[Gough et al., 2001] and Pfam [Sonnhammer et al., 1997] domain assignments on the full-length amino acid sequence were made and the corresponding AASs were evaluated using our unweighted method. We found several biologically interesting SNV differences between the landrace and elite wheat varieties (see Supp. Table S5). For example, wheat contig F0Z7V0F01D2DA5 had a SNP at position 172 in the casein kinase II beta subunit domain with phenotypic consequences predicted to affect the flower developmental stages and vegetative growth. The casein kinase II beta subunit domain has a putative function in flowering time regulation in the model plant Arabidopsis [Ogiso et al., 2010] and is likely to be biologically significant as European domestic wheat will have been selected to grow under shortened seasons and different day lengths to the landraces. Next, wheat contig GIZP4PP04H5FGF had a SNP at position 219, which lies within the Pfam starch synthase catalytic domain. Once again, this is likely to be biologically significant as the quantity and properties of starch are important to the baking properties of cultivated wheat and will thus have been under strong selection. Finally, wheat contig 09781 had a SNP at position 368 in the cysteine proteinase domain with predicted
