BackgroundLactose provides an easily-digested energy source for neonates, and is the primary carbohydrate in milk in most species. Bovine lactose is also a key component of many human food products. However, compared to analyses of other milk components, the genetic control of lactose has been little studied. Here we present the first GWAS focussed on analysis of milk lactose traits.ResultsUsing a discovery population of 12,000 taurine dairy cattle, we detail 27 QTL for lactose concentration and yield, and subsequently validate the effects of 26 of these loci in a distinct population of 18,000 cows. We next present data implicating causative genes and variants for these QTL. Fine mapping of these regions using imputed, whole genome sequence-resolution genotypes reveals protein-coding candidate causative variants affecting the ABCG2, DGAT1, STAT5B, KCNH4, NPFFR2 and RNF214 genes. Eleven of the remaining QTL appear to be driven by regulatory effects, suggested by the presence of co-locating, co-segregating eQTL discovered using mammary RNA sequence data from a population of 357 lactating cows. Pathway analysis of genes representing all lactose-associated loci shows significant enrichment of genes located in the endoplasmic reticulum, with functions related to ion channel activity mediated through the LRRC8C, P2RX4, KCNJ2 and ANKH genes. A number of the validated QTL are also found to be associated with additional milk volume, fat and protein phenotypes.ConclusionsOverall, these findings highlight novel candidate genes and variants involved in milk lactose regulation, whose impacts on membrane transport mechanisms reinforce the key osmo-regulatory roles of lactose in milk.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-4320-3) contains supplementary material, which is available to authorized users.

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.

X chromosome inactivation (XCI) is a process by which 1 of the 2 copies of the X chromosomes present in female mammals is inactivated. The transcriptional silencing of one X chromosome achieves dosage compensation between XX females and XY males and ensures equal expression of X-linked genes in both sexes. Although all mammals use this form of dosage compensation, the complex mechanisms that regulate XCI vary between species, tissues, and development. These mechanisms include not only varying levels of inactivation, but also the nature of inactivation, which can range from being random in nature to driven by parent of origin. To date, no data describing XCI in calves or adult cattle have been reported and we are reliant on data from mice to infer potential mechanisms and timings for this process. In the context of dairy cattle breeding and genomic prediction, the implications of X chromosome inheritance and XCI in the mammary gland are particularly important where a relatively small number of bulls pass their single X chromosome on to all of their daughters. We describe here the use of RNA-seq, whole genome sequencing and Illumina BovineHD BeadChip (Illumina, San Diego, CA) genotypes to assess XCI in lactating mammary glands of dairy cattle. At a population level, maternally and paternally inherited copies of the X chromosome are expressed equally in the lactating mammary gland consistent with random inactivation of the X chromosome. However, average expression of the paternal chromosome ranged from 10 to 90% depending on the individual animal. These results suggest that either the mammary gland arises from 1 or 2 stem cells, or a nongenetic mechanism that skews XCI exists. Although a considerable amount of future work is required to fully understand XCI in cattle, the data reported here represent an initial step in ensuring that X chromosome variation is captured and used in an appropriate manner for future genomic selection.

Mid pregnancy shearing of ewes has been associated with a short-to medium-term increase in maternal thyroid hormone concentrations. To determine the role of this elevation in the observed changes in lamb birth weight and fibre characteristics, ewes in mid pregnancy were either: shorn at day 70 of pregnancy with thyroid glands left intact (Shorn), unshorn with intact thyroid glands (Unshorn), thyroidectomised but left unshorn with a short-term elevation in thyroxine (T4) concentrations in mid pregnancy (Tx+T4), or unshorn with intact thyroid gland and prolonged elevation in T4 concentrations (+T4). The Tx+T4 regime successfully increased maternal thyroid hormone for a short period post-treatment, while the +T4 regime increased maternal thyroid hormone levels for a prolonged period during mid to late pregnancy. Lambs born to Shorn ewes were significantly (P < 0.05) heavier than those born to Tx+T4 and +T4 ewes and tended to be heavier than those born to Unshorn ewes (P = 0.10). Birth weights of lambs born to Tx+T4 and +T4 ewes did not differ from those born to Unshorn ewes. Ewe treatment had no effect on lamb wool follicle characteristics or fibre diameter, coefficient of variation of mean fibre diameter, yield, or loose wool bulk; but treatment tended to affect colour (P = 0.05) and staple length (P = 0.09). These results suggest that an elevation in A04064; maternal thyroid hormones is not the sole endocrine mechanism responsible for either the birth weight effect or changes in fibre characteristics observed in lambs born to mid pregnancy shorn ewes. However, it is still possible that an elevation of T4 and T3 concentrations in conjunction with other factors are required to achieve the observed effects.

Sulfur amino acid supplementation increases wool production in sheep at low planes of nutrition but it is unclear whether there is any benefit of supplementation at planes of nutrition above maintenance and what implications this might have for wool quality characteristics. This experiment directly investigated the interaction between sulfur supplementation and plane of nutrition in terms of wool growth and fibre characteristics. Twenty-four Romney ewes, acclimatised in individual metabolism units over a 7-week pre-treatment period, were allocated to 1 of 4 treatment groups based on a 22 factorial arrangement. Groups were low (L) or high (H) intake (0.8 or 1.3 maintenance, respectively) with continuous intravenous infusion of either saline (–Cys) or cysteine (+Cys, 2 g/day). During the 3-month treatment period, measurements were obtained for liveweight, plasma cysteine concentration, wool sulfur concentration and output, clean wool growth, mean fibre diameter (MFD), length growth rate (LGR), colour, loose wool bulk, handle, and crimp frequency and character. Clean wool growth response (P < 0.05) to cysteine supplementation was greater for the L sheep (6.06 v. 4.31 g/100 cm2) than the H sheep (7.20 v. 6.13 g/100 cm2). The response to supplementation in LGR (P < 0.01) was similar in both H (14%) and L (20%) sheep. There was no response in MFD due to sulfur supplementation, although fibre diameter measurements made along the fibres suggest that there was a response in L but not H sheep (P < 0.1). Wool sulfur concentration and output increased as a result of cysteine supplementation but concentration increased more in L (30.6 v. 24.5 mg S/g; P < 0.01) than in H sheep (28.4 v. 26.2 mg S/g). Qualitative electrophoresis analyses suggested that the increase in wool sulfur was achieved primarily by an increase in ultra-high-sulfur proteins. Crimp frequency and character were both significantly (P < 0.01) enhanced by cysteine supplementation. It is concluded that cysteine supplementation, at feed intakes that commonly occur in the commercial situation, can produce a useful increase in wool growth. This growth increase is primarily accomplished by increasing length growth rate rather than fibre diameter, which should also improve the value of the wool fibre produced.