• Accuracy of predicting milk yield from alternative milk recording schemes

      Berry, Donagh; Olori, V. E.; Cromie, A. R.; Veerkamp, Roel F.; Rath, Myles V; Dillon, Pat; Teagasc Walsh Fellowship Programme (Cambridge University Press, 2005-02)
      The effect of reducing the frequency of official milk recording and the number of recorded samples per test-day on the accuracy of predicting daily yield and cumulative 305-day yield was investigated. A control data set consisting of 58 210 primiparous cows with milk test-day records every 4 weeks was used to investigate the influence of reduced milk recording frequencies. The accuracy of prediction of daily yield with one milk sample per test-day was investigated using 41 874 testday records from 683 cows. Results show that five or more test-day records taken at 8-weekly intervals (A8) predicted 305-day yield with a high level of accuracy. Correlations between 305-day yield predicted from 4-weekly recording intervals (A4) and from 8-weekly intervals were 0.99, 0.98 and 0.98 for milk, fat and protein, respectively. The mean error in estimating 305-day yield from the A8 scheme was 6.8 kg (s.d. 191 kg) for milk yield, 0.3 kg (s.d. 10 kg) for fat yield, and −0.3 kg (s.d. 7 kg) for protein yield, compared with the A4 scheme. Milk yield and composition taken during either morning (AM) or evening (PM) milking predicted 24-h yield with a high degree of accuracy. Alternating between AM and PM sampling every 4 weeks predicted 305-day yield with a higher degree of accuracy than either all AM or all PM sampling. Alternate AM-PM recording every 4 weeks and AM + PM recording every 8 weeks produced very similar accuracies in predicting 305-day yield compared with the official AM + PM recording every 4 weeks.
    • Additive genetic, non-additive genetic and permanent environmental effects for female reproductive performance in seasonal calving dairy females

      Kelleher, Margaret M.; Buckley, Frank; Evans, R. D.; Berry, Donagh; Department of Agriculture, Food and the Marine, Ireland (Teagasc (Agriculture and Food Development Authority), Ireland, 2016-09-08)
      Excellent reproductive performance (i.e. 365-day calving interval) is paramount to herd profit in seasonal-calving dairy systems. Reproductive targets are currently not being achieved in Irish dairy herds. Furthermore, most research on the genetics of reproductive performance in dairy cattle has focused primarily on lactating cows and relatively few studies have attempted to quantify the genetic contribution to differences in reproductive performance in nulliparae. The objective of the present study was to estimate the contribution of both the additive and non-additive genetic components, as well as the permanent environmental component, to phenotypic variation in the reproductive traits in nulliparous, primiparous and multiparous seasonal-calving dairy females. Reproductive phenotypes were available on up to 202,525 dairy females. Variance components were estimated using (repeatability where appropriate) linear animal mixed models; fixed effects included in the mixed models were contemporary group, parity (where appropriate), breed proportion, inter-breed specific heterosis coefficients and inter-breed specific recombination loss coefficients. Heritability of the reproductive traits ranged from 0.004 (pregnancy rate to first service) to 0.17 (age at first service in nulliparae), while repeatability estimates for the reproductive traits in cows ranged from 0.01 (calving interval) to 0.11 (pregnant in the first 42 days of the breeding season). Breed-specific heterosis regression coefficients suggest that, relative to the parental mean, a first-cross Holstein–Jersey crossbred was almost 7 days younger at first calving, had a 9-day shorter calving interval, a 6 percentage unit greater pregnancy rate in the first 42 days of the breeding season and a 3 percentage unit greater survival rate to next lactation. Heifer calving rate traits were strongly genetically correlated with age at first calving (–0.97 to –0.66) and calving rate in the first 42 days of the calving season for first parity cows (0.77 to 0.56), but genetic correlations with other cow reproductive traits were weak and inconsistent. Calving interval was strongly genetically correlated with the majority of the cow traits; 56%, 40%, and 92% of the genetic variation in calving interval was explained by calving to the first service interval, number of services and pregnant in the first 42 days of the breeding season, respectively. Permanent environmental correlations between the reproductive performance traits were generally moderate to strong. The existence of contributions from non-additive genetic and permanent environmental effects to phenotypic differences among cows suggests the usefulness of such information to rank cows on future expected performance; this was evidenced by a stronger correlation with future reproductive performance for an individual cow index that combined additive genetic, non-additive genetic and permanent environmental effects compared to an index based solely on additive genetic effects (i.e. estimated breeding values).
    • Administration of a live culture of Lactococcus lactis DPC 3147 into the bovine mammary gland stimulates the local host immune response, particularly IL-1β and IL-8 gene expression

