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The vegetable SNP database: An integrated resource for plant breeders and scientists

文献类型： 外文期刊

作者： Yang, Jingjing 1 ; Zhang, Jian 1 ; Du, Heshan 1 ; Zhao, Hong 1 ; Li, Haizhen 1 ; Xu, Yong 1 ; Mao, Aijun 1 ; Zhang, Xiaofei 1 ; Fu, Yiqian 1 ; Xia, Yang 1 ; Wen, Changlong 1 ;

作者机构： 1.Beijing Acad Agr & Forestry Sci, Beijing Vegetable Res Ctr, Beijing 100097, Peoples R China

2.Beijing Key Lab Vegetable Germplasms Improvement, Beijing 100097, Peoples R China

3.Key Lab Biol & Genet Improvement Hort Crops North, Beijing 100097, Peoples R China

4.State Key Lab Vegetable Germplasm Innovat, Tianjin 300380, Peoples R China

关键词： VegSNPDB; SNP database; Alpha SNP; Vegetable; Genetic research

期刊名称：GENOMICS （ 影响因子：4.31； 五年影响因子：4.38 ）

ISSN： 0888-7543

年卷期： 2022 年 114 卷 3 期

页码：

收录情况： SCI

摘要： Single nucleotide polymorphisms (SNPs) are widely used in genetic research and molecular breeding. To date, the genomes of many vegetable crops have been assembled, and hundreds of core germplasms for each vegetable have been sequenced. However, these data are not currently easily accessible because they are stored on different public databases. Therefore, a vegetable crop SNP database should be developed that hosts SNPs demonstrated to have a high success rate in genotyping for genetic research (herein, "alpha SNPs"). We constructed a database (VegSNPDB, http://www.vegsnpdb.cn/) containing the sequence data of 2032 germplasms from 16 vegetable crop species. VegSNPDB hosts 118,725,944 SNPs of which 4,877,305 were alpha SNPs. SNPs can be searched by chromosome number, position, SNP type, genetic population, or specific individuals, as well as the values of MAF, PIC, and heterozygosity. We hope that VegSNPDB will become an important SNP database for the vege-table research community.

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