Phylogenetic relationships among species of Setaria (Paniceae; Panicoideae; Poaceae) in Korea: insights from nuclear (ITS and kn1) and chloroplast DNA sequence data

The genus Setaria (tribe Paniceae, subfamily Panicoideae, family Poaceae) comprises approximately 125 species, including agriculturally important food crop (Setaria italica) and globally distributed weed species (S. viridis, S. faberi, S. verticillata, and S. pumila). As an ongoing attempt to determine phylogenetic relationships among species of Setaria in East Asia, we generated phylogeny of Setaria based on a total of 44 accessions representing all the species in Korea. We sequenced two nuclear loci (nrDNA ITS and kn1) and three chloroplast DNA non-coding regions (trnL-trnF, psbJ-petA, and trnQ-rps16) and conducted maximum parsimony, maximum likelihood and Bayesian Inference analyses. The results identified two groups of Setaria in Korea, i.e., S. glauca (=S. pumila) group and S. viridis-S. faberi complex (S. viridis, S. italica, S. faberi, and S. x pycnocoma) group. Only one representative perennial species (i.e., S. chondrachne) in Korea is sister to the S. viridis-S. faberi clade. A minimum of two independent origins of S. faberi, a putative allotetraploid, is suggested in this study, but the contribution from B genome (i.e., S. adhaerens) was not supported. The origin of tetraploid, perennial species of Setaria in Korea, S. chondrachne, is uncertain, but this study suggests possible autotetraploidy and close relationship of S. chondrachne with A genome type species in S. viridis-S. faberi clade. We also documented possible ancient gene flow between D genome (i.e., S. glauca var. dura) and A genome (e.g., S. viridis) in this study.