      Beecher, Christine; Daly, Mairead; Berry, Donagh; Klostermann, Katja; Flynn, James; Meaney, William J; Hill, Colin; McCarthy, Tommie V; Ross, R Paul; Giblin, Linda; et al. (Cambridge University Press: Published for the Institute of Food Research and the Hannah Research Institute, 18/05/2009)
      Mastitis is one of the most costly diseases to the dairy farming industry. Conventional antibiotic therapy is often unsatisfactory for successful treatment of mastitis and alternative treatments are continually under investigation. We have previously demonstrated, in two separate field trials, that a probiotic culture, Lactococcus lactis DPC 3147, was comparable to antibiotic therapy to treat bovine mastitis. To understand the mode of action of this therapeutic, we looked at the detailed immune response of the host to delivery of this live strain directly into the mammary gland of six healthy dairy cows. All animals elicited signs of udder inflammation 7 h post infusion. At this time, clots were visible in the milk of all animals in the investigation. The most pronounced increase in immune gene expression was observed in Interleukin (IL)-1b and IL-8, with highest expression corresponding to peaks in somatic cell count. Infusion with a live culture of a Lc. lactis leads to a rapid and considerable innate immune response.
    • Association between body condition score and live weight in pasture-based Holstein-Friesian dairy cows

      Berry, Donagh; MacDonald, Kevin A.; Penno, John W.; Roche, John R. (Cambridge University Press: Published for the Institute of Food Research and the Hannah Research Institute, 2006-11)
      The objective was to quantify the strength of the relationship between body condition score (BCS) and live weight (LW) in pasture-based Holstein-Friesian dairy cattle, and to determine the kg LW per unit BCS. A total of 26021 test-day records with information on both BCS (1–10 scale, where 1 is emaciated and 10 is obese) and LW across 1110 lactations from one research farm were used in the analysis. Correlation and regression analyses were used to determine the degree of association between BCS and LW in different parities, stages of the inter-calving interval and years. Correlations between BCS and LW were relatively consistent, with the mean correlation between BCS and LW across all data of 0·55 implying that differences in BCS explain approximately 30% of the variation in LW. Significantly different regressions of LW on BCS were present within stage of inter-calving interval by parity subclasses. Excluding calving, LW per unit BCS varied from 17 kg (early to mid lactation in parity 1) to 36 kg (early lactation in parity 4 and 5). However, LW per unit BCS was greatest at calving varying from 44 kg in first parity animals to 62 kg in second parity animals. On average, 1 BCS unit equated to 31 kg LW across all data.
    • Association of bovine leptin polymorphisms with energy output and energy storage traits in progeny tested Holstein-Friesian dairy cattle sires

