*2.4. Genotyping and Population Structure*

The HWWAMP panel was previously genotyped using the 90 K SNP wheat iSelect assay and the marker data is available at the T3 wheat database [50]. The majority of SNPs included in the 90 K SNP assay were SNPs discovered using RNA-seq transcripts from 19 hexaploid and 18 tetraploid wheat lines in addition to SNPs previously discovered in hexaploid wheat [51]. The source of majority of SNPs, being RNA-Seq transcripts, resulted in nonrandom distribution of SNPs in the genome [52,53]. Additional details on the wheat iSelect assay have been presented previously [54]. The dataset comprised a total of 16,054 SNPs across 299 genotypes. In order to avoid spurious marker–trait associations, SNP markers with minor allele frequency <0.05 and missing data of >20% were excluded from the analysis. Genotypes with >20% missing SNP sites (Dawn and Parker) were also excluded from the analyses (leaving 14,661 SNPs). The population structure of the HWWAMP was studied using principal component analysis (PCA). The PCA was performed using TASSEL (version 5.0, Buckler Lab, Ithaca, NY, USA) [55] and a biplot of PC1 versus PC2 was generated.
