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

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

doi:10.1016/j.ygeno.2022.110348

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

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

Authors

Jingjing Yang¹, Jian Zhang¹, Heshan Du¹, Hong Zhao¹, Haizhen Li¹, Yong Xu¹, Aijun Mao¹, Xiaofei Zhang¹, Yiqian Fu¹, Yang Xia¹, Changlong Wen²

Affiliations

¹ 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.
² 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; State Key Laboratory of Vegetable Germplasm Innovation, Tianjin 300380, China. Electronic address: wenchanglong@nercv.org.

PMID: 35339630
DOI: 10.1016/j.ygeno.2022.110348

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.

Keywords: Alpha SNP; Genetic research; SNP database; VegSNPDB; Vegetable.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Base Sequence
Crops, Agricultural / genetics
Genome, Plant
Humans
Plant Breeding
Polymorphism, Single Nucleotide*
Vegetables* / genetics