Genetic Diversity and Genome Wide Association Analysis of Major Characters of Foxtail Millet, an Emerging Model for the Panicoideae Grasses and C4 Photosynthesis

Due to its small diploid genome (~515Mb), short growing cycle and small morphological stature, foxtail millet (Setaria italica) and its wild ancestor green foxtail (S. viridis) is on the fast track becoming a model system for the Panicoideae grasses, which include maize, sorghum, pearl millet and other important cereals and biofuel grasses. Foxtail millet is also widely recognized as a model to decipher the molecular biology of C4 photosynthesis. Related knowledge of foxtail millet population diversity will for sure promoting the development of this model system. There are about 38,000 accessions of foxtail millet gremlins stored in different gene banks world wide and two core collections were constructed in China and ICRISAT (International Crops Research Institute for the Semi-Arid Tropics) respectively. Previous studies of using RFLP, AFLP, ISSR and SSR markers indicated that the Chinese accessions are much more diversified than samples from other regions. A high level of genetic diversity of an average of number of alleles of 20.9 per locus was identified using 77 SSR markers evaluating 250 Chinese foxtail millet landraces and four clusters were referred which well corresponded with geographical origin (Wang et al., 2012). A haplotype map of 0.8 million SNP of genome variation was constructed by re-sequencing 916 world wide foxtail millet landraces and cultivars, the level of genetic diversity as revealed was similar to that of indica rice (Oryza sativa). Two divergent groups that are strongly correlated with early and late flowering time, corresponding with north and south geographical distribution, were classified. Phenotyping of 47 morphological and agronomical characteristics in five different environments identified 512 loci, among which 59 association signals for the same traits were shared on at least two phenotyping locations. Genome wide variation comparison between Chinese landraces and improved cultivars revealed 36 selective sweeps that seem to have occurred during modern breeding selection (Jia et al., 2013). Those fundamental data will for sure promote foxtail millet and green foxtail becoming a novel model of the grasses family and help the improvement of foxtail millet as a rain-fed crop for the developing countries.