• Analysis of DRB1 exon 2 genotyping by STR size analysis in Suffolk and Texel sheep breeds

      Sayers, Gearoid; Mitchel, S; Ryan, Marion T; Stear, Michael J.; Hanrahan, James P; Sweeney, Torres; Department of Agriculture, Food and the Marine; Wellcome Trust; RSF16; 061354 (Teagasc (Agriculture and Food Development Authority), Ireland, 2004)
      Alleles of the DRB1 exon 2 locus of the major histocompatibility complex have recently been associated with genetic resistance to gastrointestinal nematodes in sheep. While sequence-based typing is the standard method for allele discrimination, a rapid, high throughput method for DRB1 exon 2 genotyping is required if such information is to be incorporated into national breeding programmes. Previous studies have highlighted a simple tandem repeat (STR) located within intron 2 of the DRB1 gene, which could potentially be used to accurately assess the allele present within the adjacent exon 2. The aims of this study were firstly to compare two methods of STR analysis, Genescan™ and autoradiography, and secondly to investigate if STR analysis of DRB1 intron 2 could be used to accurately assess the profile of DRB1 exon 2. Six DRB1 exon 2 alleles were identified by sequence-based typing in Suffolk (n = 31) and eight in Texel (n = 60) sheep. The results indicated that Genescan™ was a more accurate method of STR analysis than autoradiography. The expected 1:1 correspondence between STR size, analysed by Genescan™ and DRB1 exon 2 allele, determined by sequence-based typing, was not observed. However, the correspondence was found to be degenerate, whereby some alleles were associated with two STR sizes. Thus, irrespective of the STR size identified, STR analysis by Genescan™ identified the correct allele in all cases within both populations of animals studied. However, the Genescan™ method of allele identification cannot be used for Suffolk × Texel crossbred progeny or in other breeds where the relationship between STR size and DRB1 exon 2 allele is not known.
    • Anti-Müllerian hormone in grazing dairy cows: Identification of factors affecting plasma concentration, relationship with phenotypic fertility, and genome-wide associations

      Gobikrushanth, M.; Purfield, Deirdre C; Canadas, E. R.; Herlihy, Mary M.; Kenneally, J.; Murray, Margaret; Kearney, Francis; Colazo, M. G.; Ambrose, D. J.; Butler, Stephen; et al. (Elsevier, 2019-09-11)
      The objectives of this study were to (1) characterize the distribution and variability of plasma anti-Müllerian hormone (AMH) concentration; (2) evaluate factors associated with phenotypic variation in plasma AMH; (3) examine the associations between categories of plasma AMH and reproductive outcomes [pregnancy to first artificial insemination (P/AI), and pregnancy rates within 21, 42, and 84 d after the mating start date (MSD)]; (4) estimate pedigree and genomic heritability for plasma AMH; and (5) identify and validate SNP associated with phenotypic variation in plasma AMH. Plasma AMH concentration (pg/mL) was determined from a blood sample collected (mean ± standard deviation) 10 ± 2 d after first insemination at detected estrus (IDE) in 2,628 first- and second-parity Irish dairy cows. Overall, plasma AMH had a positively skewed distribution with mean (± standard deviation), median, minimum, and maximum concentrations of 326 ± 231, 268, 15, and 2,863 pg/mL, respectively. Plasma AMH was greatest for Jersey, followed by Holstein × Jersey, Holstein × Norwegian Red, and Holstein cows (410, 332, 284, and 257 pg/mL, respectively). Second-parity cows had greater plasma AMH than first-parity cows (333 vs. 301 pg/mL, respectively). Samples collected at 7 and 8 d after first IDE had lesser plasma AMH than those collected on d 9, 10, 11, 12, and 13 after first IDE (291 and 297 vs. 317, 319, 331, 337, and 320 pg/mL). Plasma AMH was not associated with either body condition score at first IDE or the interval from calving to MSD. Cows were categorized into low (≤150 pg/mL; n = 526; lowest 20%), intermediate (>150 to ≤461 pg/mL; n = 1,576; intermediate 60%), and high AMH (>461 pg/mL; n = 526; highest 20%) groups based on plasma AMH, and associations with reproductive outcomes were tested. Cows with high and intermediate plasma AMH had 1.42- and 1.51-times-greater odds of becoming pregnant within 84 d after the MSD than those with low plasma AMH (90.3 and 90.8 vs. 86.8%, respectively); however, P/AI and pregnancy rate within 21 and 42 d after the MSD did not differ among AMH categories. Plasma AMH was moderately heritable (pedigree heritability of 0.40 ± 0.06 and genomic heritability of 0.45 ± 0.05), and 68 SNP across Bos taurus autosomes 7 and 11 were associated with phenotypic variation in plasma AMH. Out of 68 SNP, 42 were located in a single quantitative trait locus on Bos taurus autosome 11 that harbored 6 previously identified candidate genes (NR5A1, HSPA5, CRB2, DENND1A, NDUFA8, and PTGS) linked to fertility-related phenotypes in dairy cows.
    • Application of Meta-Analysis and Machine Learning Methods to the Prediction of Methane Production from In Vitro Mixed Ruminal Micro-Organism Fermentation

