : J. Hou :C. Hao : L. Wang :Y. Dong :X. Zhang (*)Key Laboratory of Crop Germplasm Resources and Utilization,Ministry of Agriculture/Institute of Crop Science, ChineseAcademy of Agricultural Sciences,Beijing 100081, Chinae-mail: [email protected]

H. GeKey Laboratory of Huanghuaihai Crop Genetic Improvement andBiotechnology, Ministry of Agriculture/Crop Research Institute,Qingdao Academy of Agricultural Sciences,Qingdao 266100, China

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correlated with dry matter accumulation during developmentas determined by yield at harvest in rice grain, tomato, andpotatoes (Kato 1995; Sun et al. 1992; Zrenner et al. 1995).SUS is an important factor contributing to differences inkernel weight based on the observation that kernels withsignificantly higher water contents and achieving maximumdry weights have correspondingly higher SUS activities(Dale and Housley 1986).

Besides the important role in starch biosynthesis men-tioned above, SUS has many other functions. Ruan et al.(2003) noted that suppression of SUS activity by 70% ormore in the ovule epidermis led to a fiberless phenotype.SUS was believed to be involved in cell wall biosynthesisby providing UDP-glucose directly to cellulose synthase(King et al. 1997; Ruan and Chourey 1998; Haigler et al.2001). In addition, SUS protein may be involved inproviding energy for uploading assimilates into the phloem.During later stages of seed development in Arabidopsis,SUS localizes specifically to the companion cells within thesilique wall, indicating that SUS activity in the embryo mayuse sucrose to provide precursors for the biosynthesis ofstorage proteins and lipids (Fallahi et al. 2008). This resultis consistent with previous localization studies in citrusfruit, maize leaves (Nolte and Koch 1993), and radishhypocotyls (Rouhier and Usuda 2001), where SUS proteinmay be involved in providing energy for phloem loading/unloading processes (van Bel and Knoblauch 2000).

A multigene family encodes several SUS isoforms in plants,including maize (Carlson et al. 2002), pea (Barratt et al. 2001),rice (Wang et al. 1992; Huang et al. 1996; Harada et al. 2005;Hirose et al. 2008), and lotus (Horst et al. 2007). Within agiven species the Sus genes share greater sequence similaritieswith their counterparts in other species than they do to eachother (Shaw et al. 1994; Baud et al. 2004). Different types ofSus genes have different expression profiles and play diverseroles during the development of sink organs (Baud et al.2004; Fallahi et al. 2008). In maize, two paralogous genes,Sh1 and sus1, encode two biochemically similar isozymes ofsucrose synthase, SUS1 and SUS2, respectively. Chourey etal. (1998) concluded that the SUS1 isozyme plays a dominantrole in providing the substrate for cellulose biosynthesis,whereas the SUS2 protein is needed mainly for generatingprecursors for starch biosynthesis.

Two genes corresponding to the SUS1 and SUS2proteins were also characterized in barley and wheat. Inbarley, these two genes were located on chromosomes 7HSand 2HS, respectively (Sánchez de la Hoz et al. 1992)whereas in wheat, Sus1 and Sus2 were on the short arms ofhomoeologous group 7 chromosomes (Maraña et al. 1988).In both barley and wheat the two genes showed differentexpression patterns; Sus2 expressed only in the endosperm,whereas Sus1 mRNA was expressed in roots and leaves(Martinez de Ilarduya et al. 1993; Maraña et al. 1990).

Thus diverse functions of SUS apparently correspondedto the different SUS isoforms and to different types of Susgenes. Even the same Sus gene may have differenthaplotypes with different effects on agronomic traits. Thepurposes of this study were to determine the sequencevariation in the wheat TaSus2 gene specifically expressed inendosperm, to evaluate its association with importantagronomic traits in Chinese wheat cultivars, and to identifysuperior TaSus2 haplotypes and develop molecular markersfor marker assisted selection (MAS) breeding in wheat.

Materials and methods

Plant materials

Three diploid progenitor species of common wheat,Triticum urartu (AA) accession UR203 (CAAS GermplasmBank), Aegilops speltoides (SS) Y2046, and Aegilopstauschii (DD) Y2009, the Thalictrum orientale (AABB)TR5 and 61 wheat accessions including 26 moderncultivars and 35 landraces, were used in sequencing todetect single-nucleotide polymorphisms (SNPs) and hap-lotypes for the TaSus2 gene.

Two hundred and forty-five wheat accessions (Electronicsupplementary Table 1) from the Chinese wheat mini-corecollection representing more than 70% of the wheat geneticdiversity of China using only 1% of the Chinese basiccollection (Hao et al. 2008), 348 modern varieties in theChinese wheat core collection (Electronic supplementaryTable 2), and 384 European wheat cultivars (SupplementaryTable 3) were used for validation of TaSus2-2Btgw. Themini-core and core collections were selected from 23,705accessions collected or bred in China (Zhang et al. 2002;Dong et al. 2003; Hao et al. 2008). During the 2002, 2005,and 2006 wheat-growing seasons, the above 245 varietieswere planted at the CAAS Luoyang Experiment Station inHenan province (111.6°E, 33.8°N). The European cultivarswere planted only in 2006. Each variety was planted in two2-m rows spaced 25 cm apart, with 40 plants in each row.The field management followed the local normal agricul-tural practice.

A recombinant inbred line (RIL) population with 184lines derived from Xiaoyan 54×Jing 411 (Electronicsupplementary Table 4), kindly provided by Dr. TongYiping, Institute of Genetics and Developmental Biology,Chinese Academy of Sciences, was used for mapping.

DNA and RNA extraction

Genomic DNAwas extracted from lyophilized mixed youngleaves of seven seedlings as described by Sharp et al. (1988).Isolation and reverse transcription of total RNA followed

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Guo et al. (2010). RNA was extracted from immatureembryos 15 days after anthesis using TRIzol reagent andcDNA were synthesized with the SuperScript II System(Invitrogen) according to the manufacturer’s instructions.

Cloning and genome structure analysis of the TaSus2 gene

Based on the known sequence (GenBank accession No.AJ000153) (Guerin et al. unpublished, http://www.ncbi.nlm.nih.gov/nuccore/3393043) the primer pair Sus2-167 and Sus2-168 was designed to amplify the TaSus2 gene, and then toobtain the genomic DNA sequence from leaf tissue DNA andthe cDNA sequence from the developing endosperm RNA ofChinese Spring wheat. The polymerase chain reactions(PCRs) were carried out using LA Taq polymerase (TaKaRaBiotechnology (Dalian)), a 3′→5′ proof reading polymerase,in a reaction volume of 15 μl, containing 80 ng genomicDNA, 7.5 μl 2× PCR buffer, 1.0 μl 10 μM forward andreverse primers, respectively, 0.24 μl 25 mM dNTPs, and 0.75unit LA Taq polymerase. PCR was carried out using a PTC-100™ Programmable Thermal Controller (MJ Research) asfollows: initial denaturation at 95°C for 3 min; followed by 30cycles of 95°C for 30 s, 62°C for 1 min, and 72°C for 4 min,with a final extension of 72°C for 10 min. The PCR productswere electrophoresed on 1.0% agarose gels, stained withethidium bromide, and visualized under UV light.

