Our study is the first to report SNP characterization within bovine FADS1 and FADS2 genes in Canadian Holstein cows, and association with milk SFAs, MUFAs and PUFAs. FADS1 and FADS2 genes code for Δ-5 and Δ-6 desaturases, respectively and these enzymes are crucial in the endogenous synthesis of LC-PUFAs from the precursor essential FAs, LA and ALA, obtained from the diet. Numerous human studies have indicated that, changes in the levels of individual FAs are related to FADS enzyme activity [27–30] and recently, Merino et al  reported that genetic variants in FADS1 and FADS2 genes in humans can alter desaturase activity. Furthermore, it has been shown in humans that genetic variants of FADS1 and FADS2 influence blood lipid and breast milk essential FAs in pregnancy and lactation . In this study, mutations were detected in the coding as well as non-coding (introns and 3′UTR) regions of studied genes. Mutations in these regions have been variously shown to associate significantly with economically important traits in farm animals, affect gene expression or function of resultant protein products [35, 36].
The reported non-synonymous mutation within FADS2 gene has either valine or alanine at position 294 of the protein. These two amino acids are both nonpolar amino acids with aliphatic side chain groups. This change in amino acid does not seem to affect the structure and function of the resultant protein which may explain why no significant association was recorded between this SNP and any of studied FAs.
Significant associations were recorded between one PUFA (C20:5n3), and the synonymous FADS1 (FADS1-07, rs42187261) mutation. According to allele substitution results, allele T, the major allele with frequency of 57% in studied individuals, was superior in increasing the content of C20:5n3. It is worthwhile to point out that positive influence of this SNP on oleic acid and other health promoting FAs was significant before FDR correction, but not after FDR correction. Stearic acid (C18:0), a SFA and one of the main products of extensive biohydrogenation of USFAs in the ruminal environment is desaturated by the SCD1 enzyme  to oleic acid. The influence of this SNP (FADS1-07, rs42187261), together with favorable associations with SNPs detected within the SCD1 gene [38–40] may contribute to desaturate products of ruminal biohydrogenation or SFAs to much needed health promoting FAs. Furthermore, this mutation (rs42187261) also favored increase in the content of one individual SFA (C23:0). This study shows only a moderate correlation between C23:0 and C20:5n3 (r2 = 0.459). Furthermore, C23:0 is not among SFAs (C16:0, C14:0 and C12:0) which were associated with raised plasma low density lipoprotein cholesterol levels . Since most SFAs in milk are synthesized de novo in the mammary gland through the activities of enzymes other than FADS1 and FADS2 while USFAs arise mostly from dietary sources, the effect of this mutation (rs42187261) may be more relevant for USFAs. Furthermore, very low and in most cases negative correlations were recorded between PUFAs positively influenced in this study and SFAs; implying that the effect of the rs42187261, rs109772589 and rs136261927 mutations can be useful in the positive management of these PUFAs.
Synonymous mutations have generally been regarded as silent mutations, that is, have no effect on protein structure and function. Recent evidence, however, indicates that silent mutations are able to cause changes in protein expression, conformation and function . Numerous recent GWAS studies have revealed substantial contributions of synonymous SNPs to human disease risk and other complex traits [42–45]. Evidence suggest that synonymous SNPs can result in aberrant mRNA splicing , affect mRNA stability and thus protein expression and enzymatic activity , affect protein conformation and have functional and clinical consequences . Consequently, Chamary and Hurst  estimated that 5-10% of human genes contain at least one region in which silent mutations could be harmful. Synonymous SNPs are generally not included in most association studies between SNPs and milk fat traits in ruminants. Therefore, important information that can assist in breeding programs could be missed. Our result on the synonymous FADS1 (FADS1-07, rs42187261) mutation support the concept of using both non-synonymous and synonymous mutations in animal breeding.
Our study also recorded a significant association between one intronic SNP (FADS1-01, rs136261927) and one MUFA (C20:3n6). Reports of significant associations between intronic SNPs in several lipogenic genes and milk fat traits as well as other production traits have emerged . For example, intronic SNPs in the SCD1 (g.6926A > G) and FASN genes (g.8948C > T, ss491228481) were recently shown to be significantly associated with milk yield, fat yield and protein yield in Chinese Holstein cows . Mutations in intronic regions are known to play important regulatory roles in mammalian gene expression, including roles in transcription regulation, polyadenylation, mRNA export, translational efficiency, and the rate of mRNA decay . Our study further points to the importance of non-coding region SNPs in the modulation of gene expression and resultant effects on milk yield traits.