Research in the ABRD encompasses nutrition, fertility, breeding, health and welfare. Research activities focus on producing profitable animals and the corresponding management strategies to deliver the productivity, sustainability and product quality targets set out in Ireland’s Food Harvest 2020 vision. The ABRD uses a powerful combination of established animal science techniques, as well as cutting-edge molecular and computational biology tools, to answer relevant industry research questions. Our focus is on dairy and beef cattle and sheep. We have developed animal models that are divergent for a range of economically important traits.

Recent Submissions

  • Development of a benchmarking system for Irish beef farms using data envelopment analysis

    Finneran, Eoghan; Crosson, Paul (2013)
    Agricultural extension trends have involved greater use of collaborative “discussion group” dissemination approaches. These discussion groups involve regular participatory meetings between a consistent cohort of farmers and extension practitioners with occasional input from industry and research stakeholders. In Ireland, policy change, small farm scale and low incomes are some of the factors incentivising beef farmers and industry to seek increased whole-farm income efficiency. Whole-farm comparative analysis may provide a means of identifying and explaining efficiency drivers at farm level. This article describes the development of BEEFMARK, a benchmarking model with potential to act as a tool to facilitate farmer-farmer and farmer-adviser group learning within discussion groups. BEEFMARK utilised Data Envelopment Analysis (DEA) to measure beef farm income and scale efficiency and to identify and characterise efficient peer farms which act as benchmarks for similarly structured, but lower efficiency farms. Market derived gross output (€) per livestock unit was positively associated with farm efficiency while greater overhead and concentrate feed expenditure was negatively associated with income and scale efficiency.
  • The Structural and Functional Capacity of Ruminal and Cecal Microbiota in Growing Cattle Was Unaffected by Dietary Supplementation of Linseed Oil and Nitrate

    Popova, Milka; McGovern, Emily; McCabe, Matthew; Martin, Cécile; Doreau, Michel; Arbre, Marie; Meale, Sarah J.; Morgavi, Diego P.; Waters, Sinead M.; INRA; French ministry of Foreign Affairs and International Development; French ministry of National Education, Higher Education, and Research; FACCE-JPI (Frontiers, 2017-05-24)
    Microorganisms in the digestive tract of ruminants differ in their functionality and ability to use feed constituents. While cecal microbiota play an important role in post-rumen fermentation of residual substrates undigested in the rumen, limited knowledge exists regarding its structure and function. In this trial we investigated the effect of dietary supplementation with linseed oil and nitrate on methane emissions and on the structure of ruminal and cecal microbiota of growing bulls. Animals were allocated to either a CTL (control) or LINNIT (CTL supplemented with 1.9% linseed and 1.0% nitrates) diet. Methane emissions were measured using the GreenFeed system. Microbial diversity was assessed using amplicon sequencing of microbial genomic DNA. Additionally, total RNA was extracted from ruminal contents and functional mcrA and mtt genes were targeted in amplicon sequencing approach to explore the diversity of functional gene expression in methanogens. LINNIT had no effect on methane yield (g/kg DMI) even though it decreased methane production by 9% (g/day; P < 0.05). Methanobrevibacter- and Methanomassiliicoccaceae-related OTUs were more abundant in cecum (72 and 24%) compared to rumen (60 and 11%) irrespective of the diet (P < 0.05). Feeding LINNIT reduced the relative abundance of Methanomassiliicoccaceae mcrA cDNA reads in the rumen. Principal component analysis revealed significant differences in taxonomic composition and abundance of bacterial communities between rumen and cecum. Treatment decreased the relative abundance of a few Ruminococcaceae genera, without affecting global bacterial community structure. Our research confirms a high level of heterogeneity in species composition of microbial consortia in the main gastrointestinal compartments where feed is fermented in ruminants. There was a parallel between the lack of effect of LINNIT on ruminal and cecal microbial community structure and functions on one side and methane emission changes on the other. These results suggest that the sequencing strategy used here to study microbial diversity and function accurately reflected the absence of effect on methane phenotypes in bulls treated with linseed plus nitrate.
  • Grazing of dairy cows on pasture versus indoor feeding on total mixed ration: Effects on low-moisture part-skim Mozzarella cheese yield and quality characteristics in mid and late lactation

    Gulati, Arunima; Galvin, Norann; Hennessy, Deirdre; McAuliffe, Stephen; O’Donovan, Michael; McManus, Jennifer J.; Fenelon, Mark; Guinee, Timothy P.; Department of Agriculture, Food and the Marine, Ireland; Dairy Levy Trust; 11/sf/309 (Elsevier for American Dairy Science Association, 2018-08-16)
    This study investigated the effects of 3 dairy cow feeding systems on the composition, yield, and biochemical and physical properties of low-moisture part-skim Mozzarella cheese in mid (ML; May–June) and late (LL; October–November) lactation. Sixty spring-calving cows were assigned to 3 herds, each consisting of 20 cows, and balanced on parity, calving date, and pre-experimental milk yield and milk solids yield. Each herd was allocated to 1 of the following feeding systems: grazing on perennial ryegrass (Lolium perenne L.) pasture (GRO), grazing on perennial ryegrass and white clover (Trifolium repens L.) pasture (GRC), or housed indoors and offered total mixed ration (TMR). Mozzarella cheese was manufactured on 3 separate occasions in ML and 4 in LL in 2016. Feeding system had significant effects on milk composition, cheese yield, the elemental composition of cheese, cheese color (green to red and blue to yellow color coordinates), the extent of flow on heating, and the fluidity of the melted cheese. Compared with TMR milk, GRO and GRC milks had higher concentrations of protein and casein and lower concentrations of I, Cu, and Se, higher cheese-yielding capacity, and produced cheese with lower concentrations of the trace elements I, Cu, and Se and higher yellowness value. Cheese from GRO milk had higher heat-induced flow and fluidity than cheese from TMR milk. These effects were observed over the entire lactation period (ML + LL), but varied somewhat in ML and LL. Feeding system had little, or no, effect on gross composition of the cheese, the proportions of milk protein or fat lost to cheese whey, the texture of the unheated cheese, or the energy required to extend the molten cheese. The differences in color and melt characteristics of cheeses obtained from milks with the different feeding systems may provide a basis for creating points of differentiation suited to different markets.
  • Genetic variability in the humoral immune response to bovine herpesvirus-1 infection in dairy cattle and genetic correlations with performance traits