PCR products were excised from gels and purified with aPCR product purification kit DP-1502 (Tiangen, Beijing).The purified products were then cloned using the pGEM-TEasy Cloning Vector (Tiangen, Beijng) and transformedinto Top 10 competent Escherichia coli cells by the heatshock method. Positive clones were selected by colonyPCR and their plasmids were extracted with a plasmidextraction kit DP-1002 (Tiangen, Beijng). DNA sequencingwas performed by ABI 3730XI DNA Analyzer (AppliedBiosystems). To verify the results, each PCR product wassequenced in both directions.

The genomic DNA sequences of TaSus2 gene werealigned using the software DNAStar (http://www.dnastar.com/). The genomic structure of the TaSus2 gene wasdetermined by aligning the amplified genomic DNAsequences and their corresponding cDNA sequences.

Genome-specific primer design and TaSus2 chromosomelocation

The allohexaploid nature of common wheat predicts that therewould be orthologous TaSus2 genes for each family in the A,B, and D genomes. Based on DNA variations among thegenomic sequences of the TaSus2 gene in each genome, fivepairs of genome-specific primers were designed using thePrimer Premier 5.0 software (http://www.premierbiosoft.com/)(Table 1).

A set of Chinese Spring nullisomic-tetrasomic lines, wasemployed to verify the chromosomal locations of theTaSus2 genes with the genome-specific primers (Table 1).Furthermore, using data for the Xiaoyan 54×Jing 411 RILpopulation with 184 individuals, this gene was mappedusing the MAPMAKER/EXP version 3.0 (Lander andBotstein 1989)

Single-nucleotide polymorphism identification

SNPs were identified using the DNAStar software (http://www.dnastar.com/).

Agarose gel-based co-dominant allele-specific-polymerasechain reaction primer designs

To assay SNPs, we used the agarose gel-based co-dominantallele-specific (ACAS) or allele-specific AS-PCR methoddeveloped by Kanazin et al. (2000), and applied, forexample, in Arabidopsis (Drenkard et al. 2000), soybean

Table 1 Primer sequences used in this study

Primer name Sequence (5′–3′) Tm (°C)a

Sus2-167 For1 CGCCCTGAGCCGCATCCACA

62

Sus2-168 Rev1 CGCTCGCCCGCCATTTATTTCTCT

Sus2-AJ1 For2 GAAGAGGACAGCAATGGG

60

Sus2-AJ323 Rev2 TCACATACTCCCAGACGC

Sus2-2A-1452f For3 CTGAAAGTTTAAACTGGAACTACC

60

Sus2-2A-2190r Rev3 CATTAGGAATCAATTATAAGTTTATAAC

Sus2-2D-674f For4 CCTGTGATGTTCAGCTCTTGATCTAT

62

Sus2-2D-1206r Rev4 CTTTCAGTTGGCTCATAGATAGTG

Sus2-SNP-185 For5 TAAGCGATGAATTATGGC

Sus2-SNP-589H1 Rev5-1 GGTGTCCTTGAGCTTCTCG

60

Sus2-SNP-589H2 Rev5-2 GGTGTCCTTGAGCTTCTgG

60

Sus2-SNP-589H3 Rev5-3 GGTGTCCTTGAGCTTCcgG

60

Sus2-SNP-227 For6 ctataGTATGAGCTGGATCAATGGC

Sus2-SNP-589L1 Rev6-1 GGTGTCCTTGAGCTTCTCA

60

Sus2-SNP-589L2 Rev6-2 GGTGTCCTTGAGCTTCTgA

60

Sus2-SNP-589L3 Rev6-3 GGTGTCCTTGAGCTTCcgA

60

For forward, Rev reversea Annealing temperature (°C)

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(Kim et al. 2005; Yuan et al. 2007), maize (Shin et al.2006), rice (Hayashi et al. 2004, 2006), and wheat (Wei etal. 2009). Allele-specific primers were designed using thefact that a 3′ mismatch does not prime a PCR at a specificannealing temperature (Sommer et al. 1992). Also, becausewheat is allohexaploid (2n=6×=42), genome-specificprimes were designed from the DNA variations among thedifferent genomic wheat sequences, as the forward (orreverse) primer in ACAS-PCR. For each SNP locus, wedesigned allele-specific forward (or reverse) primers (eachmatching one of the SNP variants at the 3′-end) and thegenomic-specific reverse (or forward) primers with match-ing melting temperatures (Fig. 1, Electronic supplementaryFig. 1). The primers were designed in such a way that thedifference in length between the two PCR fragments wasmore than 40 bp, allowing the alleles to be easily separatedon agarose gels.

PCR were performed as follows: 95°C for 3 min;followed by 30 cycles of 95°C for 30 s, 60°C for 1 min,and 72°C for 30 s, with a final extension of 72°C for10 min. The two amplified products for the same SNP locuswere then mixed and separated on standard 1.5% agarosegels (or 6% denaturing polyacrylamide gels). Finally, thegenotypes of the SNP were assessed according to themolecular weights of the PCR amplified products.

Statistical analyses

Population structure involving 78 SSR markers used inconstruction of the core- and mini-core collections (Hao etal. 2008) was analyzed using Structure2.1 (Pritchard 2001).

Various traits, including number of fertile tillers per plant,1,000 grain weight (TGW), grain number per spike,heading date, maturity date, plant height, spike length,spike number, grain number in the spikelet with themaximum number of grains, first internode length, flagleaf length, and flag leaf width, were measured in threecropping seasons (2001–2002, 2004–2005, 2005–2006) toexamine the association between each trait and the ACASmarker in 89 modern varieties and 156 landrace accessions,respectively. One-way analyses of variance were performedwith the SPSS System for Windows version 12.0 (SPSSInc., Chicago, IL, USA) to determine association differ-ences between two haplotypes.

The QTLs searching in grasses species was carried out atGramene (http://www.gramene.org) and the CMap site onthe Cnetre for Comparative Genomics web site at MurdochUniversity (http://ccg.murdoch.edu.au/cmap/ccg-live/). Therice sequence blast was based on Rice Genome AnnotationProject (http://rice.plantbiology.msu.edu/).

Results

Cloning, characterization, and chromosome assignmentsof the TaSus2 gene

The TaSus2 genomic DNA sequences were amplified bythe primer pair Sus2-167 and Sus2-168 (Table 1) fromcommon wheat Chinese Spring (AABBDD), and threediploid accessions T. urartu UR203 (AA), A. speltoidesY2046 (SS), and A. tauschii Y2009 (DD). Three TaSus2genes were amplified from Chinese Spring and one fromeach diploid.

To assign the specific chromosome locations of the threeTaSus2 genes, five genome-specific primer sets weredesigned based on genomic sequence differences amongthe TaSus2 genes (Table 1). The genomic DNAs of ChineseSpring, T. orientale, T. urartu, A. speltoides, A. tauschii andthe homologous group 2 Chinese Spring nulli-tetrasomiclines were amplified using these genomic-specific primerpairs. The TaSus2 genes were located on chromosomes 2A,2B and 2D (Fig. 2). Using genetic and molecular data forthe Xiaoyan 54×Jing 411 RIL population, TaSus2-2B waslocated in chromosome 2BS where it was flanked by SSRmarkers Xbarc102.2 and Xbarc91 (Fig. 3), which aresituated in deletion bin 2BS-1-0.53-0.75 (Sourdille et al.2004).

