Genome change in wheat observed through the structure and expression of α/β-gliadin genes

To better understand genome structure and the expression of alpha/beta-gliadin multigenes in hexaploid wheat, bacterial artificial chromosome (BAC) clones containing alpha/beta-gliadin genes from the three loci, Gli-A2, Gli-B2, and Gli-D2, were screened. Based on their restriction fragment patterns, we selected five BAC clones, namely, two clones for Gli-A2, two clones for Gli-B2, and one clone for Gli-D2, to fully sequence. Approximately 200 kb was sequenced for each locus. In total, twelve alpha/beta-gliadin intact genes and four pseudogenes were found, and retrotransposons or other transposons existed in each BAC clone. Dot-plot analysis revealed the pattern of genome segmental duplication within each BAC. We calculated time since duplication of each set of alpha/beta-gliadin genes and insertion of retrotransposons. Duplication of all adjacent genes within the same BAC clone took place before or after allotetrapolyploidization, but duplication of certain genes occurred before diploid differentiation of wheat species. Retrotransposons were also inserted before and after the segmental duplication events. Furthermore, translocation of alpha/beta-gliadin genes from chromosomes 1 to 6 apparently occurred before the diversification of various wheat genomes. Duplication of genome segments containing alpha/beta-gliadin genes and retrotransposons were brought about through unequal crossing-over or saltatory replication and alpha/beta-gliadin genes per se were duplicated without any recombination events. Out of twelve intact alpha/beta-gliadin genes detected from their sequences, nine were expressed, although their patterns of expression were distinct. Since they have similar cis-elements and promoter structures, the mechanisms underlying their distinct gene expression and possible applications are discussed.