Haplotype diversity and evolutionary history of the Lr34 locus of wheat

Leaf rust caused by Puccinia triticina is a major disease of wheat, and genetic resistance remains the best strategy for managing it. The resistance gene Lr34 has been key in the genetic management of wheat leaf rust worldwide. However, little is known about the geo-genetic diversity, history and origin of this unique gene. This study was conducted to provide a comprehensive analysis of the genetic diversity at the Lr34 locus of a world wheat germplasm collection. A total of 52 alleles were detected for the 10 Lr34 markers. On the basis of the Lr34-specific markers, the world collection was divided into five major haplotypes (H), of which H1 was consistently associated with the resistance phenotype Lr34+. Phenotypic data confirmed the susceptible phenotypes of H2, H3 and H4 and the susceptible or intermediate phenotype of H5. SNP12 (C/T) was the only mutation differentiating the resistant haplotype from the susceptible ones. Combined analysis of the 10 markers resulted in dividing the major haplotypes into 118 different sub-haplotypes. Structure and clustering analyses grouped them into two main clusters and seven sub-clusters. Variance between the main clusters represented the largest proportion of the total variation. H2, the only haplotype found in Aegilops tauschii, is the ancestral haplotype and H1 (Lr34+) likely arose after the advent of hexaploid wheat. Analysis of geographical distribution showed that H1 was more frequent in the Asian germplasm while H2 dominated the European germplasm. Lr34, a gain-of-function mutation, is hypothesized to have originated in Asia.