      Giblin, Linda; Butler, Stephen T.; Kearney, Breda M.; Waters, Sinead M.; Callanan, Michael J.; Berry, Donagh; Department of Agriculture, Food and the Marine, Ireland; Irish Dairy Levy Research Trust; Teagasc Walsh Fellowship Programme; RSF-06-0353; et al. (Biomed Central, 29/07/2010)
      Background: Leptin modulates appetite, energy expenditure and the reproductive axis by signalling via its receptor the status of body energy stores to the brain. The present study aimed to quantify the associations between 10 novel and known single nucleotide polymorphisms in genes coding for leptin and leptin receptor with performance traits in 848 Holstein-Friesian sires, estimated from performance of up to 43,117 daughter-parity records per sire. Results: All single nucleotide polymorphisms were segregating in this sample population and none deviated (P > 0.05) from Hardy-Weinberg equilibrium. Complete linkage disequilibrium existed between the novel polymorphism LEP-1609, and the previously identified polymorphisms LEP-1457 and LEP-580. LEP-2470 associated (P < 0.05) with milk protein concentration and calf perinatal mortality. It had a tendency to associate with milk yield (P < 0.1). The G allele of LEP-1238 was associated (P < 0.05) with reduced milk fat concentration, reduced milk protein concentration, longer gestation length and tended to associate (P < 0.1) with an increase in calving difficulty, calf perinatal mortality and somatic cells in the milk. LEP-963 exhibited an association (P < 0.05) with milk fat concentration, milk protein concentration, calving difficulty and gestation length. It also tended to associate with milk yield (P < 0.1). The R25C SNP associated (P < 0.05) with milk fat concentration, milk protein concentration, calving difficulty and length of gestation. The T allele of the Y7F SNP significantly associated with reduced angularity (P < 0.01) and reduced milk protein yield (P < 0.05). There was also a tendency (P < 0.1) for Y7F to associate with increased body condition score, reduced milk yield and shorter gestation (P < 0.1). A80V associated with reduced survival in the herd (P < 0.05). Conclusions Several leptin polymorphisms (LEP-2470, LEP-1238, LEP-963, Y7F and R25C) associated with the energetically expensive process of lactogenesis. Only SNP Y7F associated with energy storage. Associations were also observed between leptin polymorphisms and calving difficulty, gestation length and calf perinatal mortality. The lack of an association between the leptin variants investigated with calving interval in this large data set would question the potential importance of these leptin variants, or indeed leptin, in selection for improved fertility in the Holstein-Friesian dairy cow.
    • Associations between colostrum management, passive immunity, calf-related hygiene practices, and rates of mortality in preweaning dairy calves

      Barry, John; Bokkers, Eddie A.M.; Berry, Donagh; de Boer, Imke J.M.; McClure, J. Trenton; Kennedy, Emer; Teagasc Walsh Fellowship Programme (Elsevier, 2019-09-11)
      Calves are particularly vulnerable to health issues before weaning and experience high rates of mortality. Poor colostrum quality or substandard colostrum management, combined with poor hygiene, can increase disease susceptibility, contributing to elevated mortality rates. This study aimed to assess colostrum and calf management together with subsequent mortality rates in preweaning calves. Forty-seven Irish spring-calving, pasture-based dairy herds were enrolled in the study. To investigate whether colostrum and hygiene practices change as the calving season progresses, each farm was visited in both the first and last 6 wk of the calving season. The concentration of IgG in 250 colostrum samples and 580 calf serum samples was determined by radial immunodiffusion assay. Mean colostrum IgG concentration was 85 mg/mL, and mean calf serum IgG concentration was 30.9 and 27.1 mg/mL, respectively, in the first and last 6 wk of the calving season. Smaller herd size and younger age at sampling were associated with higher calf serum IgG concentration. Dairy breed calves were associated with higher serum IgG concentrations compared with beef breed calves; no association was detected based on sex. For feeding equipment hygiene, we assessed the presence of protein residues and found that hygiene levels tended to worsen from the first to the final 6 wk of the calving season. We found no association between feeding equipment hygiene and herd size or 28-d calf mortality rate. Colostrum and calf management practices were not associated with either calf serum IgG concentration or 28-d calf mortality rate. We found that IgG concentration in colostrum produced in Irish dairy herds was generally good, although large variation existed, emphasizing the need for assessment of colostrum before feeding. Results also suggested that hygiene practices associated with calf rearing can be improved, particularly in the latter half of the calving season.
    • Associations between herd size, rate of expansion and production, breeding policy and reproduction in spring-calving dairy herds

