Background: Gene duplication can provide genetic basis for the evolution. The neo/sub-functionalization of redundant copies can promote plant growth and development, improve environmental adaptability, and even form new species.
Methods: We systematically identified the duplication genes and their origin of maize by comprehensively utilizing methods of homologous clustering, chromosomal collinearity, Ks analysis and phylogenetic analysis. The distinction of duplicated genes was analyzed by comparing the gene structure, sequence composition, expression, and functional differentiation.
Results: More than 70% of the genes in the maize genome have been found to be duplication genes, and mainly derived from the whole-genome duplication (WGD). The gene structure of the WGD genes is more complex, with rich components and long CDS. The GC content of WGD genes contributes to the bimodal distribution, indicating that a part of the duplicated gene contains abundant GC bases. The expression level of WGD genes is high and possesses tissue-specificity. The functionally differentiated duplication genes are mainly involved in the growth and stress response of maize.
Conclusions: The results of this study indicate that duplication genes produced by WGD provide new adaptability to maize growth, morphogenesis, and biotic and abiotic stress resistance, which are important to the evolution of maize.