An organism-wide ATAC-seq peak catalog for the bovine and its use to identify regulatory variants.

We report the generation of an organism-wide catalog of 976,813 cis-acting regulatory elements for the bovine detected by the assay for transposase accessible chromatin using sequencing (ATAC-seq). We regroup these regulatory elements in 16 components by nonnegative matrix factorization. Correlation between the genome-wide density of peaks and transcription start sites, correlation between peak accessibility and expression of neighboring genes, and enrichment in transcription factor binding motifs support their regulatory potential. Using a previously established catalog of 12,736,643 variants, we show that the proportion of single-nucleotide polymorphisms mapping to ATAC-seq peaks is higher than expected and that this is owing to an approximately 1.3-fold higher mutation rate within peaks. Their site frequency spectrum indicates that variants in ATAC-seq peaks are subject to purifying selection. We generate eQTL data sets for liver and blood and show that variants that drive eQTL fall into liver- and blood-specific ATAC-seq peaks more often than expected by chance. We combine ATAC-seq and eQTL data to estimate that the proportion of regulatory variants mapping to ATAC-seq peaks is approximately one in three and that the proportion of variants mapping to ATAC-seq peaks that are regulatory is approximately one in 25. We discuss the implication of these findings on the utility of ATAC-seq information to improve the accuracy of genomic selection.

Comparison of environment quality measurements between 3 types of calf housing in the United Kingdom.

Preweaning calves are kept in a range of housing types that offer variable protection against the weather and provide differing internal environments. This cross-sectional observational study assessed the effect of housing type (shed, polytunnel, or hutches) on internal environmental parameters, using 2 blocks of 8-wk measurements from 10 commercial dairy farms in the south of England, covering both summer and winter periods. Continuous measurements for internal and external temperature and humidity were recorded by data logger placed within the calf housing and used to calculate the temperature-humidity index (THI). Weekly point readings were also taken for temperature, humidity, light, air speed, ammonia level, and airborne particulate matter. Airborne bacterial levels were determined at wk 2, 5, and 8 by incubating air samples at 35°C for 24 h in aerobic conditions. Data were analyzed using linear mixed models. Housing type influenced THI significantly in both seasons. In summer, calves were exposed to heat stress conditions (THI ≥72) for 39, 31, and 14 of 46 d in polytunnel housing, hutches, and sheds, respectively. The maximum summer temperature (37.0°C) was recorded in both hutch and polytunnel housing, with sheds remaining consistently cooler (maximum 31.0°C). In winter, the lowest minimum internal temperature recorded was in hutches at -4.5°C, with both the sheds and polytunnel, but not hutches, providing a significant increase in temperature compared with the external environment. Hutches remained ≤ 10°C for 86% of the winter study period. Light levels were reduced in all housing types compared with the external environment. The particulate matter in air that is capable of reaching the lungs (particulate matter <10 µm) was highest in sheds, intermediate in hutches, and lowest in polytunnel housing (0.97 ± 3.75, 0.37 ± 0.44, and 0.20 ± 0.24 mg/m3, respectively). This was mirrored by airborne bacterial numbers, which were also highest in sheds (8,017 ± 2,141 cfu/m3), intermediate in hutches (6,870 ± 2,084 cfu/m3), and lowest in the polytunnel (3,357 ± 2,572 cfu/m3). Round, white, catalase-positive, and oxidase-negative colonies were most prevalent, likely indicating Staphylococcus species. This study demonstrated that UK calves are routinely exposed to either heat or cold stress, especially when housed in hutches or polytunnels. Sheds had the highest levels of particulate matter and airborne bacteria, both known contributory factors for respiratory disease. These findings demonstrate that all calf housing systems result in environmental compromises that could have long-term impacts on calf health and growth; therefore, further studies should identify husbandry and housing modifications to mitigate these factors.

Hepatic Global Transcriptomic Profiles of Holstein Cows According to Parity Reveal Age-Related Changes in Early Lactation.