      Ellis, Jennifer L.; Alaiz-Moretón, Héctor; Navarro-Villa, Alberto; McGeough, Emma J.; Purcell, Peter; Powell, Christopher D.; O’Kiely, Padraig; France, James; López, Secundino; Department of Agriculture, Food and the Marine; et al. (MDPI AG, 2020-04-21)
      In vitro gas production systems are utilized to screen feed ingredients for inclusion in ruminant diets. However, not all in vitro systems are set up to measure methane (CH4) production, nor do all publications report in vitro CH4. Therefore, the objective of this study was to develop models to predict in vitro CH4 production from total gas and volatile fatty acid (VFA) production data and to identify the major drivers of CH4 production in these systems. Meta-analysis and machine learning (ML) methodologies were applied to a database of 354 data points from 11 studies to predict CH4 production from total gas production, apparent DM digestibility (DMD), final pH, feed type (forage or concentrate), and acetate, propionate, butyrate and valerate production. Model evaluation was performed on an internal dataset of 107 data points. Meta-analysis results indicate that equations containing DMD, total VFA production, propionate, feed type and valerate resulted in best predictability of CH4 on the internal evaluation dataset. The ML models far exceeded the predictability achieved using meta-analysis, but further evaluation on an external database would be required to assess generalization ability on unrelated data. Between the ML methodologies assessed, artificial neural networks and support vector regression resulted in very similar predictability, but differed in fitting, as assessed by behaviour analysis. The models developed can be utilized to estimate CH4 emissions in vitro.
    • Application of next generation sequencing for the elucidation of genes and pathways involved in the host response to bovine respiratory syncytial virus

      Johnston, D; Earley, B; McCabe, M. S.; Blackshields, G.; Lemon, K.; Duffy, C.; McMenamy, M.; Cosby, S. L.; Kim, J.; Taylor, J. F.; et al. (2021-06-16)
      Objective: To identify genes and pathways involved in the host response to bovine respiratory syncytial virus.
    • The application of transcriptomic data in the authentication of beef derived from contrasting production systems

      Sweeney, Torres; Lejeune, Alexandre; Moloney, Aidan; Monahan, Frank J; Gettigan, Paul M; Downey, Gerard; Park, Stephen D. E.; Ryan, Marion T; Department of Agriculture, Food and the Marine (Biomed Central, 2016-09-21)
      Background Differences between cattle production systems can influence the nutritional and sensory characteristics of beef, in particular its fatty acid (FA) composition. As beef products derived from pasture-based systems can demand a higher premium from consumers, there is a need to understand the biological characteristics of pasture produced meat and subsequently to develop methods of authentication for these products. Here, we describe an approach to authentication that focuses on differences in the transcriptomic profile of muscle from animals finished in different systems of production of practical relevance to the Irish beef industry. The objectives of this study were to identify a panel of differentially expressed (DE) genes/networks in the muscle of cattle raised outdoors on pasture compared to animals raised indoors on a concentrate based diet and to subsequently identify an optimum panel which can classify the meat based on a production system. Results A comparison of the muscle transcriptome of outdoor/pasture-fed and Indoor/concentrate-fed cattle resulted in the identification of 26 DE genes. Functional analysis of these genes identified two significant networks (1: Energy Production, Lipid Metabolism, Small Molecule Biochemistry; and 2: Lipid Metabolism, Molecular Transport, Small Molecule Biochemistry), both of which are involved in FA metabolism. The expression of selected up-regulated genes in the outdoor/pasture-fed animals correlated positively with the total n-3 FA content of the muscle. The pathway and network analysis of the DE genes indicate that peroxisome proliferator-activated receptor (PPAR) and FYN/AMPK could be implicit in the regulation of these alterations to the lipid profile. In terms of authentication, the expression profile of three DE genes (ALAD, EIF4EBP1 and NPNT) could almost completely separate the samples based on production system (95 % authentication for animals on pasture-based and 100 % for animals on concentrate- based diet) in this context. Conclusions The majority of DE genes between muscle of the outdoor/pasture-fed and concentrate-fed cattle were related to lipid metabolism and in particular β-oxidation. In this experiment the combined expression profiles of ALAD, EIF4EBP1 and NPNT were optimal in classifying the muscle transcriptome based on production system. Given the overall lack of comparable studies and variable concordance with those that do exist, the use of transcriptomic data in authenticating production systems requires more exploration across a range of contexts and breeds.
    • Artificial rearing affects piglets pre-weaning behaviour, welfare and growth performance

