Phylogeny of Rice Genomes with Emphasis on Origins of Allotetraploid Species

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 an...

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Bibliographic Details
Published in:Proceedings of the National Academy of Sciences - PNAS 1999-12, Vol.96 (25), p.14400-14405
Main Authors: Ge, Song, Sang, Tao, Lu, Bao-Rong, Hong, De-Yuan
Format: Article
Language:English
Subjects:
Adh1 gene
Adh2 gene
Alcohol Dehydrogenase - genetics
Base Sequence
Biological Sciences
Biological taxonomies
Chloroplasts - genetics
Diploidy
Evolution
Genes
Genetic loci
Genome, Plant
Genomes
Genomics
matK gene
Molecular Sequence Data
Oryza - classification
Oryza - genetics
Oryza schlechteri
Parsimony
Phylogenetics
Phylogeny
Plants
Polymerase Chain Reaction
Polyploidy
Porteresia coarctata
Rice
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Summary: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.
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.96.25.14400