• Labour efficiency on-farm

      O'Brien, Bernadette; Gleeson, David E; O’Donovan, K.; Ruane, D.; Kinsella, J.; Mee, John F; Boyle, Laura; McNamara, John (Teagasc, 2007-01-01)
      Improvements in milking efficiency have a greater influence than any other aspect of the dairy farmers work on overall farm labour inputs (Whipp, 1992). In order to facilitate the examination of milking process labour inputs, the milking process may be divided into the following three components: herding pre and post milking (transfer of cows to and from the milking parlour); milking (milking tasks / work routines within the parlour); and washing (washing of milking machine and yard). Meanwhile, within milking specifically, the number of cows milked per operator per hour is the best measure of both the performance of the operator and the milking installation (Clough, 1978). This is affected by the following three factors: the milking times of the cows, the number and arrangement of the milking units, and the operator’s work routine (Whipp, 1992). The addition of extra milking units will only increase milking performance if the operator has idle time during milking (Hansen, 1999).
    • Land Drainage - A farmer’s practical guide to draining grassland in Ireland

      Tuohy, Patrick; Fenton, Owen; O'Loughlin, James; Humphreys, James (Teagasc, 30/07/2013)
      No drainage work should be carried out before the drainage characteristics of the soil are established by a site and soil test pit investigation. • Two types of drainage system exist: a groundwater drainage system and a shallow drainage system. The design of the system depends entirely on the drainage characteristics of the soil. • Distinguishing between the two types of drainage systems essentially comes down to whether or not a permeable layer is present (at a workable depth) that will allow the flow of water with relative ease. If such a layer is evident, a piped drain system at that depth is likely to be effective. If no such layer is found during soil test pit investigations, it will be necessary to improve the drainage capacity of the soil. This involves a disruption technique such as moling, gravel moling or subsoiling in tandem with collector drains. • Drains are not effective unless they are placed in a free draining soil layer or complimentary measures (mole drainage, subsoiling) are used to improve soil drainage capacity. If water is not moving through the soil in one or other of these two ways, the water table will not be lowered. • Outfall level must not dictate the drainage system depth. If a free draining layer is present, it must be utilised. • Drain pipes should always be used for drains longer than 30 m. If these get blocked it is a drainage stone and not a drainage pipe issue. • Drainage stone should not be filled to the top of the field trench except for very limited conditions (the bottom of an obvious hollow). Otherwise it is an extremely expensive way of collecting little water. • Most of the stone being used for land drainage today is too big. Clean aggregate in the 10–40 mm (0.4 to 1.5 inch approx) grading band should be used. Generally you get what you pay for. • Subsoiling is not effective unless a shallow impermeable layer is being broken or field drains have been installed prior to the operation. Otherwise it will not have any long-term effect and may do more harm than good. • Most land drainage systems are poorly maintained. Open drains should be clean and as deep as possible and field drains feeding into them should be regularly rodded or jetted.
    • Leukocyte profile, gene expression, acute phase response, and metabolite status of cows with sole hemorrhages

