Abstract
BackgroundVarious enzyme inhibitors act on key insect gut digestive hydrolases, including alpha-amylases and proteinases. Alpha-amylase inhibitors have been widely investigated for their possible use in strengthening a plant's defense against insects that are highly dependent on starch as an energy source. We attempted to unravel the diversity of monomeric alpha-amylase inhibitor genes of Israeli and Golan Heights' wild emmer wheat with different ecological factors (e.g., geography, water, and temperature). Population methods that analyze the nature and frequency of allele diversity within a species and the codon analysis method (comparing patterns of synonymous and non-synonymous changes in protein coding sequences) were used to detect natural selection.ResultsThree hundred and forty-eight sequences encoding monomeric alpha-amylase inhibitors (WMAI) were obtained from 14 populations of wild emmer wheat. The frequency of SNPs in WMAI genes was 1 out of 16.3 bases, where 28 SNPs were detected in the coding sequence. The results of purifying and the positive selection hypothesis (p < 0.05) showed that the sequences of WMAI were contributed by both natural selection and co-evolution, which ensured conservation of protein function and inhibition against diverse insect amylases. The majority of amino acid substitutions occurred at the C-terminal (positive selection domain), which ensured the stability of WMAI. SNPs in this gene could be classified into several categories associated with water, temperature, and geographic factors, respectively.ConclusionsGreat diversity at the WMAI locus, both between and within populations, was detected in the populations of wild emmer wheat. It was revealed that WMAI were naturally selected for across populations by a ratio of dN/dS as expected. Ecological factors, singly or in combination, explained a significant proportion of the variations in the SNPs. A sharp genetic divergence over very short geographic distances compared to a small genetic divergence between large geographic distances also suggested that the SNPs were subjected to natural selection, and ecological factors had an important evolutionary role in polymorphisms at this locus. According to population and codon analysis, these results suggested that monomeric alpha-amylase inhibitors are adaptively selected under different environmental conditions.
Highlights
Various enzyme inhibitors act on key insect gut digestive hydrolases, including alpha-amylases and proteinases
Characterization of monomeric a-amylase inhibitors Genomic PCR amplifications were conducted by specific wheat monomeric a-amylase inhibitor (WMAI) cloning primers, and desired PCR products were detected in accessions of wild emmer wheat
Our results demonstrated that the polymorphism of monomeric a-amylase inhibitor genes in wild emmer wheat was correlated with the ecogeographic distribution of the accessions
Summary
Various enzyme inhibitors act on key insect gut digestive hydrolases, including alpha-amylases and proteinases. Population methods that analyze the nature and frequency of allele diversity within a species and the codon analysis method (comparing patterns of synonymous and non-synonymous changes in protein coding sequences) were used to detect natural selection. Two major classes of methods are currently in use to detect natural selection: population methods, based on analyzing the nature and frequency of allele diversity within a species, and codon analysis methods, based on comparing patterns of synonymous and non-synonymous changes in protein coding sequences. Purifying selection is expected to act against mutations that have deleterious effects on protein structure by causing changes to functionally important amino acid residues or by altering the regulation of gene expression [4]. The ratio of the observed non-synonymous mutation rate to the synonymous mutation rate can be utilized as an estimate of selective pressure, where dN/dS < 1 suggests that most amino acid substitutions have been eliminated by the purifying selection, while a dN/dS > 1 indicates positive selection [6]
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