The aim of the Teagasc Animal and Grassland Research & Innovation Programme is to increase the profitability, competitiveness and sustainability of Irish livestock production through research and innovation.

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  • Sharpea and Kandleria are lactic acid producing rumen bacteria that do not change their fermentation products when co-cultured with a methanogen

    Kumar, Sandeep; Treloar, Bryan P.; Teh, Koon Hoong; McKenzie, Catherine M.; Henderson, Gemma; Attwood, Graeme T.; Waters, Sinéad M.; Patchett, Mark L.; Janssen, Peter H.; Teagasc Walsh Fellowship Programme; et al. (Elsevier, 2018-07-25)
    Sharpea and Kandleria are associated with rumen samples from low-methane-emitting sheep. Four strains of each genus were studied in culture, and the genomes of nine strains were analysed, to understand the physiology of these bacteria. All eight cultures grew equally well with d-glucose, d-fructose, d-galactose, cellobiose, and sucrose supplementation. d-Lactate was the major end product, with small amounts of the mixed acid fermentation products formate, acetate and ethanol. Genes encoding the enzymes necessary for this fermentation pattern were found in the genomes of four strains of Sharpea and five of Kandleria. Strains of Sharpea produced traces of hydrogen gas in pure culture, but strains of Kandleria did not. This was consistent with finding that Sharpea, but not Kandleria, genomes contained genes coding for hydrogenases. It was speculated that, in co-culture with a methanogen, Sharpea and Kandleria might change their fermentation pattern from a predominately homolactic to a predominately mixed acid fermentation, which would result in a decrease in lactate production and an increase in formation of acetate and perhaps ethanol. However, Sharpea and Kandleria did not change their fermentation products when co-cultured with Methanobrevibacter olleyae, a methanogen that can use both hydrogen and formate, and lactate remained the major end product. The results of this study therefore support a hypothesis that explains the link between lower methane yields and larger populations of Sharpea and Kandleria in the rumens of sheep.
  • Blood immune transcriptome analysis of artificially fed dairy calves and naturally suckled beef calves from birth to 7 days of age

    Surlis, C.; Earley, Bernadette; McGee, Mark; Keogh, K.; Cormican, Paul; Blackshields, G.; Tiernan, K.; Dunn, A.; Morrison, S.; Arguello, A.; et al. (Nature Publishing Group, 2018-10-18)
    Neonatal calves possess a very immature and naïve immune system and are reliant on the intake of maternal colostrum for passive transfer of immunoglobulins. Variation in colostrum management of beef and dairy calves is thought to affect early immune development. Therefore, the objective of this study was to examine changes in gene expression and investigate molecular pathways involved in the immune-competence development of neonatal Holstein dairy calves and naturally suckled beef calves using next generation RNA-sequencing during the first week of life. Jugular whole blood samples were collected from Holstein (H) dairy calves (n = 8) artificially fed 5% B.W. colostrum, and from beef calves which were the progenies of Charolais-Limousin (CL; n = 7) and Limousin-Friesian beef suckler cows (LF; n = 7), for subsequent RNA isolation. In dairy calves, there was a surge in pro-inflammatory cytokine gene expression possibly due to the stress of separation from the dam. LF calves exhibited early signs of humoral immune development with observed increases in the expression genes coding for Ig receptors, which was not evident in the other breeds by 7 days of age. Immune and health related DEGs identified as upregulated in beef calves are prospective contender genes for the classification of biomarkers for immune-competence development, and will contribute towards a greater understanding of the development of an immune response in neonatal calves.
  • RNA-seq analysis of bovine adipose tissue in heifers fed diets differing in energy and protein content

    Waerp, Hilde K. L.; Waters, Sinead M; McCabe, Matthew S.; Cormican, Paul; Salte, Ragnar; Research Council of Norway; TINE SA Norwegian dairies; Felleskjøpet agricultural cooperative; Animalia AS; 199448 (PLOS, 2018-09-20)
    Adipose tissue is no longer considered a mere energy reserve, but a metabolically and hormonally active organ strongly associated with the regulation of whole-body metabolism. Knowledge of adipose metabolic regulatory function is of great importance in cattle management, as it affects the efficiency and manner with which an animal converts feedstuff to milk, meat and fat. However, the molecular mechanisms regulating metabolism in bovine adipose tissue are still not fully elucidated. The emergence of next-generation sequencing technologies has facilitated the analysis of metabolic function and regulation at the global gene expression level. The aim of this study was to investigate the effect of diets differing in protein and energy density level on gene expression in adipose tissue of growing replacement dairy heifers using next-generation RNA sequencing (RNAseq). Norwegian Red heifers were fed either a high- or low-protein concentrate (HP/LP) and a high- or low-energy roughage (HE/LE) diet from 3 months of age until confirmed pregnancy to give four treatments (viz, HPHE, HPLE, LPHE, LPLE) with different growth profiles. Subcutaneous adipose tissue sampled at 12 months of age was analyzed for gene expression differences using RNAseq. The largest difference in gene expression was found between LPHE and LPLE heifers, for which 1092 genes were significantly differentially expressed, representing an up-regulation of mitochondrial function, lipid, carbohydrate and amino acid metabolism as well as changes in the antioxidant system in adipose tissue of LPHE heifers. Differences between HPHE and HPLE heifers were much smaller, and dominated by genes representing NAD biosynthesis, as was the significantly differentially expressed genes (DEG) common to both HE-LE contrasts. Differences between HP and LP groups within each energy treatment were minimal. This study emphasizes the importance of transcriptional regulation of adipose tissue energy metabolism, and identifies candidate genes for further studies on early-stage obesity and glucose load in dairy cattle.
  • Forage type influences milk yield and ruminal responses to wheat adaptation in late-lactation dairy cows

