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

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 limitat...

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Bibliographic Details
Published inAgronomy (Basel) Vol. 13; no. 8; p. 2100
Main Authors Cho, Yeonghun, Lim, Insu, Ha, Jungmin
Format Journal Article
LanguageEnglish
Published Basel MDPI AG 01.08.2023
Subjects
Alleles
Breeding
Chromosomes
Cultivars
Cultivation
DNA methylation
Domestication
Enzymes
Evolution
Gene transfer
Genes
Genetic diversity
genome compatibility
Genomes
Glucose
Grain cultivation
introgression breeding
Oryza
Phylogenetics
Phylogeny
Plant breeding
Population genetics
Rice
rice (genus Oryza)
Species
Species diversity
Synteny
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Summary: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.
ISSN:2073-4395
2073-4395
DOI:10.3390/agronomy13082100