Genomic and Evolutionary Relationship of Foxtail Millet with its Setaria Relatives, a Genomic Model for Biofuel Grasses

Because of two of its species, foxtail millet (Setaria italica) and green foxtail (S. viridis) are emerging as novel models for the Panicoideae grasses including switch grass (Panicum virgatum), napiergrass (Pennisetum purpureum), pearl millet (Pennisetum glaucum), and maize (Zea mays), the genus Setaria of the grasses Poaceae family captures more and more attention. Although it is generally thought that there are about 125 species in this genus, the actual number of species world wide is ambiguous. Genomic and evolutionary kinship of widely distributed Setaria species lay the foundational knowledge of this group grasses. The diploid A genome was first described in green foxtail in the 1940s by Li et al., the wild ancestor of domesticated foxtail millet. The B genome of diploid S. adhaerans was identified by GISH (Genomic In Situ Hybridization) in 2001 by Benabdelmouna et al., and giant foxtail (S. faberi) and bristle foxtail (S. verticillata) were identified as being tetraploid, and composed of A and B genomes. The diploid genome of S. grisebachii was identified as being different from both A and B genomes, and designated as C genome by Wang et al. in 2009. Three other genomes of D (yellow foxtail, S. glauca), E (S. plicate) and F (S. arenaria) were identified by a combination of analyses by GISH and 5S rDNA and knotted 1 genomic sequences by Zhao et al., and those 6 types from A to F are all of the genomes so far identified. No detailed research on the evolutionary kinship of those 6 genomes has been conducted as of presently. Evolutionary phylogeny based on genomic sequences, revealed that genome A, B, and C are closely related, and it seems that A is a little closer to C than to B. No diploid species of genomes D, E and F have been identified so far, and samples of those 3 genomes exhibited multiploidy, including tetraploidy, hexaploidy and octploidy. Our sequence data indicated that the F genome is far from the A, B and C genomes, and that the genomes of D and E are somewhere between A, B, C, and F. For a clear understanding of the genetic relationship of the Setaria genus, more detailed work is needed.