The three celebrated Institutes, namely, Institute of Crop Sciences/National Key Facilities for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 2) BGI, Bei Shan Industrial Zone, Yantian District, Shenzhen 518083, China and 3) the International Rice Research Institute, Metro Manila 1301, Philippines, in a combined effort re-sequenced 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.
The report enumerated here represents an international resequencing effort of 3,000 rice genomes. The data reported here serve 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.