    Ring, S. C.; Graham, D. A.; Sayers, Riona; Byrne, N.; Kelleher, M. M.; Doherty, M. L.; Berry, Donagh P.; Department of Agriculture, Food and the Marine (Elsevier for American Dairy Science Association, 2018-04-26)
    Bovine herpesvirus-1 (BoHV-1) is a viral pathogen of global significance that is known to instigate several diseases in cattle, the most notable of which include infectious bovine rhinotracheitis and bovine respiratory disease. The genetic variability in the humoral immune response to BoHV-1 has, to our knowledge, not ever been quantified. Therefore, the objectives of the present study were to estimate the genetic parameters for the humoral immune response to BoHV-1 in Irish female dairy cattle, as well as to investigate the genetic relationship between the humoral immune response to BoHV-1 with milk production performance, fertility performance, and animal mortality. Information on antibody response to BoHV-1 was available to the present study from 2 BoHV-1 sero-prevalence research studies conducted between the years 2010 to 2015, inclusive; after edits, BoHV-1 antibody test results were available on a total of 7,501 female cattle from 58 dairy herds. National records of milk production (i.e., 305-d milk yield, fat yield, protein yield, and somatic cell score; n = 1,211,905 milk-recorded cows), fertility performance (i.e., calving performance, pregnancy diagnosis, and insemination data; n = 2,365,657 cows) together with animal mortality data (i.e., birth, farm movement, death, slaughter, and export events; n = 12,853,257 animals) were also available. Animal linear mixed models were used to quantify variance components for BoHV-1 as well as to estimate genetic correlations among traits. The estimated genetic parameters for the humoral immune response to BoHV-1 in the present study (i.e., heritability range: 0.09 to 0.16) were similar to estimates previously reported for clinical signs of bovine respiratory disease in dairy and beef cattle (i.e., heritability range: 0.05 to 0.11). Results from the present study suggest that breeding for resistance to BoHV-1 infection could reduce the incidence of respiratory disease in cattle while having little or no effect on genetic selection for milk yield or milk constituents (i.e., genetic correlations ranged from −0.13 to 0.17). Moreover, even though standard errors were large, results also suggest that breeding for resistance to BoHV-1 infection may indirectly improve fertility performance while also reducing the incidence of mortality in older animals (i.e., animals >182 d of age). Results can be used to inform breeding programs of potential genetic gains achievable for resistance to BoHV-1 infection in cattle.
  • Perinatal immuno/inflammatory responses in the presence or absence of bovine fetal infection

    Jawor, Paulina; Mee, John F; Stefaniak, Tadeusz; The National Centre for Research and Development; PBS2/A8/20/2013 (Biomed Central, 2018-11-01)
    Background It is known that the bovine fetus can mount an immune and inflammatory reaction to infection, but it is not known whether there is a contemporaneous maternal response. Nor is it known whether the response of calves which die perinatally, with or without infection, differs from that of live perinates. Hence, the objective of this study was to determine if acute phase reactant and immunoglobulin concentrations differed between calves (and their dams) in three groups: live calves (CC; n = 21) and dead calves with (PM INF+; n = 22) or without (PM INF-; n = 89) in utero infection. In calf plasma, serum amyloid A, haptoglobin, immunoglobulins M, G1 and G2 and interleukin-6 were measured. In dam serum, SAA and Hp was measured and in amniotic and abomasal fluid, IL-6 was measured. Results Live calves had higher plasma concentrations of SAA and IL-6 than dead calves with (PM INF+) or without (PM INF-) in utero infection. Calves in the PM INF-, but not PM INF+ group, had higher Hp concentrations than calves in the CC group. Calves in the PM INF+ group had higher IgG1 concentrations than calves in the PM INF- and CC groups. Except for higher IgG1 and IgG2 concentrations, biomarker values did not differ significantly between dead calves with or without in utero infection. Live calves had higher IL-6 concentrations in abomasal fluid compared to PM INF- calves. There were no significant differences in blood biomarker concentrations between dams of the three groups of calves. Amniotic fluid IL-6 concentrations were higher from the dams of control calves than the dams of uninfected calves. Conclusions Differences in biomarkers (higher Hp and IgG1; lower SAA and IL-6) between perinatal mortalities and live perinates probably reflect differences between these two groups in age at sampling (SAA and IL-6) and in utero infection (IgG1). Out of the six analytes measured in calves, only IgG1 and IgG2 were biomarkers of (chronic) in utero infection.
  • Intestinal microbiota profiles associated with low and high residual feed intake in chickens across two geographical locations

