Genetic Diversity and Population Structure of Elite Foxtail Millet [Setaria italica (L.) P. Beauv.] Germplasm in China

China is among the countries that have the most severe water deficiency. Due to its excellent drought tolerance, foxtail millet [Setaria italica (L.) P. Beauv.] has become one of the important cereal crops in China. Information on genetic diversity and population structure of foxtail millet may facilitate effective use of limited genetic resources in breeding programs. In this study, a selected panel of 128 accessions was screened with 79 simple sequence repeat (SSR) markers to investigate genetic diversity and population structure of foxtail millet. The panel was selected from 3356 germplasm collections from three major ecological areas of China: North, Northwest, and Northeast China. The mean genetic diversity was 0.75 and the mean polymorphism information content (PIC) was 0.72, indicating a high level of genetic diversity across the panel. Structure analysis identified six groups, which matches with their pedigree information, in general, but not with their geographic origins. Germplasm in Group 2 (G2) have unique geographic origins and pedigrees, which is different from other five groups; thus, crosses of accessions in this group to accessions from other groups are more likely to generate expected recombination for developing both conventional and hybrid cultivars.