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, linkagedisequilibrium (LD) patterns have not been systematically characterizedacross the genome of Asian rice (Oryza sativa). Such informationis critical to fully exploit the genome sequence for mappingcomplex traits using association techniques. Here we characterizeLD in five 500-kb regions of the rice genome in three majorcultivated rice varieties (indica, tropical japonica, and temperatejaponica) and in the wild ancestor of Asian rice, Oryza rufipogon.Using unlinked SNPs to determine the amount of background linkagedisequilibrium in each population, we find that the extent ofLD is greatest in temperate japonica (probably >500 kb),followed by tropical japonica ( $~$ 150 kb) and indica ( $~$ 75 kb). LDextends over a shorter distance in O. rufipogon (<<40kb) than in any of the O. sativa groups assayed here. The differencesin the extent of LD among these groups are consistent with differencesin outcrossing and recombination rate estimates. As well asheterogeneity between groups, our results suggest variationin LD patterns among genomic regions. We demonstrate the feasibilityof genomewide association mapping in cultivated Asian rice usinga modest number of SNPs.