Feed efficiency in dairy sheep: An insight from the milk transcriptome

Introduction

As higher feed efficiency in dairy ruminants means a higher capability to transform feed nutrients into milk and milk components, differences in feed efficiency are expected to be partly linked to changes in the physiology of the mammary glands. Therefore, this study aimed to determine the biological functions and key regulatory genes associated with feed efficiency in dairy sheep using the milk somatic cell transcriptome.

Material and methods

RNA-Seq data from high (H-FE, n = 8) and low (L-FE, n = 8) feed efficiency ewes were compared through differential expression analysis (DEA) and sparse Partial Least Square-Discriminant analysis (sPLS-DA).

Results

In the DEA, 79 genes were identified as differentially expressed between both conditions, while the sPLS-DA identified 261 predictive genes [variable importance in projection (VIP) > 2] that discriminated H-FE and L-FE sheep.

Discussion

The DEA between sheep with divergent feed efficiency allowed the identification of genes associated with the immune system and stress in L-FE animals. In addition, the sPLS-DA approach revealed the importance of genes involved in cell division (e.g., KIF4A and PRC1) and cellular lipid metabolic process (e.g., LPL, SCD, GPAM, and ACOX3) for the H-FE sheep in the lactating mammary gland transcriptome. A set of discriminant genes, commonly identified by the two statistical approaches, was also detected, including some involved in cell proliferation (e.g., SESN2, KIF20A, or TOP2A) or encoding heat-shock proteins (HSPB1). These results provide novel insights into the biological basis of feed efficiency in dairy sheep, highlighting the informative potential of the mammary gland transcriptome as a target tissue and revealing the usefulness of combining univariate and multivariate analysis approaches to elucidate the molecular mechanisms controlling complex traits.

Effects of PUFA-Rich Dietary Strategies on Ruminants' Mammary Gland Gene Network: A Nutrigenomics Review

Although the inclusion of polyunsaturated fatty acids (PUFAs) in ruminants' diets appears to be a well-documented strategy to enrich milk with PUFAs, several gene networks that regulate milk synthesis and mammary gland homeostasis could be impaired. The objective of this literature review is to assess the effects of nutritional strategies focused on enriching milk with PUFAs on gene networks regulating mammary gland function and lipogenesis, as well as the impact of feed additives and bioactive compounds with prominent antioxidant potential on immune-oxidative transcriptional profiling, as a part of mammary gland homeostasis and health. The findings support the conclusion that PUFAs' inclusion in ruminants' diets more strongly downregulate the stearoyl-CoA desaturase (SCD) gene compared to other key genes involved in de novo fatty acid synthesis in the mammary gland. Additionally, it was revealed that seed oils rich in linoleic and linolenic acids have no such strong impact on networks that regulate lipogenic homeostasis compared to marine oils rich in eicosapentaenoic and docosahexaenoic acids. Furthermore, ample evidence supports that cows and sheep are more prone to the suppression of lipogenesis pathways compared to goats under the impact of dietary marine PUFAs. On the other hand, the inclusion of feed additives and bioactive compounds with prominent antioxidant potential in ruminants' diets can strengthen mammary gland immune-oxidative status. Considering that PUFA's high propensity to oxidation can induce a cascade of pro-oxidant incidences, the simultaneous supplementation of antioxidant compounds and especially polyphenols may alleviate any side effects caused by PUFA overload in the mammary gland. In conclusion, future studies should deeply investigate the effects of PUFAs on mammary gland gene networks in an effort to holistically understand their impact on both milk fat depression syndrome and homeostatic disturbance.

Milk Fat Depression and Trans-11 to Trans-10 C18:1 Shift in Milk of Two Cattle Farming Systems