      O'Driscoll, Keelin; McCabe, Matthew; Earley, Bernadette; Marie Curie Intra-European Fellowship; 252611 (Elsevier, 2017-08-23)
      Sole hemorrhages result from disruption to normal claw horn formation and are caused by a variety of internal and external factors. Evidence suggests that they are painful, although they do not usually cause clinical lameness and are difficult to detect by observing cow gait. Little is known about how or whether sole hemorrhages affect the cow systemically. This study compared hematology profile, leukocyte gene expression, and physiological responses of cows with no/mild hemorrhages (category 1; n = 17), moderate hemorrhages (category 2; n = 18), and severe hemorrhages (category 3; n = 12). At approximately 100 d in milk, all cows in the study herd (n = 374) were locomotion scored before hoof examination. The cows included in the study were not clinically lame and had no other hoof disorder. Blood samples were taken from all cows within 24 h of selection. Leukocyte counts were obtained using an automated cell counter, cortisol and dehydroepiandrosterone (DHEA) concentration by ELISA, and plasma haptoglobin, urea, total protein, creatine kinase and glucose were analyzed on a clinical chemistry analyzer. Expression of 16 genes associated with lameness or stress were estimated using real-time quantitative PCR. Data from cows within each category were compared using the Mixed procedure in SAS (version 9.3; SAS Institute Inc., Cary, NC). Fixed effects included hemorrhage severity category and lactation number, with days in milk and body condition score included as covariates. Locomotion score worsened as sole hemorrhage category worsened. Locomotion score of category 1 cows tended to be lower than that of category 2 cows and was lower than that of category 3 cows. The locomotion score of category 3 cows was also greater than that of categories 1 and 2 combined. Category had no effect on leukocyte number, on any of the individual leukocyte cell numbers or percentages, cortisol or DHEA concentration, cortisol:DHEA ratio, or relative expression of any of the genes investigated, and we detected no differences in plasma glucose, protein, or creatine kinase concentrations between categories. However, category 3 cows had greater plasma concentrations of haptoglobin and tended to have lesser concentrations of plasma urea than category 1 and 2 cows. The differences in gait between cows with no or minor sole hemorrhages and cows with severe hemorrhages indicate that hemorrhages may be associated with discomfort or pain. Nevertheless, the only physiological measure that changed with increasing locomotion score was plasma haptoglobin concentration. Haptoglobin has previously been found to be elevated in lame cows, and thus shows promise as a marker for limb pain.
    • Live animal measurements, carcass composition and plasma hormone and metabolite concentrations in male progeny of sires differing in genetic merit for beef production

      Clarke, A. M.; Drennan, Michael J; McGee, Mark; Kenny, David A.; Evans, Ross D; Berry, Donagh P. (Cambridge University Press, 2009-07)
      In genetic improvement programmes for beef cattle, the effect of selecting for a given trait or index on other economically important traits, or their predictors, must be quantified to ensure no deleterious consequential effects go unnoticed. The objective was to compare live animal measurements, carcass composition and plasma hormone and metabolite concentrations of male progeny of sires selected on an economic index in Ireland. This beef carcass index (BCI) is expressed in euros and based on weaning weight, feed intake, carcass weight and carcass conformation and fat scores. The index is used to aid in the genetic comparison of animals for the expected profitability of their progeny at slaughter. A total of 107 progeny from beef sires of high (n = 11) or low (n = 11) genetic merit for the BCI were compared in either a bull (slaughtered at 16 months of age) or steer (slaughtered at 24 months of age) production system, following purchase after weaning (8 months of age) from commercial beef herds. Data were analysed as a 2 × 2 factorial design (two levels of genetic merit by two production systems). Progeny of high BCI sires had heavier carcasses, greater (P < 0.01) muscularity scores after weaning, greater (P < 0.05) skeletal scores and scanned muscle depth pre-slaughter, higher (P < 0.05) plasma insulin concentrations and greater (P < 0.01) animal value (obtained by multiplying carcass weight by carcass value, which was based on the weight of meat in each cut by its commercial value) than progeny of low BCI sires. Regression of progeny performance on sire genetic merit was also undertaken across the entire data set. In steers, the effect of BCI on carcass meat proportion, calculated carcass value (c/kg) and animal value was positive (P < 0.01), while a negative association was observed for scanned fat depth pre-slaughter and carcass fat proportion (P < 0.01), but there was no effect in bulls. The effect of sire expected progeny difference (EPD) for carcass weight followed the same trends as BCI. Muscularity scores, carcass meat proportion and calculated carcass value increased, whereas scanned fat depth, carcass fat and bone proportions decreased with increasing sire EPD for conformation score. The opposite association was observed for sire EPD for fat score. Results from this study show that selection using the BCI had positive effects on live animal muscularity, carcass meat proportion, proportions of high-value cuts and carcass value in steer progeny, which are desirable traits in beef production.
    • Long-term stability of RNA in post-mortem bovine skeletal muscle, liver and subcutaneous adipose tissues

