Welcome to CropSNPdb

The Crop SNP database (CropSNPdb) is a data resource for crop variation identified using genotyping arrays. The current database build
contains Brassica, hexaploid bread wheat (Triticum aestivum) barley (Hordeum vulgare), lentil (Lens culinaris), chickpea (Cicer) and field pea (Pisum) genotypes from the Brassica 60k, the wheat 90k and the Infinium Wheat Barley 40K Illumina arrays.

CropSNPdb includes genotypes called from 526 Brassica lines from published datasets and 309 wheat lines from T3 Wheat, plus all 32,656 Australian Grains Genebank wheat accessions (landraces, cultivars, breeding lines and genetic stocks from 110 countries) genotyped with the Wheat Barley 40K array (AGG Wheat Release 260619), and 709 barley lines from OzBarley (Australian elite cultivars and landraces, Wheat Barley 40K array, with greenhouse phenotypes; plus 108,970 gene-based RNA-seq SNPs for the 214 elite lines), and 324 lentil lines of the AGILE Lentil Diversity Panel (459,938 exome-capture SNPs from KnowPulse, with days to flowering and maturity from 18 site-years), and 279 chickpeas, mostly wild C. reticulatum and C. echinospermum from south-eastern Turkey plus cultivated lines (2.0 million whole-genome SNPs; von Wettberg et al. 2018), and 696 pea accessions on the Cameor v2 genome: the USDA Pea Single Plant Plus Collection (456 accessions, 270,306 GBS SNPs; Powers et al. 2021) and the AMS panel of Aubert et al. 2023 (240 accessions, 641,081 SNPs; Kreplak et al. 2026).

Features
  • Simple interface for querying and downloading public crop genotyping array data
  • Genotypes can be viewed as in table format and as a track in the genome browser GBrowse
  • Search function allows cultivar comparison and querying of genomic region
  • SNPs returned from a Search can be downloaded as a genotype table or visualised via a link to a genome viewer
  • Bulk download of all SNPs per chromosome in genotype format is available to facilitate further analysis.
Genome builds
Tutorial

Applied Bioinformatics Group. Version 1.0, August 2018. Contact us: Dave.Edwards@uwa.edu.au