Cows can live for over 20 years, but their productive lifespan averages only around 3 years after first calving. Liver dysfunction can reduce lifespan by increasing the risk of metabolic and infectious disease. This study investigated the changes in hepatic global transcriptomic profiles in early lactation Holstein cows in different lactations. Cows from five herds were grouped as primiparous (lactation number 1, PP, 534.7 ± 6.9 kg, n = 41), or multiparous with lactation numbers 2-3 (MP2-3, 634.5 ± 7.5 kg, n = 87) or 4-7 (MP4-7, 686.6 ± 11.4 kg, n = 40). Liver biopsies were collected at around 14 days after calving for RNA sequencing. Blood metabolites and milk yields were measured, and energy balance was calculated. There were extensive differences in hepatic gene expression between MP and PP cows, with 568 differentially expressed genes (DEGs) between MP2-3 and PP cows, and 719 DEGs between MP4-7 and PP cows, with downregulated DEGs predominating in MP cows. The differences between the two age groups of MP cows were moderate (82 DEGs). The gene expression differences suggested that MP cows had reduced immune functions compared with the PP cows. MP cows had increased gluconeogenesis but also evidence of impaired liver functionality. The MP cows had dysregulated protein synthesis and glycerophospholipid metabolism, and impaired genome and RNA stability and nutrient transport (22 differentially expressed solute carrier transporters). The genes associated with cell cycle arrest, apoptosis, and the production of antimicrobial peptides were upregulated. More surprisingly, evidence of hepatic inflammation leading to fibrosis was present in the primiparous cows as they started their first lactation. This study has therefore shown that the ageing process in the livers of dairy cows is accelerated by successive lactations and increasing milk yields. This was associated with evidence of metabolic and immune disorders together with hepatic dysfunction. These problems are likely to increase involuntary culling, thus reducing the average longevity in dairy herds.

Proportion of Concentrate in the Diet of Early Lactation Dairy Cows Has Contrasting Effects on Circulating Leukocyte Global Transcriptomic Profiles, Health and Fertility According to Parity.

The functionality of circulating leukocytes in dairy cows is suppressed after calving, with negative energy balance as a risk factor. Leukocyte transcriptomic profiles were compared separately in 44 multiparous (MP) and 18 primiparous (PP) Holstein-Friesian cows receiving diets differing in concentrate proportion to test whether immune dysfunction could be mitigated by appropriate nutrition. After calving, cows were offered either (1) low concentrate (LC); (2) medium concentrate (MC) or (3) high concentrate (HC) diets with proportions of concentrate to grass silage of 30%:70%, 50%:50% and 70%:30%, respectively. Cow phenotype data collected included circulating metabolites, milk yield and health and fertility records. RNA sequencing of circulating leukocytes at 14 days in milk was performed. The HC diet improved energy balance in both age groups. There were more differentially expressed genes in PP than MP cows (460 vs. 173, HC vs. LC comparison) with few overlaps. The MP cows on the LC diet showed upregulation of the complement and coagulation cascade and innate immune defence mechanisms against pathogens and had a trend of more cases of mastitis and poorer fertility. In contrast, the PP cows on the HC diet showed greater immune responses based on both gene expression and phenotypic data and longer interval of calving to conception. The leukocytes of MP and PP cows therefore responded differentially to the diets between age, nutrient supply and immunity affecting their health and subsequent fertility.

Global transcriptomic profiles of circulating leucocytes in early lactation cows with clinical or subclinical mastitis.

Bovine mastitis, an inflammatory disease of the mammary gland, is classified as subclinical or clinical. Circulating neutrophils are recruited to the udder to combat infection. We compared the transcriptomic profiles in circulating leukocytes between healthy cows and those with naturally occurring subclinical or clinical mastitis. Holstein Friesian dairy cows from six farms in EU countries were recruited. Based on milk somatic cell count and clinical records, cows were classified as healthy (n = 147), subclinically (n = 45) or clinically mastitic (n = 22). Circulating leukocyte RNA was sequenced with Illumina NextSeq single end reads (30 M). Differentially expressed genes (DEGs) between the groups were identified using CLC Genomics Workbench V21, followed by GO enrichment analysis. Both subclinical and clinical mastitis caused significant changes in the leukocyte transcriptome, with more intensive changes attributed to clinical mastitis. We detected 769 DEGs between clinical and healthy groups, 258 DEGs between subclinical and healthy groups and 193 DEGs between clinical and subclinical groups. Most DEGs were associated with cell killing and immune processes. Many upregulated DEGs in clinical mastitis encoded antimicrobial peptides (AZU1, BCL3, CAMP, CATHL1, CATHL2, CATHL4,CATHL5, CATHL6, CCL1, CXCL2, CXCL13, DEFB1, DEFB10, DEFB4A, DEFB7, LCN2, PGLYRP1, PRTN3, PTX3, S100A8, S100A9, S100A12, SLC11A1, TF and LTF) which were not upregulated in subclinical mastitis. The use of transcriptomic profiles has identified a much greater up-regulation of genes encoding antimicrobial peptides in circulating leukocytes of cows with naturally occurring clinical compared with subclinical mastitis. These could play a key role in combatting disease organisms.