    Russo, Victoria M.; Leury, B.J.; Kennedy, Emer; Hannah, M.C.; Auldist, M.J.; Wales, W.J.; Agriculture Victoria Research; Dairy Australia; Teagasc; The University of Melbourne (Elsevier, 2018-08-23)
    The effects of different wheat adaptation strategies on ruminal fluid pH, dry matter intake (DMI) and energy-corrected milk (ECM) were measured in 28 late-lactation dairy cows. Cows were fed either perennial ryegrass (PRG) hay or alfalfa hay and had no previous wheat adaptation. Wheat was gradually substituted for forage in 3 even increments, over 6 or 11 d, until wheat made up 40% of DMI (∼8 kg of dry matter/cow per day). We found no differences in DMI between adaptation strategies (6 or 11 d) within forage type; however, cows fed alfalfa hay consumed more overall and produced more ECM. The rate of ruminal pH decline after feeding, as well as the decrease in mean, minimum, and maximum ruminal pH with every additional kilogram of wheat was greater for cows fed alfalfa hay. Cows fed alfalfa hay and on the 6-d adaptation strategy had the lowest mean and minimum ruminal fluid pH on 3 consecutive days and were the only treatment group to record pH values below 6.0. Despite ruminal pH declining to levels typically considered low, no other measured parameters indicated compromised fermentation or acidosis. Rather, cows fed alfalfa hay and adapted to wheat over 6 d had greater ECM yields than cows on the 11-d strategy. This was due to the 6-d adaptation strategy increasing the metabolizable energy intake in a shorter period than the 11-d strategy, as substituting wheat for alfalfa hay caused a substantial increase in the metabolizable energy concentration of the diet. We found no difference in ECM between adaptation strategies when PRG hay was fed, as there was no difference in metabolizable energy intake. The higher metabolizable energy concentration and lower intake of the PRG hay meant the increase in metabolizable energy intake with the substitution of wheat was less pronounced for cows consuming PRG hay compared with alfalfa hay. Neither forage type nor adaptation strategy affected time spent ruminating. The higher intakes likely contributed to the lower ruminal pH values from the alfalfa hay treatments. However, both forages allowed the rumen contents to resist the large declines in ruminal pH typically seen during rapid grain adaptation. Depending on the choice of base forage, rapid grain introduction may not result in poor adaptation. In situations where high-energy grains are substituted for a low-energy, high-fiber basal forage, rapid introduction could prove beneficial over gradual strategies.
  • Effect of equine chorionic gonadotropin treatment during a progesterone-based timed artificial insemination program on reproductive performance in seasonal-calving lactating dairy cows

    Randi, Federico; Sánchez, José Maria; Herlihy, Mary M.; Valenza, Alessio; Kenny, David A.; Butler, Stephen T.; Lonergan, Patrick; Department of Agriculture, Food and the Marine; 13S515; 13S528 (Elsevier, 2018-08-23)
    The aim of this study was to investigate the effect of progesterone (P4)-based timed artificial insemination (TAI) programs on fertility in seasonal-calving, pasture-based dairy herds. A total of 1,421 lactating dairy cows on 4 spring-calving farms were stratified based on days in milk (DIM) and parity and randomly allocated to 1 of 3 treatments: (1) control: no hormonal treatment; cows inseminated at detected estrus; (2) P4-Ovsynch: cows received a 7-d P4-releasing intravaginal device (PRID Delta; CEVA Santé Animale, Libourne, France) with 100 μg of a gonadotropin-releasing hormone (GnRH) analog (Ovarelin; CEVA Santé Animale) at PRID insertion, a 25-mg injection of PGF2α (Enzaprost; CEVA Santé Animale) at PRID removal, GnRH at 56 h after device removal and TAI 16 h later; (3) P4-Ovsynch+eCG: the same as P4-Ovsynch, but cows received 500 IU of equine chorionic gonadotropin (eCG; Syncrostim; CEVA Santé Animale) at PRID removal. At 10 d before mating start date (MSD), all cows that were ≥35 DIM were examined by transrectal ultrasound to assess presence or absence of a corpus luteum; body condition score (BCS) was also recorded. Pregnancy diagnosis was performed by transrectal ultrasonography 30 to 35 d after insemination. Overall pregnancy/AI (P/AI) was not different between groups (50.9, 49.8, and 46.3% for control, P4-Ovsynch, and P4-Ovsynch+eCG, respectively) but the 21-d pregnancy rate was increased by the use of synchronization (35.0, 51.7, and 47.2%, respectively). Compared with the control group, synchronization significantly reduced the interval from MSD to conception (34.6, 23.0, and 26.5 d, respectively) and consequently reduced the average days open (98.0, 86.0, and 89.0 d). Across all treatment groups, DIM at the start of synchronization affected P/AI (42.3, 49.5, and 53.9% for <60, 60–80, and >80 DIM, respectively), but neither parity (46.5, 50.4, and 48.4% for parity 1, 2, and ≥3, respectively) nor BCS (44.0, 49.4, and 58.6% for ≤2.50, 2.75–3.25, and ≥3.50, respectively) affected the likelihood of P/AI. Two-way interactions between treatment and DIM, parity, or BCS were not detected. In conclusion, the use of TAI accelerated pregnancy establishment in cows in a pasture-based system by reducing days open, but eCG administration at PRID removal did not affect P/AI.
  • The relationship between serum insulin-like growth factor-1 (IGF-1) concentration and reproductive performance, and genome-wide associations for serum IGF-1 in Holstein cows

