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Sequence diversity, haplotype analysis, association mapping and functional marker development in the waxy and starch synthase IIa genes for grain-yield-related traits in hexaploid wheat (Triticum aestivum L.)

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Abstract

Development of high-yielding cereal crops could meet increasing global demands for food, feed and bio-fuels. Wheat is one of the world’s most important cereal crops. The biosynthesis of starch is the major determinant of yield in wheat. Two starch biosynthesis genes, the waxy (Wx) genes and the starch synthase IIa (SSIIa) genes, were amplified and sequenced in 92 diverse wheat genotypes using genome-specific primers. Nucleotide diversity, haplotype analysis and association mapping were performed. The first exon (5′-UTR) and the first intron of the three homoeologous Wx genes were isolated using expressed sequence tag sequences. The Wx genes contained 12 exons separated by 11 introns. SNP (single nucleotide polymorphism) frequency ranged from 1 SNP/3,648 bp for Wx-D1 to 1 SNP/135 bp for SSIIa-A1, with an average of 1 SNP/230 bp. The average SNP frequencies in exon and intron regions were 1 SNP/322 bp and 1 SNP/228 bp, respectively. Thirty, 23 and 5 SNPs were identified and formed five, six and five haplotypes for SSIIa-A1, SSIIa-B1 and SSIIa-D1, respectively. However, no association was found between these SNPs and seven yield-related traits. Twenty-two, 15 and 1 SNPs were detected and formed nine, five and two haplotypes for Wx-A1, Wx-B1 and Wx-D1, respectively. Three unique nucleotides C+A+T at SNP5, SNP6 and SNP12 formed Wx-B1-H3, which was significantly associated with increased grain weight, thousand kernel weight, and total starch content in three spring wheat genotypes and five winter wheat genotypes. Cost-effective and co-dominant SNP markers were developed using temperature-switch (TS)-PCR and are being used for marker-assisted selection of doubled haploid lines with enhanced grain yield and starch content in winter wheat breeding programs.

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Acknowledgments

We thank Dr. J. Raupp, the Wheat Genetic and Genomic Resources Center (WGGRC), Department of Plant Pathology, Kansas State University, for providing the nulli-tetrasomic lines of Chinese Spring (CS). The seed of wheat genotypes was kindly supplied by Dr. H. Bockelman of the Germplasm Resources Information Network (GRIN), USDA-ARS, USA, D. Kessler of the Plant Gene Resources of Canada (PGRC), Agriculture and Agri-Food Canada, Canada, and Dr. Zdeněk Stehno of Gene Bank, Crop Research Institute, Czech Republic, respectively. This work was supported by NSERC (National Science and Engineering Research Council of Canada) and Husky Energy Inc.

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  1. Department of Plant Science, University of Manitoba, 66 Dafoe Road, Winnipeg, MB, R3T 2N2, Canada

    Xiu-Qiang Huang & Anita Brûlé-Babel

  2. Pioneer Hi-Bred Production LP, 12111 Mississauga Road, Caledon, ON, L7C 1X1, Canada

    Xiu-Qiang Huang

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  1. Xiu-Qiang Huang
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Correspondence to Xiu-Qiang Huang or Anita Brûlé-Babel.

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Huang, XQ., Brûlé-Babel, A. Sequence diversity, haplotype analysis, association mapping and functional marker development in the waxy and starch synthase IIa genes for grain-yield-related traits in hexaploid wheat (Triticum aestivum L.). Mol Breeding 30, 627–645 (2012). https://doi.org/10.1007/s11032-011-9649-8

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