    Siegerstetter, Sina-Catherine; Schmitz-Esser, Stephan; Magowan, Elizabeth; Wetzels, Stefanie Urimare; Zebeli, Qendrim; Lawlor, Peadar G; O'Connell, Niamh E.; Metzler-Zebeli, Barbara U.; European Union; 311794 (PLOS, 2017-11-15)
    Intestinal microbe-host interactions can affect the feed efficiency (FE) of chickens. As inconsistent findings for FE-associated bacterial taxa were reported across studies, the present objective was to identify whether bacterial profiles and predicted metabolic functions that were associated with residual feed intake (RFI) and performance traits in female and male chickens were consistent across two different geographical locations. At six weeks of life, the microbiota in ileal, cecal and fecal samples of low (n = 34) and high (n = 35) RFI chickens were investigated by sequencing the V3-5 region of the 16S rRNA gene. Location-associated differences in α-diversity and relative abundances of several phyla and genera were detected. RFI-associated bacterial abundances were found at the phylum and genus level, but differed among the three intestinal sites and between males and females. Correlation analysis confirmed that, of the taxonomically classifiable bacteria, Lactobacillus (5% relative abundance) and two Lactobacillus crispatus-OTUs in feces were indicative for high RFI in females (P < 0.05). In males, Ruminococcus in cecal digesta (3.1% relative abundance) and Dorea in feces (<0.1% relative abundance) were best indicative for low RFI, whereas Acinetobacter in feces (<1.5% relative abundance) related to high RFI (P < 0.05). Predicted metabolic functions in feces of males confirmed compositional relationships as functions related to amino acid, fatty acid and vitamin metabolism correlated with low RFI, whereas an increasing abundance of bacterial signaling and interaction (i.e. cellular antigens) genes correlated with high RFI (P < 0.05). In conclusion, RFI-associated bacterial profiles could be identified across different geographical locations. Results indicated that consortia of low- abundance taxa in the ileum, ceca and feces may play a role for FE in chickens, whereby only bacterial FE-associations found in ileal and cecal digesta may serve as useful targets for dietary strategies.
  • CowPI: A Rumen Microbiome Focussed Version of the PICRUSt Functional Inference Software

    Wilkinson, Toby J.; Huws, Sharon A.; Edwards, Joan E.; Kingston-Smith, Alison H.; Siu-Ting, Karen; Hughes, Martin; Rubino, Francesco; Friedersdorff, Maximillian; Creevey, Christopher J.; Biotechnology and Biological Sciences Research Council; BBSRC Institute Strategic Programme; Irish Research Council; BBS/OS/GC/000011B; BB/E/W/10964A01; ELEVATEPD/2014/69 (Frontiers, 2018-05-25)
    Metataxonomic 16S rDNA based studies are a commonplace and useful tool in the research of the microbiome, but they do not provide the full investigative power of metagenomics and metatranscriptomics for revealing the functional potential of microbial communities. However, the use of metagenomic and metatranscriptomic technologies is hindered by high costs and skills barrier necessary to generate and interpret the data. To address this, a tool for Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) was developed for inferring the functional potential of an observed microbiome profile, based on 16S data. This allows functional inferences to be made from metataxonomic 16S rDNA studies with little extra work or cost, but its accuracy relies on the availability of completely sequenced genomes of representative organisms from the community being investigated. The rumen microbiome is an example of a community traditionally underrepresented in genome and sequence databases, but recent efforts by projects such as the Global Rumen Census and Hungate 1000 have resulted in a wide sampling of 16S rDNA profiles and almost 500 fully sequenced microbial genomes from this environment. Using this information, we have developed “CowPI,” a focused version of the PICRUSt tool provided for use by the wider scientific community in the study of the rumen microbiome. We evaluated the accuracy of CowPI and PICRUSt using two 16S datasets from the rumen microbiome: one generated from rDNA and the other from rRNA where corresponding metagenomic and metatranscriptomic data was also available. We show that the functional profiles predicted by CowPI better match estimates for both the meta-genomic and transcriptomic datasets than PICRUSt, and capture the higher degree of genetic variation and larger pangenomes of rumen organisms. Nonetheless, whilst being closer in terms of predictive power for the rumen microbiome, there were differences when compared to both the metagenomic and metatranscriptome data and so we recommend, where possible, functional inferences from 16S data should not replace metagenomic and metatranscriptomic approaches. The tool can be accessed at http://www.cowpi.org and is provided to the wider scientific community for use in the study of the rumen microbiome.
  • Evaluating Established Methods for Rumen 16S rRNA Amplicon Sequencing With Mock Microbial Populations

    McGovern, Emily; Waters, Sinead M.; Blackshields, Gordon; McCabe, Matthew S.; FACCE-JPI; Teagasc Walsh Fellowship Programme; 2014231 (Frontiers, 2018-06-25)
    The rumen microbiome scientific community has utilized amplicon sequencing as an aid in identifying potential community compositional trends that could be used as an estimation of various production and performance traits including methane emission, animal protein production efficiency, and ruminant health status. In order to translate rumen microbiome studies into executable application, there is a need for experimental and analytical concordance within the community. The objective of this study was to assess these factors in relation to selected currently established methods for 16S phylogenetic community analysis on a microbial community standard (MC) and a DNA standard (DS; ZymoBIOMICSTM). DNA was extracted from MC using the RBBC method commonly used for microbial DNA extraction from rumen digesta samples. 16S rRNA amplicon libraries were generated for the MC and DS using primers routinely used for rumen bacterial and archaeal community analysis. The primers targeted the V4 and V3–V4 region of the 16S rRNA gene and samples were subjected to both 20 and 28 polymerase chain reaction (PCR) cycles under identical cycle conditions. Sequencing was conducted using the Illumina MiSeq platform. As the bacteria contained in the microbial mock community were well-classified species, and for ease of explanation, we used the results of the Basic Local Alignment Search Tool classification to assess the DNA, PCR cycle number, and primer type. Sequence classification methodology was assessed independently. Spearman’s correlation analysis indicated that utilizing the repeated bead beating and column method for DNA extraction in combination with primers targeting the 16S rRNA gene using 20 first-round PCR cycles was sufficient for amplicon sequencing to generate a relatively accurate depiction of the bacterial communities present in rumen samples. These results also emphasize the requirement to develop and utilize positive mock community controls for all rumen microbiomic studies in order to discern errors which may arise at any step during a next-generation sequencing protocol.
  • Improved detection of biomarkers in cervico-vaginal mucus (CVM) from postpartum cattle

