• Bayesian evaluation of budgets for endemic disease control: An example using management changes to reduce milk somatic cell count early in the first lactation of Irish dairy cows

      Archer, Simon C.; McCoy, Finola; Wapenaar, Wendela; Green, Martin J.; Teagasc Walsh Fellowship Programme (Elsevier, 2013-10-21)
      The aim of this research was to determine budgets for specific management interventions to control heifer mastitis in Irish dairy herds as an example of evidence synthesis and 1-step Bayesian micro-simulation in a veterinary context. Budgets were determined for different decision makers based on their willingness to pay. Reducing the prevalence of heifers with a high milk somatic cell count (SCC) early in the first lactation could be achieved through herd level management interventions for pre- and peri-partum heifers, however the cost effectiveness of these interventions is unknown. A synthesis of multiple sources of evidence, accounting for variability and uncertainty in the available data is invaluable to inform decision makers around likely economic outcomes of investing in disease control measures. One analytical approach to this is Bayesian micro-simulation, where the trajectory of different individuals undergoing specific interventions is simulated. The classic micro-simulation framework was extended to encompass synthesis of evidence from 2 separate statistical models and previous research, with the outcome for an individual cow or herd assessed in terms of changes in lifetime milk yield, disposal risk, and likely financial returns conditional on the interventions being simultaneously applied. The 3 interventions tested were storage of bedding inside, decreasing transition yard stocking density, and spreading of bedding evenly in the calving area. Budgets for the interventions were determined based on the minimum expected return on investment, and the probability of the desired outcome. Budgets for interventions to control heifer mastitis were highly dependent on the decision maker's willingness to pay, and hence minimum expected return on investment. Understanding the requirements of decision makers and their rational spending limits would be useful for the development of specific interventions for particular farms to control heifer mastitis, and other endemic diseases.
    • Beef Cross Breeding of Dairy and Beef Cows

      Keane, Michael G. (Teagasc, 2011-03-01)
      Summary The rationale for crossing dairy cows with beef bulls is to increase the beef productivity and value of the progeny. The proportion of dairy cows available for beef crossing is determined by the dairy herd replacement rate. The performance of cross-bred cattle is generally superior to the mean of the parent breeds because of heterosis. This is most pronounced for reproduction, maternal and calf survival traits. Crossing dairy cows with early maturing beef breeds (e.g. Angus, Hereford) has little effect on growth but improves carcass conformation and reduces feed intake. Crossing with most late maturing beef breeds also improves carcass conformation and reduces feed intake, but in addition, growth rate, kill-out proportion and carcass muscle proportion are increased. Cross breeding can have small negative effects on dam milk production, and subsequent reproduction can be impaired following a long gestation or difficult calving. There is little advantage in crossing with double muscled sire breeds (e.g. Belgian Blue, Piedmontese) compared with the larger conventional late maturing breeds (e.g. Charolais, Blonde d'Aquitaine). There are few effects of sire breed on meat quality.
    • Beef production from feedstuffs conserved using new technologies to reduce negative environmental impacts

      O'Kiely, Padraig; Crosson, Paul; Hamilton, William J.; Little, Enda; Stacey, Pamela; Walsh, Karl; Black, Alistair D; Crowley, James C.; Drennan, Michael J; Forristal, Dermot; et al. (Teagasc, 2007-12-01)
      Most (ca. 86%) Irish farms make some silage. Besides directly providing feed for livestock, the provision of grass silage within integrated grassland systems makes an important positive contribution to effective grazing management and improved forage utilisation by grazing animals, and to effective feed budgeting by farmers. It can also contribute to maintaining the content of desirable species in pastures, and to livestock not succumbing to parasites at sensitive times of the year. Furthermore, the optimal recycling of nutrients collected from housed livestock can often be best achieved by spreading the manures on the land used for producing the conserved feed. On most Irish farms, grass silage will remain the main conserved forage for feeding to livestock during winter for the foreseeable future. However, on some farms high yields of whole-crop (i.e. grain + straw) cereals such as wheat, barley and triticale, and of forage maize, will be an alternative option provided that losses during harvesting, storage and feedout are minimised and that input costs are restrained. These alternative forages have the potential to reliably support high levels of animal performance while avoiding the production of effluent. Their production and use however will need to advantageously integrate into ruminant production systems. A range of technologies can be employed for crop production and conservation, and for beef production, and the optimal options need to be identified. Beef cattle being finished indoors are offered concentrate feedstuffs at rates that range from modest inputs through to ad libitum access. Such concentrates frequently contain high levels of cereals such as barley or wheat. These cereals are generally between 14% to 18% moisture content and tend to be rolled shortly before being included in coarse rations or are more finely processed prior to pelleting. Farmers thinking of using ‘high-moisture grain’ techniques for preserving and processing cereal grains destined for feeding to beef cattle need to know how the yield, conservation efficiency and feeding value of such grains compares with grains conserved using more conventional techniques. European Union policy strongly encourages a sustainable and multifunctional agriculture. Therefore, in addition to providing European consumers with quality food produced within approved systems, agriculture must also contribute positively to the conservation of natural resources and the upkeep of the rural landscape. Plastics are widely used in agriculture and their post-use fate on farms must not harm the environment - they must be managed to support the enduring sustainability of farming systems. There is an absence of information on the efficacy of some new options for covering and sealing silage with plastic sheeting and tyres, and an absence of an inventory of the use, re-use and post-use fate of plastic film on farms. Irish cattle farmers operate a large number of beef production systems, half of which use dairy bred calves. In the current, continuously changing production and market conditions, new beef systems must be considered. A computer package is required that will allow the rapid, repeatable simulation and assessment of alternate beef production systems using appropriate, standardised procedures. There is thus a need to construct, evaluate and utilise computer models of components of beef production systems and to develop mathematical relationships to link system components into a network that would support their integration into an optimal system model. This will provide a framework to integrate physical and financial on-farm conditions with models for estimating feed supply and animal growth patterns. Cash flow and profit/loss results will be developed. This will help identify optimal systems, indicate the cause of failure of imperfect systems and identify areas where applied research data are currently lacking, or more basic research is required.
    • Behavioural responses of pasture based dairy cows to short term management in tie-stalls

