蔬菜单核苷酸多态性数据库：植物育种者和科学家的综合资源。

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

作者信息

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

机构信息

Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing 100097, China; Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing 100097, China.

出版信息

Genomics. 2022 May;114(3):110348. doi: 10.1016/j.ygeno.2022.110348. Epub 2022 Mar 23.

DOI:10.1016/j.ygeno.2022.110348

PMID:35339630

Abstract

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 vegetable research community.

摘要

单核苷酸多态性（SNPs）在基因研究和分子育种中被广泛应用。迄今为止，许多蔬菜作物的基因组已完成组装，且每种蔬菜的数百份核心种质已进行测序。然而，目前这些数据不易获取，因为它们存储在不同的公共数据库中。因此，应开发一个蔬菜作物SNP数据库，该数据库收录那些在基因研究基因分型中已证明具有高成功率的SNPs（本文中称为“α SNPs”）。我们构建了一个数据库（VegSNPDB，http://www.vegsnpdb.cn/），其中包含来自16种蔬菜作物的2032份种质的序列数据。VegSNPDB收录了118,725,944个SNPs，其中4,877,305个为α SNPs。可通过染色体编号、位置、SNP类型、遗传群体或特定个体以及最小等位基因频率（MAF）、多态信息含量（PIC）和杂合度的值来搜索SNPs。我们希望VegSNPDB将成为蔬菜研究领域的一个重要SNP数据库。