QTL Mapping for Leaf Rust Resistance in a Common Wheat Recombinant Inbred Line Population of Doumai/Shi4185

Leaf rust, a devastating fungal disease caused by <i>Puccinia triticina</i> (Pt), severely impacts wheat quality and yield. Identifying genetic loci for wheat leaf rust resistance, developing molecular markers, and breeding resistant varieties is the most environmentally friendly and economical strategy for disease control. This study utilized a recombinant inbred line (RIL) population of Doumai and Shi4185, combined with the wheat 90 K single nucleotide polymorphisms (SNPs) chip data and maximum disease severity (MDS) of leaf rust from four environments, to identify adult plant resistance (APR) loci through linkage mapping. Additionally, kompetitive allele-specific PCR (KASP) markers suitable for breeding were developed, and genetic effects were validated in a natural population. In this study, 5 quantitative trait loci (QTL) on chromosomes 1B (2), 2A and 7B (2) were identified through inclusive composite interval mapping, and named as <i>QLr.lfnu-1BL1</i>, <i>QLr.lfnu-1BL2</i>, <i>QLr.lfnu-2AL</i>, <i>QLr.lfnu-7BL1</i> and <i>QLr.lfnu-7BL2</i>, respectively, explaining 4.54-8.91% of the phenotypic variances. The resistance alleles of <i>QLr.lfnu-1BL1</i> and <i>QLr.lfnu-1BL2</i> originated from Doumai, while the resistance alleles of <i>QLr.lfnu-2AL</i>, <i>QLr.lfnu-7BL1</i> and <i>QLr.lfnu-7BL2</i> came from Shi4185. Among these, <i>QLr.lfnu-1BL2</i>, <i>QLr.lfnu-7BL1</i> and <i>QLr.lfnu-7BL2</i> overlapped with previously reported loci, whereas <i>QLr.lfnu-1BL1</i> and <i>QLr.lfnu-2AL</i> are likely to be novel. Two KASP markers, <i>QLr.lfnu-2AL</i> and <i>QLr.lfnu-7BL</i>, were significantly associated with leaf rust resistance in a diverse panel of 150 wheat varieties mainly from China. Totally, 34 potential candidate genes encoded the NLR proteins, receptor-like kinases, signaling kinases and transcription factors were selected as candidate genes for the resistance loci. These findings will provide stable QTL, available breeding KASP markers and candidate genes, and will accelerate the progresses of wheat leaf rust resistance improvement through marker-assisted selection breeding.