      Schmitt, Océane; O'Driscoll, Keelin; Boyle, Laura; Baxter, Emma M.; Department of Agriculture, Food and the Marine; 13S428 (Elsevier, 2018-11-02)
      One strategy adopted on farms to deal with managing large litters involves removing piglets from their mothers at seven days old to be reared in specialised accommodation with milk replacer. Effects on piglet behaviour, growth and some aspects of welfare were evaluated in this study by comparing 10 pairs of two litters (one sow-reared: SR, one artificially-reared: AR) selected at seven days-old at a similar weight. Piglet behaviour was recorded for 20 min following transfer of AR piglets to the artificial-rearing enclosure (D0) and for 20 min hourly between 09:00 h and 17:00 h (8 h) on D5 and D12. Hourly 5 min live observations were also undertaken. Qualitative Behavioural Assessment (QBA) was conducted on D14 to evaluate piglets’ emotional state. Survival and illness events were recorded until weaning. On D0, D1, D8 and D15 piglets were weighed and scored for tear staining, dirtiness of the face and severity of lesions on the snout, limbs, ear and tail. Survival and illness rates, as well as the rates of behaviours/min were analysed using GLMMs. Weights and QBA scores were analysed using GLM. Lesions, tear staining and dirtiness scores were averaged per litter and analysed using GLM. When AR piglets were transferred to the artificial-rearing enclosure, their behaviour was not different to SR piglets. Over the two observation days, AR piglets performed more belly-nosing (F1,76.53 = 42.25; P < 0.001), nursing-related displacements (F1,79 = 19.32, P < 0.001), visits to the milk cup (compared to nursing bouts; F1,73.8 = 38.42, P < 0.001), and oral manipulation of littermates’ ears (F1,91.95 = 12.79, P < 0.001) and tails (F1,58.54 = 15.63, P < 0.001) than SR piglets. However, SR piglets played alone (F1,88.99 = 8.29, P < 0.005) and explored their environment (F1,99.42 = 4.52, P < 0.05) more frequently than AR piglets. The QBA scores indicated a lower emotional state in AR piglets (t25.1=-3.25, P < 0.05). Survival rate and overall illness rate of piglets were similar between the treatments. AR piglets experienced a growth check following their transfer to the artificial-rearing enclosure and remained lighter than SR piglets through to weaning (6.53 ± 0.139 kg vs. 7.97 ± 0.168 kg, t256 = 9.79, P < 0.001). Overall, snout lesion scores were not different between the treatments, but AR piglets had lower limb (F1,10.1 = 5.89, P < 0.05) and ear (F1,14.5 = 24.89, P < 0.001) lesion scores and higher tail lesion scores (F1,34.5 = 15.54, P < 0.001). AR piglets were dirtier (F1,17.4 = 23.38, P < 0.001) but had lower tear staining scores (F1,19.1 = 68.40, P < 0.001) than SR piglets. In conclusion, artificial rearing impaired piglets’ behaviour, welfare and growth.
    • Associating cow characteristics with mobility scores in pasture-based dairy cows