      Jago, J. G.; Berry, Donagh (Cambridge University Press, 2011-04)
      Dairy herd size is expected to increase in many European countries, given the recent policy changes within the European Union. Managing more cows may have implications for herd performance in the post-quota era. The objective of this study was to characterise spring-calving herds according to size and rate of expansion, and to determine trends in breeding policy, reproduction and production performance, which will inform industry of the likely implications of herd expansion. Performance data from milk recording herds comprising 775 795 lactations from 2555 herds for the years 2004 to 2008 inclusive were available from the Irish Cattle Breeding Federation. Herds were classified into Small (average of 37 cows), Medium (average of 54 cows) and Large (average of 87 cows) and separately into herds that were not expanding (Nil expansion), herds expanding on average by three cows per year (Slow expansion) and herds expanding on average by eight cows per year (Rapid expansion). There was no association between rate of expansion and 305-day fat and protein yield. However, 305-day milk yield decreased and milk protein and fat percentage increased with increasing rate of expansion. There were no associations between herd size and milk production except for protein and fat percentage, which increased with increasing herd size. Average parity number of the cows decreased as rate of expansion increased and tended to decrease as herd size increased. In rapidly expanding herds, cow numbers were increased by purchasing more cattle. The proportion of dairy sires relative to beef sires used in the breeding programme of expanding herds increased and there was more dairy crossbreeding, albeit at a low rate. Similarly, large herds were using more dairy sires and fewer beef sires. Expanding herds and large herds had superior reproductive performance relative to non-expanding and small herds. Animals in expanding herds calved for the first time at a younger age, had a shorter calving interval and were submitted for breeding by artificial insemination at a higher rate. The results give confidence to dairy producers likely to undergo significant expansion post-quota such that, despite managing more cows, production and reproductive performance need not decline. The management skills required to achieve these performance levels need investigation.
    • Associations between the K232A polymorphism in the diacylglycerol-O-transferase 1 (DGAT1) gene and performance in Irish Holstein-Friesian dairy cattle

      Berry, Donagh; Howard, Dawn J.; O'Boyle, Padraig; Waters, Sinead M.; Kearney, J.F.; McCabe, Matthew (Teagasc, Oak Park, Carlow, Ireland, 2010)
      Selection based on genetic polymorphisms requires accurate quantification of the effect or association of the polymorphisms with all traits of economic importance. The objective of this study was to estimate, using progeny performance data on 848 Holstein-Friesian bulls, the association between a non-conservative alanine to lysine amino acid change (K232A) in exon 8 of the diacylglycerol-O-transferase 1 (DGAT1) gene and milk production and functionality in the Irish Holstein-Friesian population. The DGAT1 gene encodes the diacylglycerol-O-transferase microsomal enzyme necessary to catalyze the final step in triglyceride synthesis. Weighted mixed model methodology, accounting for the additive genetic relationships among animals, was used to evaluate the association between performance and the K232A polymorphism. The minor allele frequency (K allele) was 0.32. One copy of the K allele was associated (P < 0.001) with 77 kg less milk yield, 4.22 kg more fat yield, 0.99 kg less protein yield, and 1.30 and 0.28 g/kg greater milk fat and protein concentration, respectively; all traits were based on predicted 305-day production across the first five lactations. The K232A polymorphism explained 4.8%, 10.3% and 1.0% of the genetic variance in milk yield, fat yield and protein yield, respectively. There was no association between the K232A polymorphism and fertility, functional survival, calving performance, carcass traits, or any conformation trait with the exception of rump width and carcass conformation. Using the current economic values for the milk production traits in the Irish total merit index, one copy of the K allele is worth €5.43 in expected profitability of progeny. Results from this study will be useful in quantifying the cost-benefit of including the K232A polymorphism in the Irish national breeding programme.
    • Body condition score and live-weight effects on milk production in Irish Holstein-Friesian dairy cows

