The Extent of Linkage Disequilibrium in Rice (Oryza sativa L.)

Genetics - Tập 177 Số 4 - Trang 2223-2232 - 2007
Kristie A. Mather1, Ana L. Caicedo1, Nicholas R. Polato2, Kenneth M. Olsen1, Susan R. McCouch2, Michael D. Purugganan3,1
1Department of Genetics, North Carolina State University, Raleigh, North Carolina 27695
2Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853 and
3Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003

Tóm tắt

Abstract 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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Thông tin
Thông tin xuất bản

Genetics

Tập 177 Số 4

2223-2232

Thông tin tác giả