Genomic regions associated with both summer and winter bovine milk fatty acids

In genome-wide association studies (GWAS) many thousands of single nucleotide polymorphisms (SNPs) are being tested for associations. In general it is expected that only a small proportion of the SNPs will have a true association and only those that have an effect that is large enough will be significant. Setting a significance threshold is finding the balance between limiting the number of false positives and maintaining sufficient power. Replication of results is a strategy to separate false positives from true associations. The aim of this study was to perform a GWAS for bovine milk fatty acids in summer milk samples to confirm regions of the bovine genome associated with bovine milk fatty acids in winter milk samples detected in our previous GWAS. Two milk samples from 2,000 first lactation dairy cows were collected. The first milk sample was taken in winter, when Dutch cows are mainly kept indoors. The second milk sample, from the same set of cows, was taken in summer, when Dutch cows are often grazing outdoors for a part of the day. Milk fat composition was measured by gas chromatography. The most abundant fatty acids, i.e. C4:0-C18:0, C10:1-C18:1 and CLA, were analyzed. Summer milk contained more unsaturated fat and less saturated fat than winter milk, e.g. fat contained on average 29.2% C16:0 and 20.6% C18:1 in summer, and 32.6% C16:0 and 18.2% C18:1 in winter. Phenotypic correlations between winter and summer samples were low: 0.40-0.57 for short and medium chain fatty acids, and 0.36-0.40 for long chain fatty acids. Genetic correlations between winter and summer samples were very high (0.77-1), suggesting that summer and winter milk all genetically the same trait. The cows were genotyped for 50,000 markers. For each individual marker we determined whether there was a significant association with the milk fatty acids. This GWAS of fatty acids from summer milk samples confirms many associations that were previously detected in a GWAS of fatty acids from winter milk samples, including eight ‘new’ regions that were not considered in the individual studies. Three of these regions had major effects, the region around DGAT1 on chromosome 14, a large region on chromosome 19, and the region around SCD1 on chromosome 26. Winter and summer -log10(P-values) of confirmed SNPs showed a correlation of 0.89. Winter and summer additive SNP effects of confirmed SNPs showed a correlation of 0.97. The high correlation implies that the effect of the QTL is similar in winter as in summer. The confirmation of these regions gives more certainty that these regions are involved in milk fatty acid synthesis and are worthwhile to analyse further in fine mapping studies.

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