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

Ravel, C.; Faye, Annie; Ben-Sadoun, Sarah; Ranoux, Marion; Dardevet, Mireille; Dupuits, Cécile; Exbrayat, Florence; Poncet, Charles; Sourdille, Pierre; Branlard, Gérard

doi:10.1007/s00122-019-03505-y

Cited by 29 publications

(34 citation statements)

References 59 publications

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“…Besides, the reported molecular markers were useful for high-throughput HMW-GS identification, and KASP assay makers for HMW-GS identification were recently developed for rapid genotyping [33,35]. However, it still requires independent experiments for each HMW-GS.…”

Section: Discussionmentioning

confidence: 99%

“…Interestingly, the protein weight of HMW-GS on Lab-on-a-chip was shown to be higher than that observed on SDS-PAGE, and the electrophoresis pattern of HMW-GS on Lab-on-a-chip was different from SDS-PAGE. Useful molecular markers, such as Kompetitive Allele-Specific PCR (KASP) and single-nucleotide polymorphism (SNP) markers, were developed to identify the allelic variation for the Glu-1 loci [32,33]. These molecular markers are useful for the high-throughput identification of allelic variations of genetic resources and the screening of breeding lines for quality improvement [33].…”

Section: Introductionmentioning

confidence: 99%

“…Useful molecular markers, such as Kompetitive Allele-Specific PCR (KASP) and single-nucleotide polymorphism (SNP) markers, were developed to identify the allelic variation for the Glu-1 loci [32,33]. These molecular markers are useful for the high-throughput identification of allelic variations of genetic resources and the screening of breeding lines for quality improvement [33]. However, they do not have the ability to examine all allelic variations at the same time.…”

Section: Introductionmentioning

confidence: 99%

“…However, they do not have the ability to examine all allelic variations at the same time. Therefore, owing to the above, there is a sustaining need for the development of allelic specific markers for HMW-GS identification [33].…”

Section: Introductionmentioning

confidence: 99%

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Rapid and Easy High-Molecular-Weight Glutenin Subunit Identification System by Lab-on-a-Chip in Wheat (Triticum aestivum L.)

Shin

Cha

Lee

et al. 2020

Plants

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Lab-on-a-chip technology is an emerging and convenient system to easily and quickly separate proteins of high molecular weight. The current study established a high-molecular-weight glutenin subunit (HMW-GS) identification system using Lab-on-a-chip for three, six, and three of the allelic variations at the Glu-A1, Glu-B1, and Glu-D1 loci, respectively, which are commonly used in wheat breeding programs. The molecular weight of 1Ax1 and 1Ax2* encoded by Glu-A1 locus were of 200 kDa and 192 kDa and positioned below 1Dx subunits. The HMW-GS encoded by Glu-B1 locus were electrophoresed in the following order below 1Ax1 and 1Ax2*: 1Bx13 ≥ 1Bx7 = 1Bx7OE > 1Bx17 > 1By16 > 1By8 = 1By18 > 1By9. 1Dx2 and Dx5 showed around 4-kDa difference in their molecular weights, with 1Dy10 and 1Dy12 having 11-kDa difference, and were clearly differentiated on Lab-on-a-chip. Additionally, some of the HMW-GS, including 1By8, 1By18, and 1Dy10, having different theoretical molecular weights showed similar electrophoretic mobility patterns on Lab-on-a-chip. The relative protein amount of 1Bx7OE was two-fold higher than that of 1Bx7 or 1Dx5 and, therefore, translated a significant increase in the protein amount in 1Bx7OE. Similarly, the relative protein amounts of 8 & 10 and 10 & 18 were higher than each subunit taken alone. Therefore, this study suggests the established HMW-GS identification system using Lab-on-a-chip as a reliable approach for evaluating HMW-GS for wheat breeding programs.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Rapid and Easy High-Molecular-Weight Glutenin Subunit Identification System by Lab-on-a-Chip in Wheat (Triticum aestivum L.)

Shin

Cha

Lee

et al. 2020

Plants

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show abstract

“…Thus, using the currently available KASP assays alone will not provide the full composition of alleles, but KASP are ideal to be used in MAS when certain allele combinations are to be selected. Attempts to develop markers for other Glu-B1, Glu-D1 and Glu-D3 alleles are ongoing [26]. At CIMMYT with a very well-established wheat quality laboratory the designed KASP assays presented in this study are currently used to verify uncertain SDS-PAGE results during the evaluation of advanced breeding lines in preliminary yield trails.…”

Section: Plos Onementioning

confidence: 99%

SNP markers for low molecular glutenin subunits (LMW-GSs) at the Glu-A3 and Glu-B3 loci in bread wheat

et al. 2020

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The content and composition of seed storage proteins is largely responsible for wheat enduse quality. They mainly consist of polymeric glutenins and monomeric gliadins. According to their electrophoretic mobility, gliadins and glutenins are subdivided into several fractions. Glutenins are classified as high molecular weight or low molecular weight glutenin subunits (HMW-GSs and LMW-GSs, respectively). LMW-GSs are encoded by multigene families located at the orthologous Glu-3 loci. We designed a set of 16 single-nucleotide polymorphism (SNP) markers that are able to detect SDS-PAGE alleles at the Glu-A3 and Glu-B3 loci. The SNP markers captured the diversity of alleles in 88 international reference lines and 27 Mexican cultivars, when compared to SDS-PAGE and STS markers, however, showed a slightly larger percent of multiple alleles, mainly for Glu-B3. SNP markers were then used to determine the Glu-1 and Glu-3 allele composition in 54 CIMMYT historical lines and demonstrated to be useful tool for breeding programs to improve wheat end product properties.

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STAC: A tool to leverage genetic marker data for crop research and breeding

Carle,

Kiszonas,

Garland‐Campbell

et al. 2023

Agrosystems Geosci & Env

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As genotyping by sequencing (GBS) becomes more prevalent and cost‐effective, there is a benefit in being able to apply the data to solve a variety of problems. However, high degrees of missing data and overreliance on single nucleotide polymorphisms (SNPs), while ignoring other forms of genetic variation, frequently plague attempts to make full use of GBS sequence data. Here we have developed two R scripts to serve as a tool in haplotype determination at loci of interest within biparental populations. One of these scripts, Sparse Tag Allele Caller (STAC), provides both automated calling and visual representations of the data around a locus of interest to assist in rapid data compilation decision‐making. The other script, STAC Integrate, allows automated quality control and logic‐based integration of presence/absence data with SNP data, while also rendering global overviews of recombination and coverage across the genome. These scripts are designed to be used together to maximize the utility of the available data. These tools were validated on a biparental population of wheat that was genotyped through GBS. They successfully enabled haplotype determination of a locus that was difficult to directly genotype, and their systemic accuracy was demonstrated in multiple populations and species. These scripts may serve as a tool for researchers attempting to make better use of GBS and other genetic marker data for both research and crop breeding decisions.

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

Cited by 29 publications

References 59 publications

Rapid and Easy High-Molecular-Weight Glutenin Subunit Identification System by Lab-on-a-Chip in Wheat (Triticum aestivum L.)

Rapid and Easy High-Molecular-Weight Glutenin Subunit Identification System by Lab-on-a-Chip in Wheat (Triticum aestivum L.)

SNP markers for low molecular glutenin subunits (LMW-GSs) at the Glu-A3 and Glu-B3 loci in bread wheat

STAC: A tool to leverage genetic marker data for crop research and breeding

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