Nucleotide diversity and minisatellite in chloroplast Asp(GUC)-Thr(GGU) region in Elymus trachycaulus complex, Elymus alaskanus and Elymus caninus

Nucleotide variation in chloroplast Asp(GUC)-Thr(GGU) intergenic region and genetic relationships among this group were examined among Elymus trachycaulus complex, Elymus alaskanus and Elymus caninus. The estimates of nucleotide diversity (π) ranged from 0.00111 for Elymus virescens to 0.03086 for E. caninus. Highest nucleotide diversity was found for E. caninus among the taxa analyzed here and followed by Elymus hyperarcticus. E. virescens accessions are genetically very uniform. Phylogenetic analysis suggested that E. caninus is paraphyletic. Elymus violaceus is genetically distinct from both E. alaskanus and E. trachycaulus. Our result indicates that Asp (GUC)-Thr (GGU) intergenic region has a high rate of evolutionary in Elymus species. Large indels detected in this region appear to have a highly rate of evolution and are thus more prone to homoplasy. We also first reported a minisatellite discovered in Asp (GUC)-Thr (GGU) region in Elymus species. The minisatellite identified here is an excellent candidate marker for studying population structures of Elymus species.