A novel chimeric low-molecular-weight glutenin subunit gene from the wild relatives of wheat Aegilops kotschyi and Ae. juvenalis:: Evolution at the Glu-3 Loci

Four LMW-m and one novel chimeric (between LMAV-i and LMW-m types) glutenin subunit (LMW-GS) genes from Aegilops neglecta, (UUMM), Ae. kotschyi (UUSS), and Ae. (DDMMUU) were isolated and characterized. Sequence structures showed that the 4 LMW-m-type genes, assigned to the M genome of Ae. neglecta, displayed a high homology with those from hexaploid common wheat. The novel chimeric gene, designed as AjkLMW-i, was isolated form both Ae. kotschyi and Ae. juvenalis and shown to be located on the U genome. Phylogentic analysis demonstrated that it had higher identity to the LMW-m-type than the LMW-i-type genes. A total of 20 single nucleotide polymorphisms (SNPs) were detected among the 4 LMW-m genes, with 13 of these being nonsynonymous SNPs that resulted in amino acid substitutions in the deduced mature proteins. Phylogenetic analysis demonstrated that it had higher identity to the LMW-m-type than the LMW-i-type genes. The divergence time estimation showed that the M and D genomes were closely related and diverged at 5.42 million years ago (NRA) while the differentiation between the U and A genomes was 6.82 MYA. We propose that, in addition to homologous recombination, all illegitimate recombination event on the U genome may have occurred 6.38 MYA and resulted in the generation of the chimeric gene which may be an important genetic mechanism for the origin and evolution of LMW-GS Glu-3 alleles as well as other prolamin genes.