      Enriquez-Hidalgo, Daniel; Lemos Teixeira, Dayane; Lewis, Eva; Buckley, Frank; O'Driscoll, Keelin; Boyle, Laura; UNIVERSA Fellowship (Elsevier, 2017-09-22)
      Dairy cows in experimental grazing herds are often confined for metabolic measurements. The objective of this study was to establish effects of transfer from pasture, to tie-stalls in a metabolism house, then back to pasture, on lying behaviour and locomotion score of lactating cows: Holstein-Friesian (H, n = 16), Jersey (J, n = 16) and H × J (HJ, n = 16). Cows were transferred to tie-stalls on d 1 for 12 days, and were offered freshly cut ryegrass according to herbage allowance (HERB) and genotype: J low = 14; J high = 17; H and HJ low = 16; and H and HJ high = 20 kg DM/d. Lying behaviour was recorded on four days: −2, −1 (Pre-confinement), 3 (Early confinement), 10, 11 (Late confinement), 13 and 14 (Post-confinement) relative to transfer (d 1) using dataloggers, and was also video-recorded during the first 15 h. Locomotion score was recorded on days −4, −3, 12 and 16. No effects of HERB on lying variables were observed during the first 15 h in confinement, but J cows made more lying intentions (21.0 vs. 12.2; P < 0.05) and tended (P = 0.07) to have a shorter latency to lie. Cows spent less (P < 0.001) time lying in early confinement (07:22:29 h/d) than on any of the other occasions (9:12:50 h/d). Cows had more (P < 0.001) and shorter (P < 0.001) lying bouts in confinement than while at pasture. Low HERB cows spent more time lying than high HERB cows (09:54:55 vs. 09:09:33 h/d; P < 0.01). J had higher locomotion scores than H (9.2 ± 0.2 vs.7.8 ± 0.2; P < 0.001), and tended (P = 0.09) to have higher scores than HJ (8.5 ± 0.2) cows. Locomotion scores were lowest pre confinement, highest at turnout (d 12), and intermediate after that at pasture (d 16) (7.6 ± 0.2, 9.3 ± 0.2 and 8.6 ± 0.3, respectively; P < 0.01). On transfer to the metabolism house cows showed disrupted patterns of lying although daily lying time returned to levels similar to pasture by late confinement. Confinement also resulted in a short-term deterioration in locomotory ability, which although improving, was still evident 4 days following the cows return to pasture with Jersey cows being more affected than the other genotypes. These findings suggest that longer adaptation periods and temporary release to loafing areas may improve both the validity of data collected and cow welfare.
    • Bi-directional gene set enrichment and canonical correlation analysis identify key diet-sensitive pathways and biomarkers of metabolic syndrome.

