Genome-Wide Syntenic and Evolutionary Analysis of 30 Key Genes Found in Ten Oryza Species

Abstract

Rice is a vital staple food crop worldwide, providing nutrition and sustenance to a significant portion of the global population. The genetic diversity of cultivated rice species has been significantly reduced during domestication, resulting in the loss of favorable alleles. To overcome this limitation, wild rice species have been used in introgression breeding programs to introduce beneficial alleles. In this study, we performed syntenic and phylogenetic analyses for 10 Oryza species, comprising both cultivar and wild species. Pairwise syntenic analysis revealed 3885 synteny blocks containing 1,023,342 gene pairs among 10 species. O. nivara contained the most blocks that were syntenous with the other nine species. In total, 425 paralogous and orthologous genes were identified for 30 key genes involved in rice breeding. His1 (43), GS3 (28), and qSW5/GW5 (27) had the most paralogous and orthologous genes. For GS3 and qSW5/GW5, two gene transfer events were detected. These findings have implications for rice breeding strategies, particularly with respect to gene pyramiding and introgression breeding programs. This research will contribute to the development of elite cultivars with improved quality and yield to meet the growing global demand for high-quality rice.