Targeted Discovery of Single‐Nucleotide Polymorphisms in an Unmarked Wheat Chromosomal Region Containing the Hessian Fly Resistance Gene H33

Abstract

The durum wheat [Triticum turgidum L. subsp. durum (Desf.) Husn.] Hessian fly [Mayetiola destructor (Say)] resistance gene H33 was previously introgressed into common wheat (T. aestivum L.) and mapped to chromosome 3AS. However, H33 located to a region that is 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 markers flanking economically important genes is a common problem in self‐pollinating crops because of low polymorphism and, in the case of wheat, a large genome size. H33 is currently effective against all virulent Hessian fly populations tested from the southeastern United States, a region where deployed resistance genes are beginning to fail; thus, effort was needed to identify tightly linked flanking markers to use this valuable gene in marker‐assisted selection (MAS). To target the 25.1‐cM segment adjacent to H33 for marker discovery, eight resistant and four susceptible plants were selected for genotyping‐by‐sequencing (GBS). Four single‐nucleotide polymorphisms (SNPs) were identified, with the closest marker being only 6.7 cM away and converted into high‐throughput polymerase chain reaction (PCR)‐based markers for the Kompetitive Allele Specific PCR (KASP) assay. In addition, 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.