      Bahar, Bojlul; Monahan, Frank J; Moloney, Aidan P; Schmidt, Olaf; MacHugh, David E; Sweeney, Torres; National Development Plan 2000-2006; Teagasc Walsh Fellowship Programme (Biomed Central, 2007-11-29)
      Background: Recovering high quality intact RNA from post-mortem tissue is of major concern for gene expression studies in animals and humans. Since the availability of post-mortem tissue is often associated with substantial delay, it is important that we understand the temporal variation in the stability of total RNA and of individual gene transcripts so as to be able to appropriately interpret the data generated from such studies. Hence, the objective of this experiment was to qualitatively and quantitatively assess the integrity of total and messenger RNA extracted from bovine skeletal muscle, subcutaneous adipose tissue and liver stored at 4°C at a range of time points up to 22 days post-mortem. These conditions were designed to mimic the environment prevailing during the transport of beef from the abattoir to retail outlets. Results: The 28S and 18S rRNA molecules of total RNA were intact for up to 24 h post-mortem in liver and adipose tissues and up to 8 days post-mortem in skeletal muscle. The mRNA of housekeeping genes (GAPDH and ACTB) and two diet-related genes (RBP5 and SCD) were detectable up to 22 days post-mortem in skeletal muscle. While the mRNA stability of the two housekeeping genes was different in skeletal muscle and liver, they were similar to each other in adipose tissue. After 22 days post-mortem, the relative abundance of RBP5 gene was increased in skeletal muscle and in adipose tissue and decreased in liver. During this period, the relative abundance of SCD gene also increased in skeletal muscle whereas it decreased in both adipose tissue and liver. Conclusion: Stability of RNA in three tissues (skeletal muscle, subcutaneous adipose tissue and liver) subjected to long-term post-mortem storage at refrigeration temperature indicated that skeletal muscle can be a suitable tissue for recovering biologically useful RNA for gene expression studies even if the tissue is subjected to post-mortem storage for weeks, whereas adipose tissue and liver should be processed within 24 hours post-mortem.
    • Machine learning algorithms for the prediction of conception success to a given insemination in lactating dairy cows

      Henpstalk, K.; McParland, Sinead; Berry, Donagh P.; European Commission (Elsevier for American Dairy Science Association, 2015-06)
      The ability to accurately predict the conception outcome for a future mating would be of considerable benefit for producers in deciding what mating plan (i.e., expensive semen or less expensive semen) to implement for a given cow. The objective of the present study was to use herd- and cow-level factors to predict the likelihood of conception success to a given insemination (i.e., conception outcome not including embryo loss); of particular interest in the present study was the usefulness of milk mid-infrared (MIR) spectral data in augmenting the accuracy of the prediction model. A total of 4,341 insemination records with conception outcome information from 2,874 lactations on 1,789 cows from 7 research herds for the years 2009 to 2014 were available. The data set was separated into a calibration data set and a validation data set using either of 2 approaches: (1) the calibration data set contained records from all 7 farms for the years 2009 to 2011, inclusive, and the validation data set included data from the 7 farms for the years 2012 to 2014, inclusive, or (2) the calibration data set contained records from 5 farms for all 6 yr and the validation data set contained information from the other 2 farms for all 6 yr. The prediction models were developed with 8 different machine learning algorithms in the calibration data set using standard 10-times 10-fold cross-validation and also by evaluating in the validation data set. The area under curve (AUC) for the receiver operating curve varied from 0.487 to 0.675 across the different algorithms and scenarios investigated. Logistic regression was generally the best-performing algorithm. The AUC was generally inferior for the external validation data sets compared with the calibration data sets. The inclusion of milk MIR in the prediction model generally did not improve the accuracy of prediction. Despite the fair AUC for predicting conception outcome under the different scenarios investigated, the model provided a reasonable prediction of the likelihood of conception success when the high predicted probability instances were considered; a conception rate of 85% was evident in the top 10% of inseminations ranked on predicted probability of conception success in the validation data set.
    • Major management factors associated with the variation in reproductive performance of Irish dairy herds