Milk fat depression (MFD) syndrome, a consistent decrease in milk fat content, is related to important changes in fatty acid composition due to feed imbalances and the consequent ruminal metabolism alteration. Milk produced in two different farming systems was compared: Holstein Friesian fed with unified in intensive production and Podolica raised on a pasture in an extensive system. Milk chemical characteristics and fatty acid composition were determined comparing milk with a normal fat level (>3.8%) to milk with a low fat level (<3.2%) in each breeding system. Holstein Friesian milk showed the decrease in trans-11 and increase in trans-10 C18:1 (shift from trans-11 to trans-10 C18:1) in low fat with respect to normal fat milk with a consequent decrease in the trans-11/trans-10 C18:1 ratio. Even conjugated linoleic acid (CLA), C18:2 cis-9, trans-11, was lower while CLA trans-10, cis-12 was higher in low fat milk than in normal fat milk from Holstein Friesian. These changes, that are indicators of MFD syndrome, were not found in Podolica milk between fat levels. Holstein Friesian milk showed less short-chain fatty acids (9.48 % vs. 11.05%, p < 0.001), trans vaccenic acid (C18:1 trans-11, 0.51% vs. 3.39%, p < 0.001), rumenic acid (CLA C18:2 cis-9, trans-11, 0.32% vs. 1.45%, p < 0.001) and total CLA (0.53% vs. 1.91%, p < 0.001) contents than Podolica milk. Further losses of these human healthy nutrients in low fat Friesian milk reduced the nutritional quality of the milk, while the milk from animals raised on the pasture was of better quality even when the level of fat was low.

Transcriptome Adaptation of the Ovine Mammary Gland to Dietary Supplementation of Extruded Linseed

Several dietary strategies were adopted to reduce saturated fatty acids and increase beneficial fatty acids (FA) for human health. Few studies are available about the pathways/genes involved in these processes. Illumina RNA-sequencing was used to investigate changes in the ovine mammary gland transcriptome following supplemental feeding with 20% extruded linseed. Comisana ewes in mid-lactation were fed a control diet for 28 days (control period) followed by supplementation with 20% DM of linseed panel for 28 days (treatment period). Milk production was decreased by 30.46% with linseed supplementation. Moreover, a significant reduction in fat, protein and lactose secretion was also observed. Several unsaturated FAs were increased while short and medium chain saturated FAs were decreased by linseed treatment. Around four thousand (1795 up- and 2133 down-regulated) genes were significantly differentially regulated by linseed supplementation. The main pathways affected by linseed supplementation were those involved in the energy balance of the mammary gland. Principally, the mammary gland of fed linseed sheep showed a reduced abundance of transcripts related to the synthesis of lipids and carbohydrates and oxidative phosphorylation. Our study suggests that the observed decrease in milk saturated FA was correlated to down-regulation of genes in the lipid synthesis and lipid metabolism pathways.

Individual differences in responsiveness to diet-induced milk fat depression in dairy sheep and goats

Both sheep and goats can display very different individual degrees of milk fat depression (MFD), which might explain some apparent contradictions in the literature. Because the antilipogenic effect of certain fatty acids (FA) is the most likely origin of MFD, characterizing the milk FA profile of animals showing different degrees of MFD seems a helpful step to understand the physiological basis of the tolerance or susceptibility to the syndrome. Analyzing whether specific traits may predetermine a particular responsiveness would also be of relevance to meet this aim. However, information about these aspects is scant, not only in goats and sheep but in ruminants in general. This study was conducted with 25 Murciano-Granadina does and 23 Assaf ewes that were fed a total mixed ration without lipid supplementation for 3 wk (control period). Then, all animals received the same basal diet supplemented with 2% of fish oil (FO) for 5 additional weeks (MFD period). At the end of this second period, and on the basis of the extent of FO-induced decreases in milk fat concentration, the 5 most responsive (RESPON+) and the 5 least responsive (RESPON-) animals were selected within each species, 20 in total. Milk yield and composition, including a comprehensive FA profile, were examined at the end of each period. By design, between-group variation in milk fat concentration and yield was substantial, but no significant interaction with the effect of species was detected. Reductions in these 2 performance traits averaged 6% in RESPON- and 26% in RESPON+. Results do not allow suggesting that responsiveness to MFD would be clearly predetermined neither by the studied performance traits nor by milk FA profile, although a certain relationship with energy balance might exist. Furthermore, variations in ewes and does displaying different individual degrees of MFD may be associated with changes in certain candidate milk fat inhibitors, such as trans-10 18:1 and cis-9 16:1, whereas trans-10,cis-12 conjugated linoleic acid would only have a minor role in determining MFD severity. Alterations in the molar yield of de novo and preformed FA suggest relevant differences in the mechanisms underlying MFD in RESPON+ and RESPON-, with interspecies effects being observed only in more tolerant animals. Further research is still required to elucidate key determinants of responsiveness to MFD.