Acute bovine viral diarrhea virus infection inhibits expression of interferon tau-stimulated genes in bovine endometrium.

Bovine viral diarrhea virus (BVDV) can evade host detection by downregulation of interferon signaling pathways. Infection of cows with noncytopathic (ncp) BVDV can cause early embryonic mortality. Upregulation of type I interferon stimulated genes (ISGs) by blastocyst-secreted interferon tau (IFNT) is a crucial component of the maternal recognition of pregnancy (MRP) in ruminants. This study investigated the potential of acute BVDV infection to disrupt MRP by modulating endometrial ISG expression. Endometrial cells from 10 BVDV-free cows were cultured and treated with 0 or 100 ng/ml IFNT for 24 h in the absence or presence of ncpBVDV infection to yield four treatment groups: CONT, ncpBVDV, IFNT, or ncpBVDV+IFNT. ncpBVDV infection alone only upregulated TRIM56, but reduced mRNA expression of ISG15, MX2, BST2, and the proinflammatory cytokine IL1B. As anticipated, IFNT treatment alone significantly increased expression of all 17 ISGs tested. In contrast to the limited effect of ncpBVDV alone, the virus markedly inhibited IFNT-stimulated expression of 15 ISGs tested (ISG15, HERC5, USP18, DDX58, IFIH1, IFIT1, IFIT3, BST2, MX1, MX2, RSAD2, OAS1Y, SAMD9, GBP4, and PLAC8), together with ISG15 secreted protein. Only TRIM56 and IFI27 expression was unaltered. IL1B expression was reduced by the combined treatment. These results indicate that acute ncpBVDV infection may decrease uterine immunity and lead to MRP failure through inhibition of IFNT-stimulated endometrial ISG production. This in turn could reduce fertility and predispose cows to uterine disease, while evasion of the normal uterine immune response by ncpBVDV may contribute to maintenance and spreading of this economically important disease.

Influence of hyaluronan on endometrial receptivity and embryo attachment in sheep.

An increasing number of reports suggests a role of hyaluronan (HA) in female reproduction and interest in its application in assisted reproduction is rising. However, there are contrasting data about the effectiveness of adding HA to the embryo-transfer medium on improving pregnancy rates. Using sheep as an experimental model, the studies reported here analysed the impact of HA infusion into the uterus on embryo attachment to uterine luminal epithelium (LE) and expression of selected markers of uterine receptivity. On Day 14 after natural mating (pre-attachment), uterine horns were infused with either (n=4 each): PBS (control), HA (1mg mL-1), HA+hyaluronidase 2 (Hyal2; 300IU mL-1) or 4-methyl-umbelliferone (HA-synthesis inhibitor; 4MU, 1mM). HA immunostaining on uterine sections collected on Day 17 was negative in the 4MU group and weak in the HA+Hyal2 group. In contrast to 4MU, which resulted in 100% attachment, HA infusion blocked embryo attachment in all treated animals. This was accompanied by the disappearance of mucin 1 and increased expression of osteopontin and CD44v6 in the LE of uteri with attached embryos. In conclusion, the presence of HA at the embryo-maternal interface during embryo implantation resulted in reduced endometrial receptivity and inhibited the interaction of trophoblasts with the LE, whereas clearance of HA favoured embryo attachment.

BVDV alters uterine prostaglandin production during pregnancy recognition in cows.