    Adnane, Mounir; Kelly, Paul; Chapwanya, Aspinas; Meade, Kieran G; O’Farrelly, Cliona; The Algerian Ministry for High Education and Scientific Research; University of Tiaret, Algeria; Department of Agriculture, Food and the Marine, Ireland; ofarrecl-HRB-HRA_POR/2012/37; 13/S/472 (Biomed Central, 2018-09-29)
    Background In the postpartum cow, early diagnosis of uterine disease is currently problematic due to the lack of reliable, non-invasive diagnostic methods. Cervico-vaginal mucus (CVM) is an easy to collect potentially informative source of biomarkers for the diagnosis and prognosis of uterine disease in cows. Here, we report an improved method for processing CVM from postpartum dairy cows for the measurement of immune biomarkers. CVM samples were collected from the vagina using gloved hand during the first two weeks postpartum and processed with buffer alone or buffer containing different concentrations of the reducing agents recommended in standard protocols: Dithiothriotol (DTT) or N-Acetyl-L-Cysteine (NAC). Total protein was measured using the bicinchoninic acid (BCA) assay; interleukin 6 (IL-6), IL-8 and α1-acid glycoprotein (AGP) were measured by ELISA. Results We found that use of reducing agents to liquefy CVM affects protein yield and the accuracy of biomarker detection. Our improved protocol results in lower protein yields but improved detection of cytokines and chemokines. Using our modified method to measure AGP in CVM we found raised levels of AGP at seven days postpartum in CVM from cows that went on to develop endometritis. Conclusion We conclude that processing CVM without reducing agents improves detection of biomarkers that reflect uterine health in cattle. We propose that measurement of AGP in CVM during the first week postpartum may identify cows at risk of developing clinical endometritis.
  • Spatial patterns of Fasciola hepatica and Calicophoron daubneyi infections in ruminants in Ireland and modelling of C. daubneyi infection

    Naranjo-Lucena, Amalia; Munita Corbalán, María P; Martínez-Ibeas, Ana M; McGrath, Guy; Murray, Gerard; Casey, Mícheál; Good, Barbara; Sayers, Riona; Mulcahy, Grace; Zintl, Annetta; European Union; Department of Agriculture, Food and the Marine, Ireland; 635408); 13/S/405 (Biomed Central, 2018-09-29)
    Background Fasciola hepatica has always represented a threat to Irish livestock because the Irish climate is highly suitable for the main local intermediate host of the parasite, the snail Galba truncatula. The recent clinical emergence of infections due to Calicophoron daubneyi has raised the question of whether the two parasites, which share a niche during part of their life-cycles, interact in some way. Here, we used geographical information systems (GIS) to analyse the distribution of both parasites in cattle and sheep. We also developed the first predictive model of paramphistomosis in Ireland. Results Our results indicated that, in cattle, liver fluke infection is less common than rumen fluke infection and does not exhibit the same seasonal fluctuations. Overall, we found that cattle had a higher likelihood of being infected with rumen fluke than sheep (OR = 3.134, P < 0.01). In addition, infection with one parasite increased the odds of infection with the other in both host species. Rumen fluke in cattle showed the highest spatial density of infection. Environmental variables such as soil drainage, land cover and habitat appeared to be the most important risk factors for C. daubneyi infection, followed by rainfall and vegetation. Overall the risk of infection with this parasite was predicted to be higher in the west of the country. Conclusions This study shows differences between the infection rates and spatial patterns of bovine and ovine infections with F. hepatica and C. daubneyi in Ireland. Whether the reasons for this are due to susceptibility, exposure and/or management factors is yet to be determined. Furthermore, the rumen fluke model indicates distinct risk factors and predicted distribution to those of F. hepatica, suggesting potential biological differences between both parasite species.
  • Residual feed intake phenotype and gender affect the expression of key genes of the lipogenesis pathway in subcutaneous adipose tissue of beef cattle