      Morine, Melissa J; McMonagle, Jolene; Toomey, Sinead; Reynolds, Clare M; Moloney, Aidan P; Gormley, Isobel C; O Gaora, Peadar; Roche, Helen M.; Department of Agriculture, Food and the Marine; Irish Research Council for Science, Engineering and Technology; et al. (Biomed Central, 2010-10-07)
      Background Currently, a number of bioinformatics methods are available to generate appropriate lists of genes from a microarray experiment. While these lists represent an accurate primary analysis of the data, fewer options exist to contextualise those lists. The development and validation of such methods is crucial to the wider application of microarray technology in the clinical setting. Two key challenges in clinical bioinformatics involve appropriate statistical modelling of dynamic transcriptomic changes, and extraction of clinically relevant meaning from very large datasets. Results Here, we apply an approach to gene set enrichment analysis that allows for detection of bi-directional enrichment within a gene set. Furthermore, we apply canonical correlation analysis and Fisher's exact test, using plasma marker data with known clinical relevance to aid identification of the most important gene and pathway changes in our transcriptomic dataset. After a 28-day dietary intervention with high-CLA beef, a range of plasma markers indicated a marked improvement in the metabolic health of genetically obese mice. Tissue transcriptomic profiles indicated that the effects were most dramatic in liver (1270 genes significantly changed; p < 0.05), followed by muscle (601 genes) and adipose (16 genes). Results from modified GSEA showed that the high-CLA beef diet affected diverse biological processes across the three tissues, and that the majority of pathway changes reached significance only with the bi-directional test. Combining the liver tissue microarray results with plasma marker data revealed 110 CLA-sensitive genes showing strong canonical correlation with one or more plasma markers of metabolic health, and 9 significantly overrepresented pathways among this set; each of these pathways was also significantly changed by the high-CLA diet. Closer inspection of two of these pathways - selenoamino acid metabolism and steroid biosynthesis - illustrated clear diet-sensitive changes in constituent genes, as well as strong correlations between gene expression and plasma markers of metabolic syndrome independent of the dietary effect. Conclusion Bi-directional gene set enrichment analysis more accurately reflects dynamic regulatory behaviour in biochemical pathways, and as such highlighted biologically relevant changes that were not detected using a traditional approach. In such cases where transcriptomic response to treatment is exceptionally large, canonical correlation analysis in conjunction with Fisher's exact test highlights the subset of pathways showing strongest correlation with the clinical markers of interest. In this case, we have identified selenoamino acid metabolism and steroid biosynthesis as key pathways mediating the observed relationship between metabolic health and high-CLA beef. These results indicate that this type of analysis has the potential to generate novel transcriptome-based biomarkers of disease.
    • Bioeconomic modelling of male Holstein-Friesian dairy calf-to-beef production systems on Irish farms

      Ashfield, A.; Wallace, Michael; Prendiville, Robert; Crosson, Paul (Teagasc (Agriculture and Food Development Authority), Ireland, 2014)
      With the abolition of milk quota in 2015 and increase in the use of Holstein-Friesian sires in recent years there is predicted to be an increase in the number of male Holstein-Friesian animals available for beef production. In broad terms, farmers have two options for finishing these animals; as bulls or steers. In either case, Irish beef cattle systems are based on maximising lifetime live-weight gain from grass-based diets. Managing the relationship between the supply and demand for grazed grass is complicated in these pasture-based systems due to the seasonal variability in grass growth. The Grange Dairy Beef Systems Model (GDBSM) was used to simulate the relationship between grazed grass supply and demand and then determine the profitability of Holstein-Friesian male animals finished as bulls at 16 (B16), 19 (B19) and 22 (B22) months of age and steers at 24 (S24) months of age. Combinations of these cattle finishing options were also evaluated. The most profitable system was S24. All systems were very sensitive to variations in beef and concentrate prices and less sensitive to calf price changes with fertiliser price changes having very little effect. Bull systems were more sensitive than the steer system to variation in beef, calf and concentrate prices. There was no advantage of combination systems in terms of utilisation of grass grown or net margin.
    • Biologic response of animals to husbandry stress with implications for biomedical models

      Earley, Bernadette; Buckham-Sporer, Kelly; Gupta, Sandeep; Pang, Wanyong; Ting, Simon (Dove Press, 2010-08-04)
      The quality of life of animals is defined by a range of parameters including health, physiology, and behavior. Stress is defined as any damaging strain, force, or agent which stimulates a physiologic defense reaction and is capable under certain circumstances of producing pathologic lesions. Disruption to normal homeostasis can impinge on other biologic processes such as metabolism, cardiovascular activity, immune function, and behavior. In general, chronic stress is considered to have a greater potential impact on animal health and welfare than acute stress, because the animals are exposed and reacting to the stressor(s) for longer periods, thereby causing prolonged disruption to homeostasis and related biologic processes. Impaired coping responses may trigger specific alterations in behavior, organ damage, reduced performance, increased susceptibility to disease, and subfertility. At a molecular level, immune function is mediated by the release of cytokines, nonantibody messenger molecules from a variety of cells of the immune system and from other cells, such as endothelial cells. Biochemical alterations in immune function are, in part, induced by plasma hormone concentration changes elicited by a stressor subsequent to activation of the sympathetic nervous system, the sympathetic adrenomedullary axis, and the hypothalamo–pituitary–adrenocortical axis.
    • Blood immune transcriptome analysis of artificially fed dairy calves and naturally suckled beef calves from birth to 7 days of age

      Surlis, Carla; Earley, Bernadette; McGee, Mark; Keogh, Kate; Cormican, Paul; Blackshields, Gordon; Tiernan, Katie; Dunn, Amanda; Morrison, Steven; 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.
    • Blood parameters as biomarkers in a Salmonella spp. disease model of weaning piglets