    Gobikrushanth, M.; Purfield, Deirdre C; Colazo, M. G.; Wang, Z.; Butler, Stephen T.; Ambrose, D. J.; Growing Forward 2; Alberta Livestock and Meat Agency; Alberta Milk; Teagasc Walsh Fellowship Programme; et al. (Elsevier, 2019-07-19)
    The objectives of this study were to determine (1) factors associated with serum concentration of insulin-like growth factor-1 (IGF-1); (2) the relationship between serum IGF-1 concentration during the first week postpartum and ovarian cyclicity status by 35 d postpartum (DPP); (3) an optimum serum IGF-1 concentration threshold predictive of pregnancy to first artificial insemination (P/AI), including its diagnostic values; (4) the associations among categories of serum IGF-1 concentration and reproductive outcomes (P/AI and pregnancy risk up to 150 and 250 DPP); and (5) single nucleotide polymorphisms (SNP) associated with phenotypic variation in serum IGF-1 concentration in dairy cows. Serum IGF-1 concentration was determined at 7 (±2.4; ±standard error of the mean) DPP in 647 lactating Holstein cows (213 primiparous, 434 multiparous) from 7 herds in Alberta, Canada. The overall mean, median, minimum, and maximum serum IGF-1 concentrations during the first week postpartum were 37.8 (±1.23), 31.0, 20.0, and 225.0 ng/mL, respectively. Herd, age, parity, precalving body condition score, and season of blood sampling were all identified as factors associated with serum IGF-1 concentrations. Although serum IGF-1 concentration during the first week postpartum had no association with ovarian cyclicity status by 35 DPP in primiparous cows, it was greater in cyclic than in acyclic multiparous cows (32.2 vs. 27.4 ng/mL, respectively). The optimum serum IGF-1 thresholds predictive of P/AI were 85.0 ng/mL (sensitivity = 31.9%; specificity = 89.1%) and 31.0 ng/mL (sensitivity = 45.5%; specificity = 66.9%) for primiparous and multiparous cows, respectively. When cows were grouped into either high or low IGF-1 categories (greater or less than or equal to 85.0 ng/mL for primiparous cows and greater or less than or equal to 31.0 ng/mL for multiparous cows, respectively), primiparous cows with high IGF-1 had 4.43 times greater odds of P/AI and a tendency for higher pregnancy risk up to 150 DPP than those with low IGF-1, but not up to 250 DPP. Likewise, multiparous cows with high IGF-1 had 1.61 times greater odds of P/AI than those with low IGF-1. Pregnancy risk up to 150 and 250 DPP, however, did not differ between IGF-1 categories in multiparous cows. Moreover, 37 SNP across 10 Bos taurus autosomes were associated with variation in serum IGF-1 concentration, and 4 previously identified candidate genes related to fertility that were in linkage disequilibrium with some of these SNP were also identified.
  • Measuring labor input on pasture-based dairy farms using a smartphone

    Deming, J.; Gleeson, David E; O'Dwyer, T.; O'Brien, Bernadette; Kinsella, J.; Dairy Research Ireland; Teagasc Walsh Fellowship Programme (Elsevier, 2018-07-19)
    With the cessation of milk quotas in the European Union, dairy herd sizes increased in some countries, including Ireland, with an associated increase in labor requirement. Second to feed costs, labor has been identified as one of the highest costs on pasture-based dairy farms. Compared with other European Union countries, Ireland has historically had low milk production per labor unit; thus, optimization of labor efficiency on farm should be addressed before or concurrently with herd expansion. The objective of this study was to quantify current levels of labor input and labor efficiency on commercial pasture-based dairy farms and to identify the facilities and management practices associated with increased labor efficiency. Thirty-eight dairy farms of varying herd sizes, previously identified as labor-efficient farms, were enrolled on the study and data were collected over 3 consecutive days each month over a 12-mo period, starting in May 2015 and finishing in August of 2016. This was achieved through the use of a smartphone application. For analysis purposes, farms were categorized into 1 of 3 herd size categories (HSC): farms with <150 cows (HSC 1), 150–249 cows (HSC 2), or ≥250 cows (HSC 3). Overall farm labor input increased with HSC with 3,015, 4,499, and 6,023 h worked on HSC 1, 2, and 3, respectively. A higher proportion of work was carried out by hired staff as herd size increased. Labor efficiency was measured as total hours input to the dairy enterprise divided by herd size. Labor efficiency improved as herd size increased above 250 cows with 17.3 h/cow per yr observed for HSC 3; labor efficiency was similar for HSC 1 and 2, at 23.8 and 23.3 h/cow per yr, respectively. A large range of efficiency was observed within HSC. The labor requirements had a distinct seasonal pattern across the 3 HSC with the highest input observed in springtime (February to April) primarily due to calving and calf-care duties, milking, and winter feeding. The lowest input was observed in wintertime (November to January) when cows were dry. Particular facilities and management practices were associated with efficiency within certain tasks, the most notable in regard to milking and winter feeding practices. Additionally, the most efficient farms used contractors to perform a higher proportion of machinery work on farm than the least efficient farms.
  • A national methodology to quantify the diet of grazing dairy cows

