Structural organization and functional divergence of high isoelectric point -amylase genes in bread wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.)

BackgroundHigh isoelectric point -amylase genes (Amy1) play major roles during cereal seed germination, and are associated with unacceptable high residual -amylase activities in ripe wheat grains. However, in wheat and barley, due to extremely high homology of duplicated copies, and large and complex genome background, the knowledge on this multigene family is limited.ResultsIn the present work, we identified a total of 41 Amy1 genes among 13 investigated grasses. By using genomic resources and experimental validation, the exact copy numbers and chromosomal locations in wheat and barley were determined. Phylogenetic and syntenic analyses revealed tandem gene duplication and chromosomal rearrangement leading to separation of Amy1 into two distinct loci, Amy1 and Amy1. The divergence of Amy1 from Amy1 was driven by adaptive selection pressures performed on two amino acids, Arg(97) and Asn(233) (P>0.95*). The predicted protein structural alteration caused by substitution of Asp(233)Asn in the conserved starch binding surface site, and significantly expressional differentiation during seed germination and grain development provided evidence of functional divergence between Amy1 and Amy1 genes. We screened out candidate copies (TaAmy1-A1/A2 and TaAmy1-D1) associated with high residual -amylase activities in ripe grains. Furthermore, we proposed an evolutionary model for expansion dynamics of Amy1 genes.ConclusionsOur study provides comprehensive analyses of the Amy1 multigene family, and defines the fixation of two spatially structural Amy1 loci in wheat and barley. Potential functional divergence between them is reflected by their sequence features and expressional patterns, and driven by gene duplication, chromosome rearrangement and natural selections during gene family evolution. Furthermore, the discrimination of differentially effective copies during seed germination and/or grain development will provide guidance to manipulation of -amylase activity in wheat and barley breeding for better yield and processing properties.