Pacific Northwest and Southeast U.S. stripe rust data

This dataset consists of genotypic, phenotypic, and covariate SNP data for two panels of soft red winter wheat (<i>Triticum aestivum</i>) evaulated for stripe rust (<i>Puccinia striiformis</i>; Yr) resistance: the Historical Eastern (HE) panel, consisting of 273 genotypes, and the Southeastern Elite (SE) panel, consisting of 588 genotypes. The HE panel was grown in Central Ferry, WA in 2013; Mount Vernon, WA in 2013 and 2014; the Spillman Agronomy Farm in Pullman, WA in 2014; the Whitlow Agronomy Farm in Pullman, WA in 2013 and 2014; and the Milo J. Shult Agricultural Research and Extension Center in Fayetteville, AR in 2013 and 2014. The SE panel was grown at the same location in Fayetteville, AR and in Plains, GA in 2018 and 2019.<br><br>Genotypic data is supplied in variant call format (VCF) files. A file of filtered, pre-imputed data is supplied (HEP-SEP_Yr_50miss_prefilt.vcf.gz), as well as a file of imputed data (HEP-SEP_Yr_50miss_postimp_filt.vcf.gz). SNP calling was performed using TASSEL-GBS in TASSEL 5.2.50 for both panels jointly, aligning against the v1 Chinese Spring reference genome assembly. The raw SNP data was filtered to remove SNPs with minor allele frequency &lt; 5%, &gt; 50% missing data rate, or with &gt; 10% heterozygous call frequency. Following filtering, missing data was imputed using Beagle 5.0. Following imputation, SNP data was filtered a second time using the same minor allele frequency and heterozygous call thresholds listed above. The imputed data was thinned to only retain a single SNP in groups of SNPs in perfect linkage disequilibrium (r² = 1).<br><br>Phenotypic data consists of within-environment means for the HE panel (HEP_Yr_pheno_env_means.csv) and the SE panel (SEP_Yr_pheno_env_means.csv). Stripe rust severity (SEV) and infection type (IT) were rated for the HE panel, while only SEV was rated for the SE panel. The SE data has been converted to percentiles within each environment, as it was originally collected on two different scales.<br><br>Covariate SNP data (HEP-SEP_Yr_KASP_covars.csv) consists of data from LGC Genomics KASP assays for the <i>Yr17/Lr37/Sr38</i> locus on chromosome 2A, evaluated in both the HE and SE panels, and the <i>Yr30/Sr2</i> locus on chromosome 3B, evaluated in the HE panel only. Note that the <i>Yr30/Sr2</i> locus contains a null allele.<br><br>Finally, environments_info.csv contains general information on all of the testing environments used in the study.<br>