2014-2015 TCAP ABB mid-Atlantic Virginia

Genotypic, phenotypic, and covariate SNP data collected on a panel of soft winter wheat grown in Blacksburg, Virginia and Warsaw, Virginia in the 2013-2014 and 2014-2015 winter wheat growing seasons as part of the USDA-NIFA Tritaceae Coordinated Agricultural Project (TCAP) mid-Atlantic allele-based breeding (ABB) panel. Genotypic data is supplied in variant call format (VCF) files, both unimputed and following imputation with Beagle 4.1.

Unimputed genotypic data was filtered to remove SNPs with minor allele frequency < 5%, > 50% missing data content, or with > 15% heterozygous calls. Following imputation, the genotypic data was refiltered for minor allele frequency and portion of heterozygous calls using the same thresholds listed above. The imputed data was thinned to only retain a single SNP in groups of SNPs in perfect linkage disequilibrium (r2 = 1).