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ARS Home » Plains Area » Manhattan, Kansas » Center for Grain and Animal Health Research » Hard Winter Wheat Genetics Research » Research » Publications at this Location » Publication #315079
Title: Genotyping-By-Sequencing (GBS) identified SNP tightly linked to QTL for pre-harvest sprouting resistance

Author
item LIN, MENG - Kansas State University
item CAI, SHIBIN - Kansas State University
item WANG, SHAN - Kansas State University
item LIU, SHUBING - Kansas State University
item ZHANG, GUORONG - Kansas State University
item Bai, Guihua

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/31/2015
Publication Date: 4/8/2015
Citation: Lin, M., Cai, S., Wang, S., Liu, S., Zhang, G., Bai, G. 2015. Genotyping-By-Sequencing (GBS) identified SNP tightly linked to QTL for pre-harvest sprouting resistance. Theoretical and Applied Genetics. DOI: 10.1007/S00122-015-2513-1.

Interpretive Summary: Pre-harvest sprouting (PHS) of wheat reduces both wheat grain yield and the end-use quality. Growing PHS resistant cultivars is the most effective approach to reduce PHS damage. The PHS resistance in wheat is controlled by quantitative trait loci (QTL). DNA markers tightly linked to the QTL for PHS resistance can help accurately to transfer QTL into new cultivars. In this study, we conduct both field and greenhouse experiments to evaluate PHS resistance in a recombinant inbred population developed from a cross between a PHS-resistant parent ‘Tutoumai A’ and a PHS-susceptible parent 'Siyang 936' and lab experiment to identify DNA markers using Genotyping-By-Sequencing (GBS), a next-generation sequencing based technology. We identified four QTL for PHS resistance and one QTL on chromosome 4A shows the largest and more consistent effect on PHS resistance. Two single nucleotide polymorphism (SNP) markers, GBS109947 and GBS212432, were mapped to the major QTL region on chromosome 4AL, and delimited the QTL to a 2.9 cM interval. Some GBS-derived SNP were converted into Kompetitive Allele Specific PCR (KASP) assays that can be easily used for marker-assisted selection to improve PHS resistance.

Technical 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 Kompetitive Allele Specific PCR (KASP) assays that can be easily used for marker-assisted selection to improve PHS resistance.