URL: | http://ricevarmap.ncpgr.cn/ |
Full name: | Rice Variation Map |
Description: | RiceVarMap v2.0 is a comprehensive database for rice genomic variation and its functional annotation. It provides curated information of 17,397,026 genomic variations (including 14,541,446 SNPs and 2,855,580 small INDELs ) from sequencing data of 4,726 rice accessions. These variations were identified using GATK software based on the assembly Os-Nipponbare-Reference-IRGSP-1.0. |
Year founded: | 2015 |
Last update: | 2023-01-31 |
Version: | v2.0 |
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Country/Region: | China |
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University/Institution: | Huazhong Agricultural University |
Address: | Wuhan 430070,China |
City: | Wuhan |
Province/State: | Hubei |
Country/Region: | China |
Contact name (PI/Team): | Weibo Xie |
Contact email (PI/Helpdesk): | weibo.xie@mail.hzau.edu.cn |
An inferred functional impact map of genetic variants in rice. [PMID: 34214659]
Interpreting the functional impacts of genetic variants (GVs) is an important challenge for functional genomic studies in crops and next-generation breeding. Previous studies in rice (Oryza sativa) have focused mainly on the identification of GVs, whereas systematic functional annotation of GVs has not yet been performed. Here, we present a functional impact map of GVs in rice. We curated haplotype information for 17 397 026 GVs from sequencing data of 4726 rice accessions. We quantitatively evaluated the effects of missense mutations in coding regions in each haplotype based on the conservation of amino acid residues and obtained the effects of 918 848 non-redundant missense GVs. Furthermore, we generated high-quality chromatin accessibility (CA) data from six representative rice tissues and used these data to train deep convolutional neural network models to predict the impacts of 5 067 405 GVs for CA in regulatory regions. We characterized the functional properties and tissue specificity of the GV effects and found that large-effect GVs in coding and regulatory regions may be subject to selection in different directions. Finally, we demonstrated how the functional impact map could be used to prioritize causal variants in mapping populations. This impact map will be a useful resource for accelerating gene cloning and functional studies in rice, and can be freely queried in RiceVarMap V2.0 (http://ricevarmap.ncpgr.cn). |
RiceVarMap: a comprehensive database of rice genomic variations. [PMID: 25274737]
Rice Variation Map (RiceVarMap, http:/ricevarmap.ncpgr.cn) is a database of rice genomic variations. The database provides comprehensive information of 6,551,358 single nucleotide polymorphisms (SNPs) and 1,214,627 insertions/deletions (INDELs) identified from sequencing data of 1479 rice accessions. The SNP genotypes of all accessions were imputed and evaluated, resulting in an overall missing data rate of 0.42% and an estimated accuracy greater than 99%. The SNP/INDEL genotypes of all accessions are available for online query and download. Users can search SNPs/INDELs by identifiers of the SNPs/INDELs, genomic regions, gene identifiers and keywords of gene annotation. Allele frequencies within various subpopulations and the effects of the variation that may alter the protein sequence of a gene are also listed for each SNP/INDEL. The database also provides geographical details and phenotype images for various rice accessions. In particular, the database provides tools to construct haplotype networks and design PCR-primers by taking into account surrounding known genomic variations. These data and tools are highly useful for exploring genetic variations and evolution studies of rice and other species. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. |