Rice, Oryza sativa L., is the staple food for half the world’s population. By 2030, rice production must increase by at least 25% 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.
Here, we include data from an international effort resequencing a core collection of 3,000 rice accessions from 89 countries as a global public good. The 3,000 sequenced rice genomes had an average sequencing depth of 14X, average genome coverage and mapping rates of 94.0% and 92.5%, respectively.
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.
Keywords: Oryza sativa, genetic resources, genome diversity, next generation sequencing
The 3000 rice genomes sequence data are now completely uploaded into the INSDC databases (the Sequence Read Archives (SRA) at EBI, DDBJ and NCBI), and available for easy download from the links noted below, rather than from GigaDB. NB - the mapping of each file as previously stored in GigaDB to the relevant location on the EBI FTP server can be found in the file seq_file_mapping_to_SRA.txt.
Please choose the appropriate geographical location:
Europe: EBI - PRJEB6180
USA: NCBI - PRJEB6180
Asia: DDBJ - ERP005654
Any inquires can be directed to any /all of the following members of the consortium:
Gengyun Zhang BGI, Shenzhen, China
Zhikang Li Chinese Academy of Agricultural Sciences, Beijing, China
Tian-Qing Zheng Chinese Academy of Agricultural Sciences, Beijing, China
Kenneth L. McNally International Rice Research Institute, Metro Manila, Philippines
Read the peer-reviewed publication(s):
Li, J.-Y., Wang, J., & Zeigler, R. S. (2014). The 3,000 rice genomes project: new opportunities and challenges for future rice research. GigaScience, 3(1). doi:10.1186/2047-217x-3-8
(2014). The 3,000 rice genomes project. GigaScience, 3(1). doi:10.1186/2047-217x-3-7
Wang, W., Mauleon, R., Hu, Z., Chebotarov, D., Tai, S., Wu, Z., … Zhang, F. (2018). Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature, 557(7703), 43–49. doi:10.1038/s41586-018-0063-9
Accessions (data included in GigaDB):