The Rice 3000 Genomes Project Data.

Dataset type: Genomic
Data released on May 27, 2014

The 3000 Rice Genomes Project (2014): The Rice 3000 Genomes Project Data. GigaScience Database. http://dx.doi.org/10.5524/200001

DOI10.5524/200001


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

Additional details

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

Related datasets:

doi:10.5524/200001 IsReferencedBy doi:10.5524/100199

Accessions (data included in GigaDB):

ENA: PRJEB6180

Projects:







File NameSample IDData TypeFile FormatSizeRelease Date 
Tabular dataCSV5.02 KB2014-04-28
ReadmeTEXT1.8 KB2014-04-28
External linkUNKNOWN0 KB2014-10-29
Tabular dataEXCEL421.32 KB2014-10-29
Tabular dataTEXT23.33 MB2014-04-28
Displaying 1-5 of 5 File(s).
Date Action
October 13, 2015 File rice3K_sequence_data_at_EBI updated
October 19, 2015 File rice3K_sequence_data_at_EBI updated
October 19, 2015 File readme.txt updated
October 20, 2015 File rice3K_sequence_data_at_EBI updated
October 20, 2015 File consortium_list.csv updated
October 20, 2015 File rice_line_metadata_20141029.xlsx updated
October 20, 2015 File seq_file_mapping_to_SRA.txt updated
October 23, 2015 File seq_file_mapping_to_SRA.txt updated
October 23, 2015 File seq_file_mapping_to_SRA.txt updated
October 23, 2015 File rice3K_sequence_data_at_EBI updated
October 23, 2015 File rice3K_sequence_data_at_EBI updated
October 26, 2015 File rice_line_metadata_20141029.xlsx updated
October 28, 2015 File rice3K_sequence_data_at_EBI updated
November 1, 2015 File rice_line_metadata_20141029.xlsx updated
November 2, 2015 File rice_line_metadata_20141029.xlsx updated
November 2, 2015 File rice3K_sequence_data_at_EBI updated
November 3, 2015 File consortium_list.csv updated
November 3, 2015 File readme.txt updated
November 3, 2015 File rice3K_sequence_data_at_EBI updated
November 3, 2015 File seq_file_mapping_to_SRA.txt updated
November 4, 2015 File consortium_list.csv updated
November 4, 2015 File consortium_list.csv updated
November 4, 2015 File readme.txt updated
November 4, 2015 File rice_line_metadata_20141029.xlsx updated
November 4, 2015 File rice_line_metadata_20141029.xlsx updated
November 4, 2015 File rice_line_metadata_20141029.xlsx updated
November 4, 2015 File rice3K_sequence_data_at_EBI updated
November 5, 2015 File seq_file_mapping_to_SRA.txt updated
November 5, 2015 File rice_line_metadata_20141029.xlsx updated
November 6, 2015 File rice_line_metadata_20141029.xlsx updated
November 8, 2015 File rice_line_metadata_20141029.xlsx updated
November 9, 2015 File rice_line_metadata_20141029.xlsx updated
May 8, 2018 Manuscript Link added : 10.1038/s41586-018-0063-9