      Barba-Vidal, Emili; Buttow Roll, Victor Fernando; Manzanilla, Edgar G; Torrente, Carlos; Moreno Munoz, Jose Antonio; Perez, Jose Francisco; Martin-Orue, Susana Maria; Spanish Ministry of Education and Science; Laboratorios Ordesa S.L.; CNPQ Brazil; et al. (PLOS, 2017-10-26)
      Background The weaning pig is used as an experimental model to assess the impact of diet on intestinal health. Blood parameters (BP) are considered a useful tool in humans, but there is very scarce information of such indicators in the weaning pig. The objective of the present study is to evaluate the use of different BP as indicators in an experimental model of salmonellosis. Methodology Seventy-two 28-day-old piglets were divided into four groups in a 2x2 factorial arrangement, with animals receiving or not a probiotic combination based on B. infantis IM1® and B. lactis BPL6 (109 colony forming units (cfu)/d) and orally challenged or not a week later with Salmonella Typhimurium (5x108 cfu). Blood samples of one animal per pen (N = 24) were taken four days post-inoculation for the evaluation of different BP using an I-stat® System and of plasmatic concentrations of zinc, iron and copper. Principal findings Results reported marginal deficiencies of zinc in piglets at weaning. Moreover, plasmatic zinc, copper and iron presented good correlations with weight gain (r 0.57, r -0.67, r 0.54 respectively; P < 0.01). Blood electrolytes (Na+, Cl- and K+) decreased (P < 0.01) only when the performance of the animals was seriously compromised and clinical symptoms were more apparent. Acid-base balance parameters such as HCO3-, TCO2 and BEecf significantly correlated with weight gain, but only in the challenged animals (r -0.54, r -0.55, and r -0.51, respectively; P < 0.05), suggesting metabolic acidosis depending on Salmonella infection. Glucose was affected by the challenge (P = 0.040), while Htc and Hgb increased with the challenge and decreased with the probiotic (P < 0.05). Furthermore, correlations of Glu, Htc and Hgb with weight gain were observed (P < 0.05). Overall, BP could be regarded as simple, useful indexes to assess performance and health of weaning piglets.
    • Body and carcass measurements, carcass conformation and tissue distribution of high dairy genetic merit Holstein, standard dairy genetic merit Friesian and Charolais x Holstein-Friesian male cattle

      McGee, Mark; Keane, Michael G.; Neilan, R.; Moloney, Aidan P; Caffrey, Patrick J. (Teagasc, Oak Park, Carlow, Ireland, 2007)
      The increased proportion of Holstein genes in the dairy herd may have undesirable consequences for beef production in Ireland. A total of 72 spring-born calves, (24 Holstein (HO), 24 Friesian (FR) and 24 Charolais X Holstein-Friesian (CH)) were reared from calfhood to slaughter. Calves were artificially reared indoors and spent their first summer at pasture following which they were assigned to a 3 breeds (HO, FR and CH) 2 production systems (intensive 19-month bull beef and extensive 25-month steer beef) 2 slaughter weights (560 and 650 kg) factorial experiment. Body measurements of all animals were recorded at the same time before the earliest slaughter date. After slaughter, carcasses were graded and measured and the pistola hind-quarter was separated into fat, bone and muscle. HO had significantly higher values for withers height, pelvic height and chest depth than FR, which in turn had higher values than CH. HO had a longer back and a narrower chest than either FR or CH, which were not significantly different. Carcass length and depth, pistola length, and leg length were 139.2, 134.4 and 132.0 (s.e. 0.81), 52.1, 51.3 and 47.7 (s.e. 0.38), 114.4, 109.0 and 107.0 (s.e. 0.65) and 76.7, 71.9 and 71.4 (s.e. 0.44) cm for HO, FR and CH, respectively. Breed differences in pistola tissue distribution between the joints were small and confined to the distal pelvic limb and ribs. There were relatively small breed differences in the distribution of pistola muscle weight between individual muscles. Body measurements were significantly greater for animals on the intensive system (bulls) than the extensive system (steers) in absolute terms, but the opposite was so when they were expressed relative to live weight. The only significant difference in relative carcass measurements between the production systems was for carcass depth, which was lower for the intensive compared with the extensive system. Increasing slaughter weight significantly increased all carcass measurements in absolute terms but reduced them relative to weight. It is concluded that there were large differences between the breed types in body and carcass measurements, and hence in carcass shape and compactness but differences in tissue distribution were small.
    • Body condition score and live-weight effects on milk production in Irish Holstein-Friesian dairy cows

