Rapid identification of adult plant wheat stripe rust resistance gene <italic>YrC271</italic> using high-throughput SNP array-based bulked segregant analysis

Abstract

<p id="C3">Wheat cultivar C271 registered as PI 210904 in the USDA National Small Grains Collection was developed from Punjab Pakistan in 1953 and it confers adult plant resistance (APR) to stripe rust both in the United States and China for many years. In the present study, we dissected the genetic basis of stripe rust resistance on 229 F_2:3 populations produced by crossing Jinmai 79 and C271 in the fields of Yangling and Jiangyou. Bulked segregant analysis coupled with wheat 660K SNP array placed the majority of SNPs differences on chromosome arm 3BS. After using allele-specific quantitative PCR based genotyping assay (AQP) to confirm the SNPs, a linkage map was constructed and a major locus was detected across all environments based on IciMapping v4.1 software. The QTL, designated as <italic>YrC271</italic>, was flanked by SNP markers <italic>AX-109001377 </italic>and <italic>AX-111087256</italic> with a genetic interval of 1.9 cM corresponding to a physical distance of 1.9 Mb in RefSeq v.1.0 (positions 6.1-8.0 Mb). Comparative genomics analysis was performed to detect the collinear genomic regions of different hexaploid wheat accessions (<italic>Triticum aestivum</italic>), <italic>T</italic>. <italic>dicoccoides</italic>, and <italic>T. turgidum. </italic>More than 340 SNPs in the physical region were extracted for haplotype analysis in a panel of over 1484 worldwide common wheat accessions, and five major haplotypes (Hap1, Hap2, Hap3, Hap4, and Hap5) were identified. And the favorable haplotype Hap1 was highly associated with stripe rust resistance. <italic>YrC271</italic> appeared to be similar to <italic>YrC271</italic> based on comparison of relative distance, stripe rust responses, and pedigree analyses, but allelism tests, cloning or precise phenotypic comparisons would be needed for confirmation. The <italic>YrC271</italic> region provided the opportunity for further map-based cloning and haplotypes analysis enabled pyramiding favorable alleles into commercial cultivars by marker-assisted selection.