Development of single nucleotide polymorphism-based functional molecular markers from the Lr22a gene sequence in wheat (Triticum aestivum)

The adult-plant leaf rust resistant gene Lr22a confers broadly effective resistance against the fungal pathogen Puccinia triticina Eriks. (Pt) in wheat that has not been extensively utilized in wheat cultivars. The objective of this study was to develop robust functional molecular markers using the Lr22a gene sequence to facilitate integration of Lr22a in breeding programmes. The Lr22a coding sequence was used to identify isolated SNPs and four kompetitive allele specific polymerase chain reaction (PCR) (KASP) markers were developed. For marker testing, a F_2:3 population was developed by crossing a near-isogenic line RL4495 (Lr22a carrier) with Thatcher and phenotyped with Pt race TDBJ and genotyped with a 90K iSelect SNP array, four KASP markers and two SSR markers. A linkage map of chromosome arm 2DS that included Lr22a was constructed. The KASP markers co-segregated with Lr22a and were validated for cross-applicability on a panel of wheat lines. KASP markers Kwh636, Kwh637 and Kwh638 reliably detected the presence or absence of Lr22a. The markers developed in this study will facilitate Lr22a selection in breeding programmes.