Three cDNA clones for TaSus2 gene were amplifiedfrom Chinese Spring developing endosperm by the primerpair Sus2-167 and Sus2-168 (Table 1). These correspondedto the genomic DNA sequences. In order to obtain the full-length cDNA and complete genomic DNA sequences of thethree TaSus2 genes, the primer pair Sus2-AJ1 and Sus2-

(1)

(2)

CgGg

TgAg

423bp

589H

589L

381bp

185

227

Fig. 1 Schematic diagram showing the ACAS-PCR approach used tovalidate SNP. The 589 M and 589 F primers contain SNP variants atthe 3′end and, in addition, have a mismatch with a nonspecific allelein the second nucleotides in the 3′end. The 185 and 227 primers aregenome-specific primers. The two amplified products for the sameSNP locus (1) and (2) were then mixed and separated on standard1.5% agarose gels. The names of primers 589H, 589L, 185 and 227are Sus2-SNP-589H2, Sus2-SNP-589L2, Sus2-SNP-185, and Sus2-SNP-227, respectively in Table 1

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AJ323 (Table 1) was designed and amplified fromChinese Spring. Alignment of the genomic DNA sequen-ces and cDNA sequences of the TaSus2 gene showed thatthe complete genomic DNA sequences of TaSus2-2A,TaSus2-2B, and TaSus2-2D were 4,370, 4,380, and4,128 bp, respectively, each with 15 exons and 14 introns,as well as the 5′and 3′ flanking sequences (Fig. 4).Except for a 250 bp deletion in the first intron of TaSus2-2D, the exon-intron structures and sequences of the threegenes showed high similarity. Moreover, the exon-intronstructure of TaSus2 was very similar to that of barleyHvSus2 (GenBank Y15802.1), indicating a close phylo-genetic relationship. The exons of the barley and wheatTaSus2 genes showed high sequence identities, rangingfrom 90.6% to 99.0%, the introns similarities were61.7–90.0%.

SNP identification and SNP marker development

Three TaSus2 genes (TaSus2-2A, TaSus2-2B, and TaSus2-2D)were amplified by the primer pair Sus2-167 and Sus2-168from 61 common or bread wheat accessions consisting of 26modern varieties and 35 landraces. After aligning thesequences we found that TaSus2-2A and TaSus2-2D werecompletely conserved and that TaSus2-2B was polymorphic.Three SNPs were identified, within the first intron (137 T>C),

one in the second exon (589 T>C) and one in the ninthintron (2668A>G) (Fig. 4). The three SNPs formed twohaplotypes (TTA and CCG), which were designated Hap-Land Hap-H, respectively.

ACAS-PCR primer sets for SNP 589 T>C workedwell and behaved co-dominantly. The forward primers(Sus2-SNP-185 and Sus2-SNP-227) for ACAS-PCR weregenome-specific, and the reverse primers were allele-specific with an artificial mismatch in the 3′-end (Supple-mentary Fig. 1). In addition to the SNP-variant at the3′-end of the reverse primers, when no nucleotidemismatch (Sus2-SNP-589L1 and Sus2-SNP-589H1) ortwo mismatches (Sus2-SNP-589L3 and Sus2-SNP-589H3) occurred in the 3′-end, the ACAS-PCR primersets for SNP 589T>C produced PCR products from bothor neither haplotypes. Thus only when one mismatch(Sus2-SNP-589L2 and Sus2-SNP-589H2) occurred, theACAS-PCR primers sets reliably discriminated betweenthe two alleles (Supplementary Fig. 2). The two primersets Sus2-SNP-185 and Sus2-SNP-589H2, Sus2-SNP-227,and Sus2-SNP-589L2, corresponding to the haplotypesHap-H and Hap-L, respectively, were selected as an SNPmarker (TaSus2-2Btgw) to screen the 61 original varieties.The haplotypes detected by the TaSus2-2Btgw fully agreedwith those deduced from the sequences obtained onABI3730.

Sus2-SNP-185/589L2

Sus2-2D-674f/1206r

Sus2-SNP-227/589L2

Sus2-2A-1452f/ 2190r

818bp

766bp

423bp

381bp

Fig. 2 PCR-based chromosome locationas of TaSus2 orthologs.Absence of a band indicates the specific sequence is located on thecorresponding null genome or chromosomes. The size of theamplification product is shown on the left and the primer pair onthe right. For primer pairs Sus2-SNP-185/589L2 and Sus2-SNP-227/589L2, the target PCR target product is present in N2AT2B, N2AT2D,N2DT2A, N2DT2B, Triticum aestivum (6×) and Thalictrumorientale (AABB), However, no target PCR product is present in

N2BT2A, N2BT2D, Triticum urartu, Aegilops tauschii. The primerpairs Sus2-SNP-185/589L2 and Sus2-SNP-227/589L2 are therefore2B chromosome-specific. Compared with the TaSus2-2B amplifiedfrom Chinese Spring and T. orientale (AABB), there is a 250 bpdeletion in Sus2 amplified from Aegilops speltoides Y2046 (Electronicsupplementary sequence). There is no target PCR product identified inA. speltoides 2,046 (2×) because the primers Sus2-SNP-185 and Sus2-SNP-227 are included in this 250 bp region

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Association between haplotypes at TaSus2-2B and TGW

The new primer sets (Sus2-SNP-185 and Sus2-SNP-589H2,Sus2-SNP-227 and Sus2-SNP-589L2) amplified 423 and381 bp fragments in 245 wheat accessions from the Chinesewheat mini-core collection, corresponding to the haplotypesHap-H and Hap-L, respectively (Fig. 5). Based on the 78SSR markers used in constructing the core- and mini-corecollections (Hao et al. 2008), these accessions wereclustered into two sub-sets, landraces and modern varieties,by the Structure2.1 program (Pritchard 2001). Thus weaccepted the kinship value as K=2 (Electronic supplemen-tary Fig. 3). Associations of PCR band profiles with 12mean trait values of 89 modern Chinese varieties and 156landrace accessions were then carried out separately(Table 2). No significant differences between the haplo-

types were detected among the landraces except for headingdate in 2005 (P=0.03).

Among modern varieties there was a significant differ-ence between haplotype means for TGW in all 3 years withthe average TGW for Hap-H being 4.26 g higher than Hap-Lacross seasons. Leaf width for Hap-L was significantly lessthan for Hap-H in both seasons in which it was measured.There were significant differences (P<0.05) in plant heightin 2005 and 2006, but not in 2002 (P=0.39). Grain numberfor Hap-L was consistently less than for Hap-H, but wassignificant only in 2002 (Table 2). These results suggestedthat the main effect of TaSus2-2B is its contribution to TGW,and that Hap-H is a superior allele for grain yield. A yieldQTL was also mapped in the genomic region flankingTaSus2 in the Xiaoyan 54×Jing 411 RIL population (Tong etal., unpublished).

