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Development of haplotype-specific molecular markers for the low-molecular-weight glutenin subunits

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Abstract

Low-molecular-weight glutenin subunits (LMW-GSs) are one of the major components of gluten, and their allelic variation has been widely associated with different wheat end-use quality parameters. These proteins are encoded by multigene families located at the orthologous Glu-3 loci (Glu-A3, Glu-B3, and Glu-D3); the genes at each locus are divided by large intergenic and highly recombinogenic regions. Among the methods used for the LMW-GS allele identification, polymerase chain reaction (PCR)-based molecular markers have the advantages of being simple, accurate, and independent from the plant stage of development. However, the available LMW-GS molecular markers are either incapable of capturing the complexity of the LMW-GS gene family or difficult to interpret. In the present study, we report the development of a set of PCR-based molecular markers specific for the LMW-GS haplotypes present at each Glu-3 locus. Based on the LMW-GS gene sequences available in GenBank, single nucleotide polymorphisms (SNPs) specific for each Glu-3 haplotype were identified and the relevant PCR primers were designed. In total, we developed three molecular markers for the Glu-A3 and Glu-B3 loci, respectively, and five molecular markers for the Glu-D3 locus. The markers were tested on 44 bread wheat varieties previously characterized for their LMW-GS genic profile and found to be equally or more efficient than previously developed LMW-GS PCR-based markers. This set of markers allows an easier and less ambiguous identification of specific LMW-GS haplotypes associated with gluten strength and can facilitate marker-assisted breeding for wheat quality.

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Acknowledgments

The authors thank Dr. Derick Jiwan for constructive suggestions on this work. Stacey Sykes and Shawna Vogl assisted in the preparation and submission of the manuscript.

Funding

This research was supported in part by NIFA AFRI Grant No. 2013-67013-21226 and CRIS Project 2090-43440-007-00-D.

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Authors and Affiliations

  1. Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA

    Maria I. Ibba

  2. USDA-ARS Western Wheat Quality Laboratory, Pullman, WA, USA

    Alecia M. Kiszonas & Craig F. Morris

Authors
  1. Maria I. Ibba
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  2. Alecia M. Kiszonas
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  3. Craig F. Morris
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Corresponding author

Correspondence to Craig F. Morris.

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Mention of trademark or proprietary products does not constitute a guarantee or warranty of a product by the US Department of Agriculture and does not imply its approval to the exclusion of other products that may also be suitable. This article is in the public domain and not copyrightable.

Electronic supplementary material

Supplementary Fig. 1

Analysis of the PCR products obtained from Chinese Spring and its ditelosomic lines by using the haplotype-specific LMW-GS molecular markers. L: Thermo Scientific GeneRuler 1Kb DNA ladder; Dt1AL: Chinese Spring ditelosomic 1AL; Dt1BL: Chinese Spring ditelosomic 1BL; Dt1DL: Chinese Spring ditelosomic 1DL; CS: Chinese Spring (DOCX 1041 kb)

Supplementary Fig. 2

Electropherograms of the haplotype-specific LMW-GS marker results obtained from Chinese Spring (DOCX 376 kb)

Supplementary Fig. 3

(a) Location of the Glu-A3-3 primer sets on the A3646 genes. Red arrows indicate the location of the primers highlighted in the box. (b) Elecropherograms associated with the different A3-646 genic profile resulting from the capillary electrophoresis separation. Blue peaks represent PCR amplicons. The numbers in the green boxes indicate the PCR amplicon length. The genes associated with the amplicons are reported in blue. (DOCX 186 kb)

Supplementary Fig. 4

(a) Location of the Glu-B3-3 primer sets on the B3-688 genes. Red arrows indicate the location of the primers highlighted in the box. (b) Elecropherograms associated with the different B3-688 genic profile resulting from the capillary electrophoresis separation. Blue peaks represent PCR amplicons. The numbers in the green boxes indicate the PCR amplicon length. The genes associated with the amplicons are reported in blue. (DOCX 197 kb)

Supplementary File 1

(DOCX 27 kb)

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Ibba, M.I., Kiszonas, A.M. & Morris, C.F. Development of haplotype-specific molecular markers for the low-molecular-weight glutenin subunits. Mol Breeding 38, 68 (2018). https://doi.org/10.1007/s11032-018-0827-9

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