      Buckley, Frank; Dillon, Pat; Mee, John F (Teagasc, 2007-01-01)
      The results highlight the importance of BCS in achieving good reproductive performance. The likelihood of reproductive success was best predicted by BCS around the time of breeding and, for cows calving in good BCS (3.0 or greater) the level of BCS loss between calving and first service. A low BCS pre-calving (<2.75) was associated with prolonged calving to first service, and calving to conception intervals. Very high BCS pre-calving (>3.5) results in excessive BCS loss (>0.5) post-calving. On the basis of these findings a pre-calving BCS of no greater than 3.25 is a sensible target for pasture-based spring calving systems in Ireland. It is necessary to maintain BCS at 2.75 or greater during the breeding season, and loss of body condition between calving and first service should be restricted to 0.5 BCS units.
    • Management practices as risk factors for the presence of bulk milk antibodies to Salmonella, Neospora caninum and Leptospira interrogans serovar hardjo in Irish dairy herds

      O'Doherty, E.; Berry, Donagh P.; O'Grady, L.; Sayers, Riona (Cambridge University Press, 2014-03-24)
      A survey of management practices in 309 Irish dairy herds was used to identify risk factors for the presence of antibodies to Salmonella, Neospora caninum and Leptospira interrogans serovar hardjo in extensively managed unvaccinated dairy herds. A previous study documented a herd-level seroprevalence in bulk milk of 49%, 19% and 86% for Salmonella, Neospora caninum and leptospira interrogans serovar hardjo, respectively in the unvaccinated proportion of these 309 herds in 2009. Association analyses in the present study were carried out using multiple logistic regression models. Herds where cattle were purchased or introduced had a greater likelihood of being positive to leptospira interrogans serovar hardjo (P<0.01) and Salmonella (P<0.01). Larger herds had a greater likelihood of recording a positive bulk milk antibody result to leptospira interrogans serovar hardjo (P<0.05). Herds that practiced year round calving were more likely to be positive to Neospora caninum (P<0.05) compared to herds with a spring-calving season, with no difference in risk between herds that practiced split calving compared to herds that practiced spring calving. No association was found between presence of dogs on farms and prevalence of Neospora caninum possibly due to limited access of dogs to infected materials including afterbirths. The information from this study will assist in the design of suitable control programmes for the diseases under investigation in pasture-based livestock systems.
    • Management practices as risk factors for the presence of bulk milk antibodies to Salmonella, Neospora caninum and Leptospira interrogans serovar hardjo in Irish dairy herds

      O'Doherty, Eugene; Berry, Donagh P.; O'Grady, L.; Sayers, Riona (Cambridge University Press, 2014-03-24)
      A survey of management practices in 309 Irish dairy herds was used to identify risk factors for the presence of antibodies to Salmonella, Neospora caninum and Leptospira interrogans serovar hardjo in extensively managed unvaccinated dairy herds. A previous study documented a herd-level seroprevalence in bulk milk of 49%, 19% and 86% for Salmonella, Neospora caninum and leptospira interrogans serovar hardjo, respectively in the unvaccinated proportion of these 309 herds in 2009. Association analyses in the present study were carried out using multiple logistic regression models. Herds where cattle were purchased or introduced had a greater likelihood of being positive to leptospira interrogans serovar hardjo (P<0.01) and Salmonella (P<0.01). Larger herds had a greater likelihood of recording a positive bulk milk antibody result to leptospira interrogans serovar hardjo (P<0.05). Herds that practiced year round calving were more likely to be positive to Neospora caninum (P<0.05) compared to herds with a spring-calving season, with no difference in risk between herds that practiced split calving compared to herds that practiced spring calving. No association was found between presence of dogs on farms and prevalence of Neospora caninum possibly due to limited access of dogs to infected materials including afterbirths. The information from this study will assist in the design of suitable control programmes for the diseases under investigation in pasture-based livestock systems.
    • Managing variability in decision making in swine growing-finishing units