Usually, population structure can be observed in moderncultivars due to breeding activities, especially in outcross-ing crops such as maize (Pritchard 2001, Flint-Garcia et al.2003). In inbred crops, such as wheat, germplasm exchangeand intercrossing have reduced the divisions betweengeographic and breeding populations, thus diminishingpopulation structure (Hao et al. 2008). The genetic structureof modern varieties was also analyzed with Structure2.1using the 78 SSR markers. The modern varieties wereclustered into two sub-groups (Electronic supplementaryFig. 4). However, no obvious bias for either Hap-H or Hap-Lwas detected in either sub-group (sub-group 1, 36% Hap-Hand 55% Hap-L; sub-group 2, 20% Hap-H and 78% Hap-L).It seems therefore, that any population structure existing inChinese modern varieties did not strongly affect haplotypeassociations of TaSus2.

Comparative genomics analysis of TaSus2 in grassesand QTLs co-localized with its orthologous genesin rice and maize

TaSus2-2B was mapped on chromosome 2BS, and wasflanked by SSR markers Xbarc102.2 and Xbarc91 (Fig. 3).Xbarc91 co-localized with important agronomic traits QTLs(wheat 2B Con July 2010. http://ccg.murdoch.edu.au/cmap/ccg-live/cgi-bin/cmap/viewer?ref_map_set_acc=843;ref_map_accs=3794), including the thousand kernel weightQTL, QTkw.sfr-2B (Fig. 6, Supplementary Fig. 5). In 226F5 recombinant inbred lines (RILs) from a cross betweenwheat and spelt, QTkw.sfr-2B was detected, which couldexplain more than 5–9% phenotypic variance (Zanetti et al.2001).

A TaSus2 orthologues gene (LOC_Os07g42490.2) wasphysically mapped at 25,429,604 to 254,339,10 bp on ricechromosome 7L. The cDNA sequence homologies betweenLOC_Os07g42490.2 (GenBank EF122474.1) and TaSus2-2A, TaSus2-2B, TaSus2-2D were 88.6%, 88.7%, 88.9%,

Chro. 2B

swes184wmc314

1.8

wms210barc1138.2cfd238

11.1

barc200

25.0

wmc407.21.1

wms429

11.3

barc183

9.5

barc71.3

barc131.2

barc102.27.7

Tasus2-2Btgw

6.5

barc914.3

barc18barc160

0.7

wms55.1

0.7

barc1155

1.6

ag24.2

12.3

wms191.1

13.5

wms388

9.8

cfd73.12.3

cfd267.2

12.1

barc223.210.2

Fig. 3 TaSus2-2Btgw mapon chromosome 2BS for RILpopulation from Xiaoyan54×Jing 411. The TaSus2-2Btgw

marker was located in chromo-some 2BS and flanked by SSRmarkers Xbarc102.2 andXbarc91

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respectively. LOC_Os07g42490.2 was co-localized withQTLs controlling yield traits (Japanese rice-Gramene anno-tated nipponbare sequence 2006, http://gramene.agrinome.org/db/cmap/map_details?ref_map_set_acc=grjp2008a;ref_map_accs=grjp2008a-07;highlight=grjp2008a-07-20980010), including grain yield QTL AQE031 (Fig. 6,Electronic supplementary Fig. 6), detected in Oryzasativa×Oryza glumaepatula BC2F2 family populationwith LOD value 3.26. Markers RM11 and STSG86 wereco-localized markers with this QTL, respectively explain-ing 12.9% and 13.9% of the yield variation (Brondani etal. 2002).

In maize, the orthologues gene for TaSus2 is Sus1. Thehomology between Sus1 (GenBank NM_001111853) andTaSus2 was 84.3%. Gene Sus1 was physically mapped in bin9.04 on chromosome 9 (Causse et al. 1995), and co-localizedwith several QTLs (Maize Bins QTL 2005, http://www.gramene.org/db/cmap/viewer?ref_map_set_acc=maize-bins-

qtl;ref_map_accs=maize-bins-qtl9), such as AQFS092 andAQFS1068 affecting seed weight (Fig. 6, Electronic supple-mentary Fig. 7). Significant association between Acp1, amarker in bin 9.04, and grain weight QTL AQFS092 wasfound, and variation at the Acp1 locus explained at least 5%of the phenotypic variation (Abler et al. 1991). AQFS1068 isa major QTL for kernel weight, and accounted for 15% ofthe variation (Melchinger et al. 1998).

Distribution of Hap-H at TaSus2-2B in different decades

The release dates (Hao et al. 2006) of 348 modern varietiesreleased in China since the 1940s were used to examinechanges in TGW over 10 year intervals of the past sixdecades (1940s, 1950s, 1960s, 1970s, 1980s, and 1990s).Over that period the frequency of Hap-H showed anincreasing trend from zero in the 1940s to 44% in varietiesreleased during the 1990s (Fig. 7).

423bp381bp

Hap-H Hap-L

423bp 381bp

M 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 a

b

Fig. 5 Test of polymorphism for PCR fragments amplified withprimer pairs Sus2-SNP-185 and Sus2-SNP-589H2, and Sus2-SNP-227and Sus2-SNP-589L2 in different cultivars on 1.5% agarose (a) and6% denaturing polyacrylamide gels (b) 1 Xiaoyan 54, 2 ZM017079, 3ZM009126, 4 ZM017936, 5 ZM017231, 6 ZM003131, 7 ZM022727,

8 ZM003069, 9 ZM003663, 10 ZM001912, 11 ZM003793, 12ZM003650, 13 ZM002685, 14 ZM003747, 15 ZM002659, 16ZM009411, 17 ZM015719, 18 ZM009097, 19 Jing411, 20 ChineseSpring, M 100 bp DNA ladder (Trans, BM301) in (a); PBR322 DNA/mspl (Biolabs, N3032) in (b)

TaSus2-2B

111 133 156 195 122 218 102 181 126 167 225 319 251 140 49

394 69 88 403 98 102 76 76 78 84 80 93 104 90 6 8

2

2 7 7 7 9 4

9

TaSus2-2A

111

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

133 154 195 122 220 100 178 126 167 225 319 251 140 49

386 71 90 410 79 105 87 76 77 85 77 93 104 917 7 1

0

7 7 1

49

TaSus2-2D

111 133 155 195 120 218 102 181 126 167 225 319 251 140 49

141 78 87 407 87 105 77 78 74 84 80 94 104 91 7 1

0

8 7 4

4

137T>C 589T>C 2668A>G

TAG

SNP

ATG

Fig. 4 The exon-intron structure of the TaSus2 gene from wheat 2A,2B and 2D homoeologs. The numbered solid arrows denote exons,and the lines between exons represent introns. The numbers under

exons and introns indicate their size (bp). The locations of SNPs inTaSus2-2B are indicated by arrows

Funct Integr Genomics (2011) 11:49–61 55

Page 8

Tab

le2

Com

parisonof

means

for12

agrono

mic

traitsbetweentwohaplotyp

esof

theTaSu

s2-2Blocusin

mod

ernChinese

varietiesandland

race

accessions

(means±SD)

Trait/HT

2002

2005

2006

Hap

-LHap

-HFvalue

PHap

-LHap

-HFvalue

PHap

-LHap

-HFvalue

P

Mod

ernvariety

FT

7.77

8±2.76

56.85

0±3.51

41.41

40.23

89.90

7±3.98

19.20

9±4.69

10.44

10.50

98.82

4±3.05

57.94

4±2.39

11.64

30.20

4

TGW

(g)

