Development and validation of diagnostic markers for wheat stem rust resistance gene Sr43

Stem rust, caused by Puccinia graminis Pers. f. sp. tritici Eriks. & E. Henn (Pgt), is one of the most widely spread fungal diseases in wheat (Triticum aestivum) worldwide. Sr43 originated from Thinopyrum ponticum and showed broad-spectrum resistance to stem rust. Recently, Sr43 has been cloned, which encodes an unusual protein kinase fused to two domains of unknown function. However, high-throughput Sr43 diagnostic markers are not available to assist wheat breeding. In this study, we identified sequence variation within or near the conserved domains of Sr43 by comparing the Sr43 sequence to its homologs in the wheat pangenome accessions and developed two kompetitive allele-specific PCR (KASP) markers (Sr43-KASP1 and Sr43-KASP2) for Sr43. The Sr43-marker alleles at both marker loci co-segregated with the corresponding phenotypes in a BC₂F_2:3 segregating population developed by backcrossing RWG34 (Sr43⁺) to a hard winter wheat (HWW) “Jagger” (Sr43⁻). The Sr43 resistance marker alleles were not detected in a US HWW panel (RGON2020) where Sr43 is absent. The results confirmed that Sr43-KASP1 and Sr43-KASP2 are diagnostic for Sr43 and will facilitate the effective deployment of Sr43 to improve stem rust resistance in wheat breeding programs.