Abstract
Milk is composed of a complex mixture of lipids, proteins, carbohydrates and various vitamins and minerals as a source of nutrition for young mammals. The composition of milk varies between individuals, with lipid composition in particular being highly heritable. Recent reports have highlighted a region of bovine chromosome 27 harbouring variants affecting milk fat percentage and fatty acid content. We aimed to further investigate this locus in two independent cattle populations, consisting of a Holstein-Friesian x Jersey crossbreed pedigree of 711 F2 cows, and a collection of 32,530 mixed ancestry Bos taurus cows. Bayesian genome-wide association mapping using markers imputed from the Illumina BovineHD chip revealed a large quantitative trait locus (QTL) for milk fat percentage on chromosome 27, present in both populations. We also investigated a range of other milk composition phenotypes, and report additional associations at this locus for fat yield, protein percentage and yield, lactose percentage and yield, milk volume, and the proportions of numerous milk fatty acids. We then used mammary RNA sequence data from 212 lactating cows to assess the transcript abundance of genes located in the milk fat percentage QTL interval. This analysis revealed a strong eQTL for AGPAT6, demonstrating that high milk fat percentage genotype is also additively associated with increased expression of the AGPAT6 gene. Finally, we used whole genome sequence data from six F1 sires to target a panel of novel AGPAT6 locus variants for genotyping in the F2 crossbreed population. Association analysis of 58 of these variants revealed highly significant association for polymorphisms mapping to the 5′UTR exons and intron 1 of AGPAT6. Taken together, these data suggest that variants affecting the expression of AGPAT6 are causally involved in differential milk fat synthesis, with pleiotropic consequences for a diverse range of other milk components.
Highlights
The lactating mammary gland is a sophisticated secretory organ, producing a complex mixture of lipids, proteins, carbohydrates and various vitamins and minerals as a source of nutrition for the developing young
When estimating the combined effect of markers partitioned into 1 Mbp windows throughout the genome, this signal was the second largest milk fat percentage quantitative trait loci (QTL) genome-wide, with the largest effect estimated for the well-studied diacylglycerol acyltransferase 1 (DGAT1) locus on chromosome 14 (Table S2)
Our analysis suggests pleiotropic effects on a wide range of other milk components, including the individual proportions of milk fatty acids, milk volume, and protein and lactose content and yield
Summary
The lactating mammary gland is a sophisticated secretory organ, producing a complex mixture of lipids, proteins, carbohydrates and various vitamins and minerals as a source of nutrition for the developing young. In Bos taurus, large scale genetic studies have led to the identification of numerous genomic regions affecting the abundance of major milk components [2,3,4,5]. Quantitative trait loci (QTL) for differential milk composition have been detected on most bovine autosomes, few of the causative genes underlying these signals have been identified. Of those genes with confirmed effects, the most studied is diacylglycerol acyltransferase 1 (DGAT1). The effects of DGAT1 on milk fat composition reflect its role as a key acyltransferase of the mammary triglyceride synthesis pathway, responsible for catalysing diacylglycerol to triacylgycerol [8]
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