Embryonic mortality in cows is at least in part caused by failure of pregnancy recognition (PR). Evidence has shown that bovine viral diarrhoea virus (BVDV) infection can disrupt pregnancy. Prostaglandins (PG) play important roles in many reproductive processes, such as implantation. The aim of this study was to investigate the effect of BVDV infection on uterine PG production and PR using an in vitro PR model. Bovine uterine endometrial cells isolated from ten BVDV-free cows were cultured and treated with 0 or 100ng/mL interferon-τ (IFNT) in the absence or presence of non-cytopathic BVDV (ncpBVDV). PGF2α and PGE2 concentrations in the spent medium were measured using radioimmunoassays, and in the treated cells expression of the genes associated with PG production and signalling was quantified using qPCR. The results showed that the IFNT challenge significantly stimulated PTGS1 and PTGER3 mRNA expression and PGE2 production; however, these stimulatory effects were neutralised in the presence of ncpBVDV infection. ncpBVDV infection significantly increased PTGS1 and mPGES1 mRNA expression and decreased AKR1B1 expression, leading to increased PGE2 and decreased PGF2α concentrations and an increased PGE2:PGF2α ratio. The other tested genes, including PGR, ESR1, OXTR, PTGS2, PTGER2 and PTGFR, were not significantly altered by IFNT, ncpBVDV or their combination. Our study suggests that BVDV infection may impair PR by (1) inhibiting the effect of IFNT on uterine PG production and (2) inducing an endocrine switch of PG production from PGF2α to PGE2 to decrease uterine immunity, thereby predisposing the animals to uterine disease.

Global transcriptomic profiling of bovine endometrial immune response in vitro. I. Effect of lipopolysaccharide on innate immunity.

The dysregulation of endometrial immune response to bacterial lipopolysaccharide (LPS) has been implicated in uterine disease and infertility in the postpartum dairy cow, although the mechanisms are not clear. Here, we investigated whole-transcriptomic gene expression in primary cultures of mixed bovine epithelial and stromal endometrial cells. Cultures were exposed to LPS for 6 h, and cellular response was measured by bovine microarray. Approximately 30% of the 1006 genes altered by LPS were classified as being involved in immune response. Cytokines and chemokines (IL1A, CX3CL1, CXCL2, and CCL5), interferon (IFN)-stimulated genes (RSAD2, MX2, OAS1, ISG15, and BST2), and the acute phase molecule SAA3 were the most up-regulated genes. Ingenuity Pathway Analysis identified up-regulation of many inflammatory cytokines and chemokines, which function to attract immune cells to the endometrium, together with vascular adhesion molecules and matrix metalloproteinases, which can facilitate immune cell migration from the tissue toward the uterine lumen. Increased expression of many IFN-signaling genes, immunoproteasomes, guanylate-binding proteins, and genes involved in the intracellular recognition of pathogens suggests important roles for these molecules in the innate defense against bacterial infections. Our findings confirmed the important role of endometrial cells in uterine innate immunity, whereas the global approach used identified several novel immune response pathways triggered by LPS in the endometrium. Additionally, many genes involved in endometrial response to the conceptus in early pregnancy were also altered by LPS, suggesting one mechanism whereby an ongoing response to infection may interfere with the establishment of pregnancy.

Global transcriptomic profiling of bovine endometrial immune response in vitro. II. Effect of bovine viral diarrhea virus on the endometrial response to lipopolysaccharide.

Infection with noncytopathic bovine viral diarrhea virus (ncpBVDV) is associated with uterine disease and infertility. This study investigated the influence of ncpBVDV on immune functions of the bovine endometrium by testing the response to bacterial lipopolysaccharide (LPS). Primary cultures of mixed epithelial and stromal cells were divided into four treatment groups (control [CONT], BVDV, CONT+LPS, and BVDV+LPS) and infected with ncpBVDV for 4 days followed by treatment with LPS for 6 h. Whole-transcriptomic gene expression was measured followed by Ingenuity Pathway Analysis. Differential expression of 184 genes was found between CONT and BVDV treatments, showing interplay between induction and inhibition of responses. Up-regulation of TLR3, complement, and chemotactic and TRIM factors by ncpBVDV all suggested an ongoing immune response to viral infection. Down-regulation of inflammatory cytokines, chemokines, CXCR4, and serine proteinase inhibitors suggested mechanisms by which ncpBVDV may simultaneously counter the host response. Comparison between BVDV+LPS and CONT+LPS treatments showed 218 differentially expressed genes. Canonical pathway analysis identified the key importance of interferon signaling. Top down-regulated genes were RSAD2, ISG15, BST2, MX2, OAS1, USP18, IFIT3, IFI27, SAMD9, IFIT1, and DDX58, whereas TRIM56, C3, and OLFML1 were most up-regulated. Many of these genes are also regulated by IFNT during maternal recognition of pregnancy. Many innate immune genes that typically respond to LPS were inhibited by ncpBVDV, including those involved in pathogen recognition, inflammation, interferon response, chemokines, tissue remodeling, cell migration, and cell death/survival. Infection with ncpBVDV can thus compromise immune function and pregnancy recognition, thereby potentially predisposing infected cows to postpartum bacterial endometritis and reduced fertility.