      Agostini, Piero, d S; Manzanilla, Edgar, G; de Blas, Carlos; Fahey, Alan, G; da Silva, Caio, A; Gasa, Josep; Spanish Ministerio de Ciencia e Innovación; Agencia Española de Cooperación Internacional para el Desarrollo; AGL2011-29960 (Biomed Central, 2015-09-01)
      Analysis of data collected from pig farms may be useful to understand factors affecting pig health and productive performance. However, obtaining these data and drawing conclusions from them can be done at different levels and presents several challenges. In the present study, information from 688 batches of growing-finishing (GF) pigs (average initial and final body weight of 19.1 and 108.5 kg respectively) from 404 GF farms integrated in 7 companies was obtained between July 2008 and July 2010 in Spain by survey. Management and facility factors associated with feed conversion ratio (FCR) and mortality were studied by multiple linear regression analysis in each single company (A to G) and in an overall database (OD). Factors studied were geographic location of the farm, trimester the pigs entered the farm, breed of sire and sex segregation in pens (BREGENSEG), use of circovirus vaccine, number of origins the pigs were obtained from, age of the farm, percentage of slatted floor, type of feeder, drinker and ventilation, number of phases and form of feed, antibiotic administration system, water source, and number and initial weight of pigs. Results In two or more companies studied and/or in OD, the trimester when pigs were placed in the farm, BREGENSEG, number of origins of the pigs, age of the farm and initial body weight were factors associated with FCR. Regarding mortality, trimester of placement, number of origins of the pigs, water source in the farm, number of pigs placed and the initial body weight were relevant factors. Age of the farm, antibiotic administration system, and water source were only provided by some of the studied companies and were not included in the OD model, however, when analyzed in particular companies these three variables had an important effect and may be variables of interest in companies that do not record them. Conclusions Analysing data collected from farms at different levels helps better understand factors associated with productive performance of pig herds. Out of the studied factors trimester of placement and number of origins of the pigs were the most relevant factors associated with FCR and mortality.
    • Manipulating the ensilage of wilted, unchopped grass through the use of additive treatments

      McEniry, Joseph; O'Kiely, Padraig; Clipson, N.W.J.; Forristal, P.D.; Doyle, E.M.; Teagasc Walsh Fellowship Programme (Teagasc, Oak Park, Carlow, Ireland, 2007)
      Baled silage composition frequently differs from that of comparable conventional precision-chop silage. The lower final concentration of fermentation products in baled silage makes it more conducive to the activities of undesirable microorganisms. Silage additives can be used to encourage beneficial microbial activity and/or inhibit detrimental microbial activity. The experiment was organised in a 2 (chop treatments) × 6 (additive treatments) × 2 (stages of ensilage) factorial arrangement of treatments (n = 3 silos/treatment) to suggest additive treatments for use in baled silage production that would help create conditions more inhibitory to the activities of undesirable microorganisms and realise an outcome comparable to precision-chop silage. Chopping the herbage prior to ensiling, in the absence of an additive treatment, improved the silage fermentation. In the unchopped herbage, where the fermentation was poorer, the lactic acid bacterial inoculant resulted in an immediate increase (P < 0.001) in lactic acid concentration and a faster decline (P < 0.001) in pH with a subsequent reduction in butyric acid (P < 0.001) and ammonia-N (P < 0.01) concentrations. When sucrose was added in addition to the lactic acid bacterial inoculant, the combined treatment had a more pronounced effect on pH, butyric acid and ammonia-N values at the end of ensilage. The formic acid based additive and the antimicrobial mixture restricted the activities of undesirable microorganisms resulting in reduced concentrations of butyric acid (P < 0.001) and ammonia-N (P < 0.01). These additives offer a potential to create conditions in baled silage more inhibitory to the activities of undesirable microorganisms.
    • Manipulation of grass supply to meet feed demand

