Axiom 2.0 assay manual workflow user guide rev3

A list of SNPs was submitted to Affymetrix for probeset design. For each SNP, one single probeset was included in the TaBW280K SNP array. 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 (APT) and SNPolisher^™ (http://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 4 on all the samples. As a second step, the SNPs failing the QC criteria (“Other” and “NoMinorHom”) were reprocessed using an inbred penalty of 16. Probesets classified as OTVs by SNPolisher were analyzed with OTV_caller in the two steps. The TaBW280K SNP array can be purchased from Affymetrix.

Since the CC was established based only on 37 SSRs (Balfourier et al., 2007 (link)), it cannot scan the entire genome of wheat. Therefore, the CC genotype was further determined with the Axiom^® 35k breeders SNP array (Affymetrix, CA, USA) (Allen et al., 2017 (link)) to screen the entire genome and re-analyze subpopulation structure. Genotyping was performed on an Affymetrix GeneTitan system following Affymetrix’s manual (Axiom^® 2.0 Assay Manual Workflow User Guide Rev3). SNP callings were performed using modified versions of Affymetrix Power Tools (APT) and SNPolisher™(Affymetrix, CA, USA) to account for the wheat genome’s specificity. Genotype scoring was performed in Affymetrix Genotyping Console using recommended QC metrics (0.82 DQC, 97 QC call rate) (Przewieslik-Allen et al., 2021 (link)). Among 35,143 SNPs, SNPs with a minor allele frequency (MAF) of 5% or less were removed.
Genocore (Jeong et al., 2017 (link)) and CoreHunter (Thachuk et al., 2009 (link)) programs were used to select the K-wheat mini CC based on the whole genome SNPs. Genocore selected subsets using -d 0.001 and -cv 200 parameters. Core Hunter selected subsets using default options.