Abstract
Backgroundα-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.ResultsThe influence of ecological factors on the genetic structure of dimeric α-amylase inhibitor genes was evaluated by specific SNP markers. A total of 244 dimeric α-amylase inhibitor genes were obtained from 13 accessions in 10 populations. Seventy-five polymorphic positions and 74 haplotypes were defined by sequence analysis. Sixteen out of the 75 SNP markers were designed to detect SNP variations in wild emmer wheat accessions from different populations in Israel. The proportion of polymorphic loci P (5%), the expected heterozygosity He, and Shannon's information index in the 16 populations were 0.887, 0.404, and 0.589, respectively. The populations of wild emmer wheat showed great diversity in gene loci both between and within populations. Based on the SNP marker data, the genetic distance of pair-wise comparisons of the 16 populations displayed a sharp genetic differentiation over long geographic distances. The values of P, He, and Shannon's information index were negatively correlated with three climatic moisture factors, whereas the same values were positively correlated by Spearman rank correlation coefficients' analysis with some of the other ecological factors.ConclusionThe populations of wild emmer wheat showed a wide range of diversity in dimeric α-amylase inhibitors, both between and within populations. We suggested that SNP markers are useful for the estimation of genetic diversity of functional genes in wild emmer wheat. These results show significant correlations between SNPs in the α-amylase inhibitor genes and ecological factors affecting diversity. Ecological factors, singly or in combination, explained a significant proportion of the variations in the SNPs, and the SNPs could be classified into several categories as ecogeographical predictors. It was suggested that the SNPs in the α-amylase inhibitor genes have been subjected to natural selection, and ecological factors had an important evolutionary influence on gene differentiation at specific loci.
Highlights
Wild emmer wheat, Triticum dicoccoides, the progenitor of bread and pasta wheats, presumably originated in and adaptively diversified from, northeastern Israel into the Near East Fertile Crescent [1]
The estimates of molecular diversity derived from PCRbased techniques such as amplified restriction fragment length polymorphism (AFLP), microsatellites, single nucleotide polymorphism (SNP), and sequence comparisons are several-fold higher than enzymatic diversity [6]
SNPs are identified in ESTs, the polymorphisms could be directly used to map functional and expressed genes, rather than DNA sequences derived from conventional RAPD and AFLP techniques, which are typically not functional genes [7,8,9]
Summary
Triticum dicoccoides, the progenitor of bread and pasta wheats, presumably originated in and adaptively diversified from, northeastern Israel into the Near East Fertile Crescent [1]. In this center of diversity, wild emmer wheat harbors rich genetic diversity and resources [1]. Previous studies in T. dicoccoides and other cereals have shown significant nonrandom adaptive molecular genetic differentiation at single and multilocus structures in either protein-coding regions or randomly amplified polymorphic DNAs among micro-ecological environments [2,3]. The majority of SNPs in coding regions (cSNPs) are single-base substitutions, which may or may not result in amino acid changes. Some cSNPs may alter a functionally important amino acid residue, and these are of interest for their potential links with phenotypes [10]
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