The Extent of Linkage Disequilibrium in Rice (Oryza sativa L.)
| Autor: | Susan R. McCouch, Nicholas R. Polato, Ana L. Caicedo, Michael D. Purugganan, Kenneth M. Olsen, Kristie A. Mather |
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| Rok vydání: | 2007 |
| Předmět: |
Crops
Agricultural Recombination Genetic Genetics education.field_of_study Linkage disequilibrium Oryza sativa Base Sequence biology Genetic Linkage Molecular Sequence Data Population food and beverages Oryza Single-nucleotide polymorphism Outcrossing Investigations biology.organism_classification Polymorphism Single Nucleotide Oryza rufipogon Genome Linkage Disequilibrium Japonica education Genome Plant |
| Zdroj: | Genetics. 177:2223-2232 |
| ISSN: | 1943-2631 |
| DOI: | 10.1534/genetics.107.079616 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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