ena-STUDY-BGI-28-04-2014-03:33:36:055-14
The 3000 Rice Genomes Project
Background Rice, Oryza sativa L., is the staple food for half the world's population. By 2030, rice production must increase by at least 50% to keep pace with population growth. Accelerated genetic gains in rice improvement are needed to mitigate the effects of climate change and loss of arable land and to ensure global food supply.  Results Here, we briefly report an international effort on resequencing a core collection of 3000 rice accessions from 89 countries, and its deposition into GigaDB.org (http://dx.doi.org/10.5524/200001) and SRA as a global public good. The 3,000 sequenced rice genomes had an average sequencing depth of 14X, average genome coverages and mapping rates of 94.0% and 92.5%, respectively. About 18.9 million 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.  Conclusions This data provides 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 at a higher level of detail the genomic diversity within O. sativa. 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. Purified seeds of the sequenced accessions are (or will be available) from the IRGC or CNCGB as genetic stocks. Information on obtaining seeds from the IRGC can be found at this link (http://irri.org/our-work/seeds) and from the CNCGB can be found at this site (http://icgr.caas.net.cn/cgris_english.html).
Background Rice, Oryza sativa L., is the staple food for half the world's population. By 2030, rice production must increase by at least 50% to keep pace with population growth. Accelerated genetic gains in rice improvement are needed to mitigate the effects of climate change and loss of arable land and to ensure global food supply.  Results Here, we briefly report an international effort on resequencing a core collection of 3000 rice accessions from 89 countries, and its deposition into GigaDB.org (http://dx.doi.org/10.5524/200001) and SRA as a global public good. The 3,000 sequenced rice genomes had an average sequencing depth of 14X, average genome coverages and mapping rates of 94.0% and 92.5%, respectively. About 18.9 million 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.  Conclusions This data provides 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 at a higher level of detail the genomic diversity within O. sativa. 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. Purified seeds of the sequenced accessions are (or will be available) from the IRGC or CNCGB as genetic stocks. Information on obtaining seeds from the IRGC can be found at this link (http://irri.org/our-work/seeds) and from the CNCGB can be found at this site (http://icgr.caas.net.cn/cgris_english.html).