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SNP markers for early identification of high molecular weight glutenin subunits (HMW-GSs) in bread wheat

Key message

A set of eight SNP markers was developed to facilitate the early selection of HMW-GS alleles in breeding programmes.

Abstract

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.

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Abbreviations

Bx7OE:

Overexpressed Bx7 allele

HMW-GS:

High molecular weight glutenin subunit

KASP:

Kompetitive allele-specific PCR

LMW-GS:

Low molecular weight glutenin subunit

SDS-PAGE:

Sodium dodecyl sulphate–polyacrylamide gel electrophoresis

SNP:

Single-nucleotide polymorphism

SSP:

Seed storage proteins

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Acknowledgements

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).

Author information

CR, PS and GB designed the experiment. CR analysed the sequences and designed the primers for SNP genotyping. AF extracted grain proteins and performed electrophoresis (SDS-PAGE). FE carried out DNA extraction. MR, MD, CD and FE genotyped the SNPs. CP supervised SNP genotyping. CR and SBS analysed the data. CR wrote the manuscript. All authors commented on the manuscript.

Correspondence to Catherine Ravel.

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Communicated by Aimin Zhang.

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Supplementary material 2 (PDF 595 kb)

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)

Fig. S2. Alignment of CDS at Glu-A1-1. This is a bioedit file with tags. Start and stop codons are indicated in yellow. SNPs chosen for typing HMW-GS are in red. SNPs in the repetitive domains are in grey (BIO 10 kb)

Fig. S3. Alignment of the region upstream of the start codon for Glu-D1-1. This is a bioedit file with tags. Start codons, the chosen SNPs and remaining SNPs are indicated in yellow, red and grey, respectively (BIO 5 kb)

Fig. S4. Alignment of the promoter region and CDS for Glu-D1-2. This is a bioedit file with tags. Start and stop codons, the chosen SNP and the remaining SNPs are indicated in yellow, red and grey, respectively (BIO 6 kb)

Fig. S5. Alignment of the promoter region and CDS for Glu-B1-1. This is a bioedit file with tags. Start and stop codons, the chosen SNP and the remaining SNPs are indicated in yellow, red and grey, respectively (BIO 60 kb)

Fig. S6. Alignment of the promoter region, CDS and UTRs for Glu-B1-2. This is a bioedit file with tags. Start and stop codons are indicated in yellow, while the chosen SNPs are indicated in red (BIO 66 kb)

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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

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