Phylogenetic and population genomic analysis of foxtail millet (Setaria italica) landraces via ddRAD-seq, with emphasis on Japanese germplasm

Abstract

We clarified the phylogeny and population structure of foxtail millet (Setaria italica (L.) P. Beauv.) landraces using ddRAD-seq, which also enabled us to focus in detail on Japanese landraces. The results were compared with those of previous phylogenetic studies based on transposon display and genotyping of individual genes involved in domestication and diversification under natural and artificial selection. Foxtail millet landraces were found to cluster into distinct geographical groups. The comparison revealed that certain genes, such as Heading date 1, began diverging soon after domestication. In contrast, genes such as Pseudo-response regulator 37 appeared to have differentiated before geographic divergence, likely in response to environmental adaptation. However, genes such as Waxy loci diversified after geographic separation under human selection. Implication of introgression between geographically distant groups was also observed, for example, between French and East Asian landraces. In Japan, two distinct landrace groups were identified: one closely related to Korean landraces and the other showing genetic similarity to accessions from Taiwan and the Batan Islands of the Philippines. The latter group is predominantly distributed in the Nansei Islands (Okinawa Prefecture), indicating multiple introductions and complex dispersal histories of foxtail millet in Japan.