title: The extent of linkage disequilibrium in rice (Oryza sativa L.).
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 (approximately 150 kb) and indica (approximately 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.
authors.affiliation: Department of Genetics, North Carolina State University, Raleigh 27695, USA.
authors.forename: Kristie A
authors.initials: KA
authors.lastname: Mather
authors.forename: Ana L
authors.initials: AL
authors.lastname: Caicedo
authors.forename: Nicholas R
authors.initials: NR
authors.lastname: Polato
authors.forename: Kenneth M
authors.initials: KM
authors.lastname: Olsen
authors.forename: Susan
authors.initials: S
authors.lastname: McCouch
authors.forename: Michael D
authors.initials: MD
authors.lastname: Purugganan
mesh_terms: D001483:Base Sequence; D018556:Crops, Agricultural / Q000235:genetics; D008040:Genetic Linkage; D018745:Genome, Plant; D015810:Linkage Disequilibrium; D008969:Molecular Sequence Data; D012275:Oryza / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D011995:Recombination, Genetic