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Genotyping-by-sequencing (GBS) identified SNP tightly linked to QTL for pre-harvest sprouting resistance

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Using a GBS-SNP map, a QTL for pre-harvest sprouting resistance on 4AL of Totoumai A was delimited to 2.9-cM interval, and SNP closely linked to several other QTL were identified.

Abstract

Pre-harvest sprouting (PHS) of wheat is a major constraint to wheat production in many wheat-growing areas worldwide, because it reduces both wheat grain yield and the end-use quality. To identify markers tightly linked to the quantitative trait loci (QTL) for PHS resistance and seed dormancy (SD), we evaluated 155 recombinant inbred lines (RIL) derived from a cross between a PHS-resistant parent ‘Tutoumai A’ and a PHS-susceptible parent ‘Siyang 936’ for single-nucleotide polymorphisms (SNP) using genotyping-by-sequencing (GBS), and for PHS resistance and SD using both field and greenhouse grown plants. Two SNP, GBS109947 and GBS212432, were mapped to a major QTL region for PHS resistance and SD on chromosome 4AL, and delimited the QTL to a 2.9-cM interval. Two and nine additional SNP were mapped to minor QTL regions for SD on chromosome 5B and 5A, respectively. Critical SNP in these QTL regions were converted into KBioscience Competitive Allele-Specific PCR (KASP) assays that can be easily used for marker-assisted selection to improve PHS resistance.

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Acknowledgments

This is contribution number 15-199-J from the Kansas Agricultural Experiment Station. This project is partly funded by the National Research Initiative Competitive Grants CAP project 2011-68002-30029 from the USDA National Institute of Food and Agriculture. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the US Department of Agriculture. USDA is an equal opportunity provider and employer.

Conflict of interest

The authors declare that they have no conflict of interest.

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Authors and Affiliations

  1. Agronomy Department, Kansas State University, Manhattan, KS, 66506, USA

    Meng Lin, Shibin Cai, Shan Wang, Shubing Liu, Guorong Zhang & Guihua Bai

  2. Hard Winter Wheat Genetics Research Unit, USDA-ARS, Manhattan, KS, 66506, USA

    Guihua Bai

  3. Food Crop Institute, Jiangsu Academy of Agricultural Science, Nanjing, China

    Shibin Cai

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  1. Meng Lin
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  2. Shibin Cai
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  4. Shubing Liu
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  6. Guihua Bai
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Correspondence to Guihua Bai.

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Communicated by A. Zhang.

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Lin, M., Cai, S., Wang, S. et al. Genotyping-by-sequencing (GBS) identified SNP tightly linked to QTL for pre-harvest sprouting resistance. Theor Appl Genet 128, 1385–1395 (2015). https://doi.org/10.1007/s00122-015-2513-1

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  • DOI: https://doi.org/10.1007/s00122-015-2513-1

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