    O'Brien, Donal; Moran, Brian; Shalloo, Laurence (Elsevier, 2018-07-04)
    The unique rumen of dairy cows allows them to digest fibrous forages and feedstuffs. Surprisingly, to date few attempts have been made to develop national methods to gain an understanding on the make-up of a dairy cow's diet, despite the importance of milk production. Consumer interest is growing in purchasing milk based on the composition of the cows' diet and the time they spend grazing. The goal of this research was to develop such a methodology using the national farm survey of Ireland as a data source. The analysis was completed for a 3-yr period from 2013 to 2015 on a nationally representative sample of 275 to 318 dairy farms. Trained auditors carried out economic surveys on farms 3 to 4 times per annum. The auditors collected important additional information necessary to estimate the diet of cows including the length of the grazing season, monthly concentrate feeding, type of forage(s) conserved, and milk production. Annual cow intakes were calculated to meet net energy requirements for production, maintenance, activity, pregnancy, growth, and live weight change using survey data and published literature. Our analysis showed that the average annual cow feed intake on a fresh matter basis ranged from 22.7 t in 2013 to 24.8 t in 2015 and from 4.8 to 5 t on a dry matter basis for the same period. Forage, particularly pasture, was the largest component of the Irish cow diet, typically accounting for 96% of the diet on a fresh matter basis and 82% of dry matter intake over the 3 yr. Within the cows' forage diet, grazed pasture was the dominant component and on average contributed 74 to 77% to the average annual cow fresh matter diet over the period. The proportion of pasture in the annual cow diet as fed was also identified as a good indicator of the time cows spend grazing (e.g., coefficient of determination = 0.85). Monthly, forage was typically the main component of the cow diet, but the average contribution of concentrate was substantial for the early spring months of January and February (30 to 35% of dry matter intake). Grazed pasture was the dominant source of forage from March to October and usually contributed 95 to 97% of the diet as fed in the summer period. Overall, the national farm survey from 2013 to 2015 shows that Irish dairy farms are very reliant on forage, particularly pasture, regardless of whether it is reported on a dry matter basis or as fed. There is potential to replicate this methodology in any regions or nations where representative farm surveys are conducted.
  • Characterization of best linear unbiased estimates generated from national genetic evaluations of reproductive performance, survival, and milk yield in dairy cows

    Dunne, F. L.; Kelleher, M. M.; Walsh, S.W.; Berry, Donagh P.; MultiRepro project; Department of Agriculture, Food and the Marine (Elsevier, 2018-05-16)
    Genetic evaluations decompose an observed phenotype into its genetic and nongenetic components; the former are termed BLUP with the solutions for the systematic environmental effects in the statistical model termed best linear unbiased estimates (BLUE). Geneticists predominantly focus on the BLUP and rarely consider the BLUE. The objective of this study, however, was to define and quantify the association between 8 herd-level characteristics and BLUE for 6 traits in dairy herds, namely (1) age at first calving, (2) calving to first service interval (CFS), (3) number of services, (4) calving interval (CIV), (5) survival, and (6) milk yield. Phenotypic data along with the fixed and random effects solutions were generated from the Irish national multi-breed dairy cow fertility genetic evaluations on 3,445,557 cows; BLUE for individual contemporary groups were collapsed into mean herd-year estimates. Data from 5,707 spring-calving herds between the years 2007 and 2016 inclusive were retained; association analyses were undertaken using linear mixed multiple regression models. Pearson coefficient correlations were used to quantify the relationships among individual trait herd-year BLUE, and transition matrices were used to understand the dynamics of mean herd BLUE estimates over years. Based on the mean annual trends in raw, BLUP, and BLUE, it was estimated that BLUE were associated with at least two-thirds of the improvement in CIV and milk production over the past 10 yr. Milk recording herds calved heifers for the first time on average 15 d younger, had an almost 2 d longer CFS but 2.3 d shorter CIV than non-milk-recording herds. Larger herd sizes were associated with worse BLUE for both CFS and CIV. Expanding herds and herds that had the highest proportion of cows born on the farm itself, on average, calved heifers younger and had shorter CIV. By separating the raw performance of a selection of herds into their respective BLUE and BLUP, it was possible to identify herds with inferior management practices that were being compensated by superior genetics; similarly, herds were identified with superior BLUE, but because of their inferior genetic merit, were not reaching their full potential. This suggests that BLUE could have a pivotal role in a tailored decision support tool that would enable producers to focus on the most limiting factor hindering them from achieving their maximum performance.
  • GWAS and eQTL analysis identifies a SNP associated with both residual feed intake and GFRA2 expression in beef cattle

    HIggins, Marc G.; Fitzsimons, Clare; McCLure, Matthew C.; McKenna, Clare; Conroy, Stephen; Kenny, David A.; McGee, MArk; Waters, Sinead M; Morris, Derek W.; Department of Agriculture, Food and the Marine; et al. (Nature Publishing Group, 2018-09-24)
    Residual feed intake (RFI), a measure of feed efficiency, is an important economic and environmental trait in beef production. Selection of low RFI (feed efficient) cattle could maintain levels of production, while decreasing feed costs and methane emissions. However, RFI is a difficult and expensive trait to measure. Identification of single nucleotide polymorphisms (SNPs) associated with RFI may enable rapid, cost effective genomic selection of feed efficient cattle. Genome-wide association studies (GWAS) were conducted in multiple breeds followed by meta-analysis to identify genetic variants associated with RFI and component traits (average daily gain (ADG) and feed intake (FI)) in Irish beef cattle (n = 1492). Expression quantitative trait loci (eQTL) analysis was conducted to identify functional effects of GWAS-identified variants. Twenty-four SNPs were associated (P < 5 × 10−5) with RFI, ADG or FI. The variant rs43555985 exhibited strongest association for RFI (P = 8.28E-06). An eQTL was identified between this variant and GFRA2 (P = 0.0038) where the allele negatively correlated with RFI was associated with increased GFRA2 expression in liver. GFRA2 influences basal metabolic rates, suggesting a mechanism by which genetic variation may contribute to RFI. This study identified SNPs that may be useful both for genomic selection of RFI and for understanding the biology of feed efficiency.
  • Cross-Fostering Implications for Pig Mortality, Welfare and Performance