Role of PTGS2-generated PGE2 during gonadotrophin-induced bovine oocyte maturation and cumulus cell expansion.

Prostaglandin E2 (PGE2) is an autocrine/paracrine factor which mediates gonadotrophin (Gn) stimulation of cumulus expansion and oocyte maturation in rodents. Its role in bovine oocyte maturation is less characterized. This study detected PTGS2 (COX2) and PGE synthases (PTGES1, PTGES2 and PTGES3) in bovine cumulus-oocyte complexes (COC). Only PTGS2 and PTGES1 expression changed during maturation. In Gn-free media, no cumulus expansion and ∼45% nuclear maturation was achieved, while Gn-induced maturation showed full cumulus expansion (score 3) and ∼87% maturation. PGE2 supplementation without Gn induced mild cumulus expansion (score 0.5-1) but increased nuclear maturation to levels similar to those obtained with Gn alone. In the presence of Gn, exogenous PGE2 did not affect expansion or nuclear maturation and subsequent embryo development. Treatment with PTGS2 selective inhibitor (NS398), PTGS2-specific siRNA or PTGER2-receptor antagonist (AH6809) resulted in ∼20-25% reduction in nuclear maturation. NS398 and AH6809 did not affect cumulus expansion. Most oocytes not reaching metaphase of second meiosis (MII) following NS398, AH6809 and PTGS2-specific siRNA treatments were at MI. After longer maturation, NS398-treated oocytes had normal MII rate and uncompromised embryo development. PGE2 has a limited role in cumulus expansion in bovine COC but is important for the timing of Gn-induced nuclear maturation. We confirmed that genes involved in the synthesis of prostaglandin E2 (PGE2) are expressed by cumulus-oocyte complexes (or eggs) of cows and that PGE2 is synthesized during oocyte maturation in the presence of gonadotrophin hormones. When we inhibited synthesis of PGE2 or blocked its receptors, oocyte maturation, but not cumulus expansion, was compromised. Further investigation showed that oocyte maturation is delayed but not arrested when PGE2 synthesis is inhibited. On the other hand, addition of exogenous PGE2 induced a high maturation rate and mild cumulus expansion only in the absence of gonadotrophin stimulation, and had no effect in the presence of gonadotrophin.

Does inbreeding contribute to pregnancy loss in Thoroughbred horses?

BACKGROUND: Excessive inbreeding increases the probability of uncovering homozygous recessive genotypes and has been associated with an increased risk of retained placenta and lower semen quality. No genomic analysis has investigated the association between inbreeding levels and pregnancy loss. OBJECTIVES: To compare genetic inbreeding coefficients (F) of naturally occurring Thoroughbred Early Pregnancy Loss (EPLs), Mid and Late term Pregnancy Loss (MLPL) and Controls. The F value was hypothesised to be higher in cases of pregnancy loss (EPLs and MLPLs) than Controls. STUDY DESIGN: Observational case-control study. METHODS: Allantochorion and fetal DNA from EPL (n = 37, gestation age 14-65 days), MLPL (n = 94, gestational age 70 days-24 h post parturition) and Controls (n = 58) were genotyped on the Axiom Equine 670K SNP Genotyping Array. Inbreeding coefficients using Runs of Homozygosity (FROH) were calculated using PLINK software. ROHs were split into size categories to investigate the recency of inbreeding. RESULTS: MLPLs had significantly higher median number of ROH (188 interquartile range [IQR], 180.8-197.3), length of ROH (3.10, IQR 2.93-3.33), and total number of ROH (590.8, IQR 537.3-632.3), and FROH (0.26, IQR 0.24-0.28) when compared with the Controls and the EPLs (p < 0.05). There was no significant difference in any of the inbreeding indices between the EPLs and Controls. The MLPLs had a significantly higher proportion of long (>10 Mb) ROH (2.5%, IQR 1.6-3.6) than the Controls (1.7%, IQR 0.6-2.5), p = 0.001. No unique ROHs were found in the EPL or MLPL populations. MAIN LIMITATIONS: SNP-array data does not allow analysis of every base in the sequence. CONCLUSIONS: This first study of the effect of genomic inbreeding levels on pregnancy loss showed that inbreeding is a contributor to MLPL, but not EPL in the UK Thoroughbred population. Mating choices remain critical, because inbreeding may predispose to MLPL by increasing the risk of homozygosity for specific lethal allele(s).

