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PMID: 10588717 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Phylogeny of rice genomes with emphasis on origins of allotetraploid species.

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 96 ·No. 25 ·1999-12-07 ·Pages 14400-5

Ge S, Sang T, Lu BR, Hong DY

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.

MeSH Terms
Alcohol Dehydrogenase/genetics Base Sequence Chloroplasts/genetics Genome, Plant Molecular Sequence Data Oryza/classification,genetics Phylogeny Polymerase Chain Reaction Polyploidy
Chemicals
Alcohol Dehydrogenase
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Ge S
Laboratory of Systematic Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China. [email protected]
Sang T
Lu B R
Hong D Y
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Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
0027-8424
DOI
10.1073/pnas.96.25.14400
Email
[email protected]
Published
1999-12-07
Pages
14400-5
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC24448
Subset
IM
Databases
GENBANK
AF148568, AF148569, AF148570, AF148571, AF148572, AF148573, AF148574, AF148575, AF148576, AF148577, AF148578, AF148579, AF148580, AF148581, AF148582, AF148583, AF148584, AF148585, AF148586, AF148587, AF148588, AF148589, AF148590, AF148591, AF148592, AF148593, AF148594, AF148595, AF148596, AF148597
External Links
PubMed source DOI: 10.1073/pnas.96.25.14400 PMC Full Text View journal details
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