    Calderón Díaz, Julia A.; García Manzanilla, Edgar; Diana, Alessia; Boyle, Laura; Department of Agriculture, Food and the Marine; Teagasc Walsh Fellowship Programme; 14/S/832 (Frontiers, 2018-06-06)
    This study aimed to (1) identify cross-fostering (CF) practices employed on a commercial farm; (2) characterize CF pigs according to litter of origin traits, and (3) investigate the implications of CF practices on pig mortality, performance and welfare. This was an observational study whereby pigs were managed according to normal farming practice. Pigs (n = 1,016) born within 1 week were classified as non-CF (NCF); CF during the first (CFW1) and second or third (CFW2+) weeks of lactation. Pigs were individually weighed and inspected for the presence of tail (TL), ear (EL) and body lesions (BL) at weaning (7.03 ± 1.61 kg) and at the end of the first (12.9 ± 3.03 kg) and second (31.9 ± 5.50 kg) weaner and grower (66.3 ± 9.12 kg) stages. Mortality was recorded through to slaughter (c. 115 kg). At slaughter, TL were scored and carcass characteristics, presence of pleurisy, enzootic pneumonia, pericarditis and heart condemnations were recorded. 40.8% of CF pigs were CFW1; ANOVA tests revealed these were born to sows with a higher number of piglets born alive than NCF pigs (14.6 ± 2.61 and 12.8 ± 2.68, respectively). The remaining 59.2% of CF pigs were CFW2+; these were, on average, 0.14 kg lighter at birth than NCF pigs. Therefore, a nested case control design was retrospectively applied whereby pigs with complete records to slaughter, were matched for these variables to investigate associations between CF weeks, welfare and performance traits. Growth performance did not differ between CF week (P > 0.05); however, CFW2+ carcasses were 4.9 kg lighter (P < 0.05) compared with NCF and CFW1 pigs. EL were more likely in CFW1 compared to NCF and CFW2+ (P < 0.05) pigs. To investigate the effect of CF week on the risk of mortality, all 1,016 pigs were used. CF pigs were at higher risk of death (P < 0.05) with similar odds in CFW1 and CFW2+ pigs compared with NCF pigs, although other underlying factors could contribute to this result. Performance and health traits were similar between CF weeks. Early cross-fostering appeared to influence the presence of ear lesions but the mechanism is likely indirect and difficult to explain.
  • The translation of animal welfare research into practice: The case of mixing aggression between pigs

    Peden, Rachel S.E.; Turner, Simon P.; Boyle, Laura; Camerlink, Irene; Scotland’s Rural College (SRUC) (Elsevier, 2018-03-10)
    Aggression between unfamiliar pigs at mixing is a major animal welfare problem in commercial farming. It has been studied since the 1970s and remains an important topic in animal welfare research. Methods to reduce pig aggression at mixing have been reviewed previously, but there has been little translation of the advocated techniques and building designs into practice. As a result, the problem persists on many commercial units. A similar situation exists for many other animal welfare issues. This article takes a new approach in not only reviewing the recent scientific literature, but also reviewing the evidence of uptake in industry. Firstly, the current state of aggression mitigation research is reviewed; including the most successful recent developments in breeding against aggression, early life socialisation, the use of pheromones and nutrition. Secondly, information is extracted from both peer reviewed and industry literature to establish the extent to which these strategies have been transferred from research to practice. Finally, we discuss why in spite of the amount of research on reducing aggression at mixing the problem has not reduced in intensive farming systems. The limited uptake in practice appears to be due to low prioritisation of the problem, the practicalities of implementation, lack of information on cost-effectiveness and ineffective communication of research to the farming community. To bridge this gap, industry must be involved in the design of practical solutions and the cost-effectiveness of these must be quantified. This approach should also be considered for other animal welfare issues under investigation. We recommend a better alignment between research questions and industry interests to increase the success of research efforts to improve animal welfare in practice.
  • Associations between exposure to bovine herpesvirus 1 (BoHV-1) and milk production, reproductive performance, and mortality in Irish dairy herds

    Sayers, RÍona; Irish Dairy Levy (Elsevier, 2016-12-09)
    As cost-benefit analyses are required to prioritize and promote disease control and eradication programs within a jurisdiction, national data relating to disease-related production losses are particularly useful. The objectives of the current study were to use Irish bovine herpesvirus 1 (BoHV-1) prevalence data in dairy herds, obtained by bulk milk sampling on 4 occasions over the 2009 lactation, to document associations between milk production, fertility performance, mortality, and BoHV-1 herd status. Bulk milk (n = 305) antibody ELISA was used to classify farms as positive or negative in terms of endemic BoHV-1. Cow-level (milk parameters only) and herd-level performance data were sourced from the Irish Cattle Breeding Federation. Ordinary linear and negative binomial regressions were used to investigate associations between milk, fertility, and mortality performance and herd-level BoHV-1 results (both categorical and continuous variables). Only slight effects on the rates of carryover cows, nonpregnant cows, and total deaths were highlighted with increasing ELISA sample/positive (%) values (incidence rate ratio = 1.001). Multiparous cows in herds BoHV-1 bulk milk antibody positive recorded a reduction in milk yield per cow per year of 250.9 L in the multivariable linear model. Milk fat and protein yields were also affected by herd BoHV-1 status, again highlighting sub-optimal milk production in BoHV-1 bulk milk-positive herds. The current study has highlighted an economical method of investigating losses due to endemic infection using repeated bulk milk sampling over a single lactation. These data can contribute to analyzing the cost-benefit of applying BoHV-1 control strategies both on farm and at a national level.
  • Effect of stocking rate and animal genotype on dry matter intake, milk production, body weight, and body condition score in spring-calving, grass-fed dairy cows