39.975

±6.90

844

.916

±5.37

18.36

70.00

5**

37.141

±6.36

141

.268

±4.46

57.41

30.00

8**

39.615

±6.08

043

.320

±5.411

6.94

30.01

0*

GN

49.582

±9.79

455

.429

±11.784

4.83

20.03

1*45

.074

±9.20

048

.355

±7.17

52.26

00.13

752

.669

±9.35

054

.912

±8.44

21.06

90.30

4

HD

177.69

1±5.35

717

7.38

1±6.84

50.04

30.83

519

7.71

2±3.69

119

7.45

8±4.32

40.07

30.78

818

2.06

8±6.19

818

0.04

0±5.87

71.93

70.16

8

RD

227.27

3±7.24

322

6.55

0±7.50

10.14

30.70

623

5.81

0±4.31

023

4.63

6±3.99

51.23

00.27

122

4.88

1±4.36

322

3.56

0±5.24

51.42

50.23

6

PH

(cm)

99.118

±20

.132

94.667

±19

.500

0.75

60.38

710

0.87

9±17

.141

90.333

±19

.219

5.98

30.01

7*10

6.10

9±17

.136

97.120

±20

.146

4.31

80.04

1*

SpL

(cm)

10.625

±2.18

610

.095

±2.311

0.86

70.35

59.08

4±1.79

98.73

5±1.65

40.62

70.43

110

.375

±2.36

99.93

6±1.77

60.69

10.40

8

SN

21.436

±2.30

821

.762

±2.42

70.29

40.58

921

.077

±1.91

921

.618

±1.88

71.27

30.26

322

.156

±1.85

722

.160

±1.52

30.00

00.99

2

MGNs

3.07

5±0.48

53.27

3±0.40

72.87

90.09

43.50

5±0.58

83.67

2±0.50

31.53

70.21

9

FIL

(cm)

31.718

±6.64

730

.810

±6.50

60.29

80.58

633

.833

±7.56

831

.716

±6.97

31.43

70.23

4

LFL(cm)

22.017

±5.07

421

.429

±3.46

80.27

00.60

517

.040

±3.64

916

.491

±3.44

60.41

00.52

4

WFL(cm)

1.65

7±0.30

61.84

9±0.16

68.43

10.00

5**

1.47

0±0.40

01.64

2±0.24

93.96

00.05

0*

Landrace

FT

8.77

6±3.04

48.41

2±2.36

30.35

90.55

18.88

4±3.23

78.88

1±2.87

40.00

00.99

510

.570

±3.82

710

.008

±2.82

00.86

00.35

5

TGW

(g)

33.668

±6.18

934

.362

±5.95

50.29

90.58

630

.817

±6.34

230

.537

±5.71

90.06

50.79

933

.534

±5.91

332

.632

±4.75

80.88

70.34

8

GN

49.313

±11.638

52.104

±11.344

1.78

10.18

440

.537

±7.22

741

.557

±7.69

60.57

10.45

153

.699

±10

.039

55.206

±9.23

70.79

50.37

4

HD

184.16

0±8.63

118

4.91

7±7.66

80.25

10.61

719

5.36

6±5.113

197.44

2±6.26

74.66

60.03

2*18

5.97

8±7.67

518

8.44

2±7.22

93.58

10.06

0

MD

231.48

8±11.512

231.42

6±4.98

60.00

10.97

223

1.65

1±3.32

923

2.50

0±4.24

41.50

20.22

322

9.22

6±7.44

423

0.90

4±6.41

21.86

70.17

4

PH

(cm)

114.17

5±16

.952

115.55

2±12

.420

0.24

20.62

410

8.57

5±12

.823

104.90

2±12

.452

2.69

40.10

312

4.46

2±12

.073

124.03

8±11.305

0.04

30.83

6

SpL

(cm)

10.659

±2.60

710

.140

±2.18

51.35

40.24

78.71

3±2.01

78.81

3±1.47

80.08

80.76

810

.754

±2.65

911.018

±2.29

70.36

20.54

8

SN

21.711

±2.56

921

.532

±2.58

60.14

50.70

420

.724

±1.78

220

.915

±1.74

60.35

10.55

523

.088

±1.84

523

.419

±1.74

41.117

0.29

2

MGNs

2.79

8±0.42

32.811±0.51

30.02

10.88

43.411±0.58

13.51

9±0.91

00.76

50.38

3

FIL

(cm)

31.420

±5.15

230

.491

±4.37

41.08

30.30

037

.349

±5.02

937

.780

±4.75

20.25

50.61

4

LFL(cm)

15.604

±3.18

915

.384

±3.14

70.16

00.69

019

.312

±3.88

118

.823

±3.22

00.59

70.44

1

WFL(cm)

1.20

8±0.21

51.23

4±0.21

30.49

90.48

11.33

5±0.23

41.39

0±0.23

91.78

90.18

3

Fratio

andprob

ability

basedon

one-way

ANOVA

FTfertile

tillers

perplant,TGW

1,00

0grainweigh

t,GNgrainnu

mberperspike,HD

headingdate,M

Dmaturity

date,P

Hplantheight,S

pLspikeleng

th,S

Nspikenu

mber,MGNgrainnu

mberin

thespikelet

with

themaxim

umnu

mberof

grains,FIL

thefirstinternod

eleng

th,LFLflag

leaf

leng

th,WFLflag

leaf

width

*P<0.05

;**

P<0.01

,sign

ificant

56 Funct Integr Genomics (2011) 11:49–61

Page 9

Geographical distribution of Hap-H at TaSus2-2B

The distribution of haplotypes among the 348 varieties wasconsidered in relation to the major agro-ecological zones(Zhuang 2003) in which they were grown. Taking intoaccount that more than 85% of the national wheat area andproduction is in zones I, II, III, IV, VI and VII comparisons

were largely restricted those areas. The frequencies ofHap-H varied across the six zones at 45% (zone III), 36%(zone II), 33% (zone VIII), 29% (zone IV) >15% (zone I)>9% (zone VI) (Electronic supplementary Table 5, Electronicsupplementary Fig. 8). The main wheat growing provincialfrequencies of Hap-H from the highest to lowest were Jiangsu(50%), Anhui (50%), Shannxi (46%), Henan (46%), Gansu(40%)>Sichuan (33%), Guizhou (31%)>Hebei (19%),Beijing (17%), Shanxi (13%), Shandong (11%)>Heilongjiang(5%). These results suggested a decline in Hap-H frequencywith increasing latitude (Fig. 8b, Electronic supplementaryTable 6).

Among 384 European wheat cultivars from 16 countriesonly 48 (13%) were Hap-H (Supplementary Table 3).These occurred mainly in the Mediterranean countries, suchas Italy, Spain and Portugal (Fig. 8a, Electronic supple-mentary Table 7).

