An interpretive review of selective sweep studies in Bos taurus cattle populations: identification of unique and shared selection signals across breeds

This review compiles the results of 21 genomic studies of European Bos taurus breeds and thus provides a general picture of the selection signatures in taurine cattle identified by genome-wide selection-mapping scans. By performing a comprehensive summary of the results reported in the literature, we compiled a list of 1,049 selection sweeps described across 37 cattle breeds (17 beef breeds, 14 dairy breeds and 6 dual-purpose breeds), and four different beef-vs-dairy comparisons, which we subsequently grouped into core selective sweep (CSS) regions, defined as consecutive signals within 1 Mb of each other. We defined a total of 409 CSSs across the 29 bovine autosomes, 232 (57%) of which were associated with a single-breed (Single-breed CSSs), 134 CSSs (33%) were associated with a limited number of breeds (Two-to-four-breed CSSs) and 39 CSSs (9%) were associated with five or more breeds (Multi-breed CSSs). For each CSS, we performed a candidate gene survey that identified 291 genes within the CSS intervals (from the total list of 5,183 BioMart-extracted genes) linked to dairy and meat production, stature and coat colour traits. A complementary functional enrichment analysis of the CSS positional candidates highlighted other genes related to pathways underlying behaviour, immune response and reproductive traits. The Single-breed CSSs revealed an over-representation of genes related to dairy and beef production, this was further supported by over-representation of production-related pathway terms in these regions based on a functional enrichment analysis. Overall, this review provides a comparative map of the selection sweeps reported in European cattle breeds and presents for the first time a characterization of the selection sweeps that are found in individual breeds. Based on their uniqueness, these breed-specific signals could be considered as divergence signals, which may be useful in characterising and protecting livestock genetic diversity

Prepartal Energy Intake Alters Blood Polymorphonuclear Leukocyte Transcriptome During the Peripartal Period in Holstein Cows

In the dairy industry, cow health and farmer profits depend on the balance between diet (ie, nutrient composition, daily intake) and metabolism. This is especially true during the transition period, where dramatic physiological changes foster vulnerability to immunosuppression, negative energy balance, and clinical and subclinical disorders. Using an Agilent microarray platform, this study examined changes in the transcriptome of bovine polymorphonuclear leukocytes (PMNLs) due to prepartal dietary intake. Holstein cows were fed a high-straw, control-energy diet (CON; NE L  = 1.34 Mcal/kg) or overfed a moderate-energy diet (OVE; NE L  = 1.62 Mcal/kg) during the dry period. Blood for PMNL isolation and metabolite analysis was collected at −14 and +7 days relative to parturition. At an analysis of variance false discovery rate <0.05, energy intake (OVE vs CON) influenced 1806 genes. Dynamic Impact Approach bioinformatics analysis classified treatment effects on Kyoto Encyclopedia of Genes and Genomes pathways, including activated oxidative phosphorylation and biosynthesis of unsaturated fatty acids and inhibited RNA polymerase, proteasome, and toll-like receptor signaling pathway. This analysis indicates that processes critical for energy metabolism and cellular and immune function were affected with mixed results. However, overall interpretation of the transcriptome data agreed in part with literature documenting a potentially detrimental, chronic activation of PMNL in response to overfeeding. The widespread, transcriptome-level changes captured here confirm the importance of dietary energy adjustments around calving on the immune system

Stress and inflammatory gene networks in bovine liver are altered by plane of dietary energy during late pregnancy

The prepartal dietary energy level is tightly correlated with the degree of tissue mobilization that the animal experiences around parturition (giving birth). To better understand the link between the dry period dietary energy management and the inflammatory status around parturition, 12 multiparous Holstein cows were fed for the entire dry period either a high-wheat straw/lower-energy diet to supply at least 100 % of the calculated net energy for lactation (NEL) (control, CON) or a higher-energy diet to supply >140 % of NEL (overfed, OVE). The blood was sampled throughout the transition period for biomarker analyses. Liver tissue samples were taken on days 1214, 7, 14, and 30 relative to parturition for triacylglycerol (TAG) composition and gene expression analysis. Fifty genes involved in inflammation, endoplasmic reticulum (ER), and oxidative stress, and cell cycle and growth were evaluated. Although blood biomarkers did not reveal signs of a greater inflammatory status compared with OVE, CON cows had a greater activation of the intrahepatic unfolded protein response prepartum. However, postpartum mRNA profiling indicated that the OVE group experienced a mild but sustained level of ER stress, with higher oxidative stress and impairment of antioxidant mechanisms. After parturition, inflammation-related genes were upregulated in OVE cows compared with CON. However, CON cows experienced a gradual increase in expression of key inflammatory transcription regulators up to 30 days postpartum which agreed with the lower plasma albumin and cholesterol, suggesting an inflammatory state. Data underscored that ER stress is not necessarily linked with inflammation during the peripartal period. Gene expression data also suggest that prepartum overnutrition could have negative effects on normal cell cycle activity. Overall, allowing cows to overconsume energy prepartum increased the hepatic pro-inflammatory response prepartum and up to the point of parturition. Subsequently, cows fed the lower-energy diet experienced a gradual increase in the inflammatory response. The lack of differences between groups in voluntary feed intake and lactation capacity suggests that nutritional management prepartum triggers different mechanisms that affect ER and oxidative stress along with inflammation. Although no clinical disorders were detected, these alterations expose animals to the development of immuno-metabolic disorders

