• Gastrointestinal nematode control practices on lowland sheep farms in Ireland with reference to selection for anthelmintic resistance

      Patten, Thomas; Good, Barbara; Hanrahan, James P; Mulcahy, Grace; de Waal, Theo (Biomed Central, 2011-03-31)
      Gastrointestinal parasitism is a widely recognised problem in sheep production, particularly for lambs. While anthelmintics have a pivotal role in controlling the effects of parasites, there is a paucity of data on how farmers use anthelmintics. A representative sample of Irish lowland farmers were surveyed regarding their parasite control practices and risk factors that may contribute to the development of anthelmintic resistance. Questionnaires were distributed to 166 lowland Irish sheep producers. The vast majority of respondents treated their sheep with anthelmintics. Lambs were the cohort treated most frequently, the majority of farmers followed a set programme as opposed to treating at sign of disease. A substantial proportion (61%) administered four or more treatments to lambs in a 'normal' year. Departures from best practice in anthelmintic administration that would encourage the development of anthelmintic resistance were observed. In conclusion, in the light of anthelmintic resistance, there is a need for a greater awareness of the principles that underpin the sustainable use of anthelmintics and practices that preserve anthelmintic efficacy should be given a very high priority in the design of helminth control programmes on each farm. To this end, given that veterinary practitioners and agricultural advisors were considered to be the farmer's most popular information resource, the capacity of these professions to communicate information relating to best practice in parasite control should be targeted.
    • Gastrointestinal tract size, total-tract digestibility, and rumen microflora in different dairy cow genotypes

      Beecher, Marion; Buckley, Frank; Waters, Sinead M.; Boland, T. M.; Enriquez-Hidalgo, D.; Deighton, M. H.; O'Donovan, Michael; Lewis, Eva (Elsevier Inc and American Dairy Science Association, 2014-04-03)
      The superior milk production efficiency of Jersey (JE) and Jersey × Holstein-Friesian (JE × HF) cows compared with Holstein-Friesian (HF) has been widely published. The biological differences among dairy cow genotypes, which could contribute to the milk production efficiency differences, have not been as widely studied however. A series of component studies were conducted using cows sourced from a longer-term genotype comparison study (JE, JE × HF, and HF). The objectives were to (1) determine if differences exist among genotypes regarding gastrointestinal tract (GIT) weight, (2) assess and quantify whether the genotypes tested differ in their ability to digest perennial ryegrass, and (3) examine the relative abundance of specific rumen microbial populations potentially relating to feed digestibility. Over 3 yr, the GIT weight was obtained from 33 HF, 35 JE, and 27 JE × HF nonlactating cows postslaughter. During the dry period the cows were offered a perennial ryegrass silage diet at maintenance level. The unadjusted GIT weight was heavier for the HF than for JE and JE × HF. When expressed as a proportion of body weight (BW), JE and JE × HF had a heavier GIT weight than HF. In vivo digestibility was evaluated on 16 each of JE, JE × HF, and HF lactating dairy cows. Cows were individually stalled, allowing for the total collection of feces and were offered freshly cut grass twice daily. During this time, daily milk yield, BW, and dry matter intake (DMI) were greater for HF and JE × HF than for JE; milk fat and protein concentration ranked oppositely. Daily milk solids yield did not differ among the 3 genotypes. Intake capacity, expressed as DMI per BW, tended to be different among treatments, with JE having the greatest DMI per BW, HF the lowest, and JE × HF being intermediate. Production efficiency, expressed as milk solids per DMI, was higher for JE than HF and JE × HF. Digestive efficiency, expressed as digestibility of dry matter, organic matter, N, neutral detergent fiber, and acid detergent fiber, was higher for JE than HF. In grazing cows (n = 15 per genotype) samples of rumen fluid, collected using a transesophageal sampling device, were analyzed to determine the relative abundance of rumen microbial populations of cellulolytic bacteria, protozoa, and fungi. These are critically important for fermentation of feed into short-chain fatty acids. A decrease was observed in the relative abundance of Ruminococcus flavefaciens in the JE rumen compared with HF and JE × HF. We can deduce from this study that the JE genotype has greater digestibility and a different rumen microbial population than HF. Jersey and JE × HF cows had a proportionally greater GIT weight than HF. These differences are likely to contribute to the production efficiency differences among genotypes previously reported.
    • Gene Fusions Derived by Transcriptional Readthrough are Driven by Segmental Duplication in Human.