Discussion

A triplicated set of TaSus2 orthologs was cloned andassigned to chromosomes 2A, 2B and 2D based ongenome-specific primers and Chinese Spring nulli-tetrasomic lines (Fig. 2). TaSus2-2B was mapped onchromosome 2BS using the Xiaoyan 54×Jing 411 RIL

Fig. 7 Hap-H frequency changes in Chinese varieties released fromthe 1940s to 1990s

Feature Types

Maize BinRFLP or SSR

Gene

QTL

barc183

Wheat 2 (0-172.2 cM)

fba38

Rice 7 (29.3 Mb)swes184wmc314

1.8

wms210barc1138.2cfd238

11.1

barc200

25.0

wmc407.21.1

wms429

11.3

barc1839.5

barc71.3

barc131.2

barc102.27.7

Tasus2-2Btgw

6.5

barc914.3

barc18barc160

0.7

wms55.1

0.7

barc1155

1.6

ag24.2

12.3

wms191.1

13.5

wms388

9.8

cfd73.12.3

cfd267.2

12.1

barc223.2

10.2

Maize 9 (62.8-92.1 cM)

Cent

bar91

25.46 Mb Loc_Os07g42570

25.37 Mb Loc_Os07g4241025. 42 Mb Loc_Os07g42490

stm506acat

sus1

AQE031 (grain yield)

QTkw.sfr-2B

(thousand kernel

weight)

AQFS092 (seed weight)

AQFS1068 (seed weight)

Cent

Bin 9.02

Bin 9.03

Bin 9.04

Bin 9.05

Wheat 2Fig. 6 Comparative mappingof TaSus2 orthologues andco-localized yield QTLsin rice (LOC_Os07g42490.2)and maize (sus1)

Funct Integr Genomics (2011) 11:49–61 57

Page 10

population (Fig. 3). In barley, HvSus2, the ortholog ofTaSus2, is also located in homeologous group 2 (2HS)(Sánchez de la Hoz et al. 1992). In an earlier report Marañaet al. (1988) located the TaSus2 genes on the short arms ofgroup-7 chromosomes. However, each of our genome-specific primers amplified products not only in ChineseSpring, but also in the nulli-tetrasomics N7AT7B,N7AT7D, N7BT7A, N7BT7D, N7DT7A, N7DT7B (Elec-tronic supplementary Fig. 9).

Three SNPs detected for the TaSus2-2B locus formedtwo haplotypes (TTA and CCG), named as Hap-L andHap-H, respectively. The two haplotypes were significantlyassociated with TGW (Table 2), suggesting that TaSus2 wasinvolved in wheat grain development. In wheat, TaSus2 ispredominantly expressed in the endosperm (Maraña et al.1990). There is little knowledge on the specific functions ofthe TaSus2 gene set, but in maize, the SUS2 proteinencoded by the sucrose synthase1 locus, considered anortholog of TaSus2, is needed mainly for generatingprecursors for starch biosynthesis (Chourey et al. 1998).Because starch in the endosperm of wheat comprises 65%to 85% of the final dry weight of the grain (Housley et al.1981; Dale and Housley 1986; Hurkman et al. 2003), wheatendosperm must contribute significantly to kernel yieldbecause of its function as a storage tissue. Previous research

also showed that SUS contributes to differences in kernelweight (Dale and Housley 1986). Therefore, the differentialeffects of the two TaSus2-2B haplotypes on grain weightdetected in the present study might be caused by differentcontributions to starch biosynthesis and thence to endo-sperm development. Haplotype Hap-H had a significantpositive effect on thousand grain weight, and it might be abeneficial allele for improving grain yield.

TGW is an agriculturally important trait that continu-ously attracts the attention of breeders, and genes contrib-uting to high TGW could be targets for selection duringwheat improvement. The frequency of TaSus2-2B haplo-type Hap-H associated with high TGW has undergone anincreasing trend during the past 60 years of Chinese wheatbreeding (Fig. 7). Wheat breeding in China has progressedrapidly since 1950 and varieties have been replaced four tosix times resulting in an increased yield potential of about10% each time (He et al. 2001). Associated with theseincreases there has been an increase in TGW from less than30 to 42 g or more (He et al. 2001, Hao et al. 2006). Theincreasing frequency of Hap-H may reflect continuousselection for high TGW.

The different geographical distribution of Hap-H inChina is also supportive. Varieties bred in region IV usuallyhave larger spikes and bigger grain size, but fewer tillers to

Heilongjiang

ShandongShanxi

Hebei

Yunnan7(2)

Guizhou

Sichuan

Gansu

ShannxiHenan

AnhuiJiangsu

Beijing

Guangdong1(0)

Fujian2(3)

Jiangxi1(0)

Jilin2(1)

Hunan4(0)

Tibet4(0)

Ningxia4(0)

Qinghai5(2)

Zhejiang4(3)

Xinjiang2(7)

Hubei2(7)

Finland

Sweden

UnitedKingdom

Poland

Italy

SpainPortugal

RomaniaFrance

Germany

Austria

Switzerland

Czechoslovakia

Hungary

Belgium

Netherlands

Bulgaria

Yugoslavia

a b

Hap-H

Hap-L

Fig. 8 Distribution of haplotypes Hap-H and Hap-L in Europe (a) and China (b)

58 Funct Integr Genomics (2011) 11:49–61

Page 11

avoid the effects of canopy structures favoring epidemics ofrusts and powdery mildew. Region II has about 40% of thenational wheat area and accounts for 45% of total wheatproduction in China (He et al. 2001). The average TGW ofvarieties in this region is 42–43 g. In regions I and VI, bycontrast, there is need for low temperature tolerance duringthe winter, and varieties in these regions usually havestronger vernalization requirements and tillering capacities,but lower TGW. The frequency of Hap-H is about 30% inregions IV and II, but only 15% and 9% in regions I and VI.Provinces with a high frequency of Hap-H, such as Henan,Shannxi, and Jiangsu, tend to have more competitive andstronger wheat breeding programs than provinces withlower frequencies, such as Heilongjiang.

The results also indicate that distribution of Hap-H isrelated to latitude. Hap-H was most frequent in Gansu,Shannxi, Henan, Anhui, and Jiangsu provinces, which haverelatively low latitudes in comparison to Heilongjiangwhere the frequency of Hap-H was its lowest (5%). InEurope, much of which is at higher latitudes than China,most (87%) wheat cultivars were Hap-L. Because ofadaptation differences, many of the varieties from Europedid not mature normally when grown in Henan province.Hence it was not possible to obtain satisfactory data forTGW. Although the frequency of Hap-H was very low inEurope, it is interesting that it was present in Italianvarieties such as Funo, St2422/464 (Zhengyin 4), St1472/506 (Zhengyin 1) and Abbondanza which were introducedto China and became successful varieties and veryimportant parents in breeding programs (He et al. 2001;Jin et al. 1983; Zhang et al. 2002; Zhuang 2003).

There was no significant association between haplotypesand TGW in Chinese landraces in the mini-core collection(Table 2). A similar phenomenon occurred in rice wherehaplotype variation associated with enhanced grain lengthin O. sativa was not evident in a collection of wild rice(Oryza rufipogon) accessions having similar frequencies ofthe same haplotypes (Takano-Kai et al. 2009). It may bethat the high genetic diversity in landrace collections mightbuffer the contributions of smaller, but significant, effectsthat can be detected against less variable genetic back-grounds. Wright et al. (1999) considered that choice ofpopulations was critical for the detection of certain traits indiverse populations via association.

