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Molecular mapping of a stripe rust resistance gene YrCf75 using bulked segregant analysis combined with single nucleotide polymorphism genotyping arrays and bulked segregant RNA-Sequencing.

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most important diseases in wheat production worldwide. Breeding and planting disease-resistant varieties are the most economical, effective and environmentally-friendly measures to prevent and control wheat stripe rust. Changfeng 75, a Chinese winter wheat variety, shows high stripe rust resistance in both seedling and adult-plant stages. The seedling tests of F1, F2, and F2:3 populations derived from Mingxian 169/Changfeng 75 inoculated with Chinese predominant Pst race CYR34 showed that the stripe rust resistance of Changfeng 75 was controlled by a single recessive gene, temporarily designated as YrCf75. Bulked segregant analysis (BSA) combined with wheat 660K single-nucleotide polymorphism (SNP) array and bulked segregant RNA-Sequencing (BSR-Seq) indicated that the proportion of polymorphic SNP on wheat chromosome 2A was the highest, which suggested that YrCf75 was likely located on chromosome 2A. Two hundred and twenty-five kompetitive allele-specific PCR (KASP) and 75 simple sequence repeat (SSR) markers on chromosome 2A were used to map YrCf75 using BSA strategy. Linkage analysis indicated that 31 pairs of KASP markers and one pair of SSR marker were linked to YrCf75, and the genetic distances of the two closest flanking KASP markers AX-1110060462 and AX-111004763 were 1.2 and 2.7 cM, respectively. YrCf75 was located on wheat chromosome 2AL. The molecular detection and allele tests showed that YrCf75 is likely a new gene, which is different from the known stripe rust resistance genes (Yr1 and Yr32) on wheat chromosome 2AL.