Molecular evolution of dimeric α-amylase inhibitor genes in wild emmer wheat and its ecological association

Background  

α-Amylase inhibitors are attractive candidates for the control of seed weevils, as these insects are highly dependent on starch as an energy source. In this study, we aimed to reveal the structure and diversity of dimeric α-amylase inhibitor genes in wild emmer wheat from Israel and to elucidate the relationship between the emmer wheat genes and ecological factors using single nucleotide polymorphism (SNP) markers. Another objective of this study was to find out whether there were any correlations between SNPs in functional protein-coding genes and the environment.     

Adaptive polymorphism of tetrameric alpha-amylase inhibitors in wild emmer wheat

α-Amylase inhibitors are attractive candidates for the control of seed weevils as these insects are highly dependent on starch as an energy source. Wheat tetrameric α-amylase inhibitor (WTAI) is a mixture (60 kDa) of 3 units: WTAI-CM2 plus 2 WTAI-CM3 plus WTAI-CM16, where none of the subunits is active on its own. A total of 334 gene sequences were obtained from 14 populations (131 accessions= genotypes) of wild emmer wheat. The frequencies of SNPs in WTAI-CM2, WTAI-CM3 and WTAI-CM16 were 1 out of 87.6, 101.4, and 108.0 bases, where 5, 5 and 4 SNPs were detected in the coding sequence, respectively. The nucleotide sequence of each unit of tetrameric α-amylase inhibitors were much more conserved than that of dimeric or monomeric inhibitors. The wild emmer wheat populations showed diversity on three WTAI loci, both between and within populations. It was revealed that WTAI were naturally selected for across populations by a ratio of dN/dS as expected. The results of purifying and positive selection hypothesis (p<0.05) also showed that the sequences of WTAI were contributed by natural selection, which ensures the protein function conservation as well as the inhibition diversity with insects amylase enzyme. Ecological factors, singly or in combination, explained a significant proportion of the variations in the SNPs. Ecological factors have an important evolutionary role in gene differentiation at these loci, and tetrameric α-amylase inhibitors are obviously adaptively selected under different environments.