Evaluation of genetic diversity, population structure, and linkage disequilibrium among elite Chinese wheat ( Triticum aestivum L.) cultivars

Abstract

Genetic diversity, population structure, and linkage disequilibrium (LD) were investigated among elite Chinese wheat ( Triticum aestivum L.) cultivars originating from northern, Huanghuai and southwest wheat growing regions in China, using 69 diverse simple sequence repeat (SSR) markers. We observed an average of 11.72 (ranging from 3 to 50) alleles per SSR locus and an average gene diversity of 0.69 (ranging from 0.10 to 0.97). These results reveal that the diversity in elite Chinese cultivars was comparable to previously reported wheat germplasm SSRs in other countries. Cluster analysis of the SSR data, based on distance, divided all cultivars into six groups (A, B, C, D, E, and F) with a genetic similarity of 0.7, in agreement with their known pedigree data. The model-based clustering method divided these cultivars into four groups, partly corresponding to geographic regions of China, indicating that the genetic diversity of Chinese wheat cultivars was likely the result of regional adaptation. LD was investigated in these genotypes to determine the prospects for whole-genome association analyses. A low overall LD level (1.95%) was found with a mean r 2 of 0.14. LD decayed within a genetic distance of 33 centiMorgans (r 2 > 0.2) in all accessions, which was a slower decay than in previous studies of other crop populations. The suggested population structure and LD analysis in this study provide the basis for future association mapping for genes and quantitative trait loci in elite Chinese cultivars.