Abstract
BackgroundRice (Oryza sativa L.) yield is limited inherently by environmental stresses, including biotic and abiotic stresses. Thus, it is of great importance to perform in-depth explorations on the genes that are closely associated with the stress-resistant traits in rice. The existing rice SNP databases have made considerable contributions to rice genomic variation information but none of them have a particular focus on integrating stress-resistant variation and related phenotype data into one web resource.ResultsRice Stress-Resistant SNP database (http://bioinformatics.fafu.edu.cn/RSRS) mainly focuses on SNPs specific to biotic and abiotic stress-resistant ability in rice, and presents them in a unified web resource platform. The Rice Stress-Resistant SNP (RSRS) database contains over 9.5 million stress-resistant SNPs and 797 stress-resistant candidate genes in rice, which were detected from more than 400 stress-resistant rice varieties. We incorporated the SNPs function, genome annotation and phenotype information into this database. Besides, the database has a user-friendly web interface for users to query, browse and visualize a specific SNP efficiently. RSRS database allows users to query the SNP information and their relevant annotations for individual variety or more varieties. The search results can be visualized graphically in a genome browser or displayed in formatted tables. Users can also align SNPs between two or more rice accessions.ConclusionRSRS database shows great utility for scientists to further characterize the function of variants related to environmental stress-resistant ability in rice.
Highlights
Rice (Oryza sativa L.) yield is limited inherently by environmental stresses, including biotic and abiotic stresses
We mainly focused on non-synonymous Single Nucleotide Polymorphism (SNP) and other major effect SNPs as they could lead to amino acid residue change and alter the functional or structural properties of the target protein
Database Content The whole genome sequencing data of 402 rice (Oryza sativa L.) varieties with different abiotic and biotic stress-resistant ability were downloaded from the 3000 rice genome re-sequencing project and other projects in NCBI SRA database
Summary
Rice (Oryza sativa L.) yield is limited inherently by environmental stresses, including biotic and abiotic stresses. Rice (Oryza sativa L.) is one of the significant cereal crops, feeding a large number of worldwide populations. It is one of the well-studied model organisms for plant research. Rice yield is limited inherently by environmental stresses, including biotic and abiotic stresses. Rice breeders try to limit yield losses from environmental stresses by incorporating resistant genes and developing more climatically resilient cultivars. It is of great importance to perform in-depth explorations on the genes that are closely associated with the stress-resistant traits in rice
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