    Coffey, Emma Louise; Delaby, Luc; Fitzgerald, S.; Galvin, Norann; Pierce, K.M.; Horan, Brendan; Dairy Research Ireland (Elsevier, 2017-06-28)
    The objective of the experiment was to quantify the effect of stocking rate (SR) and animal genotype on milk production, dry matter intake (DMI), energy balance, and production efficiency across 2 consecutive grazing seasons (2014 and 2015). A total of 753 records from 177 dairy cows were available for analysis: 68 Holstein-Friesian and 71 Jersey × Holstein-Friesian (JxHF) cows each year of the experiment under a pasture-based seasonal production system. Animals within each breed group were randomly allocated to 1 of 3 whole-farm SR treatments defined in terms of body weight per hectare (kg of body weight/ha): low (1,200 kg of body weight/ha), medium (1,400 kg of body weight/ha), and high (1,600 kg of body weight/ha), and animals remained in the same SR treatments for the duration of the experiment. Individual animal DMI was estimated 3 times per year at grass using the n-alkane technique: March (spring), June (summer), and September (autumn), corresponding to 45, 111, and 209 d in milk, respectively. The effects of SR, animal genotype, season, and their interactions were analyzed using mixed models. Milk production, body weight, and production efficiency per cow decreased significantly as SR increased due to reduced herbage availability per cow and increased grazing severity. As a percentage of body weight, JxHF cows had higher feed conversion efficiency, higher DMI and milk solids (i.e., kg of fat + kg of protein) production, and also required less energy intake to produce 1 kg of milk solids. The increased production efficiency of JxHF cows at a similar body weight per hectare in the current analysis suggests that factors other than individual cow body weight contribute to the improved efficiency within intensive grazing systems. The results highlight the superior productive efficiency of high genetic potential crossbred dairy cows within intensive pasture-based milk production systems at higher SR where feed availability is restricted.
  • Genetic and nongenetic factors associated with milk color in dairy cows

    Scarso, S.; McParland, S.; Visentin, G.; Berry, Donagh P.; McDermott, A.; De Marchi, M.; European Union (Elsevier, 2017-07-12)
    Milk color is one of the sensory properties that can influence consumer choice of one product over another and it influences the quality of processed dairy products. This study aims to quantify the cow-level genetic and nongenetic factors associated with bovine milk color traits. A total of 136,807 spectra from Irish commercial and research herds (with multiple breeds and crosses) were used. Milk lightness (Lˆ*) , red-green index (aˆ*) and yellow-blue index (bˆ*) were predicted for individual milk samples using only the mid-infrared spectrum of the milk sample. Factors associated with milk color were breed, stage of lactation, parity, milking-time, udder health status, pasture grazing, and seasonal calving. (Co)variance components for Lˆ*,aˆ* , and bˆ* were estimated using random regressions on the additive genetic and within-lactation permanent environmental effects. Greater bˆ* value (i.e., more yellow color) was evident in milk from Jersey cows. Milk Lˆ* increased consistently with stage of lactation, whereas aˆ* increased until mid lactation to subsequently plateau. Milk bˆ* deteriorated until 31 to 60 DIM, but then improved thereafter until the end of lactation. Relative to multiparous cows, milk yielded by primiparae was, on average, lighter (i.e., greater Lˆ* ), more red (i.e., greater aˆ* ), and less yellow (i.e., lower bˆ* ). Milk from the morning milk session had lower Lˆ*,aˆ*, and bˆ* Heritability estimates (±SE) for milk color varied between 0.15 ± 0.02 (30 DIM) and 0.46 ± 0.02 (210 DIM) for Lˆ* , between 0.09 ± 0.01 (30 DIM) and 0.15 ± 0.02 (305 DIM) for aˆ* , and between 0.18 ± 0.02 (21 DIM) and 0.56 ± 0.03 (305 DIM) for bˆ* For all the 3 milk color features, the within-trait genetic correlations approached unity as the time intervals compared shortened and were generally <0.40 between the peripheries of the lactation. Strong positive genetic correlations existed between bˆ* value and milk fat concentration, ranging from 0.82 ± 0.19 at 5 DIM to 0.96 ± 0.01 at 305 DIM and confirming the observed phenotypic correlation (0.64, SE = 0.01). Results of the present study suggest that breeding strategies for the enhancement of milk color traits could be implemented for dairy cattle populations. Such strategies, coupled with the knowledge of milk color traits variation due to nongenetic factors, may represent a tool for the dairy processors to reduce, if not eliminate, the use of artificial pigments during milk manufacturing.
  • Associations between paratuberculosis ELISA results and test-day records of cows enrolled in the Irish Johne's Disease Control Program

