Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 106, Issue 30, Pages 12273-12278Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.0900992106
Keywords
introgression; Oryza sativa; resequencing; SNP discovery
Categories
Funding
- International Rice Research Institute
- U. S. Department of Agriculture-Cooperative State Research, Education, and Extension [2006-35604-16628]
- Generation Challenge Program [2005-35]
- Max Planck Society
- Deutsche Forschungsgemeinschaft
- Bundesministerium Fur Wirtschaftliche Zusammenarbeit
- Ford Foundation Diversity Fellowship
- U. S. Department of Agriculture-Cooperative State Research, Education
- Extension Service-National Research Initiative-Rice-Conservation Assessment Program [2004-35317-14867]
- National Science Foundation [0606461, 0701382]
- Division Of Integrative Organismal Systems
- Direct For Biological Sciences [0701382] Funding Source: National Science Foundation
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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.
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