    McKenna, Clare; Porter, Richard; Keogh, Kate; Waters, Sinead M.; McGee, Mark; Kenny, David; Teagasc Walsh Fellowship Programme (Biomed Central, 2018-09-20)
    Background Feed accounts for up to 75% of costs in beef production systems, thus any improvement in feed efficiency (FE) will benefit the profitability of this enterprise. Residual feed intake (RFI) is a measure of FE that is independent of level of production. Adipose tissue (AT) is a major endocrine organ and the primary metabolic energy reservoir. It modulates a variety of processes related to FE such as lipid metabolism and glucose homeostasis and thus measures of inter-animal variation in adiposity are frequently included in the calculation of the RFI index. The aim of this study was to determine the effect of phenotypic RFI status and gender on the expression of key candidate genes related to processes involved in energy metabolism within AT. Dry matter intake (DMI) and average daily gain (ADG) were measured over a period of 70 d for 52 purebred Simmental heifers (n = 24) and bulls (n = 28) with an initial BW±SD of 372±39.6 kg and 387±50.6 kg, respectively. Residual feed intake was calculated and animals were ranked within gender by RFI into high (inefficient; n = 9 heifers and n = 8 bulls) and low (efficient; n = 9 heifers and n = 8 bulls) groups. Results Average daily gain ±SD and daily DMI ±SD for heifers and bulls were 1.2±0.4 kg and 9.1±0.5 kg, and 1.8±0.3 kg and 9.5±1 kg respectively. High RFI heifers and bulls consumed 10% and 15% more (P < 0.05) than their low RFI counterparts, respectively. Heifers had a higher expression of all genes measured than bulls (P < 0.05). A gender × RFI interaction was detected for HMGCS2(P < 0.05) in which high RFI bulls tended to have lower expression of HMGCS2 than low RFI bulls (P < 0.1), whereas high RFI heifers had higher expression than low RFI heifers (P < 0.05) and high RFI bulls (P < 0.05). SLC2A4 expression was consistently higher in subcutaneous AT of low RFI animals across gender. Conclusion The findings of this study indicate that low RFI cattle exhibit upregulation of the molecular mechanisms governing glucose metabolism in adipose tissue, in particular, glucose clearance. The decreased expression of SLC2A4 in the inefficient cattle may result in less efficient glucose metabolism in these animals. We conclude that SLC2A4 may be a potential biomarker for RFI in cattle.
  • Culicoides species composition and abundance on Irish cattle farms: implications for arboviral disease transmission

    Collins, Áine B; Mee, John F; Doherty, Michael L; Barrett, Damien J; England, Marion E; Teagasc Walsh Fellowship Programme (Biomed Central, 2018-08-17)
    Background Following the emergence of Schmallenberg virus (SBV) in Ireland in 2012, a sentinel herd surveillance program was established in the south of Ireland with the primary aim of investigating the species composition and abundance of Culicoides on livestock farms in the region. Methods Ultraviolet-light trapping for Culicoides was carried out on 10 sentinel farms. Each site was sampled fortnightly over 16 weeks (21st July to 5th November 2014). One Onderstepoort Veterinary Institute UV light trap was run overnight at each site and catches were transferred immediately into 70% ethanol. Culicoides were morphologically identified to species level. Collection site habitats were characterised using the Phase 1 habitat survey technique (Joint Nature Conservation Committee). Results A total of 23,929 individual Culicoides from 20 species was identified, including one species identified in Ireland for the first time, Culicoides cameroni. The most abundant species identified were Culicoides obsoletus/Culicoides scoticus (38%), Culicoides dewulfi (36%), Culicoides pulicaris (9%), Culicoides chiopterus (5%) and Culicoides punctatus (5%), comprising 93% of all Culicoides specimens identified. Collection site habitats were dominated by improved grassland and a combination of broadleaf woodland and native woodland species. Conclusions The most abundant species of Culicoides identified were the putative vectors of bluetongue virus (BTV) and SBV in northern Europe. Their presence and abundance demonstrates the potential for future transmission of arboviruses among livestock in this region.
  • Effect of feeding colostrum at different volumes and subsequent number of transition milk feeds on the serum immunoglobulin G concentration and health status of dairy calves

    Conneely, Muireann; Berry, Donagh P.; Murphy, J. P.; Lorenz, I.; Doherty, M. L.; Kennedy, Emer (Elsevier for American Dairy Science Association, 2014-09)
    Transfer of sufficient IgG to the newborn calf via colostrum is vital to provide it with adequate immunological protection and resistance to disease. The objectives of the present study were to compare serum IgG concentration and health parameters of calves (1) fed different volumes of colostrum [7, 8.5, or 10% of body weight (BW)] within 2 h of birth and (2) given 0, 2, or 4 subsequent feedings of transition milk (i.e., milkings 2 to 6 postcalving). Ninety-nine dairy calves were fed 7, 8.5, or 10% of BW in colostrum within 2 h of birth and given 0, 2, or 4 subsequent feedings of transition milk. The concentration of IgG in the serum of calves was measured at 24, 48, 72, and 642 h of age by an ELISA. The apparent efficiency of absorption for IgG was determined. Health scores were assigned to calves twice per week and all episodes of disease were recorded. The effect of experimental treatment on calf serum IgG concentration differed by the age of the calf. Calves fed 8.5% of BW in colostrum had a greater mean serum IgG concentration than calves fed 7 or 10% of BW at 24, 48, and 72 h of age. At 642 h of age, serum IgG concentrations of calves fed 8.5% of BW (24.2 g/L) and calves fed 10% of BW (21.6 g/L) did not differ, although the serum IgG concentration of calves fed 8.5% of BW was still greater than that of calves fed 7% of BW (20.7 g/L). No difference in serum IgG concentration existed between calves fed 7% of BW and those fed 10% of BW at any age. No significant effect of number of subsequent feedings of transition milk on calf serum IgG concentration was detected. The apparent efficiency of absorption of calves fed 8.5% of BW in colostrum (38%) was greater than calves fed 7% of BW in colostrum (26%) and tended to be greater than in calves fed 10% of BW (29%). Calves fed further feedings of transition milk after the initial feeding of colostrum had a lower odds (0.62; 95% confidence interval: 0.41 to 0.93) of being assigned a worse eye/ear score (i.e., a more copious ocular discharge or pronounced ear droop) and a lower odds (0.5; 95% confidence interval: 0.32 to 0.79) of being assigned a worse nasal score (i.e., a more copious and purulent nasal discharge) during the study period relative to calves that received no further feedings of transition milk. In conclusion, calves fed 8.5% of BW in colostrum within 2 h of birth achieved a greater concentration of IgG in serum in the first 3 d of life than calves fed either 7 or 10% of BW. Feeding calves transition milk subsequently reduced their odds of being assigned a worse eye/ear and nasal score.
  • Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals

