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Originally published as Genetics Published Articles Ahead of Print on November 15, 2004.
Genetics, Vol. 169, 1639-1647, March 2005, Copyright © 2005
doi:10.1534/genetics.104.033175
The Population Structure of African Cultivated Rice Oryza glaberrima (Steud.)
Evidence for Elevated Levels of Linkage Disequilibrium Caused by Admixture with O. sativa and Ecological Adaptation
Mande Semon*,
Rasmus Nielsen
,
Monty P. Jones
and
Susan R. McCouch*,1
* Department of Plant Breeding, Cornell University, Ithaca, New York 14853
Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853
FARA, Accra, Ghana
1 Corresponding author: Plant Breeding Department, Cornell University, 162 Emerson Hall, Ithaca, NY 14853.
E-mail: srm4{at}cornell.edu
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 due not 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, subspecies 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.
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