Sequence polymorphisms and relationships of dimeric α-amylase inhibitor genes in the B genomes of Triticum and S genomes of Aegilops

One hundred and fifty-nine sequences encoding dimeric α-amylase inhibitors were characterized from Triticum and Aegilops. These sequences had 375 nucleotides in length, among which there were 255 conserved sites, 50 singleton variable sites (the nucleotide polymorphism only observed in a single accession) and 70 polymorphic sites (the polymorphisms found in two or more accessions). The frequency of SNPs in the B (a.k.a. S) genomes coding α-amylase inhibitor genes was 1.7 out of 10 bases. A total of 59 haplotypes were defined, among which 4 main haplotypes occurring in more than 10 genes and 36 haplotypes with single gene were found, indicating that the dimeric α-amylase inhibitors might derive from a very limited number of ancestral genes. The phylogenetic median-joining network of the 59 haplotypes was highly star like with 5 haplotype groups, and at least 2 sub clusters emerged. Evolutionary distances of the 159 genes were calculated, and subjected to the construction of neighbour-joining trees that showed that the α-amylase inhibitor genes were divided into 5 groups, and each group had at least 2 subgroups. The neighbour-joining tree of the species indicated that the genes from common wheat and Triticum dicoccoides were closely related to those from Aegilops speltoides, and it was further supported by the median-joining networks analysis of the 59 haplotypes. These results revealed the important information on genome shaping events and processes occurring at dimeric α-amylase inhibitor genes loci and contributed to our understanding of functional aspects of the dimeric α-amylase inhibitor genes, as well as phylogenetic relationships between species.