The 3,000 rice genomes project
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 an...
| Autores principales: | , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
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Oxford University Press
2014
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| Acceso en línea: | https://hdl.handle.net/10568/165521 |
| _version_ | 1855543564057968640 |
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| author | Li, Z.K. Zhang, G.Y. McNally, K.L. |
| author_browse | Li, Z.K. McNally, K.L. Zhang, G.Y. |
| author_facet | Li, Z.K. Zhang, G.Y. McNally, K.L. |
| author_sort | Li, Z.K. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | 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. |
| format | Journal Article |
| id | CGSpace165521 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2014 |
| publishDateRange | 2014 |
| publishDateSort | 2014 |
| publisher | Oxford University Press |
| publisherStr | Oxford University Press |
| record_format | dspace |
| spelling | CGSpace1655212025-05-14T10:40:03Z The 3,000 rice genomes project Li, Z.K. Zhang, G.Y. McNally, K.L. alleles bioinformatics climatic change dna sequencing gene mapping genes genetic variation genomes nucleotide sequences single nucleotide polymorphism 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. 2014-12-01 2024-12-19T12:55:09Z 2024-12-19T12:55:09Z Journal Article https://hdl.handle.net/10568/165521 en Open Access Oxford University Press Li, Z. K.; Zhang, G. Y. and McNally, K. L.. 2014. The 3,000 rice genomes project. GigaSci, Volume 3, no. 1 |
| spellingShingle | alleles bioinformatics climatic change dna sequencing gene mapping genes genetic variation genomes nucleotide sequences single nucleotide polymorphism Li, Z.K. Zhang, G.Y. McNally, K.L. The 3,000 rice genomes project |
| title | The 3,000 rice genomes project |
| title_full | The 3,000 rice genomes project |
| title_fullStr | The 3,000 rice genomes project |
| title_full_unstemmed | The 3,000 rice genomes project |
| title_short | The 3,000 rice genomes project |
| title_sort | 3 000 rice genomes project |
| topic | alleles bioinformatics climatic change dna sequencing gene mapping genes genetic variation genomes nucleotide sequences single nucleotide polymorphism |
| url | https://hdl.handle.net/10568/165521 |
| work_keys_str_mv | AT lizk the3000ricegenomesproject AT zhanggy the3000ricegenomesproject AT mcnallykl the3000ricegenomesproject AT lizk 3000ricegenomesproject AT zhanggy 3000ricegenomesproject AT mcnallykl 3000ricegenomesproject |