Genotyping of 4,506 bread wheat accessions with the TaBW410K SNP array

Genotyping data of 4,506 bread wheat accessions obtained with the TaBW410K SNP array. The 4,506 bread wheat accessions (Balfourier et al. Science Advances 2019) were genotyped using a high-density Affymetrix Axiom SNP array containing 409,695 SNPs (Kitt et al., in prep). Genotyping was conducted on the Affymetrix GeneTitan system according to the procedure described by Affymetrix (Axiom 2.0 Assay Manual Workflow User Guide Rev3). Allele calling was carried out using a modified version of the Affymetrix proprietary software packages Affymetrix Power Tools and SNPolisher (www.affymetrix.com/estore/partners_programs/programs/developer/tools/devnettools.affx) to take into account the specificities of the wheat genome. For all SNPs, HomRO, and HomFLD were calculated (http://media.affymetrix.com/support/developer/downloads/ Tools/SNPolisher_User_Guide.pdf). The HomFLD filter was set to 3.6. As a first step, all the probesets were processed with a mild inbred penalty equal to four on all samples. As a second step, the SNPs failing the quality check criteria (“Other” and “NoMinorHom”) were reprocessed using an inbred penalty of 16. Probesets classified as OTVs by SNPolisher were analyzed with OTV_caller in two steps. SNPs were classified in six main categories according to cluster patterns produced by the Affymetrix software: PHR, OTV, monomorphic high resolution, no minor homozygous, call rate below threshold, and others. For further analyses, only PHRs and OTVs were selected. This dataset contains three files: Collection_geznotyping_matrix_410k.map: map file of 239,100 markers (PHRs or OTVs) to be used with PLINK Collection_geznotyping_matrix_410k.map: bed file of 239,100 markers (PHRs or OTVs) to be used with PLINK SNP_positions_410k.txt: position of 225,771 SNP