Genome-wide genotyping-by-sequencing (GBS) and association analysis of saturated and monounsaturated fatty acids in bovine milk identifies novel markers in Canadian Holstein cows
The effect of bovine milk fatty acids (FA) on human development and heath has fuelled concerted efforts towards exploitation of existing heritable variation for genetic improvement. Consequently, genomic regions as well as single markers associated with milk fat traits have been identified in many cattle breeds around the world. Since information on population specific markers of milk FA traits in Canadian Holstein cows is limited, we used the high throughput genotyping-by-sequencing (GBS) SNP mining method and association analysis to determine population specific markers associated with milk saturated FAs (SFAs) and monounsaturated FAs (MUFAs). Fatty acid profiles of 1,200 cows from 7 herds in Quebec were determined by gas chromatography and SNPs were genotyped by GBS method. Genome wide association analysis (GWAS) with 99,814 SNPs (>70% call rates, accuracy of imputation score >50% and MAF>0.01) out of 515,820 SNPS was accomplished with the single-locus mixed linear model procedure (EMMA) implemented in Golden Helix SNP and Variation Suite v8.0 software (www.goldenhelix.com). Genome wide significance (BH P-value<0.05, range 3.86E-05 to 0.049) was detected between 7 SFAs (C4:0, C6:0, C8:0, C13:0, C14:0, C23:0 and C24:0) and several SNPs located in intergenic, coding, splicing and 3’untranslated regions. In particular, 15 significant associations for C13:0 are coding variants located in 15 genes, and 10 for C24:0 are also coding variants with many non-synonymous SNPs. One 3’UTR variant within CHFR (E3 ubiquitin-protein ligase) gene significantly associated with C6:0 and C8:0. Furthermore, genome wide significant (BH P-value<0.05) associations were recorded between several SNPs and two individual MUFAs (oleic acid [C18:1n9c] and trans vaccenic acid [C18:1n11t]), total MUFAs and total SFAs. In particular, a synonymous variant (S25_37873086) within ACHE (acetylcholinesterase) gene significantly influenced both total MUFAs and total SFAs. Minor allele frequencies for all reported significant associations are ≥0.02. Since most of these associations are being reported for FAs for the first time with only 6 of the genes known to play a role in lipogenesis, our study has uncovered potential novel SNPs and genes that can be used in improvement of milk SFA and MUFA contents through breeding to ensure quality products for human consumption. Moreover, our results also further confirm the use of the GBS technique for identification of population-based unique SNPs for GWAS and for improvement breeding in dairy cattle.
Keywords: Genome wide genotyping-by-sequencing, genome wide association study, saturated and monounsaturated fatty acids