Blood immunometabolic indices and polymorphonuclear neutrophil function in peripartum dairy cows are altered by level of dietary energy prepartum

Cows experience some degree of negative energy balance and immunosuppression around parturition, making them vulnerable to metabolic and infectious diseases. The effect of prepartum feeding of diets to meet (control, 1.34 Mcal/kg of dry matter) or exceed (overfed, 1.62 Mcal/kg of dry matter) dietary energy requirements was evaluated during the entire dry period ( 3c45 d) on blood polymorphonuclear neutrophil function, blood metabolic and inflammatory indices, and milk production in Holstein cows. By design, dry matter intake in the overfed group (n=9) exceeded energy requirements during the prepartum period (-4 to -1 wk relative to parturition), resulting in greater energy balance when compared with the control group (n=10). Overfed cows were in more negative energy balance during wk 1 after calving than controls. No differences were observed in dry matter intake, milk yield, and milk composition between diets. Although nonesterified fatty acid concentration pre- (0.138 mEq/L) and postpartum (0.421 mEq/L) was not different between diets, blood insulin concentration was greater in overfed cows prepartum (16.7 \u3bcIU/mL) compared with controls pre- and postpartum ( 3c3.25 \u3bcIU/mL). Among metabolic indicators, concentrations of urea (4.63 vs. 6.38 mmol/L), creatinine (100 vs. 118 \u3bcmol/L), and triacylglycerol (4.0 vs. 8.57 mg/dL) in overfed cows were lower prepartum than controls. Glucose was greater pre- (4.24 vs. 4.00 mmol/L) and postpartum (3.49 vs. 3.30 mmol/L) compared with control cows. Among liver function indicators, the concentration of bilirubin increased by 2 to 6 fold postpartum in control and overfed cows. Phagocytosis capacity of polymorphonuclear neutrophils was lower prepartum in overfed cows (32.7% vs. 46.5%); phagocytosis in the control group remained constant postpartum (50%) but it increased at d 7 in the overfed group to levels similar to controls (48.4%). Regardless of prepartum diet, parturition was characterized by an increase in nonesterified fatty acid and liver triacylglycerol, as well as blood indices of inflammation (ceruloplasmin and haptoglobin), oxidative stress (reactive oxygen metabolites), and liver injury (glutamic oxaloacetic transaminase). Concentrations of the antioxidant and anti-inflammatory compounds vitamin A, vitamin E, and \u3b2-carotene decreased after calving. For vitamin A, the decrease was observed in overfed cows (47.3 vs. 27.5 \u3bcg/100 mL). Overall, overfeeding energy and higher energy status prepartum led to the surge of insulin and had a transient effect on metabolism postpartum

Acute mammary and liver transcriptome responses after an intramammary Escherichia coli lipopolysaccharide challenge in postpartal dairy cows

The study investigated the effect of an intramammary lipopolysaccharide (LPS) challenge on the bovine mammary and liver transcriptome and its consequences on metabolic biomarkers and liver tissue composition. At 7days of lactation, 7 cows served as controls (CTR) and 7 cows (LPS) received an intramammary Escherichia coli LPS challenge. The mammary and liver tissues for transcriptomic profiling were biopsied at 2.5h from challenge. Liver composition was evaluated at 2.5h and 7days after challenge, and blood biomarkers were analyzed at 2, 3, 7 and 14days from challenge. In mammary tissue, the LPS challenge resulted in 189 differentially expressed genes (DEG), with 20 down-regulated and 169 up-regulated. In liver tissue, there were 107 DEG in LPS compared with CTR with 42 down-regulated and 65 up-regulated. In mammary, bioinformatics analysis highlighted that LPS led to activation of NOD-like receptor signaling, Toll-like receptor signaling, RIG-I-like receptor signaling and apoptosis pathways. In liver, LPS resulted in an overall inhibition of fatty acid elongation in mitochondria and activation of the p53 signaling pathway. The LPS challenge induced changes in liver lipid composition, a systemic inflammation (rise of blood ceruloplasmin and bilirubin), and an increase in body fat mobilization. The data suggest that cells within the inflamed mammary gland respond by activating mechanisms of pathogen recognition. However, in the liver the response likely depends on mediators originating from the udder that affect liver functionality and specifically fatty acid metabolism (beta-oxidation, ketogenesis, and lipoprotein synthesis)