Physical mapping and identification of a candidate for the leaf rust resistance gene Lr1 of wheat

Lr1 is a dominant leaf rust resistance gene located on chromosome 5DL of bread wheat and the wild species Aegilops tauschii. In this study, three polymorphic markers (WR001, WR002, and WR003) were developed from resistance gene analogs (RGAs) clustering around the Lr1 locus. Using these and other markers, Lr1 was mapped to a genetic interval of 0.79 cM in Ae. tauschii and 0.075 cM in wheat. The CAPS marker WR003, derived from LR1RGA1, co-segregated with Lr1 in both mapping populations of wheat and Ae. tauschii. For isolation of Lr1, two genomic BAC libraries (from Ae. tauschii and hexaploid wheat) were screened using the tightly flanking marker PSR567F and a set of nested primers derived from the conserved region of the RGA sequences. Approximately 400 kb BAC contig spanning the Lr1 locus was constructed. The LR1RGA1 encoding a CC-NBS-leucine-rich repeat (LRR) type of protein was the only one of the four RGAs at the Lr1 locus, which co-segregated with leaf rust resistance. Therefore, it represents a very good candidate for Lr1. The allelic sequences of LR1RGA1 from resistant and susceptible lines revealed a divergent DNA sequence block of ∼605 bp encoding the LRR repeats 9-15, whereas the rest of the sequences were mostly identical. Within this sequence block, the 48 non-synonymous changes resulted in 44 amino acid differences. This indicates that LR1RGA1 likely evolved through one or more recombination or gene conversion events with unknown genes.