|Subramanyam, Subhashree - Purdue University|
|Xiao, Xiangye - Purdue University|
|Mcdonald, Melissa - Purdue University|
Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/16/2016
Publication Date: 4/29/2016
Citation: Subramanyam, S., Nemacheck, J.A., Xiao, X., McDonald, M., Williams, C.E. 2016. Targeted discovery of single-nucleotide polymorphisms in an unmarked wheat chromosomal region containing the Hessian fly resistance gene H33. Crop Science. 56:1106-1114. doi: 10.2135/cropsci2015.10.0630.
Interpretive Summary: The H33 gene confers wheat resistance to the Hessian fly. This gene works well in the southeastern US where other sources of resistances are failing. However the gene lacked molecular markers that were close enough to be useful for marker-assisted selection. This project targeted the region containing H33 for marker identification, resulting in several useful new markers. These were converted into a convenient format for breeders to use while moving the H33 gene into cultivars.
Technical Abstract: The highly effective Hessian fly-resistance gene, H33, was introgressed from durum wheat into common wheat and genetically mapped to chromosome 3AS, in previous research. However, H33 located to a region that is well-known to be devoid of molecular markers, with the closest flanking simple sequence repeat (SSR) markers 7.4 and 25.1 cM from the gene. This lack of available markers flanking economically important genes is a common problem in self-pollinating crops due to low polymorphism and, in the case of wheat, large genome size. However, H33 is currently effective against all virulent Hessian fly populations tested from the southeastern United States, a region where the deployed resistance genes are beginning to fail; thus, additional effort was needed to identify tightly linked flanking markers to utilize this valuable gene in marker-assisted selection. To target the 25.1 cM segment adjacent to H33 for marker discovery, samples derived from eight resistant and four susceptible plants were selected for genotyping-by-sequencing (GBS), based on their markers flanking H33. Four single nucleotide polymorphisms (SNP) were identified in the target region of chromosome 3AS, with the closest marker being only 6.7 cM away. These sequences were converted into high-throughput PCR-based markers for the Kompetitive Allele-Specific PCR (KASP) assay. In addition, restriction endonucleases were identified that cut at the SNPs for restriction profiling as an alternate to the KASP assay. Development of these cost-effective markers provided both low- and high-throughput alternatives for introgressing H33 into wheat cultivars while minimizing linkage drag associated with durum regions of chromosome 3AS.