      McCartney, Ann M; Hyland, Edel M; Cormican, Paul; Moran, Raymond J; Webb, Andrew E; Lee, Kate D; Hernandez-Rodriguez, Jessica; Prado-Martinez, Javier; Creevey, Christopher J; Aspden, Julie L; et al. (Oxford Academic, 2019-08-10)
      Gene fusion occurs when two or more individual genes with independent open reading frames becoming juxtaposed under the same open reading frame creating a new fused gene. A small number of gene fusions described in detail have been associated with novel functions, for example, the hominid-specific PIPSL gene, TNFSF12, and the TWE-PRIL gene family. We use Sequence Similarity Networks and species level comparisons of great ape genomes to identify 45 new genes that have emerged by transcriptional readthrough, that is, transcription-derived gene fusion. For 35 of these putative gene fusions, we have been able to assess available RNAseq data to determine whether there are reads that map to each breakpoint. A total of 29 of the putative gene fusions had annotated transcripts (9/29 of which are human-specific). We carried out RT-qPCR in a range of human tissues (placenta, lung, liver, brain, and testes) and found that 23 of the putative gene fusion events were expressed in at least one tissue. Examining the available ribosome foot-printing data, we find evidence for translation of three of the fused genes in human. Finally, we find enrichment for transcription-derived gene fusions in regions of known segmental duplication in human. Together, our results implicate chromosomal structural variation brought about by segmental duplication with the emergence of novel transcripts and translated protein products.
    • Genetic analysis of atypical progesterone profiles in Holstein-Friesian cows from experimental research herds

      Nyman, S.; Johanssen, K.; de Koning, D. J.; Berry, Donagh P.; Veerkamp, Roel F.; Wall, E.; Beeglund, B. (Elsevier for American Dairy Science Association, 2014-11)
      The objective of this study was to quantify the genetic variation in normal and atypical progesterone profiles and investigate if this information could be useful in an improved genetic evaluation for fertility for dairy cows. The phenotypes derived from normal profiles included cycle length traits, including commencement of luteal activity (C-LA), interluteal interval, luteal phase length. and interovulatory interval. In total, 44,977 progesterone test-day records were available from 1,612 lactations on 1,122 primiparous and multiparous Holstein-Friesian cows from Ireland, the Netherlands, Sweden, and the United Kingdom. The atypical progesterone profiles studied were delayed cyclicity, prolonged luteal phase, and cessation of cyclicity. Variance components for the atypical progesterone profiles were estimated using a sire linear mixed model, whereas an animal linear mixed model was used to estimate variance components for the cycle length traits. Heritability was moderate for delayed cyclicity (0.24 ± 0.05) and C-LA (0.18 ± 0.04) but low for prolonged luteal phase (0.02 ± 0.04), luteal phase length (0.08 ± 0.05), interluteal interval (0.08 ± 0.14), and interovulatory interval (0.03 ± 0.04). No genetic variation was detected for cessation of cyclicity. Commencement of luteal activity, luteal phase length, and interovulatory interval were moderately to strongly genetically correlated with days from calving to first service (0.35 ± 0.12, 0.25 ± 0.14, and 0.76 ± 0.24, respectively). Delayed cyclicity and C-LA are traits that can be important in both genetic evaluations and management of fertility to detect (earlier) cows at risk of compromised fertility. Delayed cyclicity and C-LA were both strongly genetically correlated with milk yield in early lactation (0.57 ± 0.14 and 0.45 ± 0.09, respectively), which may imply deterioration in these traits with selection for greater milk yield without cognizance of other traits.
    • Genetic and nongenetic factors associated with milk color in dairy cows