      O'Connor, Aisling; Bokkers, Eddie A.M.; de Boer, Imke J. M.; Hogeveen, Henk; Sayers, Riona; Byrne, Nicky; Ruelle, Elodie; Shalloo, Laurence; Department of Agriculture, Food and the Marine; Teagasc Walsh Fellowship Programme; et al. (Elsevier, 2019-07-10)
      The quality of dairy cow mobility can have significant welfare, economic, and environmental consequences that have yet to be extensively quantified for pasture-based systems. The objective of this study was to characterize mobility quality by examining associations between specific mobility scores, claw disorders (both the type and severity), body condition score (BCS), and cow parity. Data were collected for 6,927 cows from 52 pasture-based dairy herds, including mobility score (0 = optimal mobility; 1, 2, or 3 = increasing severities of suboptimal mobility), claw disorder type and severity, BCS, and cow parity. Multinomial logistic regression was used for analysis. The outcome variable was mobility score, and the predictor variables were BCS, type and severity of claw disorders, and cow parity. Three models were run, each with 1 reference category (mobility score 0, 1, or 2). Each model also included claw disorders (overgrown claw, sole hemorrhage, white line disease, sole ulcer, and digital dermatitis), BCS, and cow parity as predictor variables. The presence of most types of claw disorders had odds ratios >1, indicating an increased likelihood of a cow having suboptimal mobility. Low BCS (BCS <3.00) was associated with an increased risk of a cow having suboptimal mobility, and relatively higher parity was also associated with an increased risk of suboptimal mobility. These results confirm an association between claw disorders, BCS, cow parity, and dairy cow mobility score. Therefore, mobility score should be routinely practiced to identify cows with slight deviations from the optimal mobility pattern and to take preventive measures to keep the problem from worsening.
    • The association between herd- and cow-level factors and somatic cell count of Irish dairy cows

      McParland, Sinead; O'Brien, Bernadette; McCarthy, J.; Department of Agriculture, Food and the Marine; 10/RD/AAQUALITYMILK/TMFRC713 (Teagasc (Agriculture and Food Development Authority), Ireland, 2013)
      Somatic cell count (SCC) is an indicator of both udder health and milk quality and is measured at an animal level through national milk recording schemes. The objective of this study was to assess the animal and herd factors contributing to elevated SCC (i.e. poorer milk quality). Test day records (n = 2,658,928) from 519,456 cow lactations obtained between 2007 and 2011 were included in the analyses. Herd factors tested included the geographical region of the herd and production system operated (spring calving or mixed calving system). Animal factors tested included breed, parity and age nested within parity. Four definitions of normalised SCC (i.e. SCS) were considered: 1) average test-day SCS within a 24 hour period (TD_SCS), 2) maximum SCS (peak_SCS), 3) minimum SCS (min_SCS), and 4) average SCS (avg_SCS) recorded across cow lactation; in addition, the proportion of test day records with an SCC count >200,000 (prop_200) or >250,000 (prop_250) within cow lactation were included. Following adjustment for fixed effects, average TD_SCS was 179,308 cells per mL while avg_SCS, and average min_SCS and peak_SCS were 119,481, 50,992 and 298,813 cells per mL, respectively. All animal and herd factors had a significant effect on SCC. Older animals, animals which were younger at calving than contemporaries and Holstein animals had higher SCC than younger alternative breed animals who calved at the median age. In addition, mixed calving production systems and herds in Connaught had higher SCC than spring calving herds in the other regions of Ireland.
    • Associations between paratuberculosis ELISA results and test-day records of cows enrolled in the Irish Johne's Disease Control Program

