Rapid linkage disequilibrium decay in the Lr10 gene in wild emmer wheat (Triticum dicoccoides) populations

Recombination is a key evolutionary factor enhancing diversity. However, the effect of recombination on diversity in inbreeding species is expected to be low. To estimate this effect, recombination and diversity patterns of Lr10 gene were studied in natural populations of the inbreeder species, wild emmer wheat (Triticum dicoccoides). Wild emmer wheat is the progenitor of most cultivated wheats and it harbors rich genetic resources for disease resistance. Lr10 is a leaf rust resistance gene encoding three domains: a coiled-coil, nucleotide-binding site, and leucine-rich repeat (CC-NBS-LRR). Lr10 was sequenced from 58 accessions representing 12 diverse habitats in Israel. Diversity analysis revealed a high rate of synonymous and non-synonymous substitutions (d (S) = 0.029, d (N) = 0.018, respectively) in the NBS-LRR domains. Moreover, in contrast to other resistance genes, in Lr10 the CC domain was more diverse than the NBS-LRR domains (d (S) = 0.069 vs. 0.029, d (N) = 0.094 vs. 0.018) and was subjected to positive selection in some of the populations. Seventeen recombination events were detected between haplotypes, especially in the CC domain. Linkage disequilibrium (LD) analysis has shown a rapid decay from r (2) = 0.5 to r (2) = 0.1 within a 2-kb span. These results suggest that recombination is a diversifying force for the R-gene, Lr10, in the selfing species T. dicoccoides. This is the first report of a short-range LD decay in wild emmer wheat.