Influence of energy balance on the antimicrobial peptides S100A8 and S100A9 in the endometrium of the post-partum dairy cow.

Uterine inflammation occurs after calving in association with extensive endometrial remodelling and bacterial contamination. If the inflammation persists, it leads to reduced fertility. Chronic endometritis is highly prevalent in high-yielding cows that experience negative energy balance (NEB) in early lactation. This study investigated the effect of NEB on the antimicrobial peptides S100A8 and S100A9 in involuting uteri collected 2 weeks post partum. Holstein-Friesian cows (six per treatment) were randomly allocated to two interventions designed to produce mild or severe NEB (MNEB and SNEB) status. Endometrial samples were examined histologically, and the presence of neutrophils, macrophages, lymphocytes and natural killer cells was confirmed using haematoxylin and eosin and immunostaining. SNEB cows had greater signs of uterine inflammation. Samples of previously gravid uterine horn were used to localise S100A8 and S100A9 by immunohistochemistry. Both S100 proteins were present in bovine endometrium with strong staining in epithelial and stromal cells and in infiltrated leucocytes. Immunostaining was significantly higher in SNEB cows along with increased numbers of segmented neutrophils. These results suggest that the metabolic changes of a post-partum cow suffering from NEB delay uterine involution and promote a chronic state of inflammation. We show that upregulation of S100A8 and S100A9 is clearly a key component of the early endometrial response to uterine infection. Further studies are warranted to link the extent of this response after calving to the likelihood of cows developing endometritis and to their subsequent fertility.

Regulation of the hyaluronan system in ovine endometrium by ovarian steroids.

In this study, we investigated steroid regulation of the hyaluronan (HA) system in ovine endometrium including HA synthases (HAS), hyaluronidases, and HA receptor-CD44 using 30 adult Welsh Mountain ewes. Eight ewes were kept intact and synchronized to estrous (day 0). Intact ewes were killed on day 9 (luteal phase; LUT; n=5) and day 16 (follicular phase; FOL; n=3). The remaining ewes (n=22) were ovariectomized and then treated (i.m.) with vehicle (n=6) or progesterone (n=8) for 10 days, or estrogen and progesterone for 3 days followed by 7 days of progesterone alone (n=8). Estradiol and progesterone concentrations in plasma correlated with the stage of estrous or steroid treatment. Our results showed trends (P<0.1) and statistically significant effects (P<0.05, by t-test) indicating that LUT had lower HAS1 and HAS2 and higher HAS3 and CD44 mRNA expression compared with FOL. This was reflected in immunostaining of the corresponding HAS proteins. Similarly, in ovariectomized ewes, progesterone decreased HAS1 and HAS2 and increased HAS3 and CD44, whereas estradiol tended to increase HAS2 and decrease CD44. Sometimes, HAS mRNA expression did not follow the same trend observed in the intact animals or the protein expression. HA and its associated genes and receptors were regulated by the steroids. In conclusion, these results show that the level of HA production and the molecular weight of HA in the endometrium are regulated by ovarian steroids through differential expression of different HAS both at the gene and at the protein levels.

Investigation of transferability of BovineSNP50 BeadChip from cattle to water buffalo for genome wide association study.

