Identification and Characterization of a New Leaf Rust Resistance Gene LrGR in Bread Wheat Cultivar Graecum 48

Leaf rust, caused by Puccinia triticina (Pt), poses a serious threat to sustainable wheat production globally, and identification of leaf rust resistance genes that can be readily used in cultivar development is of agronomic importance. A recombinant inbred line (RIL) population was developed from Graecum 48 × TAM 110 to characterize a leaf rust resistance gene in Graecum 48, a winter wheat cultivar developed in Kazakhstan, and was evaluated for responses to Pt race MMPSD (isolate: Pt52-2). Together with Graecum 48 and TAM 110, a subset of 20 RILs with contrasting phenotypes were genotyped using genotyping-by-sequencing, leading to the identification of 20,379 single nucleotide polymorphic (SNP) markers. Allele distribution analyses of each SNP in the sequenced RILs identified a set of SNPs closely associated with leaf rust resistance in the terminal region of chromosome arm 2DS. Four SNPs in this region were converted to kompetitive allele-specific PCR (KASP) markers, and these markers, together with those previously mapped in the target region, were used to genotype the RIL population. Linkage analysis delimited the leaf rust resistance gene in Graecum 48, designated LrGR, to an interval of 53 Kb between 64.46 and 64.51 Mb in the Chinese Spring IWGSC RefSeq 2.1, in which Lr2 resides. A test of allelism indicated LrGR is a novel gene, and the estimated recombination frequency and genetic distance between LrGR and Lr2 were 7.87% and 7.95 cM, respectively. KASP markers flanking LrGR such as kwm1620 and kwm1632 can be used to tag LrGR in marker-assisted selection.