Most Genome Wide Association Studies (GWAS) identified quantitative traits locus (QTLs) based on their average effect over the lactation. However, it is known that additive genetic variance changes during lactation and genetic correlations among milk production traits during different lactation stages deviates from unity. We conducted a GWAS specifically for SNPs whose effects on milk protein content change during lactation, i.e. those that show significant SNP by lactation stage interaction. Significance thresholds for SNP by lactation stage interaction cannot be based on standard distributions but requires permutation of the data. We detected regions on BTA 10 and 14 with significant SNP effects as well as significant SNP by lactation stage effects. Regions on BTA 3 and 27 only showed significant SNP by lactation stage effects. Regions on BTA 6, 15, 16, 20 and 26 only showed significant effects in a traditional GWAS. These results show that a GWAS accounting for a SNP by lactation stage interaction effect can help elucidate the genetic background of milk protein content. Keywords: GWAS, genotype by lactation stage interaction, permutation, milk protein content
Proceedings of the World Congress on Genetics Applied to Livestock Production, Volume Electronic Poster Session - Biology & Species - Bovine (dairy) 2, , 469, 2018
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