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doi:10.1534/genetics.104.033175
A more recent version of this article appeared on March 1, 2005.
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The population structure of African cultivated rice (Oryza Glaberrima (Steud.): evidence for elevated levels of LD caused by admixture with O. sativa and ecological adaptation
Mande Semon 1, Rasmus Nielsen 1, Monty Jones 2 and Susan McCouch 1*
1 Cornell University
2 FARA c/o FAO Regional Office for Africa
* To whom correspondence should be addressed. E-mail: srm4{at}cornell.edu.
Submitted on July 7, 2004
Revised on November 1, 2004
Accepted on 1 November 2004
Genome-wide linkage disequilibrium (LD) was investigated for 198 accessions of Oryza glaberrima using 93 nuclear microsatellite markers. Significantly elevated levels of LD were detected, even among distantly located markers. Free recombination among loci at the population genetic level was shown (1) by a lack of decay in LD among markers on the same chromosome and (2) by a strictly increasing composite likelihood function for the recombination parameter. This suggested that the elevation in LD was not due to physical linkage but to other factors, such as population structure. A Bayesian clustering analysis confirmed this hypothesis, indicating that the sample of O. glaberrima in this study was subdivided into at least five cryptic subpopulations. Two of these subpopulations clustered with control samples of O. sativa, sub-species, indica and japonica, indicating that some O. glaberrima accessions represent admixtures. The remaining three O. glaberrima subpopulations were significantly associated with specific combinations of phenotypic traits - possibly reflecting ecological adaptation to different growing environments.
Key Words: Oryza glaberrima, linkage disequilbrium, microsatellite, population differentiation, population structure
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