The Hap-H group of modern cultivars had weakerassociations with wider leaves, greater grain numbers perplant and shorter stature; all are positive effects likely to beassociated with higher yields. More importantly, QTLscontrolling grain yield and plant height were found not onlyin the chromosome region containing TaSus2-2Btgw, butalso in the collinear regions of TaSus2 on rice and maize.(Fig. 6, Supplementary Fig. 5, 6, 7). The ACAS-PCR-basedSNP marker (TaSus2-2Btgw) related most strongly to TGW

is agarose gel-based enabling rapid assaying of largenumbers of samples in simple, rapid and low costprocedures available in most molecular-biology and plantbreeding laboratories. As the frequency of Hap-H is stillrelatively low at less than 50% in Chinese current varieties,it could be used very effectively to further improve grainweight and yield potential. It may also provide significantbenefits in northern European countries where its frequencyis very low.

Acknowledgements We gratefully appreciate the help of Prof.Robert A McIntosh, University of Sydney, with English editing anddiscussion. Thanks were also given to the group of Prof. Tong YP andLi ZS, Institute of Genetics and Developmental Biology, CAS, fortheir help in mapping the haplotypes in their RIL population. Thankswere also given to Prof. Liu ZY and Yan JB, China AgriculturalUniversity; Mao L, Chinese Academy of Agricultural Sciences, fortheir help in comparative genetic analysis. This research wassupported by the Chinese Ministry of Science and Technology(2010CB125902), funding from Ministry of Agriculture(2008ZX08009) and Modern Agricultural Technical System.

References

Abler BSB, Edwards MD, Stuber CW (1991) Isoenzymatic identifi-cation of quantitative trait loci in crosses of elite maize inbreds.Crop Sci 31:267–274

Barratt DHP, Barber L, Kruger NJ, Smith AM, Wang TL, Martin C(2001) Multiple, distinct isoforms of sucrose synthase in pea.Plant Physiol 127:655–664

Baud S, Vaultier MN, Rochat C (2004) Structure and expressionprofile of the sucrose synthase multigene family in Arabidopsis. JExp Bot 55:397–409

Brondani C, Rangel N, Brondani V, Ferreira E (2002) QTL mappingand introgression of yield-related traits from Oryza glumaepatulato cultivated rice (Oryza sativa) using microsatellite markers.Theor Appl Genet 104:1192–1203

Carlson SJ, Chourey PS, Helentjaris T, Datta R (2002) Geneexpression studies on developing kernels of maize sucrosesynthase (SuSy) mutants show evidence for a third SuSy gene.Plant Mol Biol 49:15–29

Causse M, Rocher JP, Henry AM, Charcosset A, Prioul JL, de Vienne D(1995) Genetic dissection of the relationship between carbonmetabolism and early growth in maize, with emphasis on key-enzyme loci. Mol Breed 1:259–272

Chevalier P, Lingle SE (1983) Sugar metabolism in developingkernels of wheat and barley. Crop Sci 23:272–277

Chourey PS, Nelson OE (1976) The enzymatic deficiency conditionedby the shrunken-1 mutation in maize. Biochem Genet 14:1041–1055

Chourey PS, Taliercio EW, Carlson SJ, Ruan YL (1998) Geneticevidence that the two isozymes of sucrose synthase present indeveloping maize endosperm are critical, one for cell wallintegrity and the other for starch biosynthesis. Mol Gen Genet259:88–96

Dale EM, Housley TL (1986) Sucrose synthase activity in developingwheat endosperms differing in maximum weight. Plant Physiol82:7–10

Dong YS, Cao YS, Zhang XY, Liu SC, Wang LF, You GX, Pang BS,Li LH, Jia JZ (2003) Development of candidate core collections

Funct Integr Genomics (2011) 11:49–61 59

Page 12

in Chinese common wheat germplasm. J Plant Genet Res 4:1–8 (in Chinese)

Drenkard E, Richter BG, Rozen S, Stutius LM, Angell NA, MindrinosM, Cho RJ, Oegner PJ, Davis RW, Ausubel FM (2000) A simpleprocedure for the analysis of single nucleotide polymorphismsfacilitates map-based cloning in Arabidopsis. Plant Physiol124:1483–1492

Fallahi H, Scofield GN, Badger MR, Chow WS, Furbank RT, RuanYL (2008) Localization of sucrose synthase in developing seedand siliques of Arabidopsis thaliana reveals diverse roles forSUS during development. J Exp Bot 59:3283–3295

Flint-Garcia S, Jeffry M, Thornsberry ES, Buckler IV (2003) Structureof linkage disequilibrium in plants. Annu Rev Plant Biol 54:357–374

Guo ZA, Song YX, Zhou RH, Ren ZL, Jia JZ (2010) Discovery,evaluation and distribution of haplotypes of the wheat Ppd-D1gene. New Phytol 185:841–851

Haigler CH, Ivanova-Datcheva M, Hogan PS, Salnikov VV, Hwang S,Martin K, Delmer DP (2001) Carbon partitioning to cellulosesynthesis. Plant Mol Biol 47:29–51

Hao CY, Wang LF, Zhang XY, You GX, Dong YS, Jia JZ, Liu X,Shang XW, Liu SC, Cao YS (2006) Genetic diversity in Chinesemodern wheat varieties revealed by microsatellite markers. SciChina C Life Sci 49:218–226

Hao CY, Dong YS, Wang LF et al (2008) Genetic diversity andconstruction of core collection in Chinese wheat geneticresources. Chinese Sci Bull 53:1518–1526

Harada T, Satoh S, Yoshioka T, Ishizawa K (2005) Expression ofsucrose synthase genes involved in enhanced elongation ofpondweed (Potamogeton distinctus) turions under anoxia. AnnalsBot 96:683–692

Hayashi K, Hashimoto N, Daigen M, Ashikawa I (2004) Developmentof PCR-based SNP markers for rice blast resistance genes at thePiz locus. Theor Appl Genet 108:1212–1220

Hayashi K, Yoshida H, Ashikawa I (2006) Development of PCR-based allele-specific and InDel marker sets for nine rice blastresistance genes. Theor Appl Genet 113:251–260

He ZH, Rajaram S, Xin ZY, Huang GZ (eds) (2001) A history ofwheat breeding in China. CIMMYT, Mexico DF, Mexico

Hirose T, Scofield GN, Terao T (2008) An expression analysis profilefor the entire sucrose synthase gene family in rice. Plant Sci174:534–543

Horst I, Welham T, Kelly S, Kaneko T, Sato S, Tabata S, Parniske M,Wang TL (2007) TILLING mutants of Lotus japonicus revealthat nitrogen assimilation and fixation can occur in the absence ofnodule-enhanced sucrose synthase. Plant Physiol 144:806–820

Housley TL, Kirkeis AW, Ohm HW, Patterson FL (1981) Anevaluation of seed growth in soft red winter wheat. Can J PlantSci 61:525–534

Huang J, Chen J, Yu W, Shyur L, Wang A, Sung H, Lee P, Su JC(1996) Complete structures of three rice sucrose synthaseisogenes and differential regulation of their expressions. BiosciBiotechnol Biochem 60:233–239