Nutritional Regulation of Mammary Gland Development and Milk Synthesis in Animal Models and Dairy Species

In mammals, milk is essential for the growth, development, and health. Milk quantity and quality are dependent on mammary development, strongly influenced by nutrition. This review provides an overview of the data on nutritional regulations of mammary development and gene expression involved in milk component synthesis. Mammary development is described related to rodents, rabbits, and pigs, common models in mammary biology. Molecular mechanisms of the nutritional regulation of milk synthesis are reported in ruminants regarding the importance of ruminant milk in human health. The effects of dietary quantitative and qualitative alterations are described considering the dietary composition and in regard to the periods of nutritional susceptibly. During lactation, the effects of lipid supplementation and feed restriction or deprivation are discussed regarding gene expression involved in milk biosynthesis, in ruminants. Moreover, nutrigenomic studies underline the role of the mammary structure and the potential influence of microRNAs. Knowledge from three lactating and three dairy livestock species contribute to understanding the variety of phenotypes reported in this review and highlight (1) the importance of critical physiological stages, such as puberty gestation and early lactation and (2) the relative importance of the various nutrients besides the total energetic value and their interaction.

Rumen biohydrogenation and milk fatty acid profile in dairy ewes divergent for feed efficiency

A sustainable increase in livestock production would require selection for improved feed efficiency, but the mechanisms underlying this trait and explaining its large individual variation in dairy ruminants remain unclear. This study was conducted in lactating ewes to test the hypothesis that rumen biohydrogenation (BH) would differ between high- and low-efficiency animals, and these differences would be reflected in rumen fatty acid (FA) profile and affect milk FA composition. A second aim was to identify differences in FA that may serve as biomarkers of feed efficiency. Data of daily feed intake and milk yield and composition, as well as body weight, were collected individually over a 3-wk period in 40 ewes. The difference between the mean actual and predicted feed intake (estimated through metabolizable energy requirements for maintenance, production, and body weight change) over the period was used as the feed efficiency index (FEI) to select 8 of the highest feed efficiency (H-FE) and 8 of the lowest feed efficiency (L-FE) animals. In addition, residual feed intake (RFI) was estimated as the residual term from the regression of feed intake on various energy sinks. Rumen and milk FA composition were characterized by using gas chromatography, and results were analyzed using a statistical model that included the fixed effect of the group (H-FE vs. L-FE). The FEI averaged -0.29 ± 0.046 and 0.81 ± 0.084 in H-FE and L-FE, respectively, whereas RFI averaged -0.16 ± 0.084 and 0.18 ± 0.082, respectively. The correlation coefficient between both metrics was 0.69. Feed intake was similar in both groups, but H-FE showed greater milk yield, with increases in lactose content and yield, and in milk protein and fat production. Results from rumen FA profiles included a lower proportion of 18:2n-6, cis-9 18:1, and of several of their BH metabolites, and a greater concentration of 18:0, which may indicate that the apparent BH would be more complete in more efficient sheep. Milk FA analysis suggested that the greater fat yield in the H-FE group was mostly explained by increased de novo FA synthesis, whereas their milk would have lower proportions of cis-9 18:1 and C20 to 22n-6 polyunsaturated FA than L-FE. Stepwise multiple linear regression suggested that milk C20 to 22n-6 PUFA might be convenient biomarkers to discriminate more efficient dairy sheep. Further research is needed to validate these findings (e.g., under different dietary conditions).

Effect of dietary lipids and other nutrients on milk odd- and branched-chain fatty acid composition in dairy ewes

