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Originally published as Genetics Published Articles Ahead of Print on October 18, 2007.
Genetics, Vol. 177, 2223-2232, December 2007, Copyright © 2007
doi:10.1534/genetics.107.079616
The Extent of Linkage Disequilibrium in Rice (Oryza sativa L.)
Kristie A. Mather*,1,
Ana L. Caicedo*,2,
Nicholas R. Polato
,3,
Kenneth M. Olsen*,4,
Susan McCouch and
Michael D. Purugganan*,
,5
* Department of Genetics, North Carolina State University, Raleigh, North Carolina 27695, Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853 and Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003
5 Corresponding author: Department of Biology, 1009 Main Bldg., 100 Washington Square East, New York, NY 10003.
E-mail: mp132{at}nyu.edu
Despite its status as one of the world's major crops, linkage disequilibrium (LD) patterns have not been systematically characterized across the genome of Asian rice (Oryza sativa). Such information is critical to fully exploit the genome sequence for mapping complex traits using association techniques. Here we characterize LD in five 500-kb regions of the rice genome in three major cultivated rice varieties (indica, tropical japonica, and temperate japonica) and in the wild ancestor of Asian rice, Oryza rufipogon. Using unlinked SNPs to determine the amount of background linkage disequilibrium in each population, we find that the extent of LD is greatest in temperate japonica (probably >500 kb), followed by tropical japonica (
150 kb) and indica (75 kb). LD extends over a shorter distance in O. rufipogon (<<40 kb) than in any of the O. sativa groups assayed here. The differences in the extent of LD among these groups are consistent with differences in outcrossing and recombination rate estimates. As well as heterogeneity between groups, our results suggest variation in LD patterns among genomic regions. We demonstrate the feasibility of genomewide association mapping in cultivated Asian rice using a modest number of SNPs.
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