Cattle and water buffalo belong to the same subfamily Bovinae and share chromosome banding and gene order homology. In this study, we used genome-wide Illumina BovineSNP50 BeadChip to analyze 91 DNA samples from three breeds of water buffalo (Nili-Ravi, Murrah and their crossbred with local GuangXi buffalos in China), to demonstrate the genetic divergence between cattle and water buffalo through a large single nucleotide polymorphism (SNP) transferability study at the whole genome level, and performed association analysis of functional traits in water buffalo as well. A total of 40,766 (75.5 %) bovine SNPs were found in the water buffalo genome, but 49,936 (92.5 %) were with only one allele, and finally 935 were identified to be polymorphic and useful for association analysis in water buffalo. Therefore, the genome sequences of water buffalo and cattle shared a high level of homology but the polymorphic status of the bovine SNPs varied between these two species. The different patterns of mutations between species may associate with their phenotypic divergence due to genome evolution. Among 935 bovine SNPs, we identified a total of 9 and 7 SNPs significantly associated to fertility and milk production traits in water buffalo, respectively. However, more works in larger sample size are needed in future to verify these candidate SNPs for water buffalo.

Effects of the Individual and Pair Housing of Calves on Long-Term Heifer Production on a UK Commercial Dairy Farm.

Pair housing of pre-weaning dairy calves has previously demonstrated positive impacts on their growth, health and behaviour, but longer-term effects on production are still relatively unknown. This study followed a cohort of 431 Holstein heifers, recruited from a single UK commercial dairy farm, from weaning until either culling or the end of their first lactation. All animals were allocated to either individual or pair housing as a pre-weaning calf. Following weaning, all heifers were similarly managed through group housing, feeding with total mixed rations, the use of automatic heat detection for artificial insemination and weighing every two months until conception. Farm staff identified disease occurrences, which were treated following standard operating procedures. First-lactation monthly milk recording was used to measure milk yields and somatic cell counts. Overall mortality (voluntary and involuntary) was 26.6%, with a decreased hazard of exiting the herd if the heifer was pair housed as a calf (HR 0.70; p = 0.067). The voluntary cull rate was highest in the post-insemination period (13.0%) due to poor fertility. Heifers that were pair housed as calves had significantly increased odds of developing udder health issues as a primiparous cow (OR = 1.93, p = 0.022). Despite this, the 305-day milk yields were not associated with the housing group. However, the total milk produced per calf recruited into the original study was greater for pair-housed compared with individually housed calves (8088 kg vs. 7115 kg; p = 0.071), which is likely due to the significantly higher hazard of individually housed calves exiting the herd prematurely.

Effects of Individual and Pair Housing of Calves on Short-Term Health and Behaviour on a UK Commercial Dairy Farm.

Social pair housing of calves has previously demonstrated positive impacts for calves, so this study aimed to compare the health and behaviour of calves kept in individual compared to pair housing on a single commercial UK dairy farm. A total of 457 Holstein and Jersey heifer calves were recruited and systematically allocated to individual and pair housing. Weekly visits were conducted up to 8 weeks of age, with weight and presence of clinical disease measured using both a standardized scoring system and thoracic ultrasonography. A subset of calves (n = 90) had accelerometers attached to monitor activity, with CCTV placed above a further 16 pens to allow behavioural assessments to be made via continuous focal sampling at 1 and 5 weeks of age. During the study, there was a mortality rate of 2.8%, and an average daily liveweight gain (ADLG) of 0.72 kg/day, with no significant effect of housing group (p = 0.76). However, individually housed calves had increased odds of developing disease (OR = 1.88, p = 0.014). Accelerometer data showed that housing group had no effect on lying times, with a mean of 18 h 11 min per day (SD 39 min) spent lying down. The motion index was significantly higher in pair-housed calves (F1,83 = 440.3, p < 0.01), potentially due to more social play behaviour. The total time engaged in non-nutritive oral behaviours (NNOBs) was not impacted by housing group (p = 0.72). Pair-housed calves split their time conducting NNOBs equally between inanimate objects and on their pen mates' body. Individually housed calves spent significantly more time with their head out of the front of the pen (p = 0.006), and also engaged in more self-grooming than pair-housed calves (p = 0.017), possibly due to a lack of socialization. The overall findings of this study indicate that within a UK commercial dairy management system, pair-housed calves were healthier and more active than individually housed calves, while housing group did not influence ADLG or the occurrence of NNOBs.

