A set of eight SNP markers was developed to facilitate the early selection of HMW-GS alleles in breeding programmes.
In bread wheat (Triticum aestivum), the high molecular weight glutenin subunits (HMW-GSs) are the most important determinants of technological quality. Known to be very diverse, HMW-GSs are encoded by the tightly linked genes Glu-1-1 and Glu-1-2. Alleles that improve the quality of dough have been identified. Up to now, sodium dodecyl sulphate–polyacrylamide gel electrophoresis (SDS-PAGE) of grain proteins is the most widely used for their identification. To facilitate the early selection of HMW-GS alleles in breeding programmes, we developed DNA-based molecular markers. For each accession of a core collection (n = 364 lines) representative of worldwide bread wheat diversity, HMW-GSs were characterized by both genotyping and SDS-PAGE. Based on electrophoresis, we observed at least 8, 22 and 9 different alleles at the Glu-A1, Glu-B1 and Glu-D1 loci, respectively, including new variants. We designed a set of 17 single-nucleotide polymorphism (SNP) markers that were representative of the most frequent SDS-PAGE alleles at each locus. At Glu-A1 and Glu-D1, two and three marker-based haplotypes, respectively, captured the diversity of the SDS-PAGE alleles rather well. Discrepancies were found mainly for the Glu-B1 locus. However, statistical tests revealed that two markers at each Glu-B1 gene and their corresponding haplotypes were more significantly associated with the rheological properties of the dough than were the relevant SDS-PAGE alleles. To conclude, this study demonstrates that the SNP markers developed provide additional information on HMW-GS diversity. Two markers at Glu-A1, four at Glu-B1 and two at Glu-D1 constitute a useful toolbox for breeding wheat to improve end-use value.
This is a preview of subscription content, log in to check access.
Buy single article
Instant access to the full article PDF.
Price includes VAT for USA
Subscribe to journal
Immediate online access to all issues from 2019. Subscription will auto renew annually.
This is the net price. Taxes to be calculated in checkout.
Overexpressed Bx7 allele
High molecular weight glutenin subunit
Kompetitive allele-specific PCR
Low molecular weight glutenin subunit
Sodium dodecyl sulphate–polyacrylamide gel electrophoresis
Seed storage proteins
Akhunov E, Nicolet C, Dvorak J (2009) Single nucleotide polymorphism genotyping in polyploid wheat with the Illumina GoldenGate assay. Theor Appl Genet 119:507–517. https://doi.org/10.1007/s00122-009-1059-5
Allen AM, Barker GL, Berry ST et al (2011) Transcript-specific, single-nucleotide polymorphism discovery and linkage analysis in hexaploid bread wheat (Triticum aestivum L.). Plant Biotechnol J 9:1086–1099. https://doi.org/10.1111/j.1467-7652.2011.00628.x
Balfourier F, Roussel V, Strelchenko P, Exbrayat-Vinson F, Sourdille P, Boutet G, Koenig J, Ravel C, Mitrofanova O, Beckert M, Charmet G (2007) A worldwide bread wheat core collection arrayed in a 384-well plate. Theor Appl Genet 114:1265–1275. https://doi.org/10.1007/s00122-007-0517-1
Bemborm O (2016) seqLogo: sequence logos for DNA sequence alignments. R package version 1.40.0
Bérard A, Le Paslier MC, Dardevet M, Exbrayat-Vinson F, Bonnin I, Cenci A, Haudry A, Brunel D, Ravel C (2009) High-throughput single nucleotide polymorphism genotyping in wheat (Triticum spp.). Plant Biotechnol J 7:364–374. https://doi.org/10.1111/j.1467-7652.2009.00404.x
Bordes J, Branlard G, Oury FX, Charmet G, Balfourier F (2008) Agronomic characteristics, grain quality and flour rheology of 372 bread wheats in a worldwide core collection. J Cereal Sci 48:569–579
Branlard G, Dardevet M (1985) Diversity of grain protein and bread wheat quality. 2. Correlation between high molecular-weight subunits of glutenin and flour quality characteristics. J Cereal Sci 3:345–354
Branlard G, Dardevet M, Saccomano R, Lagoutte F, Gourdon J (2001) Genetic diversity of wheat storage proteins and bread wheat quality. Euphytica 119:59–67
Bustos AD, Rubio P, Jouve N (2000) Molecular characterization of the inactive allele of the gene Glu-A1 and the development of a set of AS-PCR markers for HMW glutenins of wheat. Theor Appl Genet 100:1085–1094