      Berry, Donagh P.; Buckley, Frank; Dillon, Pat; Allied Irish Bank; Artificial Insemination Managers Association;; Holstein-Friesian Society of Great Britain and Ireland; Dairy Levy Research Trust; European Union (Cambridge University Press, 2007-10)
      The objective of the present study was to quantify the relationships among body condition score (BCS; scale 1 to 5), live weight (WT) and milk production in Irish Holstein-Friesian spring calving dairy cows. Data were from 66 commercial dairy herds during the years 1999 and 2000. The data consisted of up to 9886 lactations with records for BCS or WT at least once pre-calving, or at calving, nadir or 60 days post-calving. Change in BCS and WT was also calculated between time periods. Mixed models with cow included as a random effect were used to quantify the effect of BCS and WT, as well as change in each trait, on milk yield, milk fat concentration and milk protein concentration. Significant and sometimes curvilinear associations were observed among BCS at calving or nadir and milk production. Total 305-day milk yield was greatest in cows calving at a BCS of 4.25 units. However, cows calving at a BCS of 3.50 units produced only 68 kg less milk than cows calving at a BCS of 4.25 units while cows calving at 3.25 or 3.00 BCS units produced a further 50 and 114 kg less, respectively. Cows that lost more condition in early lactation produced more milk of greater fat and protein concentration, although the trend reversed in cows that lost large amounts of condition post-calving. Milk yield increased with WT although the marginal effect decreased as cows got heavier. Milk fat and protein concentration in early lactation also increased with WT pre-calving, calving and nadir, although WT did not significantly affect average lactation milk fat concentration.
    • The bovine paranasal sinuses: Bacterial flora, epithelial expression of nitric oxide and potential role in the in-herd persistence of respiratory disease pathogens

      Murray, Gerard; O'Neill, Ronan G.; Lee, Alison M.; McElroy, Máire; More, Simon J; Monagle, Aisling; Earley, Bernadette; Cassidy, Joseph P. (PLOS, 2017-03-10)
      The bovine paranasal sinuses are a group of complex cavernous air-filled spaces, lined by respiratory epithelium, the exact function of which is unclear. While lesions affecting these sinuses are occasionally reported in cattle, their microbial flora has not been defined. Furthermore, given that the various bacterial and viral pathogens causing bovine respiratory disease (BRD) persist within herds, we speculated that the paranasal sinuses may serve as a refuge for such infectious agents. The paranasal sinuses of clinically normal cattle (n = 99) and of cattle submitted for post-mortem examination (PME: n = 34) were examined by microbial culture, PCR and serology to include bacterial and viral pathogens typically associated with BRD: Mycoplasma bovis, Histophilus somni, Mannheimia haemolytica and Pasteurella multocida, bovine respiratory syncytial virus (BRSV) and bovine parainfluenza-3 virus (BPIV-3). Overall, the paranasal sinuses were either predominantly sterile or did not contain detectable microbes (83.5%: 94.9% of clinically normal and 50.0% of cattle submitted for PME). Bacteria, including BRD causing pathogens, were identified in relatively small numbers of cattle (<10%). While serology indicated widespread exposure of both clinically normal and cattle submitted for PME to BPIV-3 and BRSV (seroprevalences of 91.6% and 84.7%, respectively), PCR identified BPIV-3 in only one animal. To further explore these findings we investigated the potential role of the antimicrobial molecule nitric oxide (NO) within paranasal sinus epithelium using immunohistochemistry. Expression of the enzyme responsible for NO synthesis, inducible nitric oxide synthase (iNOS), was detected to varying degrees in 76.5% of a sub-sample of animals suggesting production of this compound plays a similar protective role in the bovine sinus as it does in humans.
    • Bovine proteins containing poly-glutamine repeats are often polymorphic and enriched for components of transcriptional regulatory complexes

      Whan, Vicki; Hobbs, Matthew; McWilliam, Sean; Lynn, David J; Lutzow, Ylva S; Khatkar, Mehar; Barendse, William; Raadsma, Herman; Tellam, Ross L; Dairy Australia (Biomed Central, 23/11/2010)
      Background: About forty human diseases are caused by repeat instability mutations. A distinct subset of these diseases is the result of extreme expansions of polymorphic trinucleotide repeats; typically CAG repeats encoding poly-glutamine (poly-Q) tracts in proteins. Polymorphic repeat length variation is also apparent in human poly-Q encoding genes from normal individuals. As these coding sequence repeats are subject to selection in mammals, it has been suggested that normal variations in some of these typically highly conserved genes are implicated in morphological differences between species and phenotypic variations within species. At present, poly-Q encoding genes in non-human mammalian species are poorly documented, as are their functions and propensities for polymorphic variation. Results: The current investigation identified 178 bovine poly-Q encoding genes (Q ≥ 5) and within this group, 26 genes with orthologs in both human and mouse that did not contain poly-Q repeats. The bovine poly-Q encoding genes typically had ubiquitous expression patterns although there was bias towards expression in epithelia, brain and testes. They were also characterised by unusually large sizes. Analysis of gene ontology terms revealed that the encoded proteins were strongly enriched for functions associated with transcriptional regulation and many contributed to physical interaction networks in the nucleus where they presumably act cooperatively in transcriptional regulatory complexes. In addition, the coding sequence CAG repeats in some bovine genes impacted mRNA splicing thereby generating unusual transcriptional diversity, which in at least one instance was tissue-specific. The poly-Q encoding genes were prioritised using multiple criteria for their likelihood of being polymorphic and then the highest ranking group was experimentally tested for polymorphic variation within a cattle diversity panel. Extensive and meiotically stable variation was identified. Conclusions: Transcriptional diversity can potentially be generated in poly-Q encoding genes by the impact of CAG repeat tracts on mRNA alternative splicing. This effect, combined with the physical interactions of the encoded proteins in large transcriptional regulatory complexes suggests that polymorphic variations of proteins in these complexes have strong potential to affect phenotype.
    • Breeding a better cow—Will she be adaptable?