      French, Padraig; Hennessy, Deirdre; O’Donovan, Michael; Laidlaw, S. (Teagasc, 2006-01-01)
      Grazed grass is generally the cheapest form of feed available for beef and milk production in Ireland. Grass growth is variable during the year with a peak in May/June and a secondary peak in August. There is little net growth from December to February. Grass growth is also variable across the country with higher grass growth in the south and south-west (14 to 15 t DM/ha/year) compared with approximately 11 t DM/ha/year in the north-east (Brereton, 1995). There is poor synchrony between grass supply and feed demand on beef and dairy farms. The feed demand curve for a calf to two year old beef system shows feed demand decreasing as grass supply increases, and grass supply decreasing as feed demand increases. Similarly, the feed demand curve of a spring calving dairy herd shows poor synchrony with grass supply, with a surplus of grass from about mid-April to mid-August, and a deficit for the rest of the year. Traditionally surplus grass produced during May and June is conserved as silage or hay and fed back to cattle and dairy cows during the deficit times of the year.
    • Measurements of the acid-binding capacity of ingredients used in pig diets

      Lawlor, Peadar G; Lynch, P Brendan; Caffrey, Patrick J.; O'Reilly, James J; O'Connell, M Karen (Biomed Central, 2005-08-01)
      Some feed ingredients bind more acid in the stomach than others and for this reason may be best omitted from pig starter foods if gastric acidity is to be promoted. The objective of this study was to measure the acid-binding capacity (ABC) of ingredients commonly used in pig starter foods. Ingredients were categorised as follows: (i) milk products (n = 6), (ii) cereals (n = 10), (iii) root and pulp products (n = 5), (iv) vegetable proteins (n = 11), (v) meat and fish meal (n = 2), (vi) medication (n = 3), (vii) amino acids (n = 4), (viii) minerals (n = 16), (ix) acid salts (n = 4), (x) acids (n = 10). A 0.5 g sample of food was suspended in 50 ml distilled de-ionised water with continuous stirring. This suspension was titrated with 0.1 mol/L HCl or 0.1 mol/L NaOH so that approximately 10 additions of titrant was required to reach pH 3.0. The pH readings after each addition were recorded following equilibration for three minutes. ABC was calculated as the amount of acid in milliequivalents (meq) required to lower the pH of 1 kg food to (a) pH 4.0 (ABC-4) and (b) pH 3.0 (ABC-3). Categories of food had significantly different (P < 0.01) ABC values. Mean ABC-4 and ABC-3 values of the ten categories were: (i) 623 (s.d. 367.0) and 936 (s.d. 460.2), (ii) 142 (s.d. 79.2) and 324 (s.d. 146.4), (iii) 368 (s.d. 65.3) and 804 (s.d. 126.7), (iv) 381 (s.d. 186.1) and 746 (s.d. 227.0), (v) 749 (s.d. 211.6) and 1508 (s.d. 360.8), (vi) 120 (s.d. 95.6) and 261 (s.d. 163.2), (vii) 177 (s.d. 60.7) and 1078 (s.d. 359.0), (viii) 5064 (s.d. 5525.1) and 7051 (s.d. 5911.6), (ix) 5057 (s.d. 1336.6) and 8945 (s.d. 2654.1) and (x) -5883 (s.d. 4220.5) and -2591 (s.d. 2245.4) meq HCl per kg, respectively. Within category, ABC-3 and ABC- 4 values were highly correlated: R2 values of 0.80 and greater for food categories i, iv, v, vi, vii and viii. The correlation between predicted and observed ABC values of 34 mixed diets was 0.83 for ABC-4 and 0.71 for ABC-3. It was concluded that complete diets with low ABC values may be formulated through careful selection of ingredients. The final pH to which ABC is measured should matter little as ABC-3 and ABC-4 are highly correlated.
    • Measuring labor input on pasture-based dairy farms using a smartphone

