ArticleGenomics, proteomics & bioinformatics2020
SR4R: An Integrative SNP Resource for Genomic Breeding and Population Research in Rice.
Article in Genomics, proteomics & bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 29 citations in OpenAlex.
- Img2Variety: Image-based intraspecific varieties identification across the whole growth period.Plant phenomics (Washington, D.C.) · 2026Article
- Fine Mapping and Candidate Gene Identification of ORUFILM03g000096 Gene in Weedy Rice LM8: Insights into Grain Length Regulation.Rice (New York, N.Y.) · 2025Article
- Improving grain yield and salt tolerance by optimizing plant height with beneficial haplotypes in rice (Oryza sativa).Journal of advanced research · 2025Article
- A high-throughput screening method for selecting feature SNPs to evaluate breed diversity and infer ancestry.Genome research · 2025Article
- A review of artificial intelligence-assisted omics techniques in plant defense: current trends and future directions.Frontiers in plant science · 2024Review
- A rice variation map derived from 10 548 rice accessions reveals the importance of rare variants.Nucleic acids research · 2023Article
- Genome-Wide Association Studies Using 3VmrMLM Model Provide New Insights into Branched-Chain Amino Acid Contents in Rice Grains.Plants (Basel, Switzerland) · 2023Article
- GWAS Atlas: an updated knowledgebase integrating more curated associations in plants and animals.Nucleic acids research · 2023Article
- Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2023.Nucleic acids research · 2023Article
- Development of Omni InDel and supporting database for maize.Frontiers in plant science · 2023Article
- Resequencing 250 Soybean Accessions: New Insights into Genes Associated with Agronomic Traits and Genetic Networks.Genomics, proteomics & bioinformatics · 2022Article
- Understanding the Nature of Hybrid Sterility and Divergence of Asian Cultivated Rice.Frontiers in plant science · 2022Review
- Article
- Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021.Nucleic acids research · 2021Article
- Genome Variation Map: a worldwide collection of genome variations across multiple species.Nucleic acids research · 2021Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The information commons for rice (IC4R) database is a collection of 18 million single nucleotide polymorphisms (SNPs) identified by resequencing of 5152 rice accessions. Although IC4R offers ultra-high density rice variation map, these raw SNPs are not readily usable for the public. To satisfy different research utilizations of SNPs for population genetics, evolutionary analysis, association studies, and genomic breeding in rice, raw genotypic data of these 18 million SNPs were processed by unified bioinformatics pipelines. The outcomes were used to develop a daughter database of IC4R - SnpReady for Rice (SR4R). SR4R presents four reference SNP panels, including 2,097,405 hapmapSNPs after data filtration and genotype imputation, 156,502 tagSNPs selected from linkage disequilibrium-based redundancy removal, 1180 fixedSNPs selected from genes exhibiting selective sweep signatures, and 38 barcodeSNPs selected from DNA fingerprinting simulation. SR4R thus offers a highly efficient rice variation map that combines reduced SNP redundancy with extensive data describing the genetic diversity of rice populations. In addition, SR4R provides rice researchers with a web interface that enables them to browse all four SNP panels, use online toolkits, as well as retrieve the original data and scripts for a variety of population genetics analyses on local computers. SR4R is freely available to academic users at http://sr4r.ic4r.org/.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.