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Proc Natl Acad Sci U S A. 2009 Jul 28;106(30):12273-8. doi: 10.1073/pnas.0900992106. Epub 2009 Jul 13.

Genomewide SNP variation reveals relationships among landraces and modern varieties of rice.

Author information

1
International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, The Philippines. k.mcnally@cgiar.org

Abstract

Rice, the primary source of dietary calories for half of humanity, is the first crop plant for which a high-quality reference genome sequence from a single variety was produced. We used resequencing microarrays to interrogate 100 Mb of the unique fraction of the reference genome for 20 diverse varieties and landraces that capture the impressive genotypic and phenotypic diversity of domesticated rice. Here, we report the distribution of 160,000 nonredundant SNPs. Introgression patterns of shared SNPs revealed the breeding history and relationships among the 20 varieties; some introgressed regions are associated with agronomic traits that mark major milestones in rice improvement. These comprehensive SNP data provide a foundation for deep exploration of rice diversity and gene-trait relationships and their use for future rice improvement.

PMID:
19597147
PMCID:
PMC2718348
DOI:
10.1073/pnas.0900992106
[Indexed for MEDLINE]
Free PMC Article

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