Hurkman WJ, McCue KF, Altenbach SB, Korn A et al (2003) Effectof temperature on expression of genes encoding enzymes forstarch biosynthesis in developing wheat endosperm. Plant Sci164:873–881

Jin SB, Zhuang QS, Wu ZS, Huang PM, Bo YJ (1983) Chinese wheatvarieties and their genealogies. China Agricultural PublishingHouse, Beijing, China (in Chinese)

Kanazin D, Talbert VH, Blake T (2000) Electrophoretic detection ofsingle-nucleotide polymorphisms. Biotechniques 28:710–716

Kato T (1995) Change of sucrose synthase activity in developingendosperm of rice cultivars. Crop Sci 35:827–831

Kim MY, Van K, Lestari P, Moon JK, Lee SH (2005) SNPidentification and SNAP marker development for a GmNARK

gene controlling supernodulation in soybean. Theor Appl Genet110:1003–1010

King SP, Lunn JE, Furbank RT (1997) Carbohydrate content andenzyme metabolism in developing canola siliques. Plant Physiol114:153–160

Kumar R, Singh R (1980) The relationship of starch metabolism tograin size in wheat. Phytochemistry 19:2299–2303

Lander ES, Botstein D (1989) Mapping Mendelian factors underlyingquantitative traits using RFLP linkage maps. Genetics 21:185–199

Maraña C, García-Olmedo F, Carbonero P (1990) Differentialexpression of two types of sucrose synthase-encoding genes inwheat in response to anaerobiosis, cold shock and light. Gene88:167–172

Maraña C, Garcla-Olmedo F, Carbonero P (1988) Linked sucrosesynthase genes in group-7 chromosomes in hexaploid wheat(Triticum aestivum L.). Gene 63:253–260

Martinez de Ilarduya O, Vicente-Carbajosa J, Sanchez de la Hoz P,Carbonero P (1993) Sucrose synthase genes in barley. cDNAcloning of the Ss2 type and tissue-specific expression of Ss1 andSs2. FEBS Lett 320:177–181

Melchinger AE, Utz HF, Schon CC (1998) Quantitative trait locus(QTL) mapping using different testers and independent popu-lation samples in maize reveals low power of QTL detectionand large bias in estimates of QTL effects. Genetics 149:383–403

Nolte KD, Koch KE (1993) Companion-cell specific localization ofsucrose synthase in zones of phloem loading and unloading.Plant Physiol 101:899–905

Pritchard JK (2001) Deconstructing maize population structure. NatGenet 28:203–204

Rouhier H, Usuda H (2001) Spatial and temporal distribution ofsucrose synthase in the radish hypocotyl in relation to thickeninggrowth. Plant Cell Physiol 42:583–593

Ruan YL, Chourey PS (1998) A fiberless seed mutation in cotton isassociated with lack of fiber cell initiation in ovule epidermis andalterations in sucrose synthase expression and carbon partitioningin developing seeds. Plant Physiol 118:399–406

Ruan YL, Llewellyn DJ, Furbank RT (2003) Suppression of sucrosesynthase gene expression represses cotton fiber cell initiation,elongation, and seed development. Plant Cell 15:952–964

Sánchez de la Hoz P, Vicente-Carbajosa J, Mena M, Carbonero P(1992) Homologous sucrose synthase genes in barley (Hordeumvulgare) are located in chromosomes 7H (syn.1) and 2H.Evidence for a gene translocation? FEBS Lett 310:46–50

Sharp PJ, Kreis M, Shewry PR, Gale MD (1988) Location ofb-amylase sequence in wheat and its relatives. Theor Appl Genet75:289–290

Shaw JR, Ferl RJ, Baier J, St Clair D, Carson C, McCarty DR,Hannah LC (1994) Structural features of the maize susl gene andprotein. Plant Physiol 106:1659–1665

Shin JH, Kwon SJ, Lee JK, Min HK, Kim NS (2006) Geneticdiversity of maize kernel starch-synthesis genes with SNAPs.Genome 49:1287–1296

Sommer SS, Groszbar AR, Bottema CDK (1992) PCR amplificationof specific alleles (PASA) is a general method for rapidlydetecting known single base-pair changes. Biotechniques12:82–87

Sourdille P, Singh S, Cadalen T, Brown-Guedira GL, Gay G, Qi L,Gill BS, Dufour P, Murigneux A, Bernard M (2004)Microsatellite-based deletion bin system for the establishmentof genetic-physical map relationships in wheat (Triticum aesti-vum L.). Funct Integr Genomics 4:12–25

Sun J, Loboda T, Sung SJS, CCJr B (1992) Sucrose synthase in wildtomato, Lycopersicon chmielewskii, and tomato fruit sinkstrength. Plant Physiol 98:1163–1169

60 Funct Integr Genomics (2011) 11:49–61

Page 13

Takano-Kai N, Jiang H, Kubo T, Sweeney M, Matsumoto T,Kanamori H, Padhukasahasram B, Bustamante C, YoshimuraA, Doi K, McCouch S (2009) Evolutionary history of GS3, agene conferring grain length in rice. Genetics 182:1323–1334

Tang GQ, Sturm A (1999) Antisense repression of sucrose synthase incarrot (Daucus carota L.) affects growth rather than sucrosepartitioning. Plant Mol Biol 41:465–479

Van Bel AJE, Knoblauch M (2000) Sieve element and companioncell: the story of the comatose patient and the hyperactive nurse.Funct Plant Biol 27:477–487

Wang AY, Yu WP, Juang RH, Huang JW, Sung HY, Su JC (1992)Presence of three rice sucrose synthase genes as revealed bycloning and sequencing of cDNA. Plant Mol Biol 18:1191–1194

Wei B, Jing RL, Wang CS, Jb C, Mao XG, Chang XP, Jia JZ (2009)Dreb1 genes in wheat (Triticum aestivum L.): development offunctional markers and gene mapping based on SNPs. Mol Breed23:13–22

Wright AF, Carothers AD, Pirastu M (1999) Population choice inmapping genes for complex diseases. Nat Genet 23:397–404

Yuan CP, Li YH, Liu ZX, Guan RX, Chang RZ, Qiu LJ (2007) Amethod of SNP genotyping in soybean. Soybean Sci 26:447–459

Zhang XY, Li CW, Wang LF, Wang HM, You GX, Dong YS (2002)An estimation of the minimum number of SSR alleles needed toreveal genetic relationships in wheat varieties. I. Informationfrom large-scale planted varieties and cornerstone breedingparents in Chinese wheat improvement and production. TheorAppl Genet 106:112–117

Zanetti S, Winzeler M, Feuillet C, Keller B, Messmer M (2001)Genetic analysis of bread-making quality in wheat and spelt.Plant Breed 120:13–19

Zhuang QS (2003) Chinese wheat improvement and pedigree analysis.China Agricultural Publishing House, Beijing, China (in Chinese)

Zrenner R, Salanoubat M, Willmitzer L, Sonnewald U (1995) Evidenceof the crucial role of sucrose synthase for sink strength usingtransgenic potato plants (Solanum tuberosum L.). Plant J 7:97–107

Funct Integr Genomics (2011) 11:49–61 61