      Berry, Donagh P. (Elsevier, 2017-12-08)
      Adaption is a process that makes an individual or population more suited to their environment. Long-term adaptation is predicated on ample usable genetic variation. Evolutionary forces influencing the extent and dynamics of genetic variation in a population include random drift, mutation, recombination, selection, and migration; the relative importance of each differs by population (i.e., drift is likely to be more influential in smaller populations) and number of generations exposed to selection (i.e., mutation is expected to contribute substantially to genetic variability following many generations of selection). The infinitesimal model, which underpins most genetic and genomic evaluations, assumes that each quantitative trait is controlled by an infinitely large number of unlinked and non-epistatic loci, each with an infinitely small effect. Under the infinitesimal model, selection is not expected to noticeably alter the allele frequencies, despite a potential substantial change in the population mean; the exception is in the first few generations of selection when genetic variance is expected to decline, after which it stabilizes. Despite the common use of the heritability statistic in quantitative genetics as a descriptor of adaption or response to selection, it is arguably the coefficient of genetic variation that is more informative to gauge adaptation potential and should, therefore, always be cited in such studies; for example, the heritability of fertility traits in dairy cows is generally low, yet the coefficient of genetic variation for most traits is comparable to many other performance traits, thus supporting the observed rapid genetic gain in fertility performance in dairy populations. Empirical evidence from long-term selection studies, across a range of animal and plant species, fails to support the premise that selection will deplete genetic variability. Even after 100 yr (synonymous with 100 generations) of selection in corn for high protein or oil content, there appears to be no obvious plateauing in the response to selection. Although populations in several selection experiments did reach a selection limit after multiple generations of directional selection, this does not equate to an exhaustion of genetic variance; such a declaration is supported by the observed rapid responses to reverse selection once implemented in long-term selection studies. New technologies such as genome-wide enabled selection and genome editing, as well as having the potential to accelerate genetic gain, could also increase the genetic variation, or at least reduce the erosion of genetic variance over time. In conclusion, there is no evidence, either theoretical or empirical, to indicate that dairy cow breeding programs will be unable to adapt to evolving challenges and opportunities, at least not because of an absence of ample genetic variability.
    • Breeding the dairy cow of the future: what do we need?

      Berry, Donagh P. (CSIRO, 2015-06)
      Genetics is responsible for approximately half the observed changes in animal performance in well structured breeding programs. Key characteristics of the dairy cow of the future include (1) production of a large quantity of high-value output (i.e. milk and meat), (2) good reproductive performance, (3) good health status, (4) good longevity, (5) no requirement for a large quantity of feed, yet being able to eat sufficient feed to meet its requirements, (6) easy to manage (i.e. easy calving, docile), (7) good conformation (over and above reflective of health, reproductive performance and longevity), (8) low environmental footprint, and (9) resilience to external perturbations. Pertinent and balanced breeding goals must be developed and implemented to achieve this type of animal; excluding any characteristic from the breeding goal could be detrimental for genetic gain in this characteristic. Attributes currently not explicitly considered in most dairy-cow breeding objectives include product quality, feed intake and efficiency, and environmental footprint; animal health is poorly represented in most breeding objectives. Lessons from the past deterioration in reproductive performance in the global Holstein population remind us of the consequences of ignoring or failing to monitor certain animal characteristics. More importantly, however, current knowledge clearly demonstrates that once unfavourable trends have been identified and the appropriate breeding strategy implemented, the reversal of genetic trends is achievable, even for low-heritability traits such as reproductive performance. Genetic variation exists in all the characteristics described. In the genomics era, the relevance of heritability statistics for most traits is less; the exception is traits not amenable to routine measurement in large populations. Phenotyping strategies (e.g. more detailed phenotypes, larger population) will remain a key component of an animal breeding strategy to achieve the cow of the future as well as providing the necessary tools and information to monitor performance. The inclusion of genomic information in genetic evaluations is, and will continue, to improve the accuracy of genetic evaluations, which, in turn, will augment genetic gain; genomics, however, can also contribute to gains in performance over and above support of increased genetic gain. Nonetheless, the faster genetic gain and thus reduced ability to purge out unfavourable alleles necessitates the appropriate breeding goal and breeding scheme and very close monitoring of performance, in particular for traits not included in the breeding goals. Developments in other disciplines (e.g. reproductive technologies), coupled with commercial struggle for increased market share of the breeding industry, imply a possible change in the landscape of dairy-cow breeding in the future.
    • Calf health from birth to weaning. I. General aspects of disease prevention

