SR4R:An Integrative SNP Resource for Genomic Breeding and Population Research in Rice  

作　　者：Jun Yan Dong Zou Chen Li Zhang Zhang Shuhui Song Xiangfeng Wang 

机构地区：[1]Department of Crop Genomics and Bioinformatics,College of Agronomy and Biotechnology,China Agricultural University,Beijing 100094,China [2]China National Center for Bioinformation,Beijing 100101,China [3]National Genomics Data Center&CAS Key Laboratory of Genome Sciences and Information,Beijing Institute of Genomics,Chinese Academy of Sciences,Beijing 100101,China [4]University of Chinese Academy of Sciences,Beijing 100101,China [5]Rice Research Institute,Guangdong Academy of Agricultural Sciences,Guangzhou 510640,China

出　　处：《Genomics, Proteomics & Bioinformatics》2020年第2期173-185,共13页基因组蛋白质组与生物信息学报（英文版）

基　　金：supported by the National Natural Science Foundation of China(Grant No.31871706);the Department of Agriculture of Guangdong Province(2018-36);Science and Technology Program of Guangdong Province(Grant No.2019B030316006);The Strategic Priority Research Program of the Chinese Academy of Sciences(Grant No.XDA24040201);the Youth Innovation Promotion Association of the Chinese Academy of Sciences(Grant No.2017141)

摘　　要：The information commons for rice(IC4 R)database is a collection of 18 million single nucleotide polymorphisms(SNPs)identified by resequencing of 5152 rice accessions.Although IC4 R 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 IC4 R-SnpReady for Rice(SR4 R).SR4 R 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.SR4 R 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,SR4 R 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.SR4 R is freely available to academic users at http://sr4 r.ic4 r.org/.

关 键 词：RICE SNP Database HAPMAP Panel 

分 类 号：S511[农业科学—作物学]