SR4R:An Integrative SNP Resource for Genomic Breeding and Population Research in Rice
- Author:
Yan JUN
1
;
Zou DONG
;
Li CHEN
;
Zhang ZHANG
;
Song SHUHUI
;
Wang XIANGFENG
Author Information
1. Department of Crop Genomics and Bioinformatics, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100094, China
- Keywords:
Rice;
SNP;
Database;
HapMap;
Panel
- From:
Genomics, Proteomics & Bioinformatics
2020;18(2):173-185
- CountryChina
- Language:Chinese
-
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 anal-ysis, 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, includ-ing 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 sim-ulation. SR4R thus offers a highly efficient rice variation map that combines reduced SNP redun-dancy 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 genet-ics analyses on local computers. SR4R is freely available to academic users at http://sr4r.ic4r.org/.