Time course of defense mechanisms in bovine endometrium in response to lipopolysaccharide.

Endometritis caused by uterine infection after calving reduces fertility and causes major economic losses to the dairy industry. This study investigated the time course of an inflammatory response in bovine endometrium triggered by exposure to bacterial endotoxin lipopolysaccharide (LPS). Mixed endometrial epithelial and stromal cells (9:1 ratio) were grown to confluence as a model system and treated with an optimized dose of 100 ng/ml LPS in vitro. Gene expression responses were measured using quantitative PCR, and gene products were investigated using assays of culture medium and Western blotting. Of 17 candidate genes tested initially, LPS treatment for 24 h up-regulated mRNA expression of TLR4 signaling (TLR4, CD14), cytokines (IL1B, TNF), chemokines (IL8, CXCL5), antimicrobial peptides (LAP, S100A8, S100A9, S100A12), and matrix metalloproteinases (MMP1, MMP13). A 48 h, LPS time course study showed that TNF increased first at 1 h, followed by peak expression of IL1B at 6 h, and those of S100A8, S100A12, and LAP at 12 h. The intracellular S100A8 protein content doubled at 12-24 h but with little excretion into the medium. Regarding prostaglandin biosynthesis, PTGES mRNA was slightly higher after LPS exposure, whereas expression of the PGF synthase AKR1B1 was inhibited. Despite this, LPS treatment stimulated the secretion of both PGE2 and PGF2(alpha) to a similar extent. These results suggest that the family of S100 Ca²âº binding proteins are released from damaged endometrial cells and may play a major antimicrobial role. Prostaglandin synthesis increased during the uterine infection, but we found no evidence that this was associated with a change in the PGE:PGF ratio.

Differential hepatic gene expression in the broiler chicken in response to the combined stressors of food withdrawal, catching and transport at the end of production.

Broiler (meat) chickens experience the combined acute stressors of food withdrawal, catching and transport (FCT) prior to slaughter as part of normal commercial practice at the end of their lives. This has associated physiological consequences, potentially affecting both welfare and meat quality, some of which are mediated through altered hepatic function. This study compared global hepatic gene expression between control birds and those exposed to commercial FCT using 20K chicken oligonucleotide microarrays. In response to FCT, 733 genes were differentially expressed of which 486 could be mapped onto the genome. The principal molecular and cellular functions thus affected by FCT involved lipid and carbohydrate metabolism with a suppression of mRNA expression for genes involved in lipogenesis, glycolysis and glycogenolysis and an induction of those involved in gluconeogenesis, fatty acid metabolism and ketone synthesis. There was also significant differential expression of genes associated with cellular control and immune function. These stressful events associated with FCT in commercial broiler chickens altered expression of hepatic genes associated with energy metabolism, with exhaustion of stored hepatic and pectoral muscle glycogen. A better understanding of FCT-induced stress through the use of gene expression arrays may in future inform husbandry practices, to improve both welfare and meat quality.

Associations between lipid metabolism and fertility in the dairy cow.

Dairy cows mobilise body tissues to support milk production and, because glucose supplies are limited, lipids are used preferentially for energy production. Lipogenic activity is switched off and lipolytic mechanisms in adipose tissue increase through changes in the expression of several key enzymes. This results in a loss of body condition, together with high circulating concentrations of non-esterified fatty acids. Changes in the synthesis, secretion and signalling pathways of somatotrophic hormones (insulin, growth hormone, insulin-like growth factor 1) and adipokines (e.g. leptin) are central to the regulation of these processes. A high reliance on fatty acids as an energy source in the peripartum period causes oxidative damage to mitochondria in metabolically active tissues, including the liver and reproductive tract. The expression of genes involved in insulin resistance (PDK4, AHSG) is increased, together with expression of TIEG1, a transcription factor that can induce apoptosis via the mitochondrial pathway. Polymorphisms in TFAM and UCP2, two autosomal mitochondrial genes, have been associated with longevity in dairy cows. Polymorphisms in many other genes that affect lipid metabolism also show some associations with fertility traits. These include DGAT1, SCD1, DECR1, CRH, CBFA2T1, GH, LEP and NPY. Excess lipid accumulation in oocytes and the regenerating endometrium reduces fertility via reductions in embryo survival and increased inflammatory changes, respectively.