    Bouwman, Aniek C.; et al; Purfiled, Deirdre C; Berry, Donagh P.; Department of Agriculture, Food and the Marine, Ireland; Science Foundation Ireland; German Federal Ministry of Education and Research; Deutsche Forschungsgemeinschaft; Breed4Food; European Commission; Dairy Futures Cooperative Research Centre; Genome Canada project; 11/S/112; 14/IA/2576; 0315527B; PA 2789/1-1; BO-22.04-011-001-ASG-LR; 317697 (Nature Publishing Group, 2018-02-19)
    Stature is affected by many polymorphisms of small effect in humans1. In contrast, variation in dogs, even within breeds, has been suggested to be largely due to variants in a small number of genes2,3. Here we use data from cattle to compare the genetic architecture of stature to those in humans and dogs. We conducted a meta-analysis for stature using 58,265 cattle from 17 populations with 25.4 million imputed whole-genome sequence variants. Results showed that the genetic architecture of stature in cattle is similar to that in humans, as the lead variants in 163 significantly associated genomic regions (P < 5 × 10−8) explained at most 13.8% of the phenotypic variance. Most of these variants were noncoding, including variants that were also expression quantitative trait loci (eQTLs) and in ChIP–seq peaks. There was significant overlap in loci for stature with humans and dogs, suggesting that a set of common genes regulates body size in mammals.
  • Whole genome association study identifies regions of the bovine genome and biological pathways involved in carcass trait performance in Holstein-Friesian cattle

    Doran, Anthony G.; Berry, Donagh P.; Creevy, Christopher J.; Department of Agriculture, Food and the Marine, Ireland; Teagasc Walsh Fellowship Programme; Science Foundation Ireland; Irish Cattle Breeding Federation; RSF-06-0353; 11/S/112; 2009183; 07/SK/B1236A (Biomed Central, 2014-10)
    Background Four traits related to carcass performance have been identified as economically important in beef production: carcass weight, carcass fat, carcass conformation of progeny and cull cow carcass weight. Although Holstein-Friesian cattle are primarily utilized for milk production, they are also an important source of meat for beef production and export. Because of this, there is great interest in understanding the underlying genomic structure influencing these traits. Several genome-wide association studies have identified regions of the bovine genome associated with growth or carcass traits, however, little is known about the mechanisms or underlying biological pathways involved. This study aims to detect regions of the bovine genome associated with carcass performance traits (employing a panel of 54,001 SNPs) using measures of genetic merit (as predicted transmitting abilities) for 5,705 Irish Holstein-Friesian animals. Candidate genes and biological pathways were then identified for each trait under investigation. Results Following adjustment for false discovery (q-value < 0.05), 479 quantitative trait loci (QTL) were associated with at least one of the four carcass traits using a single SNP regression approach. Using a Bayesian approach, 46 QTL were associated (posterior probability > 0.5) with at least one of the four traits. In total, 557 unique bovine genes, which mapped to 426 human orthologs, were within 500kbs of QTL found associated with a trait using the Bayesian approach. Using this information, 24 significantly over-represented pathways were identified across all traits. The most significantly over-represented biological pathway was the peroxisome proliferator-activated receptor (PPAR) signaling pathway. Conclusions A large number of genomic regions putatively associated with bovine carcass traits were detected using two different statistical approaches. Notably, several significant associations were detected in close proximity to genes with a known role in animal growth such as glucagon and leptin. Several biological pathways, including PPAR signaling, were shown to be involved in various aspects of bovine carcass performance. These core genes and biological processes may form the foundation for further investigation to identify causative mutations involved in each trait. Results reported here support previous findings suggesting conservation of key biological processes involved in growth and metabolism.
  • Mid-infrared spectrometry of milk as a predictor of energy intake and efficiency in lactating dairy cows

    McParland, Sinead; Lewis, Eva; Kennedy, Emer; Moore, S. G.; McCarthy, B.; O'Donovan, Michael; Butler, Stephen T.; Pryce, J. E.; Berry, Donagh P.; Department of Agriculture, Food and the Marine, Ireland; Marie Curie project International Research Staff Exchange Scheme SEQSEL; 13/S4/96 (Elsevier for American Dairy Science Association, 2014-09)
    Interest is increasing in the feed intake complex of individual dairy cows, both for management and animal breeding. However, energy intake data on an individual-cow basis are not routinely available. The objective of the present study was to quantify the ability of routinely undertaken mid-infrared (MIR) spectroscopy analysis of individual cow milk samples to predict individual cow energy intake and efficiency. Feed efficiency in the present study was described by residual feed intake (RFI), which is the difference between actual energy intake and energy used (e.g., milk production, maintenance, and body tissue anabolism) or supplied from body tissue mobilization. A total of 1,535 records for energy intake, RFI, and milk MIR spectral data were available from an Irish research herd across 36 different test days from 535 lactations on 378 cows. Partial least squares regression analyses were used to relate the milk MIR spectral data to either energy intake or efficiency. The coefficient of correlation (REX) of models to predict RFI across lactation ranged from 0.48 to 0.60 in an external validation data set; the predictive ability was, however, strongest (REX = 0.65) in early lactation (<60 d in milk). The inclusion of milk yield as a predictor variable improved the accuracy of predicting energy intake across lactation (REX = 0.70). The correlation between measured RFI and measured energy balance across lactation was 0.85, whereas the correlation between RFI and energy balance, both predicted from the MIR spectrum, was 0.65. Milk MIR spectral data are routinely generated for individual cows throughout lactation and, therefore, the prediction equations developed in the present study can be immediately (and retrospectively where MIR spectral data have been stored) applied to predict energy intake and efficiency to aid in management and breeding decisions.
  • Does iodine supplementation of the prepartum dairy cow diet affect serum immunoglobulin G concentration, iodine, and health status of the calf?