    Botaro, Bruno G.; Ruelle, Elodie; More, Simon J; Strain, Sam; Graham, David; O’Flaherty, Joe; Shalloo, Laurence; Department of Agriculture, Food and the Marine (Elsevier, 2017-07-12)
    The effect of the Mycobacterium avium ssp. paratuberculosis (MAP) ELISA status on test-day milk performance of cows from Irish herds enrolled in the pilot national voluntary Johne's disease control program during 2013 to 2015 was estimated. A data set comprising 92,854 cows and 592,623 complete test-day records distributed across 1,700 herds was used in this study. The resulting ELISA outcome (negative, inconclusive, and positive) of each cow within each year of the program was used to allocate the cow into different scenarios representing the MAP status. At MAPscenario1, all cows testing ELISA nonnegative (i.e., inconclusive and positive) were assigned a MAP-positive status; at MAPscenario2 only cows testing ELISA-positive were assigned a MAP-positive status; at MAPscenario3 only cows testing ELISA nonnegative (inconclusive or positive) and gathered exclusively from herds where at least 2 further ELISA nonnegative (inconclusive or positive) cows were found were assigned a MAP-positive status; at MAPscenario4 only cows testing ELISA-positive that were gathered exclusively from herds where at least 2 further ELISA-positive cows were found were assigned a MAP-positive status. Milk outputs based on test-day records were standardized for fat and protein contents (SMY) and the effect of MAP ELISA status on the SMY was estimated by a linear mixed effects model structure. The SMY mean difference recorded at test day between cows with a MAP-positive status and those with a MAP-negative status within MAPscenario1 was estimated at −0.182 kg/test day; the mean difference was −0.297 kg/test day for MAPscenario2; for MAPscenario3 mean difference between MAP-positive status and MAP test-negative cows was −0.209 kg/test day, and for MAPscenario4, the difference was −0.326 kg/test day.
  • Short communication: Uncovering quantitative trait loci associated with resistance to Mycobacterium avium ssp. paratuberculosis infection in Holstein cattle using a high-density single nucleotide polymorphism panel

    Mallikarjunappa, Sanjay; Sargolzaei, M.; Brito, L. F.; Meade, Kieran G; Karrow, N. A.; Pant, S. D.; The Semex Alliance; NSERC; the Graham Centre for Agricultural Innovation; Darcy John O'Sullivan Bequest; et al. (Elsevier, 2018-05-10)
    Mycobacterium avium ssp. paratuberculosis (MAP) is the etiological agent of Johne's disease in cattle. Johne's disease is a disease of significant economic, animal welfare, and public health concern around the globe. Therefore, understanding the genetic architecture of resistance to MAP infection has great relevance to advance genetic selection methods to breed more resistant animals. The objectives of this study were to perform a genome-wide association study of previously analyzed 50K genotypes now imputed to a high-density single nucleotide polymorphism panel (777K), aiming to validate previously reported associations and potentially identify additional single nucleotide polymorphisms associated with antibody response to MAP infection. A principal component regression-based genome-wide association study revealed 15 putative quantitative trait loci (QTL) associated with the MAP infection phenotype (serum or milk ELISA tests) on 9 different chromosomes (Bos taurus autosomes 5, 6, 7, 10, 14, 15, 16, 20, and 21). These results validated previous findings and identified new QTL on Bos taurus autosomes 15, 16, 20, and 21. The positional candidate genes NLRP3, IFi47, TRIM41, TNFRSF18, and TNFRSF4 lying within these QTL were identified. Further functional validation of these genes is now warranted to investigate their roles in regulating the immune response and, consequently, cattle resistance to MAP infection.
  • The relationship between serum anti-Müllerian hormone concentrations and fertility, and genome-wide associations for anti-Müllerian hormone in Holstein cows

    Gobikrushanth, M.; Purfield, Deirdre C; Colazo, M. G.; Butler, Stephen T.; Wang, Z.; Ambrose, D. J.; Growing Forward 2; Alberta Livestock and Meat Agency; Alberta Milk; Teagasc Walsh Fellowship Programme; et al. (Elsevier, 2018-05-07)
    The objectives of this study were to (1) evaluate factors associated with variation in circulating anti-Müllerian hormone (AMH) concentrations, (2) establish an optimum AMH threshold predictive of pregnancy to first artificial insemination (P/AI), (3) examine the relationship between AMH and fertility (P/AI, pregnancy loss between 30 and 60 d after artificial insemination, and pregnancy risk up to 250 d postpartum), and (4) identify quantitative trait loci associated with phenotypic variation of AMH concentrations in dairy cows. Serum AMH concentrations (pg/mL) were determined at 7 ± 2.4 d postpartum in 647 lactating Holstein cows (213 primiparous, 434 multiparous) from 1 research and 6 commercial dairy herds in Alberta, Canada. Of these, 589 cows were genotyped on the 26K Bovine BeadChip (Neogen Inc., Lincoln, NE) and subsequently imputed to the Illumina Bovine High Density BeadChip (Illumina, San Diego, CA) for genome-wide association analysis for variation in serum AMH concentrations. Factors associated with variation in serum AMH concentrations and the relationship between categories of AMH and aforementioned fertility outcomes were evaluated only in a subset of 460 cows that had a complete data set available. The overall mean (±standard error of the mean), median, minimum, and maximum AMH concentrations were 191.1 ± 6.3, 151.7, 13.9, and 1,879.0 pg/mL, respectively. The AMH concentrations were not associated with herd, precalving body condition score, postpartum week, and season of sampling; the lactation number, however, had a quadratic relationship with serum AMH concentrations (116.2, 204.9 204.5, and 157.9 pg/mL for first, second, third, and ≥fourth lactation, respectively). The optimum AMH threshold predictive of P/AI could not be established because the receiver operating characteristic curve analysis model was nonsignificant. Categories of AMH [low (<83.0 pg/mL; n = 92), intermediate (≥83.0 to ≤285.0 pg/mL; n = 276), and high (>285.0 pg/mL; n = 92) based on lowest 20%, intermediate 60%, and highest 20% serum AMH) had no associations with P/AI (34, 43, and 40%), pregnancy loss between 30 and 60 d after artificial insemination (20, 12, and 8%), or pregnancy risk up to 250 d postpartum. One candidate gene associated with AMH production [AMH gene on Bos taurus autosome (BTA) 7] and 4 candidate genes related to embryo development (SCAI and PPP6C genes on BTA11 and FGF18 and EEF2K genes on BTA20 and BTA25, respectively) were in linkage disequilibrium with single nucleotide polymorphisms associated with phenotypic variation in serum AMH in dairy cows.
  • Milk mid-infrared spectral data as a tool to predict feed intake in lactating Norwegian Red dairy cows

