Soybean Haplotype Map (GmHapMap) and HaplotypeMiner
Soybean Haplotype Map (GmHapMap)
Davoud Torkamaneh, Jèrôme Laroche, Babu Valliyodan, Louise S. O'Donoughe, Elroy Cober, Istvan Rajcan, Ricardo Vilela Abdelnoor, Avinash Sreedasyam, Jeremy Schmutz, Henry T. Nguyen, and François Belzile
Link to FigShare Repository
Haplotype map for soybean (GmHapMap) constructed using whole-genome sequence data for 1,007 soybean accessions yielding close to 15 million SNPs. HaplotypeMiner is a tool that allows for selection of SNPs useful in defining genes or allelic characterization at a given loci in germplasm collections.
Files available for download include the GmHapHap data in VCF (variant call format) for the 1007 accessions from the GmHapMap project, and the output from HaplotypeMiner for the same accessions. The output files from HaplotypeMiner have been combined into a single file for easy download and manipulation. The Genotypes by Gene file is in HapMap format, with the addition of gene name in the first column. This file contains all of the genes that have SNPs in them and the genotypes of each accession at those SNP positions. The Haplotypes by Gene file contains each gene that contains SNPs within it and all of the haplotypes observed for that particular gene. For these two files, variants and haplotype structure can be assessed with "grep GENE FILENAME". The Loss of Function SNPs file contains all of the SNPs that cause a loss of function (LOF) in a gene, highlighting which accessions have the LOF variant.
|Funded by the USDA-ARS. Developed by the USDA-ARS SoyBase and Legume Clade Database group at the Iowa State University, Ames, IA|