Choulet F, Alberti A, Theil S, Glover NM, Barbe V, Daron J et al (2014) Structural and functional partitioning of bread wheat chromosome 3B. Science 345(6194):1249721. https://doi.org/10.1126/science.1249721
D’Ovidio R, Masci S, Porceddu E (1996) Sequence analysis of the 5′ non-coding regions of active and inactive 1Ay HMW glutenin genes from wild and cultivated wheats. Plant Sci 14:61–69
Eagles HA, Cane K, Eastwood RF, Hollamby GJ, Kuchel H, Martin PJ, Cornish GB (2006) Contributions of glutenin and puroindoline genes to grain quality traits in southern Australian wheat breeding programs. Aust J Agric Res 57:179–186
Flint-Garcia SH, Thornsberry JM, Buckler ES IV (2003) Structure of linkage disequilibrium in plants. Annu Rev Plant Biol 54:357–374. https://doi.org/10.1146/annurev.arplant.54.031902.134907
Forde J, Malpica J-M, Halford NG, Shewry PR, Anderson OD, Greene FC, Miflin BJ (1985) The nucleotide sequence of a HMW glutenin subunit gene located on chromosome 1A of wheat (Triticum aestivum L.). Nucleic Acids Res 13:6817–6832
Gale K (2005) Diagnostic DNA markers for quality traits in wheat. J Cereal Sci 41:181–192. https://doi.org/10.1016/j.jcs.2004.09.002
Gao LF, Jia JZ, Kong XY (2016) A SNP-based molecular barcode for characterization of common wheat. PLoS ONE 11:e0150947. https://doi.org/10.1371/journal.pone.0150947
Glover NM, Daron J, Pingault L, Vandepoele K, Paux E, Feuillet C, Choulet F (2015) Small-scale gene duplications played a major role in the recent evolution of wheat chromosome 3B. Genome Biol 16:188. https://doi.org/10.1186/s13059-015-0754-6
Gobaa S, Kleijer G, Stamp P (2007) 2··, a new high molecular weight glutenin subunit coded by Glu-A1: its predicted structure and its impact on bread-making quality. Plant Breed 126:1–4. https://doi.org/10.1111/j.1439-0523.2006.01313.x
Harberd NP, Flavell RB, Thompson RD (1987) Identification of a transposon like insertion in a Glu-1 allele of wheat. Mol Gen Genet 209:326–332
Horvath A, Didier A, Koenig J, Exbrayat F, Charmet G, Balfourier F (2009) Analysis of diversity and linkage disequilibrium along chromosome 3B of bread wheat (Triticum aestivum L.). Theor Appl Genet 119:1523–1537. https://doi.org/10.1007/s00122-009-1153-8
Iba MI, Kiszonas A, Morris CF (2018) Development of haplotype-specific molecular markers for the low-molecular-weight glutenin subunits. Mol Breed 38:68. https://doi.org/10.1007/s11032-018-0827-9
Janni M, Cadonici S, Pignone D, Marmiroli N (2017) Survey and new insights in the application of PCR-based molecular markers for identification of HMW-GS at the Glu-B1 locus in durum and bread wheat. Plant Breed. https://doi.org/10.1111/pbr.12506
Jin H, Yan J, Peña RJ, Xia XC, Morgounov A, Han LM, Zhang Y, He ZH (2011) Molecular detection of high- and low-molecular-weight glutenin subunit genes in common wheat cultivars from 20 countries using allele-specific markers. Crop Pasture Sci 62:746–754. https://doi.org/10.1071/CP11134
Larkin M, Blackshields G, Brown N, Chenna R, McGettigan P, McWilliam H, Valentin F, Wallace I, Wilm A, Lopez R, Thompson J, Gibson T, Higgins D (2007) Clustal W and clustal X version 2.0. Bioinformatics 23:2947–2948. https://doi.org/10.1093/bioinformatics/btm404
Lei ZS, Gale MR, He ZH, Gianibelli C, Larroque O, Xia XC, Butow BJ, Ma W (2006) Y-type gene specific markers for enhanced discrimination of high-molecular weight glutenin alleles at the Glu-B1 locus in hexaploid wheat. J Cereal Sci 43:94–101. https://doi.org/10.1016/j.jcs.2005.08.003
Liu SX, Chao S, Anderson J (2008) New DNA markers for high molecular weight glutenin subunits in wheat. Theor Appl Genet 118:177–183. https://doi.org/10.1007/s00122-008-0886-0
Liu L, Ikeda TM, Branlard G, Pena RJ, Rogers WJ, Lerner SE, Kolman MA, Xia X, Wang L, Ma W, Appels R, Yoshida H, Wang A, Yan Y, He Z (2010) Comparison of low molecular weight glutenin subunits identified by SDS-PAGE, 2-DE, MALDI-TOF-MS and PCR in common wheat. BMC Plant Biol 10:124. https://doi.org/10.1186/1471-2229-10-124
