ArticleProceedings of the National Academy of Sciences of the United States of America1999
Phylogeny of rice genomes with emphasis on origins of allotetraploid species.
Article in Proceedings of the National Academy of Sciences of the United States of America, 1999. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 149 papers.
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149 citing papers in PubMed.
- Mapping the Molecular Evolution and Role of Wild Rice GLYIII Protein-Encoding Genes in Abiotic Stress Response.Biochemical genetics · 2026Article
- Telomere-to-telomere genome assembly of Oryza australiensis reveals transposon-driven centromere repositioning and shared EE-DD ancestry.Nature communications · 2026Article
- Harnessing salt tolerance and CScientific reports · 2026Article
- Comprehensive Evaluation of Bacterial Blight Resistance and Gene Distribution in Common Wild Rice (Plants (Basel, Switzerland) · 2026Article
- Whole-genome polymorphisms and relatedness of rice varieties circulating in the Mediterranean market.Scientific reports · 2025Article
- Diploidization in a wild rice allopolyploid is both episodic and gradual.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Oryza genome evolution through a tetraploid lens.Nature genetics · 2025Article
- Evolution and diversification of the momilactone biosynthetic gene cluster in the genus Oryza.The New phytologist · 2025Article
- Usage of wildBreeding science · 2025Article
- Tandemly duplicated Rubisco activase genes of cereals show differential evolution and response to heat stress.Plant molecular biology · 2024Article
- Tracing the intraspecies expansion of glyoxalase genes and their expanding roles across the genus Oryza.Functional & integrative genomics · 2024Article
- Genome evolution and diversity of wild and cultivated rice species.Nature communications · 2024Article
- Wild rice: unlocking the future of rice breeding.Plant biotechnology journal · 2024Review
- Selfing Promotes Spread and Introgression of Segregation Distorters in Hermaphroditic Plants.Molecular biology and evolution · 2024Article
- Phylogenomic profiles of whole-genome duplications in Poaceae and landscape of differential duplicate retention and losses among major Poaceae lineages.Nature communications · 2024Article
- Population structure and genetic differentiation analyses reveal high level of diversity and allelic richness in crop wild relatives of AA genome species of rice (Oryza sativa L.) in India.Journal of applied genetics · 2023Article
- Copy number variation of the restorer Rf4 underlies human selection of three-line hybrid rice breeding.Nature communications · 2023Article
- Complete Mitochondrial Genome Assembly of an Upland Wild Rice Species,Life (Basel, Switzerland) · 2023Article
- Mycoviruses: Antagonistic Potential, Fungal Pathogenesis, and Their Interaction withMicroorganisms · 2023Review
- Mining Salt Tolerance SNP Loci and Prediction of Candidate Genes in the Rice Bud Stage by Genome-Wide Association Analysis.Plants (Basel, Switzerland) · 2023Article
89 more citing papers are in PubMed but not listed here.
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4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The rice genus, Oryza, which comprises 23 species and 9 recognized genome types, represents an enormous gene pool for genetic improvement of rice cultivars. Clarification of phylogenetic relationships of rice genomes is critical for effective utilization of the wild rice germ plasm. By generating and comparing two nuclear gene (Adh1 and Adh2) trees and a chloroplast gene (matK) tree of all rice species, phylogenetic relationships among the rice genomes were inferred. Origins of the allotetraploid species, which constitute more than one-third of rice species diversity, were reconstructed based on the Adh gene phylogenies. Genome types of the maternal parents of allotetraploid species were determined based on the matK gene tree. The phylogenetic reconstruction largely supports the previous recognition of rice genomes. It further revealed that the EE genome species is most closely related to the DD genome progenitor that gave rise to the CCDD genome. Three species of the CCDD genome may have originated through a single hybridization event, and their maternal parent had the CC genome. The BBCC genome species had different origins, and their maternal parents had either a BB or CC genome. An additional genome type, HHKK, was recognized for Oryza schlechteri and Porteresia coarctata, suggesting that P. coarctata is an Oryza species. The AA genome lineage, which contains cultivated rice, is a recently diverged and rapidly radiated lineage within the rice genus.
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