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The 3,000 rice genomes project

The 3,000 rice genomes project

  • Correspondence: The 3,000 rice genomes project

  • † Equal contributors

Author Affiliations

Institute of Crop Sciences/National Key Facilities for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 S. Zhong-Guan-Cun St, Beijing 100081, China

BGI, Bei Shan Industrial Zone, Yantian District, Shenzhen 518083, China

International Rice Research Institute, DAPO 7777, Metro Manila 1301, Philippines

GigaScience 2014, 3:7  doi:10.1186/2047-217X-3-7

Correspondence:;;; † The list of project participants and their affiliations is given at the end of this paper.

Published: 28 May 2014



Rice, Oryza sativa L., is the staple food for half the world’s population. By 2030, the production of rice must increase by at least 25% in order to keep up with global population growth and demand. Accelerated genetic gains in rice improvement are needed to mitigate the effects of climate change and loss of arable land, as well as to ensure a stable global food supply.


We resequenced a core collection of 3,000 rice accessions from 89 countries. All 3,000 genomes had an average sequencing depth of 14×, with average genome coverages and mapping rates of 94.0% and 92.5%, respectively. From our sequencing efforts, approximately 18.9 million single nucleotide polymorphisms (SNPs) in rice were discovered when aligned to the reference genome of the temperate japonica variety, Nipponbare. Phylogenetic analyses based on SNP data confirmed differentiation of the O. sativa gene pool into 5 varietal groups – indica, aus/boro, basmati/sadri, tropical japonica and temperate japonica.


Here, we report an international resequencing effort of 3,000 rice genomes. This data serves as a foundation for large-scale discovery of novel alleles for important rice phenotypes using various bioinformatics and/or genetic approaches. It also serves to understand the genomic diversity within O. sativa at a higher level of detail. With the release of the sequencing data, the project calls for the global rice community to take advantage of this data as a foundation for establishing a global, public rice genetic/genomic database and information platform for advancing rice breeding technology for future rice improvement.

Oryza sativa; Genetic resources; Genome diversity; Sequence variants; Next generation sequencing