Milk odd- and branched-chain fatty acids (OBCFA) are largely derived from bacteria leaving the rumen, which has encouraged research on their use as biomarkers of rumen function. Targeted research has examined relationships between these fatty acids (FA) and dietary components, but interactions between the effects of lipids and other nutrients on milk OBCFA are not well characterized yet. Furthermore, factors controlling milk OBCFA in sheep are largely unknown. Thus, the present meta-analysis examined relationships between diet composition and milk OBCFA using a database compiled with lot observations from 14 trials in dairy ewes fed lipid supplements. A total of 47 lots received lipid supplements, whereas their respective controls (27 lots) were fed the same basal diets without lipid supplementation. Relationships between milk OBCFA and dietary components were first assessed through a principal component analysis (PCA) and a correlation analysis. Then, responses of milk OBCFA to variations in specific dietary components (selected on the basis of the PCA) were examined in more detail by regression analysis. According to the loading plot, dietary unsaturated C18 FA loaded opposite to major milk OBCFA (e.g., 15:0, 15:0 anteiso, and 17:0) and were strongly correlated with principal component 1, which described 46% of variability. Overall, regression equations supported this negative, and generally linear, relationship between unsaturated C18 FA levels and milk OBCFA. However, the influence of C20-22 n-3 polyunsaturated FA and saturated FA was more limited. The PCA also suggested that dietary crude protein is not a determinant of milk OBCFA profile in dairy ewes, but significant relationships were observed between some OBCFA and dietary fiber or starch, consistent with a potential role of these FA as biomarkers of rumen cellulolytic and amylolytic bacteria. In this regard, regression equations indicated that iso FA would show opposite responses to increasing levels of acid detergent fiber (positive linear coefficients) and starch (negative linear coefficients). Lipid supplementation would not largely affect these associations, supporting the potential of OBCFA as noninvasive markers of rumen function under different feeding conditions (i.e., with or without lipid supplementation). Because consumption of these FA may have nutritional benefits for humans, the use of high-fiber/low-starch rations might be recommended to maintain the highest possible content of milk OBCFA in dairy sheep.

Invited review: Role of rumen biohydrogenation intermediates and rumen microbes in diet-induced milk fat depression: An update

To meet the energy requirements of high-yielding dairy cows, grains and fats have increasingly been incorporated in ruminant diets. Moreover, lipid supplements have been included in ruminant diets under experimental or practical conditions to increase the concentrations of bioactive n-3 fatty acids and conjugated linoleic acids in milk and meat. Nevertheless, those feeding practices have dramatically increased the incidence of milk fat depression in dairy cattle. Although induction of milk fat depression may be a management tool, most often, diet-induced milk fat depression is unintended and associated with a direct economic loss. In this review, we give an update on the role of fatty acids, particularly originating from rumen biohydrogenation, as well as of rumen microbes in diet-induced milk fat depression. Although this syndrome seems to be multi-etiological, the best-known causal factor remains the shift in rumen biohydrogenation pathway from the formation of mainly trans-11 intermediates toward greater accumulation of trans-10 intermediates, referred to as the trans-11 to trans-10 shift. The microbial etiology of this trans-11 to trans-10 shift is not well understood yet and it seems that unraveling the microbial mechanisms of diet-induced milk fat depression is challenging. Potential strategies to avoid diet-induced milk fat depression are supplementation with rumen stabilizers, selection toward more tolerant animals, tailored management of cows at risk, selection toward more efficient fiber-digesting cows, or feeding less concentrates and grains.

Review: Modulating ruminal lipid metabolism to improve the fatty acid composition of meat and milk. Challenges and opportunities

Growth in demand for foods with potentially beneficial effects on consumer health has motivated increased interest in developing strategies for improving the nutritional quality of ruminant-derived products. Manipulation of the rumen environment offers the opportunity to modify the lipid composition of milk and meat by changing the availability of fatty acids (FA) for mammary and intramuscular lipid uptake. Dietary supplementation with marine lipids, plant secondary compounds and direct-fed microbials has shown promising results. In this review, we have compiled information about their effects on the concentration of putative desirable FA (e.g. c9t11-CLA and vaccenic, oleic, linoleic and linolenic acids) in ruminal digesta, milk and intramuscular fat. Marine lipids rich in very long-chain n-3 polyunsaturated fatty acids (PUFA) efficiently inhibit the last step of C18 FA biohydrogenation (BH) in the bovine, ovine and caprine, increasing the outflow of t11-18:1 from the rumen and improving the concentration of c9t11-CLA in the final products, but increments in t10-18:1 are also often found due to shifts toward alternative BH pathways. Direct-fed microbials appear to favourably modify rumen lipid metabolism but information is still very limited, whereas a wide variety of plant secondary compounds, including tannins, polyphenol oxidase, essential oils, oxygenated FA and saponins, has been examined with varying success. For example, the effectiveness of tannins and essential oils is as yet controversial, with some studies showing no effects and others a positive impact on inhibiting the first step of BH of PUFA or, less commonly, the final step. Further investigation is required to unravel the causes of inconsistent results, which may be due to the diversity in active components, ruminant species, dosage, basal diet composition and time on treatments. Likewise, research must continue to address ways to mitigate negative side-effects of some supplements on animal performance (particularly, milk fat depression) and product quality (e.g. altered oxidative stability and shelf-life).