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

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

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

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

      Hurley, A. M.; Lopez-Villalobos, N.; McParland, Sinead; Lewis, Eva; Kennedy, Emer; O'Donovan, Michael; Burke, Jennifer L.; Berry, Donagh; Irish Department of Agriculture, Food and the Marine; European Union (Elsevier, 2017-11-23)
      The objective of the present study was to investigate the phenotypic inter- and intra-relationships within and among alternative feed efficiency metrics across different stages of lactation and parities; the expected effect of genetic selection for feed efficiency on the resulting phenotypic lactation profiles was also quantified. A total of 8,199 net energy intake (NEI) test-day records from 2,505 lactations on 1,290 cows were used. Derived efficiency traits were either ratio based or residual based; the latter were derived from least squares regression models. Residual energy intake (REI) was defined as NEI minus predicted energy requirements based on lactation performance; residual energy production (REP) was defined as net energy for lactation minus predicted energy requirements based on lactation performance. Energy conversion efficiency was defined as net energy for lactation divided by NEI. Pearson phenotypic correlations among traits were computed across lactation stages and parities, and the significance of the differences was determined using the Fisher r-to-z transformation. Sources of variation in the feed efficiency metrics were investigated using linear mixed models, which included the fixed effects of contemporary group, breed, parity, stage of lactation, and the 2-way interaction of parity by stage of lactation. With the exception of REI, parity was associated with all efficiency and production traits. Stage of lactation, as well as the 2-way interaction of parity by stage of lactation, were associated with all efficiency and production traits. Phenotypic correlations among the efficiency and production traits differed not only by stage of lactation but also by parity. For example, the strong phenotypic correlation between REI and energy balance (EB; 0.89) for cows in parity 3 or greater and early lactation was weaker for parity 1 cows at the same lactation stage (0.81), suggesting primiparous cows use the ingested energy for both milk production and growth. Nonetheless, these strong phenotypic correlations between REI and EB suggested negative REI animals (i.e., more efficient) are also in more negative EB. These correlations were further supported when assessing the effect on phenotypic performance of animals genetically divergent for feed intake and efficiency based on parental average. Animals genetically selected to have lower REI resulted in cows who consumed less NEI but were also in negative EB throughout the entire lactation. Nonetheless, such repercussions of negative EB do not imply that selection for negative REI (as defined here) should not be practiced, but instead should be undertaken within the framework of a balanced breeding objective, which includes traits such as reproduction and health.
    • Characterization of best linear unbiased estimates generated from national genetic evaluations of reproductive performance, survival, and milk yield in dairy cows

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

      Berry, Donagh; Horan, Brendan; Dillon, Pat (Cambridge University Press, 2005-04)
      The objective of the present study was to compare growth curves for live weight (LW) and body size of three strains of female dairy cattle reared under common environments in Ireland. One strain (HP) was selected from a predominantly North-American/European Holstein-Friesian genetic pool selected for high milk production. The second strain (HD) represented a predominantly North-American/European Holstein-Friesian genetic pool selected for high milk production but with greater selection emphasis on functional non-production traits. The third strain (NZ) consisted of New Zealand Holstein-Friesian females of high genetic merit for profitability in New Zealand. The data consisted of 99 animals (33 animals in each strain) with records on LW, length, girth and height from birth to a minimum of 594 days of age. The von Bertalanffy growth function was fitted to each animal's records separately and least-squares analyses were used to investigate the effect of strain on birth LW/body size, parameters of the growth function and average daily gains. Average mature live weight of the HD animals (591 kg) was significantly larger than that of the HP (566 kg) or NZ (543 kg) strain; the HD strain matured more slowly. The HD (134 cm) and HP (135 cm) strains were significantly taller than the NZ (128 cm) strain. Although the data set was relatively small there are indications that dairy females of North-American genetic origin were heavier at birth, grew faster, and were heavier and taller at maturity than dairy females of New Zealand origin.
    • Concordance rate between copy number variants detected using either high- or medium-density single nucleotide polymorphism genotype panels and the potential of imputing copy number variants from flanking high density single nucleotide polymorphism haplotypes in cattle

