Population-based resequencing analysis of improved wheat germplasm at wheat leaf rust resistance locus Lr21

Little is known about the genetic impacts of modern plant breeding on specific breeding target loci. Resequencing cloned genes can identify all mutations in single genes for population-based analyses of genetic changes in improved gene pools. Ninety-five wheat cultivars released in Canada from 1845 to 2004 were sequenced at the wheat leaf rust resistance locus Lr21. Characterization of the DNA fragment of length 4,071 bp, covering the Lr21 gene from -92 to +4,261, revealed 13 SNPs, four indels, 10 haplotypes, and 4 major haplotype groups. A new SCAR marker was developed to identify the resistant haplotype and haplotype groups. Non-synonymous polymorphic sites and haplotype numbers were increased over the 100 years of wheat breeding. Nucleotide diversity of the wheat cultivars was gradually reduced from 1845 to 1993 and increased after the release of the first Lr21 wheat cultivar AC Cora in 1994. Positive selection measured with Tajima's D was observed in the cultivars released before 1935. At least two recombination events were inferred in those cultivars released before 1993. Linkage disequilibrium at the locus was decreased over time. These findings demonstrate not only the effectiveness of the wheat breeding in the improvement of leaf rust resistance, but also are useful to understand the genetic influences of a long-term artificial selection on individual loci.