Evaluation of the genetic diversity and genome-wide linkage disequilibrium of Chinese maize inbred lines

Investigation of the genetic diversity, population structure, and linkage disequilibrium of maize will assist in the selection of parental lines for enhanced efficiency of maize breeding. In the present research, we investigated genetic diversity, linkage disequilibrium, and population structure among 173 inbred lines that were commercially important and/or were parental lines used for breeding in China. Using the model-based Bayesian clustering analysis, these lines could be assigned to four subgroups, Lan, P, Reid, and TSPT, most of which were in agreement with the pedigree of information. Using 78 SSR markers, the genetic diversity was determined to be an average of 8.1 alleles per locus (range 2 to 17). The average values of PIC (Polymorphic information content) and gene diversity were 0.667 and 0.704, respectively. A total of 547 pairs of SSRs on the same chromosome demonstrated significant linkage disequilibrium (LD) at the 0.01 level. Our results suggested that this population may be suitable for future marker-phenotype association analysis. In addition, the proportions of the observed LD were higher than that those of expected LD, indicating that we be careful for a high risk of spurious association, which could be generated by population stratification when using association mapping. The genetic diversity, population structure, and LD analysis in this study provided provide a basis for future association mapping for genes and quantitative trait loci.