Population structure and linkage disequilibrium of a mini core set of maize inbred lines in China

Understanding genetic diversity, population structure, and the level and distribution of linkage disequilibrium (LD) in target populations are of great importance and the prerequisite for association mapping. In the present study, 145 genome-wide SSR markers were used to assess the genetic diversity, population structure, and LD of a set of 95 maize inbred lines which represented the Chinese maize inbred lines. Results showed that the population included a diverse genetic variation. A model-based population structure analysis subdivided the inbred lines into four subgroups that correspond to the four major empirical germplasm origins in China, i.e., Lancaster, Reid, Tangsipingtou and P. Among all of the inbred lines, 65.3% were assigned into the corresponding subgroups; others were assigned into a mixed subgroup. LD was significant at a 0.01 level between 63.89% of the SSR pairs in the entire sample and with a range of 18.75-40.28% in the subgroups. Among factors influencing LD, linkage was the major cause for LD of SSR loci. The results suggested that the population may be used in the detection of genome-wide SSR marker-phenotype association.