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

      Banos, G.; Coffey, M. P.; Veerkamp, R. F.; Berry, Donagh P.; Wall, E.; European Union; RERAD; KBBE-211708 (Cambridge University Press, 2012-01)
      This study set out to demonstrate the feasibility of merging data from different experimental resource dairy populations for joint genetic analyses. Data from four experimental herds located in three different countries (Scotland, Ireland and the Netherlands) were used for this purpose. Animals were first lactation Holstein cows that participated in ongoing or previously completed selection and feeding experiments. Data included a total of 60 058 weekly records from 1630 cows across the four herds; number of cows per herd ranged from 90 to 563. Weekly records were extracted from the individual herd databases and included seven traits: milk, fat and protein yield, milk somatic cell count, liveweight, dry matter intake and energy intake. Missing records were predicted with the use of random regression models, so that at the end there were 44 weekly records, corresponding to the typical 305-day lactation, for each cow. A total of 23 different lactation traits were derived from these records: total milk, fat and protein yield, average fat and protein percentage, average fat-to-protein ratio, total dry matter and energy intake and average dry matter intake-to-milk yield ratio in lactation weeks 1 to 44 and 1 to 15; average milk somatic cell count in lactation weeks 1 to 15 and 16 to 44; average liveweight in lactation weeks 1 to 44; and average energy balance in lactation weeks 1 to 44 and 1 to 15. Data were subsequently merged across the four herds into a single dataset, which was analysed with mixed linear models. Genetic variance and heritability estimates were greater (P,0.05) than zero for all traits except for average milk somatic cell count in weeks 16 to 44. Proportion of total phenotypic variance due to genotype-by-environment (sire-by-herd) interaction was not different (P.0.05) from zero. When estimable, the genetic correlation between herds ranged from 0.85 to 0.99. Results suggested that merging experimental herd data into a single dataset is both feasible and sensible, despite potential differences in management and recording of the animals in the four herds. Merging experimental data will increase power of detection in a genetic analysis and augment the potential reference population in genome-wide association studies, especially of difficult-to-record traits.
    • Messenger RNA Sequence Rather than Protein Sequence Determines the Level of Self-synthesis and Antigen Presentation of the EBV-encoded Antigen, EBNA1

      Tellam, Judy T; Lekieffre, Lea; Zhong, Jie; Lynn, David J; Khanna, Rajiv; National Health & Medical Research Council Australia; 496684 APP1005091; 496712 (PLOS, 2012-12-27)
      Viruses establishing persistent latent infections have evolved various mechanisms to avoid immune surveillance. The Epstein-Barr virus-encoded nuclear antigen, EBNA1, expressed in all EBV-associated malignancies, modulates its own protein levels at quantities sufficient to maintain viral infection but low enough so as to minimize an immune response by the infected host cell. This evasion mechanism is regulated through an internal purine-rich mRNA repeat sequence encoding glycine and alanine residues. In this study we assess the impact of the repeat's nucleotide versus peptide sequence on inhibiting EBNA1 self-synthesis and antigen presentation. We demonstrate that altered peptide sequences resulting from frameshift mutations within the repeat do not alleviate the immune-evasive function of EBNA1, suggesting that the repetitive purine-rich mRNA sequence itself is responsible for inhibiting EBNA1 synthesis and subsequent poor immunogenicity. Our comparative analysis of the mRNA sequences of the corresponding repeat regions of different gammaherpesvirus maintenance homologues to EBNA1 highlights the high degree of identity between the nucleotide sequences despite very little homology in the encoded amino acid sequences. These studies demonstrate the importance of gammaherpesvirus purine-rich mRNA repeat sequences on antigenic epitope generation and evasion from T-cell mediated immune control, suggesting novel approaches to prevention and treatment of latent infection by this class of virus.
    • 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; et al. (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.
    • Meta-analysis of the effect of white clover inclusion in perennial ryegrass swards on milk production