      Lorenz, Ingrid; Mee, John F; Earley, Bernadette; More, Simon J (Biomed Central, 2011-09-16)
      Calfhood diseases have a major impact on the economic viability of cattle operations. This is the first in a three part review series on calf health from birth to weaning, focusing on preventive measures. The review considers both pre- and periparturient management factors influencing calf health, colostrum management in beef and dairy calves and further nutrition and weaning in dairy calves.
    • Calf health from birth to weaning. III. Housing and management of calf pneumonia

      Lorenz, Ingrid; Earley, Bernadette; Gilmore, John; Hogan, Ian; Kennedy, Emer; More, Simon J (Biomed Central, 2011-10-21)
      Calfhood diseases have a major impact on the economic viability of cattle operations. A three part review series has been developed focusing on calf health from birth to weaning. In this paper, the last of the three part series, we review disease prevention and management with particular reference to pneumonia, focusing primarily on the pre-weaned calf. Pneumonia in recently weaned suckler calves is also considered, where the key risk factors are related to the time of weaning. Weaning of the suckler calf is often combined with additional stressors including a change in nutrition, environmental change, transport and painful husbandry procedures (castration, dehorning). The reduction of the cumulative effects of these multiple stressors around the time of weaning together with vaccination programmes (preconditioning) can reduce subsequent morbidity and mortality in the feedlot. In most studies, calves housed individually and calves housed outdoors with shelter, are associated with decreased risk of disease. Even though it poses greater management challenges, successful group housing of calves is possible. Special emphasis should be given to equal age groups and to keeping groups stable once they are formed. The management of pneumonia in calves is reliant on a sound understanding of aetiology, relevant risk factors, and of effective approaches to diagnosis and treatment. Early signs of pneumonia include increased respiratory rate and fever, followed by depression. The single most important factor determining the success of therapy in calves with pneumonia is early onset of treatment, and subsequent adequate duration of treatment. The efficacy and economical viability of vaccination against respiratory disease in calves remains unclear.
    • Candidate genes associated with the heritable humoral response to Mycobacterium avium ssp. paratuberculosis in dairy cows have factors in common with gastrointestinal diseases in humans

      McGovern, S. P.; Purfield, Deirdre C; Ring, Siobhan C.; Carthy, T. R.; Graham, David A.; Berry, Donagh P.; Department of Agriculture, Food and the Marine; Science Foundation Ireland; 14/IA/2576; 16/RC/3835 (Elsevier, 2019-03-07)
      Infection of cattle with bovine paratuberculosis (i.e., Johne's disease) is caused by Mycobacterium avium ssp. paratuberculosis (MAP) and results in a chronic incurable gastroenteritis. This disease, which has economic ramifications for the cattle industry, is increasing in detected prevalence globally; subclinically infected animals can silently shed the bacterium into the environment for years, exposing contemporaries and hampering disease-control programs. The objective of the present study was to first quantify the genetic parameters for humoral response to MAP in dairy cattle. This was followed by a genome-based association analysis and subsequent downstream bioinformatic analyses from imputed whole genome sequence SNP data. After edits, ELISA test records were available on 136,767 cows; analyses were also undertaken on a subset of 33,818 of these animals from herds with at least 5 MAP ELISA-positive cows, with at least 1 of those positive cows being homebred. Variance components were estimated using univariate animal and sire linear mixed models. The heritability calculated from the animal model for humoral response to MAP using alternative phenotype definitions varied from 0.02 (standard error = 0.003) to 0.05 (standard error = 0.008). The genome-based associations were undertaken within a mixed model framework using weighted deregressed estimated breeding values as a dependent variable on 1,883 phenotyped animals that were ≥87.5% Holstein-Friesian. Putative susceptibility quantitative trait loci (QTL) were identified on Bos taurus autosome 1, 3, 5, 6, 8, 9, 10, 11, 13, 14, 18, 21, 23, 25, 26, 27, and 29; mapping the most significant SNP to genes within and overlapping these QTL revealed that the most significant associations were with the 10 functional candidate genes KALRN, ZBTB20, LPP, SLA2, FI3A1, LRCH3, DNAJC6, ZDHHC14, SNX1, and HAS2. Pathway analysis failed to reveal significantly enriched biological pathways, when both bovine-specific pathway data and human ortholog data were taken into account. The existence of genetic variation for MAP susceptibility in a large data set of dairy cows signifies the potential of breeding programs for reducing MAP susceptibility. Furthermore, the identification of susceptible QTL facilitates greater biological understanding of bovine paratuberculosis and potential therapeutic targets for future investigation. The novel molecular similarities identified between bovine paratuberculosis and human inflammatory bowel disease suggest potential for human therapeutic interventions to be translated to veterinary medicine and vice versa.
    • Capturing the economic benefit of Lolium perenne cultivar performance