    Conneely, Muireann; Berry, Donagh P.; Sayers, Riona; Murphy, J. P.; Doherty, M. L.; Lorenz, I.; Kennedy, Emer (Elsevier for American Dairy Science Association, 2014-08)
    Absorption of adequate IgG from colostrum is critical to provide the newborn calf with adequate immunological protection and resistance to disease. Excessive iodine supplementation of the prepartum ewe reduces IgG absorption of her offspring; it is possible that excessive iodine supplementation of the prepartum dairy cow may similarly impair the ability of the calf to acquire immunological protection. The objectives of this study were to determine whether the iodine status, health status, and ability of calves to absorb IgG from colostrum were affected by prepartum iodine supplementation strategies of their dams. Dairy cows (n = 127) received one of the following levels of iodine supplementation precalving: 15 mg of iodine/kg of dietary dry matter (DM) (HI); no additional iodine supplementation (MI); 5 mg/kg of dietary DM (SI); and 15 mg of iodine/kg of DM for the first 3.5 wk of the precalving period and no additional supplementation for the second 3.5 wk (HMI). Calves were assigned to 1 of 6 experimental treatments, based on the prepartum iodine supplementation treatment of their dam and the precalving treatment group of the cows from which the colostrum fed was obtained: (1) HI_HI: born to HI dams, fed HI colostrum (i.e., colostrum produced by cows in the HI group); (2) MI_MI: born to MI dams, fed MI colostrum; (3) SI_SI: born to SI dams, fed SI colostrum; (4) HI_MI: born to HI dams, fed MI colostrum; (5) MI_HI: born to MI dams, fed HI colostrum; and (6) HMI_HMI: born to HMI dams, fed HMI colostrum. Concentration of calf serum IgG and plasma inorganic iodine (PII) was measured at 0 and 24 h of age. Apparent efficiency of absorption for IgG was determined. Health scores were assigned to calves twice weekly and all episodes of disease were recorded. Cow experimental treatment group affected calf PII at 0 h of age; the PII of calves born to HI dams (987.2 µg/L) was greater than that of calves born to MI dams (510.1 µg/L), SI (585.2 µg/L), and HMI dams (692.9 µg/L). Calf experimental treatment group affected calf PII at 24 h of age; the PII of HI_HI (1,259.2 µg/L) and HI_MI (1,177.8 µg/L) calves was greater than MI_MI (240.7 µg/L), SI_SI (302.2 µg/L), HMI_HMI (320.7 µg/L), and MI_HI (216.3 µg/L) calves. No effect of experimental treatment was observed on the concentration of IgG measured in calf serum at 24 h of age, or on apparent efficiency of absorption. Experimental treatment had no effect on the likelihood of a calf being assigned a worse nasal, eye and ear, cough, or fecal score within the study period, nor did it affect the probability of a calf receiving treatment for a disease a greater number of times. Prepartum iodine supplementation of cows at 15mg/kg of DM increased the iodine levels in their calves at birth and 24 h of age, but did not affect their ability to absorb IgG from colostrum. Supplementation with iodine above the minimum requirements established by the National Research Council was unnecessary to ensure appropriate iodine levels in calves at birth.
  • Differentially Expressed Genes in Endometrium and Corpus Luteum of Holstein Cows Selected for High and Low Fertility Are Enriched for Sequence Variants Associated with Fertility

    Moore, Stephen G.; Pryce, J. E.; Hayes, B. J.; Chamberlain, A. J.; Kemper, K. E.; Berry, Donagh P.; McCabe, Matthew; Cormican, Paul; Lonergan, P.; Fair, T.; Butler, Stephen T.; Department of Agriculture, Food and the Marine, Ireland; Teagasc Walsh Fellowship Programme; National Development Plan; Irish Dairy Levy Research Trust; 13/S/528 (Oxford University Press, 2015-11)
    Despite the importance of fertility in humans and livestock, there has been little success dissecting the genetic basis of fertility. Our hypothesis was that genes differentially expressed in the endometrium and corpus luteum on Day 13 of the estrous cycle between cows with either good or poor genetic merit for fertility would be enriched for genetic variants associated with fertility. We combined a unique genetic model of fertility (cattle that have been selected for high and low fertility and show substantial difference in fertility) with gene expression data from these cattle and genome-wide association study (GWAS) results in ∼20 000 cattle to identify quantitative trait loci (QTL) regions and sequence variants associated with genetic variation in fertility. Two hundred and forty-five QTL regions and 17 sequence variants associated primarily with prostaglandin F2alpha, steroidogenesis, mRNA processing, energy status, and immune-related processes were identified. Ninety-three of the QTL regions were validated by two independent GWAS, with signals for fertility detected primarily on chromosomes 18, 5, 7, 8, and 29. Plausible causative mutations were identified, including one missense variant significantly associated with fertility and predicted to affect the protein function of EIF4EBP3. The results of this study enhance our understanding of 1) the contribution of the endometrium and corpus luteum transcriptome to phenotypic fertility differences and 2) the genetic architecture of fertility in dairy cattle. Including these variants in predictions of genomic breeding values may improve the rate of genetic gain for this critical trait.
  • Genomic prediction of dry matter intake in dairy cattle from an international data set consisting of research herds in Europe, North America, and Australasia

