Targeted molecular mapping of the adult plant resistance gene Lr46 in wheat and introgression into hard winter wheat adapted to Kansas

Leaf rust (caused by Puccinia triticina Eriks) is a widespread fungal disease of wheat. Adult plant resistance gene Lr46 has provided effective resistance against diverse races of the pathogen for almost 30 years and is thought to be durable. Previous reports located QTL corresponding to Lr46 distally on wheat chromosome 1BL. We confirmed the linkage of 1BL markers with Lr46 in a single chromosome recombinant line population where Lr46 segregates as a single gene. Using Chinese Spring (CS) deletion stocks to map the linked SSR (simple sequence repeat) markers, we determined that Lr46 is likely present in the deletion bin 1BL 0.84--0.89. To increase marker density in this region, wheat expressed sequence tags (ESTs) that mapped in the terminal 15% of chromosome 1BL were used as queries in BLASTn searches against the rice genome sequence. Wheat ESTs with significant homology to sequences from the terminal region of chromosome 5L of rice were chosen for STS (sequence-tagged site) primer design and mapped physically and genetically. Once synteny in the region was confirmed, sequences from two BAC (bacterial artificial chromosome) clones covering the target syntenic region of rice 5L were used to identify additional wheat ESTs potentially linked to Lr46. By this method, 16 additional STS markers located in a small deletion bin comprising less than 1% of chromosome 1BL were developed. A total of eight STS markers could be mapped in two populations segregating for Lr46. Of these, two markers flanking Lr46 (3.0 cM proximal and 0.7 cM distal) were identified. The physical location of the gene was confined to a sub-microscopic deletion bin between breakpoints for deletion line 1BL-13 (0.89) and 1BL-4 (0.89). Introgression of Lr46 into hard winter wheat (HWW) germplasm adapted to Kansas was done by backcrossing. Molecular and phenotypic selections were used to develop BC2F4 lines with Lr46 in two different HWW backgrounds. After field evaluation in 2004--05, the best lines will be released as germplasm to wheat breeders. This work has resulted in a source of durable resistance in a winter wheat background and the markers for deployment of Lr46 by breeding programs.