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

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

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

      Rojas Canadas, E.; Herlihy, M.M.; Kenneally, J.; Grant, J.; Kearney, F.; Lonergan, P.; Butler, Stephen; Department of Agriculture, Food and the Marine; RSF13S528 (Elsevier for American Dairy Science Association, 2019-10-01)
      The objective of this study was to evaluate the associations between corpus luteum (CL) status, uterine health, body condition score (BCS), metabolic status, and parity at wk 3 and 7 postpartum in seasonal-calving, pasture-based, lactating dairy cows. The associations between those phenotypes and individual genetic traits were also evaluated. First- and second-parity spring-calving lactating dairy cows (n = 2,600) from 35 dairy farms in Ireland were enrolled. Farms were visited every 2 weeks; cows that were at wk 3 (range 14 to 27 DIM) and wk 7 (range 42 to 55 DIM) postpartum were examined. Body condition score was measured using a scale of 1 to 5 with 0.25 increments. Transrectal ultrasound examination was performed at wk 3 and 7 postpartum to determine presence or absence of CL and ultrasound reproductive tract score. Blood samples were collected at each visit and the concentrations of glucose, β-hydroxybutyrate (BHB), and fatty acids (FA) were analyzed by using enzymatic colorimetry. Cows were grouped into 3 BCS categories [low (≤2.5), target (≥2.75 and ≤3.25), and high (≥3.5)]; 2 CL status categories: (present or absent); 2 uterine health status (UHS) categories (normal and abnormal); and 3 metabolic status categories [good (high glucose, low fatty acids and BHB), poor (low glucose, high fatty acids and BHB), and moderate (all other combinations)]. Fisher's exact test was used to test associations between variables and was supplemented by logistic regression. We found associations between UHS (wk 3 and 7), BCS (wk 3 and 7), parity (wk 3 and 7) metabolic status (wk 3), and predicted transmitting ability for calving interval (PTA for CIV; wk 3) and CL status. Cows that had abnormal UHS, low BCS, primiparity, and poor metabolic status, and were in the quartile with the greatest PTA for CIV were less likely to have had CL present at wk 3 and 7 postpartum. We also found associations between CL status (wk 3 and 7), BCS (wk 3 and 7), parity (wk 3 and 7), and PTA for CIV (wk 3) and UHS. Cows that did not have a CL present had low BCS, primiparity, and that were in the quartile with greatest PTA for CIV, had a greater risk of abnormal UHS at wk 3 and 7 postpartum. We observed strong associations between CL status, UHS, BCS, metabolic status, parity, and individual genetic traits at wk 3 and 7 postpartum in seasonal-calving, pasture-based lactating dairy cows. Achieving target BCS and good metabolic status, and selecting cows based on PTA for CIV, are all expected to increase the likelihood of hastening the resumption of estrous cyclicity and enhancing uterine health during the postpartum period.
    • Associations between postpartum phenotypes, cow factors, genetic traits, and reproductive performance in seasonal-calving, pasture-based lactating dairy cows

      Rojas Canadas, E.; Herlihy, M.M.; Kenneally, J.; Grant, J.; Kearney, F.; Lonergan, P.; Butler, S.T.; Department of Agriculture, Food and the Marine; RSF 13S528 (American Dairy Science Association, 2020-01)
      The objective of this study was to evaluate associations between corpus luteum (CL) status, uterine health, body condition score (BCS), metabolic status, parity, genetic merit for fertility traits, and reproductive performance in pasture-based dairy cows managed for seasonal reproduction. First- and second-lactation (n = 2,600) spring-calving dairy cows from 35 dairy farms located in Ireland were enrolled in the study. Farms were visited every 2 wk, and animals that were at wk 3 (range: 14–27 d in milk) and wk 7 (range: 42–55 d in milk) postpartum were examined. Body condition score was measured using a 1-to-5 scale in 0.25-point increments. Transrectal ultrasound examination was performed at wk 3 and 7 postpartum to determine presence or absence of CL and ultrasound reproductive tract score (scale of G1–G4). Blood samples were collected at each visit, and the concentrations of glucose, β-hydroxybutyrate (BHB), and fatty acids (FA) were analyzed using enzymatic colorimetry. Animals were grouped into 3 BCS categories [low (≤2.5), target (2.75–3.25), and high (≥3.5)], 2 CL categories (present or absent), 2 uterine health status categories (normal or abnormal), and 3 metabolic status categories [good (high glucose, low FA and BHB), poor (low glucose, high FA and BHB), and moderate (all other combinations)]. Fisher's exact test was used to test for associations between variables and was supplemented by logistic regression. More cows with a CL at wk 7 were served during the first 21 d of the breeding period compared with cows without a CL. Cows classified as having a uterine score of G3 or G4 at wk 3 and 7 had lower odds of pregnancy establishment during the breeding period compared with animals with a uterine score of G1 or G2. Animals with low BCS at wk 7 had lower odds of pregnancy establishment than cows with a target BCS. Cows classified as having good metabolic status at both wk 3 and wk 7 had greater odds of pregnancy establishment during the first 21 d of the breeding season than those classified as having poor metabolic status. Overall, primiparous cows had greater reproductive performance than second-parity cows. Animals in the quartiles with the best predicted transmitting ability for survival and calving interval had better reproductive performance compared with animals in the other quartiles. Cows that had better genetic merit for fertility traits and good metabolic status, achieved target BCS, and had a favorable ultrasound reproductive tract score and a CL present at wk 7 postpartum had superior reproductive performance.
    • Avian Resistance to Campylobacter jejuni Colonization Is Associated with an Intestinal Immunogene Expression Signature Identified by mRNA Sequencing

