Welcome to the Vegetable SNP Database (VegSNPDB)
    VegSNPDB is an SNP database that provides the basic SNPs and alpha SNPs in 16 vegetables, including watermelon, melon, cucumber, zucchini, bitter gourd, wax gourd, Chinese cabbage, cabbage, lettuce, spinach, carrot, radish, tomato, pepper, eggplant, and common bean. It was built based on the sequence of 2,032 accessions. Alpha SNPs are obtained after several layers of filtration for eliminating unfavorable factors for genotyping. Therefore, they are considered superior to random SNPs. VegSNPDB allows searching for SNPs, primer design, and sequence extraction. It provides 118,725,944 basic SNPs and 4,877,305 alpha SNPs with detailed information. Users can browse and search for SNPs by chromosome number, chromosome position, SNP type, MAF, PIC, and heterozygosity. Primer design for the Kompetitive allele-specific PCR platform is supported for alpha SNPs. VegSNPDB can promote genetic mapping, evolutionary and genome-wide association studies (GWAS), genetic diversity, and marker-assisted selection (MAS). We hope that VegSNPDB will become an important SNP database for research communities investigating the 16 target vegetables.
Functions offered in VegSNPDB：
  1. 1. Browse, search, or download the SNPs of 16 vegetable species.
  2. 2. Browse, search, or download the alpha SNPs of these 16 species.
  3. 3. Design primers for alpha SNPs.
  4. 4. Extract sequence from the genomes of these 16 species.
Browse by species
no img watermelon Wax gourd tomato eggplant pepper carrot lettuce spinach cabbage Chinese cabbage radish common bean bitter gourd zucchini cucumber melon
Summary
  1. a Basic SNPs were raw SNPs filtered with MAF > 0.05, missrate <0.5, heterozygosity < 0.5.
  2. b Alpha SNPs were SNPs passed several layers of filtration and eliminated unfavorable factors for genotyping.
  3. c The proportion of alpha SNPs in basic SNPs.
Citation
  1. J. Yang, J. Zhang, H. Du, H. Zhao, H. Li, Y. Xu, A. Mao, X. Zhang, Y. Fu, Y. Xia, C. Wen, The vegetable SNP database: An integrated resource for plant breeders and scientists, Genomics, 114 (2022) 110348.