Development of SNP, KASP, and SSR Markers by BSR-Seq Technology for Saturation of Genetic Linkage Map and Efficient Detection of Wheat Powdery Mildew Resistance Gene Pm61

Abstract

The gene <i>Pm61</i> that confers powdery mildew resistance has been previously identified on chromosome arm 4AL in Chinese wheat landrace Xuxusanyuehuang (XXSYH). To facilitate the use of <i>Pm61</i> in breeding practices, the bulked segregant analysis-RNA-Seq (BSR-Seq) analysis, in combination with the information on the Chinese Spring reference genome sequence, was performed in the F_2:3 mapping population of XXSYH × Zhongzuo 9504. Two single nucleotide polymorphism (SNP), two Kompetitive Allele Specific PCR (KASP), and six simple sequence repeat (SSR) markers, together with previously identified polymorphic markers, saturated the genetic linkage map for <i>Pm61</i>, especially in the proximal side of the target gene that was short of gene-linked markers. In the newly established genetic linkage map, <i>Pm61</i> was located in a 0.71 cM genetic interval and can be detected in a high throughput scale by the KASP markers <i>Xicsk8</i> and <i>Xicsk13</i> or by the standard PCR-based markers <i>Xicscx497</i> and <i>Xicsx538</i>. The newly saturated genetic linkage map will be useful in molecular marker assisted-selection of <i>Pm61</i> in breeding for disease resistant cultivar and in its map-based cloning.