    Berry, Donagh P.; Wallén, Sini E.; Prestløkken, E.; Meuwissen, Theodorus H.E.; McParland, Sinead; the Norwegian Research Council; TINE; GENO; 225233/E40 (Elsevier, 2018-03-28)
    Mid-infrared (MIR) spectroscopy of milk was used to predict dry matter intake (DMI) and net energy intake (NEI) in 160 lactating Norwegian Red dairy cows. A total of 857 observations were used in leave-one-out cross-validation and external validation to develop and validate prediction equations using 5 different models. Predictions were performed using (multiple) linear regression, partial least squares (PLS) regression, or best linear unbiased prediction (BLUP) methods. Linear regression was implemented using just milk yield (MY) or fat, protein, and lactose concentration in milk (Mcont) or using MY together with body weight (BW) as predictors of intake. The PLS and BLUP methods were implemented using just the MIR spectral information or using the MIR together with Mcont, MY, BW, or NEI from concentrate (NEIconc). When using BLUP, the MIR spectral wavelengths were always treated as random effects, whereas Mcont, MY, BW, and NEIconc were considered to be fixed effects. Accuracy of prediction (R) was defined as the correlation between the predicted and observed feed intake test-day records. When using the linear regression method, the greatest R of predicting DMI (0.54) and NEI (0.60) in the external validation was achieved when the model included both MY and BW. When using PLS, the greatest R of predicting DMI (0.54) and NEI (0.65) in the external validation data set was achieved when using both BW and MY as predictors in combination with the MIR spectra. When using BLUP, the greatest R of predicting DMI (0.54) in the external validation was when using MY together with the MIR spectra. The greatest R of predicting NEI (0.65) in the external validation using BLUP was achieved when the model included both BW and MY in combination with the MIR spectra or when the model included both NEIconc and MY in combination with MIR spectra. However, although the linear regression coefficients of actual on predicted values for DMI and NEI were not different from unity when using PLS, they were less than unity for some of the models developed using BLUP. This study shows that MIR spectral data can be used to predict NEI as a measure of feed intake in Norwegian Red dairy cattle and that the accuracy is augmented if additional, often available data are also included in the prediction model.
  • Factors associated with profitability in pasture-based systems of milk production

    Hanrahan, L.; McHugh, Noirin; Hennessy, Thia C.; Moran, Brian; Kearney, R.; Wallace, Michael; Shalloo, Laurence (Elsevier, 2018-03-07)
    The global dairy industry needs to reappraise the systems of milk production that are operated at farm level with specific focus on enhancing technical efficiency and competitiveness of the sector. The objective of this study was to quantify the factors associated with costs of production, profitability, and pasture use, and the effects of pasture use on financial performance of dairy farms using an internationally recognized representative database over an 8-yr period (2008 to 2015) on pasture-based systems. To examine the associated effects of several farm system and management variables on specific performance measures, a series of multiple regression models were developed. Factors evaluated included pasture use [kg of dry matter/ha and stocking rate (livestock units/ha)], grazing season length, breeding season length, milk recording, herd size, dairy farm size (ha), farmer age, discussion group membership, proportion of purchased feed, protein %, fat %, kg of milk fat and protein per cow, kg of milk fat and protein per hectare, and capital investment in machinery, livestock, and buildings. Multiple regression analysis demonstrated costs of production per hectare differed by year, geographical location, soil type, level of pasture use, proportion of purchased feed, protein %, kg of fat and protein per cow, dairy farm size, breeding season length, and capital investment in machinery, livestock, and buildings per cow. The results of the analysis revealed that farm net profit per hectare was associated with pasture use per hectare, year, location, soil type, grazing season length, proportion of purchased feed, protein %, kg of fat and protein per cow, dairy farm size, and capital investment in machinery and buildings per cow. Pasture use per hectare was associated with year, location, soil type, stocking rate, dairy farm size, fat %, protein %, kg of fat and protein per cow, farmer age, capital investment in machinery and buildings per cow, breeding season length, and discussion group membership. On average, over the 8-yr period, each additional tonne of pasture dry matter used increased gross profit by €278 and net profit by €173 on dairy farms. Conversely, a 10% increase in the proportion of purchased feed in the diet resulted in a reduction in net profit per hectare by €97 and net profit by €207 per tonne of fat and protein. Results from this study, albeit in a quota limited environment, have demonstrated that the profitability of pasture-based dairy systems is significantly associated with the proportion of pasture used at the farm level, being cognizant of the levels of purchased feed.

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