      McEvoy, Mary; O'Donovan, Michael; Shalloo, Laurence; Department of Agriculture, Food and the Marine (Teagasc (Agriculture and Food Development Authority), Ireland, 2011)
      Economic values were calculated for grass traits of economic importance in Irish grass-based ruminant production systems. Traits considered were those that had the greatest potential to influence the profitability of a grazing system. These were: grass dry matter (DM) yield in spring, mid-season and autumn, grass quality (dry matter digestibility; DMD), 1st and 2nd cut silage DM yield and sward persistency. The Moorepark Dairy Systems Model was used to simulate a dairy farm. Economic values were calculated by simulating the effect of a unit change in the trait of interest while holding all other traits constant. The base scenario involved a fixed herd size and land area (40 ha), and an annual DM yield of 13 t/ha. The economic values generated under the base scenario were: € 0.152/kg for DM yield in spring, € 0.030/kg for DM yield in mid-season and € 0.103/kg for DM yield in autumn; € 0.001, € 0.008, € 0.010, € 0.009, € 0.008 and € 0.006 per 1 g/kg change in DMD for the months of April to September, respectively; € 0.03/kg for 1st cut silage DM yield, € 0.02/kg for 2nd cut silage DM yield; and − € 4.961 for a 1 percent reduction in persistency. Alternative scenarios were examined to determine the sensitivity of the economic values to changes in annual DM yield, sward utilisation and a scenario where silage production was the focus of the system. The economic values were used to calculate a total merit index for each of 20 perennial ryegrass cultivars based on production data from a 3 year plot study. The rank correlation between the merit index values for the cultivars under the base scenario and the scenario involving a reduction in herbage utilisation was 1.0, while that with the scenario involving reduced annual DM yield was 0.94. It is concluded that the total merit index can be used to identify cultivars that can generate the greatest economic contribution to a grass-based production system, regardless of system or intensity of grass production.
    • Carcass characteristics of cattle differing in Jersey proportion

      Berry, Donagh P.; Judge, Michelle; Evans, R. D.; Buckley, Frank; Cromie, A. R.; Science Foundation Ireland; Department of Agriculture, Food and Marine; Meat Technology Ireland; Enterprise Ireland; 16/RC/3835; et al. (Elsevier, 2018-09-27)
      Comparison of alternative dairy (cross-)breeding programs requires full appraisals of all revenues and costs, including beef merit. Few studies exist on carcass characteristics of crossbred dairy progeny originating from dairy herds as well as their dams. The objective of the present study was to quantify, using a national database, the carcass characteristics of young animals and cows differing in their fraction of Jersey. The data set consisted of 117,593 young animals and 42,799 cows. The associations between a combination of sire and dam breed proportion (just animal breed proportion when the dependent variable was on cows) with age at slaughter (just for young animals), carcass weight, conformation, fat score, price per kilogram, and total carcass value were estimated using mixed models that accounted for covariances among herdmates of the same sex slaughtered in close proximity in time; we also accounted for age at slaughter in young animals (which was substituted with carcass weight and carcass fat score when the dependent variable was age at slaughter), animal sex, parity of the cow or dam (where relevant), and temporal effects represented by a year-by-month 2-way interaction. For young animals, the heaviest of the dairy carcasses were from the mating of a Holstein-Friesian dam and a Holstein-Friesian sire (323.34 kg), whereas the lightest carcasses were from the mating of a purebred Jersey dam to a purebred Jersey sire which were 46.31 kg lighter (standard error of the difference = 1.21 kg). The young animal carcass weight of an F1 Holstein-Friesian × Jersey cross was 20.4 to 27.0 kg less than that of a purebred Holstein-Friesian animal. The carcass conformation of a Holstein-Friesian young animal was 26% superior to that of a purebred Jersey, translating to a difference of 0.78 conformation units on a scale of 1 to 15. Purebred Holstein-Friesians produced carcasses with less fat than their purebred Jersey counterparts. The difference in carcass price per kilogram among the alternative sire-dam breed combinations investigated was minimal, although large differences existed among the different breed types for overall carcass value; the carcass value of a Holstein-Friesian animal was 20% greater than that of a Jersey animal. Purebred Jersey animals required, on average, 21 d longer to reach a given carcass weight and fat score relative to a purebred Holstein-Friesian. The difference in age at slaughter between a purebred Holstein-Friesian animal and the mating between a Holstein-Friesian sire with a Jersey dam, and vice versa, was between 7.0 and 8.9 d. A 75.8-kg difference in carcass weight existed between the carcass of a purebred Jersey cow and that of a Holstein-Friesian cow; a 50% Holstein–Friesian-50% Jersey cow had a carcass 42.0 kg lighter than that of a purebred Holstein-Friesian cow. Carcass conformation was superior in purebred Holstein-Friesian compared with purebred Jersey cows. Results from this study represent useful input parameters to populate simulation models of alternative breeding programs on dairy farms, and to help beef farmers evaluate the cost-benefit of rearing, for slaughter, animals differing in Jersey fraction.