Liu Y, He Z, Appels R, Xia X (2012) Functional markers in wheat: current status and future prospects. Theor Appl Genet 125:1–10. https://doi.org/10.1007/s00122-012-1829-3
MacRitchie F (1999) Wheat proteins: characterization and role in flour functionality. Cereal Foods World 44(4):188–193
Marchylo BA, Lukow OM, Kruger JE (1992) Quantitative variation in high molecular weight glutenin subunit 7 in some Canadian wheats. J Cereal Sci 15:29–37
Margiotta B, Urbano M, Colaprico G (1996) Detection of y-type subunit at the Glu-A1 locus in some Swedish bread wheat lines. J Cereal Sci 23:203–211
McIntosh R, Dubcovsky J, Rogers J, Morris C, Appels R, Xia XC (2013) Catalogue of gene symbols for wheat. In: 12th International wheat genetics symposium, Yokohama, Japan
Neelam K, Brown-Guedira G, Huang L (2013) Development and validation of a breeder-friendly KASPar marker for wheat leaf rust resistance locus Lr2. Mol Breed 13:233–237. https://doi.org/10.1007/s11032-012-9773-0
Paux E, Sourdille P, Mackay I, Feuillet C (2011) Sequence-based maker development in wheat: advances and applications to breeding. Biotechnol Adv 30:1071–1088. https://doi.org/10.1016/j.biotechadv.2011.09.015
Payne PI, Lawrence GJ (1983) Catalogue of alleles for the complex gene loci, Glu-A1, Glu-B1, and Glu-D1 which code for high molecular-weight subunits of glutenin in hexaploid wheat. Cereal Res Commun 11:29–35
Payne PI, Corfield KG, Blackman JA (1979) Identification of a high-molecular-weight subunit of glutenin whose presence correlates with bread-making quality in wheats of related pedigree. Theor Appl Genet 55:153–159
Payne PI, Nightingale MA, Krattiger AF, Holt LM (1987) The relationship between HMW glutenin subunit composition and the bread-making quality of British-grown wheat varieties. J Sci Food Agric 40(1):51–65
Pirozi M, Margiotta B, Latiandra D, MacRitchie F (2008) Composition of polymeric proteins and bread-making quality of wheat lines with allelic HMW-GS differing in number of cysteines. J Cereal Sci 48:117–122
R Core Team (2016) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna
Ragupathy R, Naeem HA, Reimer E, Lukow OM, Sapirstein HD, Cloutier S (2008) Evolutionary origin of the segmental duplication encompassing the wheat GLU-B1 locus encoding the overexpressed Bx7 (Bx7OE) high molecular weight glutenin subunit. Theor Appl Genet 116:283–296. https://doi.org/10.1007/s00122-007-0666-2
Rasheed A, Xia X, Yan Y, Appels R, Mahmood T, He Z (2014) Wheat seed storage proteins: advances in molecular genetics, diversity and breeding applications. J Cereal Sci 60:11–24. https://doi.org/10.1016/j.jcs.2014.01.020
Ravel C, Praud S, Murigneux A, Canaguier A, Sapet F, Samson D, Balfourier F, Dufour P, Chalhoub B, Brunel D, Beckert M, Charmet G (2006) Single-nucleotide polymorphism frequency in a set of selected lines of bread wheat (Triticum aestivum L.). Genome 49:1131–1139. https://doi.org/10.1139/g06-067
Ravel C, Fiquet S, Boudet J, Dardevet M, Vincent J, Merlino M, Michard R, Martre P (2014) Conserved cis-regulatory modules in promoters of genes encoding wheat high-molecular-weight glutenin subunits. Front Plant Sci 5:621. https://doi.org/10.3389/fpls.2014.00621
Ribeiro M, Bancel E, Faye A, Dardevet M, Grand Ravel C, Branlard G, Igrejas G (2013) Proteogenomic characterization of novel x-type high molecular weight glutenin subunit 1Ax1.1. Int J Mol Sci 14(3):5650–5667. https://doi.org/10.3390/ijms14035650
Rimbert H, Darrier B, Navarro J, Kitt J, Choulet F, Leveugle M et al (2017) High throughput SNP discovery and genotyping in hexaploid wheat. PLoS ONE 13(1):e0186329. https://doi.org/10.1371/journal.pone.0186329
Sapone A, Bai JC, Ciacci C, Dolinsek J, Green PHR, Hadjivassiliou M, Kaukinen K, Rostami K, Sanders DS, Schumann M, Ullrich R, Villalta D, Volta U, Catassi C, Fasano A (2012) Spectrum of gluten-related disorders: consensus on new nomenclature and classification. BMC Med 10:13. https://doi.org/10.1186/1741-7015-10-13
Schwarz G, Sift A, Wenzel G, Mohler V (2003) DHPLC scoring of a SNP between promoter sequences of HMW glutenin x-type alleles at the Glu-D1 locus in wheat. J Agr Food Chem 51:4263–4267. https://doi.org/10.1021/jf0261304