      Connell, Sarah; Meade, Kieran G; Allan, Brenda; Lloyd, Andrew T; Kenny, Elaine; Cormican, Paul; Morris, Derek W.; Bradley, Daniel G; O'Farrelly, Cliona; Department of Agriculture, Food and the Marine (PLOS, 2012-08-01)
      Campylobacter jejuni is the most common cause of human bacterial gastroenteritis and is associated with several post-infectious manifestations, including onset of the autoimmune neuropathy Guillain-Barré syndrome, causing significant morbidity and mortality. Poorly-cooked chicken meat is the most frequent source of infection as C. jejuni colonizes the avian intestine in a commensal relationship. However, not all chickens are equally colonized and resistance seems to be genetically determined. We hypothesize that differences in immune response may contribute to variation in colonization levels between susceptible and resistant birds. Using high-throughput sequencing in an avian infection model, we investigate gene expression associated with resistance or susceptibility to colonization of the gastrointestinal tract with C. jejuni and find that gut related immune mechanisms are critical for regulating colonization. Amongst a single population of 300 4-week old chickens, there was clear segregation in levels of C. jejuni colonization 48 hours post-exposure. RNAseq analysis of caecal tissue from 14 C. jejuni-susceptible and 14 C. jejuni-resistant birds generated over 363 million short mRNA sequences which were investigated to identify 219 differentially expressed genes. Significantly higher expression of genes involved in the innate immune response, cytokine signaling, B cell and T cell activation and immunoglobulin production, as well as the renin-angiotensin system was observed in resistant birds, suggesting an early active immune response to C. jejuni. Lower expression of these genes in colonized birds suggests suppression or inhibition of a clearing immune response thus facilitating commensal colonization and generating vectors for zoonotic transmission. This study describes biological processes regulating C. jejuni colonization of the avian intestine and gives insight into the differential immune mechanisms incited in response to commensal bacteria in general within vertebrate populations. The results reported here illustrate how an exaggerated immune response may be elicited in a subset of the population, which alters host-microbe interactions and inhibits the commensal state, therefore having wider relevance with regard to inflammatory and autoimmune disease.
    • 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.
    • Can increased dietary fibre level and a single enrichment device reduce the risk of tail biting in undocked growing-finishing pigs in fully slatted systems?

      Chou, Jen-Yun; O'Driscoll, Keelin; Sandercock, Dale A.; D’Eath, Rick B.; Teagasc Walsh Fellowship Programme; Scotland’s Rural College; Department of Agriculture, Food and the Marine (Public Library of Science (PLoS), 2020-10-30)
      This study evaluated the effectiveness of combined dietary and enrichment strategies to manage tail biting in pigs with intact tails in a conventional fully-slatted floor housing system. A 2 × 2 × 2 factorial design was used. Pigs had either a high fibre (weaner 5.3% and finisher 11.6% of crude fibre) or standard fibre diet (weaner 3.7% and finisher 5.9% of crude fibre). In the weaner stage, pigs had either a spruce wooden post (supplied in a wall-mounted dispenser) or a rubber floor toy as a enrichment device, and in the finisher stage, they had either the same or alternate enrichment item. Six hundred and seventy-two pigs were assigned to 48 pens of 14 pigs and followed from weaning until slaughter. Individual tail lesion scores and pen level behaviours were directly recorded every 2 weeks. Twenty-six pens had tail biting outbreaks and 161 injured pigs needed removal for treatment. Pigs fed with the high fibre diet performed more tail biting (p < 0.05) and tended to have a worse tail damage scores than those fed the standard fibre diet (p = 0.08). Pigs which had the floor toy as weaners and wood as finishers tended to have fewer tail lesions in the finisher stage than their counterparts (p = 0.06). Pigs receiving the floor toy as enrichment interacted with the enrichment more frequently overall (p < 0.001) and performed fewer harmful behaviours in the weaner stage (p < 0.05). Overall, higher fibre in the diet in a relatively barren environment did not help reduce tail biting or tail lesions. Altering the fibre level in the pigs’ diet and providing a single enrichment device to undocked pigs on fully slatted floors resulted in a high level of tail biting and a large proportion of pigs with partial tail amputation.
    • 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, Tara; Graham, David A.; Berry, Donagh; 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.
    • A catalogue of validated single nucleotide polymorphisms in bovine orthologs of mammalian imprinted genes and associations with beef production traits

