Population-based resequencing analysis of wild and cultivated barley revealed weak domestication signal of selection and bottleneck in the Rrs2 scald resistance gene region

Many plant disease resistance (R) genes have been cloned, but the potential of utilizing these plant R-gene genomic resources for genetic inferences of plant domestication history remains unexplored. A population-based resequencing analysis of the genomic region near the Rrs2 scald resistance gene was made in 51 accessions of wild and cultivated barley from 41 countries. Fifteen primer pairs were designed to sample the genomic region with a total length of 10 406 bp. More nucleotide diversity was found in wild (pi = 0.01846) than cultivated (pi = 0.01507) barley samples. Three distinct groups of 29 haplotypes were detected for all 51 samples, and they were well mixed with wild and cultivated barley samples from different countries and regions. The neutrality tests by Tajima's D were not significant, but a significant (P < 0.05) case by Fu and Li's D* and F* was found in the barley cultivar samples. The estimate of selection intensity by K-a/K-s was 0.691 in wild barley and 0.580 in cultivated barley. The estimate of the minimum recombination events was 16 in wild barley and 19 in cultivated barley. A coalescence simulation revealed a bottleneck intensity of 1.5 to 2 since barley domestication. Together, the domestication signal in the genomic region was weak both in human selection and domestication bottleneck.