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 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).Phenotypic data consists of one file of raw plot observations, and one file of fitted values generated by performing spatial corrections using the 'SpATS' package in R. Trait abbreviations are as follows: FLSG flag leaf stay green; GSQM grains per square meter; GW grain weight; HD heading date; HT plant height; MAT physiological maturity date; NDVI normalized-difference vegetation index at Zadok’s GS25; PROT wet chemistry-validated whole-grain protein content; SPH seeds per head; SSQM spikes per square meter; STARCH whole-grain starch content; TKW thousand kernel weight; TWT test weight; YLD grain yield.Covariate SNP data from KASP assays is provided in a VCF file, where a 0/0 denotes the homozygous wild-type state, 0/1 denotes the heterozygous state, and 1/1 denotes the homozygous "mutant" or "positive" state.