      Scarso, S.; McParland, Sinead; Visentin, G.; Berry, Donagh P.; McDermott, A.; de Marchi, M.; European Union (Elsevier, 2017-07-12)
      Milk color is one of the sensory properties that can influence consumer choice of one product over another and it influences the quality of processed dairy products. This study aims to quantify the cow-level genetic and nongenetic factors associated with bovine milk color traits. A total of 136,807 spectra from Irish commercial and research herds (with multiple breeds and crosses) were used. Milk lightness (Lˆ*) , red-green index (aˆ*) and yellow-blue index (bˆ*) were predicted for individual milk samples using only the mid-infrared spectrum of the milk sample. Factors associated with milk color were breed, stage of lactation, parity, milking-time, udder health status, pasture grazing, and seasonal calving. (Co)variance components for Lˆ*,aˆ* , and bˆ* were estimated using random regressions on the additive genetic and within-lactation permanent environmental effects. Greater bˆ* value (i.e., more yellow color) was evident in milk from Jersey cows. Milk Lˆ* increased consistently with stage of lactation, whereas aˆ* increased until mid lactation to subsequently plateau. Milk bˆ* deteriorated until 31 to 60 DIM, but then improved thereafter until the end of lactation. Relative to multiparous cows, milk yielded by primiparae was, on average, lighter (i.e., greater Lˆ* ), more red (i.e., greater aˆ* ), and less yellow (i.e., lower bˆ* ). Milk from the morning milk session had lower Lˆ*,aˆ*, and bˆ* Heritability estimates (±SE) for milk color varied between 0.15 ± 0.02 (30 DIM) and 0.46 ± 0.02 (210 DIM) for Lˆ* , between 0.09 ± 0.01 (30 DIM) and 0.15 ± 0.02 (305 DIM) for aˆ* , and between 0.18 ± 0.02 (21 DIM) and 0.56 ± 0.03 (305 DIM) for bˆ* For all the 3 milk color features, the within-trait genetic correlations approached unity as the time intervals compared shortened and were generally <0.40 between the peripheries of the lactation. Strong positive genetic correlations existed between bˆ* value and milk fat concentration, ranging from 0.82 ± 0.19 at 5 DIM to 0.96 ± 0.01 at 305 DIM and confirming the observed phenotypic correlation (0.64, SE = 0.01). Results of the present study suggest that breeding strategies for the enhancement of milk color traits could be implemented for dairy cattle populations. Such strategies, coupled with the knowledge of milk color traits variation due to nongenetic factors, may represent a tool for the dairy processors to reduce, if not eliminate, the use of artificial pigments during milk manufacturing.
    • The genetic architecture of milk ELISA scores as an indicator of Johne's disease (paratuberculosis) in dairy cattle

      Brito, Luiz F.; Mallikarjunappa, Sanjay; Sargolzaei, Mehdi; Koeck, Astrid; Chesnais, Jacques; Schenkel, Flavio S.; Meade, Kieran G; Miglior, Filippo; Karrow, Niel A.; The Semex Alliance; et al. (Elsevier, 2018-09-13)
      Johne's disease (or paratuberculosis), caused by Mycobacterium avium ssp. paratuberculosis (MAP) infection, is a globally prevalent disease with severe economic and welfare implications. With no effective treatment available, understanding the role of genetics influencing host infection status is essential to develop selection strategies to breed for increased resistance to MAP infection. The main objectives of this study were to estimate genetic parameters for the MAP-specific antibody response using milk ELISA scores in Canadian Holstein cattle as an indicator of resistance to Johne's disease, and to unravel genomic regions and candidate genes significantly associated with MAP infection. After data editing, 168,987 milk ELISA records from 2,306 herds, obtained from CanWest Dairy Herd Improvement, were used for further analyses. Variance and heritability estimates for MAP infection status were determined using univariate linear animal models under 3 scenarios: (a) SCEN1: the complete data set (all herds); (b) SCEN2: herds with at least one suspect or test-positive animal (ELISA optical density ≥0.07); and (c) SCEN3: herds with at least one test-positive animal (ELISA optical density ≥0.11). Heritability estimates were calculated as 0.066, 0.064, and 0.063 for SCEN1, SCEN2, and SCEN3, respectively. The correlations between estimated breeding values for resistance to MAP infection and other economically important traits, when significant, were favorable and of low magnitude. Genome-wide association analyses identified important genomic regions on Bos taurus autosome (BTA)1, BTA7, BTA9, BTA14, BTA15, BTA17, BTA19, and BTA25 showing significant association with MAP infection status. These regions included 2 single nucleotide polymorphisms located 2 kb upstream of positional candidate genes CD86 and WNT9B, which play key roles in host immune response and tissue homeostasis. This study revealed the genetic architecture of MAP infection in Canadian Holstein cattle as measured by milk ELISA scores by estimating genetic parameters along with the identification of genomic regions potentially influencing MAP infection status. These findings will be of significant value toward implementing genetic and genomic evaluations for resistance to MAP infection in Holstein cattle.
    • Genetic basis of benzimidazole resistance in Teladorsagia circumcincta in Ireland