      Rafter, Pierce; Gormley, Isobel C; Parnell, Andrew C; Kearney, John F; Berry, Donagh; Science Foundation Ireland; Department of Agriculture, Food and the Marine; 14/IA/2576; 16/RC/3835 (Biomed Central, 2020-03-04)
      Background The trading of individual animal genotype information often involves only the exchange of the called genotypes and not necessarily the additional information required to effectively call structural variants. The main aim here was to determine if it is possible to impute copy number variants (CNVs) using the flanking single nucleotide polymorphism (SNP) haplotype structure in cattle. While this objective was achieved using high-density genotype panels (i.e., 713,162 SNPs), a secondary objective investigated the concordance of CNVs called with this high-density genotype panel compared to CNVs called from a medium-density panel (i.e., 45,677 SNPs in the present study). This is the first study to compare CNVs called from high-density and medium-density SNP genotypes from the same animals. High (and medium-density) genotypes were available on 991 Holstein-Friesian, 1015 Charolais, and 1394 Limousin bulls. The concordance between CNVs called from the medium-density and high-density genotypes were calculated separately for each animal. A subset of CNVs which were called from the high-density genotypes was selected for imputation. Imputation was carried out separately for each breed using a set of high-density SNPs flanking the midpoint of each CNV. A CNV was deemed to be imputed correctly when the called copy number matched the imputed copy number. Results For 97.0% of CNVs called from the high-density genotypes, the corresponding genomic position on the medium-density of the animal did not contain a called CNV. The average accuracy of imputation for CNV deletions was 0.281, with a standard deviation of 0.286. The average accuracy of imputation of the CNV normal state, i.e. the absence of a CNV, was 0.982 with a standard deviation of 0.022. Two CNV duplications were imputed in the Charolais, a single CNV duplication in the Limousins, and a single CNV duplication in the Holstein-Friesians; in all cases the CNV duplications were incorrectly imputed. Conclusion The vast majority of CNVs called from the high-density genotypes were not detected using the medium-density genotypes. Furthermore, CNVs cannot be accurately predicted from flanking SNP haplotypes, at least based on the imputation algorithms routinely used in cattle, and using the SNPs currently available on the high-density genotype panel.
    • Cow factors affecting the risk of clinical mastitis

      Berry, Donagh; Meaney, William J (Teagasc (Agriculture and Food Development Authority), Ireland, 2005)
      The objective of the present study was to identify cow risk factors associated with development of clinical mastitis (CM) in subsequent stages of lactation. A total of 3,309 lactations from spring-calving Holstein-Friesian cows were included in the analysis; parity number ranged from one to three, inclusive. A generalised estimating equations approach with a logit link function was used to account for the binary nature of the data and the unequal number of repeated records per cow. The dependent variable was the probability of developing CM in the subsequent stage of lactation. Independent variables included in the model were chosen using stepwise selection; herd, year of birth, month of calving, parity, period of lactation and previous CM history significantly affected the probability of CM. Two-way interactions between parity and period of lactation and between parity and incidence of CM in the previous lactation were also included in the model. A greater probability of developing CM is expected in cows that experienced CM in the previous lactation and/or previously within the same lactation. The probability of CM occurring in cows that experienced at least one case of CM in the previous lactation was 0.92 to 3.75 times that of a cow that experienced no CM in the previous lactation. It is possible to predict the probability of an animal developing CM in the subsequent stage of lactation when information is available on the parity and month of calving of the animal and its previous history of CM.