Classification of 17 species using DNA barcoding and SNPs, reveals gene flow among , , and .

Rapid changes in agricultural environments caused by global warming pose a major challenge to food production and safety. Common wheat () is a hexaploid plant (AABBDD) that shares large numbers of quantitative traits and resistance genes with B and D genomes of species, which are responsible for several metabolic functions and biosynthetic processes, particularly in plant adaptation to biotic as well as abiotic stresses. Comparatively, the abundance of the gene pool is much higher than that of . Therefore, we used four universal DNA barcodes for plants (ITS2, K, L, and MN) to construct a phylogenetic tree to classify the genus . Fourteen species were distinguished among a total of 17 representative species. , , and could not be grouped into any of the clusters in the phylogenetic tree, indicating that these three species could not be distinguished by four DNA barcodes. Therefore, from 2408 SNPs obtained using genotyping by sequencing (GBS), we manually screened 30 SNPs that could be potentially used to classify these three species. The results of gene flow and genetic differentiation index (Fst) showed that the genetic differentiation among the three species was small, and there was bidirectional horizontal gene transfer between the three species, which was consistent with our results that the three species were difficult to classify by DNA barcode.