Semagn K, Babu R, Hearne S, Olsen M (2014) Single nucleotide polymorphism genotyping using Kompetitive Allele Specific PCR (KASP): overview of the technology and its application in crop improvement. Mol Breed 33:1–14. https://doi.org/10.1007/s11032-013-9917-x
Shewry PR (2009) Wheat. J Exp Bot 60:1537–1553. https://doi.org/10.1093/jxb/erp058
Shewry PR, Hey S (2015) The contribution of wheat to human diet and health. Food Energy Secur 4:178–202. https://doi.org/10.1002/fes3.64
Shewry P, Halford N, Tatham A (1992) High-molecular-weight subunits of wheat glutenin. J Cereal Sci 15:105–120
Shewry PR, Popineau Y, Lafiandra D, Belton P (2001) Wheat glutenin subunits and dough elasticity: findings of the EUROWHEAT project. Trends Food Sci Technol 11:433–441. https://doi.org/10.1016/S0924-2244(01)00035-8
Shewry PR, Halford NG, Belton PS, Tatham AS (2002) The structure and properties of gluten: an elastic protein from wheat grain. Philos Trans R Soc Lond B Biol Sci 357:133–142. https://doi.org/10.1098/rstb.2001.1024
Shoen DJ, Brown AH (1993) Conservation of allelic richness in wild crop relatives is aided by assessment of genetic markers. Proc Natl Acad Sci U S A 90:10623–10627. https://doi.org/10.1073/pnas.90.22.10623
Singh N, Shepherd K, Cornish G (1991) A simplified SDS-PAGE procedure for separating LMW subunits of glutenin. J Cereal Sci 14:203–208
Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, Rozen SG (2012) Primer3—new capabilities and interfaces. Nucl Acids Res 40(15):e115. https://doi.org/10.1093/nar/gks596
Wang LH, Zhao XL, He ZH, Ma W, Appels R, Pena RJ, Xia XC (2009) Characterization of low-molecular-weight-glutenin sub-unit Glu-B3 genes and development of STS markers in common wheat (Triticum aestivum L.). Theor Appl Genet 118:525–539. https://doi.org/10.1007/s00122-008-0918-9
Wang LH, Li GY, Pena RJ, Xia XC, He ZH (2010) Development of STS markers and establishment of multiplex PCR for Glu-A3 alleles in common wheat (Triticum aestivum L.). J Cereal Sci 51:305–312. https://doi.org/10.1016/j.jcs.2010.01.005
Wang S, Wong D, Forrest K et al (2014) Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array. Plant Biotechnol J 12:787–796. https://doi.org/10.1111/pbi.12183
Xu Q, Xu J, Liu C, Chang C, Wang C, You M, Li B, Liu G (2008) PCR-based markers for identification of HMW-GS at Glu-B1x loci in common wheat. J Cereal Sci 47:394–398. https://doi.org/10.1016/j.jcs.2007.05.002
Zhang W, Gianibelli MC, Rampling LR, Gale KR (2004) Characterization and marker development for low molecular weight glutenin genes from Glu-A3 alleles of bread wheat (Triticum aestivum L). Theor Appl Genet 108:1409–1419. https://doi.org/10.1007/s00122-003-1558-8
Zhang X, Liu D, Yang W, Liu K, Sun J, Guo X, Li Y, Wang D, Ling H, Zhang A (2011) Development of a new marker system for identifying the complex members of the low-molecular-weight glutenin subunit gene family in bread wheat (Triticum aestivum L.). Theor Appl Genet 122:1503–1516. https://doi.org/10.1007/s00122-011-1550-7
The authors thank François Balfourier and Jacques Bordes for providing all the accessions of the INRA core collection and alveographic data, as well as Rachel Carol from Emendo Bioscience for English corrections. The genotyping project was conducted on the genotyping platform GENTYANE at INRA Clermont-Ferrand (gentyane.clermont.inra.fr).
Conflict of interest
On behalf of all authors, the corresponding author states that there is no conflict of interest.
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Communicated by Aimin Zhang.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Fig S1. Alignment of one sequence per Glu-1 gene. This is a bioedit file with tags. Start and stop codons are indicated in yellow. The putative TSS (transcription start site) is in blue. Grey shading indicates the repetitive domain. This domain was not used for designing primers, so alignment in this region was not manually improved (BIO 28 kb)
About this article
Cite this article
Ravel, C., Faye, A., Ben-Sadoun, S. et al. SNP markers for early identification of high molecular weight glutenin subunits (HMW-GSs) in bread wheat. Theor Appl Genet 133, 751–770 (2020). https://doi.org/10.1007/s00122-019-03505-y