    de Haas, Y.; Pryce, J. E.; Calus, M. P. L.; Wall, E.; Berry, Donagh P.; Lovendahl, P.; Krattenmacher, N.; Miglior, F.; Weigel, K.; Spurlock, D.; MacDonald, K. A.; Hulsegge, B.; Veerkamp, R. F.; European Commission; gDMI consortium; 317697 (Elsevier for American Dairy Science Association, 2015-07)
    With the aim of increasing the accuracy of genomic estimated breeding values for dry matter intake (DMI) in Holstein-Friesian dairy cattle, data from 10 research herds in Europe, North America, and Australasia were combined. The DMI records were available on 10,701 parity 1 to 5 records from 6,953 cows, as well as on 1,784 growing heifers. Predicted DMI at 70 d in milk was used as the phenotype for the lactating animals, and the average DMI measured during a 60- to 70-d test period at approximately 200 d of age was used as the phenotype for the growing heifers. After editing, there were 583,375 genetic markers obtained from either actual high-density single nucleotide polymorphism (SNP) genotypes or imputed from 54,001 marker SNP genotypes. Genetic correlations between the populations were estimated using genomic REML. The accuracy of genomic prediction was evaluated for the following scenarios: (1) within-country only, by fixing the correlations among populations to zero, (2) using near-unity correlations among populations and assuming the same trait in each population, and (3) a sharing data scenario using estimated genetic correlations among populations. For these 3 scenarios, the data set was divided into 10 sub-populations stratified by progeny group of sires; 9 of these sub-populations were used (in turn) for the genomic prediction and the tenth was used for calculation of the accuracy (correlation adjusted for heritability). A fourth scenario to quantify the benefit for countries that do not record DMI was investigated (i.e., having an entire country as the validation population and excluding this country in the development of the genomic predictions). The optimal scenario, which was sharing data, resulted in a mean prediction accuracy of 0.44, ranging from 0.37 (Denmark) to 0.54 (the Netherlands). Assuming near-unity among-country genetic correlations, the mean accuracy of prediction dropped to 0.40, and the mean within-country accuracy was 0.30. If no records were available in a country, the accuracy based on the other populations ranged from 0.23 to 0.53 for the milking cows, but were only 0.03 and 0.19 for Australian and New Zealand heifers, respectively; the overall mean prediction accuracy was 0.37. Therefore, there is a benefit in collaboration, because phenotypic information for DMI from other countries can be used to augment the accuracy of genomic evaluations of individual countries.
  • Genetic parameters of ovarian and uterine reproductive traits in dairy cows

    Carthy, T. R.; Ryan, D. P.; Fitzgerald, A. M.; Evans, R. D.; Berry, Donagh P.; Department of Agriculture, Food and the Marine, Ireland; European Commission; 11/S/133 (Elsevier for American Dairy Science Association, 2015-04)
    The objective of the study was to estimate genetic parameters of detailed reproductive traits derived from ultrasound examination of the reproductive tract as well as their genetic correlations with traditional reproductive traits. A total of 226,141 calving and insemination records as well as 74,134 ultrasound records from Irish dairy cows were used. Traditional reproductive traits included postpartum interval to first service, conception, and next calving, as well as the interval from first to last service; number of inseminations, pregnancy rate to first service, pregnant within 42 d of the herd breeding season, and submission in the first 21 d of the herd breeding season were also available. Detailed reproductive traits included resumed cyclicity at the time of ultrasound examination, incidence of multiple ovulations, incidence of early postpartum ovulation, heat detection, ovarian cystic structures, embryo loss, and uterine score; the latter was a subjectively assessed on a scale of 1 (little fluid with normal uterine tone) to 4 (large quantity of fluid with a flaccid uterine tone). Variance (and covariance) components were estimated using repeatability animal linear mixed models. Heritability for all reproductive traits were generally low (0.001–0.05), with the exception of traits related to cyclicity postpartum, regardless if defined traditionally (0.07; calving to first service) or from ultrasound examination [resumed cyclicity at the time of examination (0.07) or early postpartum ovulation (0.10)]. The genetic correlations among the detailed reproductive traits were generally favorable. The exception was the genetic correlation (0.29) between resumed cyclicity and uterine score; superior genetic merit for cyclicity postpartum was associated with inferior uterine score. Superior genetic merit for most traditional reproductive traits was associated with superior genetic merit for resumed cyclicity (genetic correlations ranged from −0.59 to −0.36 and from 0.56 to 0.70) and uterine score (genetic correlations ranged from −0.47 to 0.32 and from 0.25 to 0.52). Genetic predisposition to an increased incidence of embryo loss was associated with both an inferior uterine score (0.24) and inferior genetic merit for traditional reproductive traits (genetic correlations ranged from −0.52 to −0.42 and from 0.33 to 0.80). The results from the present study indicate that selection based on traditional reproductive traits, such as calving interval or days open, resulted in improved genetic merit of all the detailed reproductive traits evaluated in this study. Additionally, greater accuracy of selection for calving interval is expected for a relatively small progeny group size when detailed reproductive traits are included in a multitrait genetic evaluation.

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