      Magee, David A; Berkowicz, Erik W; Sikora, Klaudia M; Berry, Donagh; Park, Stephen D. E.; Kelly, Alan K; Sweeney, Torres; Kenny, David A.; Evans, R. D.; Wickham, Brian W.; et al. (Cambridge University Press, 2010-06)
      Genetic (or ‘genomic’) imprinting, a feature of approximately 100 mammalian genes, results in monoallelic expression from one of the two parentally inherited chromosomes. To date, most studies have been directed on imprinted genes in murine or human models; however, there is burgeoning interest in the effects of imprinted genes in domestic livestock species. In particular, attention has focused on imprinted genes that influence foetal growth and development and that are associated with several economically important production traits in cattle, sheep and pigs. We have re-sequenced regions in 20 candidate bovine imprinted genes in order to validate single nucleotide polymorphisms (SNPs) that may influence important production traits in cattle. Putative SNPs detected via re-sequencing were subsequently re-formatted for high-throughput SNP genotyping in 185 cattle samples comprising 138 performance-tested European Bos taurus (all Limousin bulls), 29 African B. taurus and 18 Indian B. indicus samples. Analysis of the resulting genotypic data identified 117 validated SNPs. Preliminary genotype–phenotype association analyses using 83 SNPs that were polymorphic in the Limousin samples with minor allele frequencies >0.05 revealed significant associations between two candidate bovine imprinted genes and a range of important beef production traits: average daily gain, average feed intake, live weight, feed conversion ratio, residual feed intake and residual gain. These genes were the Ras proteinspecific guanine nucleotide releasing factor gene ( RASGRF1) and the zinc finger, imprinted 2 gene ( ZIM2). Despite the relatively small sample size used in these analyses, the observed associations with production traits are supported by the purported biological function of the RASGRF1 and ZIM2 gene products. These results support the hypothesis that imprinted genes contribute significantly to important complex production traits in cattle. Furthermore, these SNPs may be usefully incorporated into future marker-assisted and genomic selection breeding schemes.
    • Cattle stratified on genetic merit segregate on carcass characteristics, but there is scope for improvement

      Berry, Donagh; Pabiou, Thierry; Brennan, Denis; Hegarthy, Patrick J; Judge, Michelle M; Science Foundation Ireland; Department of Agriculture, Food and the Marine; European Union; 16/ RC/3835 (Oxford University Press (OUP), 2019-05-03)
      The study objective was to quantify the ability of genetic merit for a generated carcass index to differentiate animals on primal carcass cut weights using data from 1,446 herds on 9,414 heifers and 22,413 steers with weights for 14 different primal carcass cuts (plus 3 generated groups of cuts). The carcass genetic merit index was compromised of carcass weight (positive weight), conformation (positive weight), and fat score (negative weight), each equally weighted within the index. The association analyses were undertaken using linear mixed models; models were run with or without carcass weight as a covariate. In a further series of analyses, carcass weight and carcass fat score were both included as covariates in the models. Whether the association between primal cut yield and carcass weight differed by genetic merit stratum was also investigated. Genetic merit was associated (P < 0.001) with the weight of all cuts evaluated even when adjusted to a common carcass weight (P < 0.01); when simultaneously adjusted to a common carcass weight and fat score, genetic merit was not associated with the weight of the cuberoll or the group cuts termed minced-meat. The weight of the different primal cuts increased almost linearly within increasing genetic merit, with the exception of the rump and bavette. The difference in mean primal cut weight between the very low and very high genetic merit strata, as a proportion of the overall mean weight of that cut in the entire data set, varied from 0.05 (bavette) to 0.28 (eye of round); the average was 0.17. Following adjustment for differences in carcass weight, there was no difference in cut weight between the very low and very high strata for the rump, chuck tender, and mince cut group; the remaining cuts were heavier in the higher index animals with the exception of the cuberoll and bavette, which were lighter in the very high index animals. The association between carcass weight and the weight of each of the evaluated primal cuts differed (P < 0.05) by genetic merit stratum for all cuts evaluated with the exception of the rump, striploin, and brisket as well as the group cuts of frying and mincing. With the exception of these 5 primal (group) cuts, the regression coefficients of primal cut weight on carcass weight increased consistently for all traits with increasing genetic merit stratum, other than for the fillet, cuberoll, bavette, chuck and neck, and heel and shank.