      Dineen, Michael; Delaby, Luc; Gilliland, T.; McCarthy, B.; Teagasc Walsh Fellowship Programme; Irish Dairy Levy (Elsevier, 2017-11-23)
      There is increased demand for dairy products worldwide, which is coupled with the realization that consumers want dairy products that are produced in a sustainable and environmentally benign manner. Forage legumes, and white clover (Trifolium repens L.; WC) in particular, have the potential to positively influence the sustainability of pasture-based ruminant production systems. Therefore, there is increased interest in the use of forage legumes because they offer opportunities for sustainable pasture-based production systems. A meta-analysis was undertaken to quantify the milk production response associated with the introduction of WC into perennial ryegrass swards and to investigate the optimal WC content of dairy pastures to increase milk production. Two separate databases were created. In the grass-WC database, papers were selected if they compared milk production of lactating dairy cows grazing perennial ryegrass-WC (GC) swards with that of cows grazing perennial ryegrass-only swards (GO). In the WC-only database, papers were selected if they contained milk production from lactating dairy cows grazing on GC swards with varying levels of WC content. Data from both databases were analyzed using mixed models (PROC MIXED) in SAS (SAS Institute, Cary, NC). Within the grass-WC database, where mean sward WC content was 31.6%, mean daily milk and milk solids yield per cow were increased by 1.4 and 0.12 kg, respectively, whereas milk and milk solids yield per hectare were unaffected when cows grazed GC compared with GO swards. Stocking rate and nitrogen fertilizer application were reduced by 0.25 cows/ha and 81 kg/ha, respectively, on GC swards compared with GO swards. These results highlight the potential of GC production systems to achieve similar levels of production to GO systems but with reduced fertilizer nitrogen inputs, which is beneficial from both an economic and environmental point of view. In the context of increased demand for dairy products, there may be potential to increase the productivity of GC systems by increasing fertilizer nitrogen use to increase stocking rate and carrying capacity while also retaining the benefit of WC inclusion on milk production per cow.
    • Meta-analysis to investigate relationships between somatic cell count and raw milk composition, Cheddar cheese processing characteristics and cheese composition

      Geary, Una; Lopez-Villalobos, N.; O'Brien, Bernadette; Garrick, D.J.; Shalloo, Laurence (Teagasc (Agriculture and Food Development Authority), Ireland, 2013)
      The relationship between elevated somatic cell count (SCC) and raw milk composition, cheese processing and cheese composition, was investigated by meta-analysis using available literature representing 45 scientific articles. With respect to raw milk composition there was a significant positive relationship between SCC and the protein and fat contents and a significant negative relationship between SCC and the lactose content. In relation to cheese processing, there was a significant negative relationship between SCC and recoveries of protein and fat. As SCC increased cheese protein content declined and cheese moisture content increased.
    • A method for assessing liner performance during the peak milk flow period

      Penry, J. F.; Upton, John; Leonardi, S.; Thompson, P. D.; Reinemann, D. J. (Elsevier, 2017-11-06)
      The objective of this study was to develop a method to quantify the milking conditions under which circulatory impairment of teat tissues occurs during the peak flow period of milking. A secondary objective was to quantify the effect of the same milking conditions on milk flow rate during the peak flow rate period of milking. Additionally, the observed milk flow rate was a necessary input to the calculation of canal area, our quantitative measure of circulatory impairment. A central composite experimental design was used with 5 levels of each of 2 explanatory variables (system vacuum and pulsator ratio), creating 9 treatments including the center point. Ten liners, representing a wide range of liner compression (as indicated by overpressure), were assessed, with treatments applied using a novel quarter-milking device. Eight cows (32 cow-quarters) were used across 10 separate evening milkings, with quarter being the experimental unit. The 9 treatments, with the exception of a repeated center point, were randomly applied to all quarters within each individual milking. Analysis was confined to the peak milk flow period. Milk flow rate (MFR) and teat canal cross sectional area (CA) were normalized by dividing individual MFR, or CA, values by their within-quarter average value across all treatments. A multiple explanatory variable regression model was developed for normalized MFR and normalized CA. The methods presented in this paper provided sufficient precision to estimate the effects of vacuum (both at teat-end and in the liner mouthpiece), pulsation, and liner compression on CA, as an indicator of teat-end congestion, during the peak flow period of milking. Liner compression (as indicated by overpressure), teat-end vacuum, vacuum in the liner mouthpiece, milk-phase time, and their interactions are all important predictors of MFR and teat-end congestion during the peak milk flow period of milking. Increasing teat-end vacuum and milk-phase time increases MFR and reduces CA (indicative of increased teat-end congestion). Increasing vacuum in the liner mouthpiece also acts to reduce CA and MFR. Increasing liner compression reduces the effects of teat-end congestion, resulting in increased MFR and increased CA at high levels of teat-end vacuum and milk-phase time. These results provide a better understanding of the balance between milking speed and milking gentleness.