Genomic variation in rice: genesis of highly polymorphic linkage blocks during domestication.

Tian Tang, Jian Lu, Jianzi Huang, Jinghong He, Susan R. McCouch, Yang Shen, Zeng Kai, Michael D. Purugganan, Suhua Shi, Chung I. Wu

Research output: Contribution to journalArticle

Abstract

Genomic regions that are unusually divergent between closely related species or racial groups can be particularly informative about the process of speciation or the operation of natural selection. The two sequenced genomes of cultivated Asian rice, Oryza sativa, reveal that at least 6% of the genomes are unusually divergent. Sequencing of ten unlinked loci from the highly divergent regions consistently identified two highly divergent haplotypes with each locus in nearly complete linkage disequilibrium among 25 O. sativa cultivars and 35 lines from six wild species. The existence of two highly divergent haplotypes in high divergence regions in species from all geographical areas (Africa, Asia, and Oceania) was in contrast to the low polymorphism and low linkage disequilibrium that were observed in other parts of the genome, represented by ten reference loci. While several natural processes are likely to contribute to this pattern of genomic variation, domestication may have greatly exaggerated the trend. In this hypothesis, divergent haplotypes that were adapted to different geographical and ecological environments migrated along with humans during the development of domesticated varieties. If true, these high divergence regions of the genome would be enriched for loci that contribute to the enormous range of phenotypic variation observed among domesticated breeds.

Original languageEnglish (US)
JournalPLoS Genetics
Volume2
Issue number11
DOIs
StatePublished - Nov 17 2006

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domestication
linkage (genetics)
genomics
rice
genome
Genome
Haplotypes
haplotypes
loci
Linkage Disequilibrium
linkage disequilibrium
disequilibrium
Oryza sativa
divergence
Oceania
human development
Genetic Selection
Pacific Ocean Islands
Human Development
natural selection

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology
  • Ecology, Evolution, Behavior and Systematics
  • Cancer Research
  • Genetics(clinical)

Cite this

Genomic variation in rice : genesis of highly polymorphic linkage blocks during domestication. / Tang, Tian; Lu, Jian; Huang, Jianzi; He, Jinghong; McCouch, Susan R.; Shen, Yang; Kai, Zeng; Purugganan, Michael D.; Shi, Suhua; Wu, Chung I.

In: PLoS Genetics, Vol. 2, No. 11, 17.11.2006.

Research output: Contribution to journalArticle

Tang, Tian ; Lu, Jian ; Huang, Jianzi ; He, Jinghong ; McCouch, Susan R. ; Shen, Yang ; Kai, Zeng ; Purugganan, Michael D. ; Shi, Suhua ; Wu, Chung I. / Genomic variation in rice : genesis of highly polymorphic linkage blocks during domestication. In: PLoS Genetics. 2006 ; Vol. 2, No. 11.
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