      Keegan, Jason D; Good, Barbara; de Waal, Theo; Fanning, June; Keane, Orla M; Department of Agriculture, Food and the Marine (Biomed Central, 2017-02-13)
      Resistance to benzimidazole (BZ) anthelmintics is common in ovine nematodes of economic importance. Single nucleotide polymorphisms (SNP) at three positions in the isotype 1 β– tubulin gene have been associated with BZ resistance and molecular tests for the detection of BZ resistance have been developed. In order to determine if such tests are practicable in Ireland the polymorphisms associated with BZ resistance must be identified. To this end, BZ-resistant nematodes were recovered from four farms in Ireland. Resistant Teladorsagia circumcincta, Cooperia curticei and Trichostrongylus colubriformis were recovered, with resistant T. circumcincta the most common and the only species studied further. Sequencing of the isotype 1 β–tubulin gene from resistant T. circumcincta identified a T - A transition, resulting in an F200Y substitution known to be responsible for BZ-resistance, on three of the farms. However, on the fourth farm the frequency of the resistant A allele was only 0.33 indicating another BZ resistance mechanism may be present on this farm. An additional polymorphism resulting in a substitution of glutamate for leucine (E198L) was also found on this farm at low frequency (0.17). No polymorphisms at position 167 were identified on any farm. Therefore, molecular tests to detect BZ resistance in T. circumcincta in Ireland could prove useful; however, they may result in some instances of resistance remaining undetected.
    • Genetic merit for fertility traits in Holstein cows: I. Production characteristics and reproductive efficiency in a pasture-based system

      Cummins, Sean B; Lonergan, P.; Evans, A.C.O.; Berry, Donagh P.; Evans, R. D.; Butler, Stephen T. (American Dairy Science Association and Elsevier Inc., 2012-03)
      The objective of the present study was to characterize the phenotypic performance of cows with similar proportions of Holstein genetics, similar genetic merit for milk production traits, but with good (Fert+) or poor (Fert−) genetic merit for fertility traits. Specifically, we tested the hypothesis that cows with a negative estimated breeding value for calving interval would have superior fertility performance and would have detectable differences in body reserve mobilization and circulating concentrations of metabolic hormones and metabolites compared with cows that had a positive estimated breeding value for calving interval. For the duration of the study, cows were managed identically as a single herd in a typical grass-based, spring-calving production system. A total of 80 lactation records were available from 26 Fert+ and 26 Fert− cows over 2 consecutive years (2008 and 2009). During yr 1, cows were monitored during a 20-wk breeding season to evaluate reproductive performance. Milk production, body condition score (scale 1 to 5), body weight, grass dry matter intake, energy balance, and metabolic hormone and metabolite data were collected during both years. The Fert+ cows had greater daily milk yield (19.5 vs. 18.7 kg/d), shorter interval from calving to conception (85.6 vs. 113.8 d), and fewer services per cow (1.78 vs. 2.83). No difference between groups in grass dry matter intake, energy balance, or body weight was observed. The Fert+ cows maintained greater BCS during mid (2.84 vs. 2.74 units) and late lactation (2.82 vs. 2.73 units). Circulating concentrations of insulin-like growth factor-I were greater throughout the gestation-lactation cycle in Fert+ cows (148.3 vs. 128.2 ng/mL). The Fert+ cows also had greater circulating concentrations of insulin during the first 4 wk of lactation (1.71 vs. 1.24 μIU/mL). Analysis of records from national herd data verified the association between genetic merit for fertility traits and phenotypic reproductive performance; Fert+ cows (n = 2,436) required 11.1 d less to recalve than did Fert− cows (n = 1,388), and the percentage of cows that successfully calved for the second time within 365 and 400 d of the first calving was 8 and 13% greater for Fert+ compared with Fert− cows, respectively. These results demonstrate that genetic merit for fertility traits had a pronounced effect on reproductive efficiency, BCS profiles, and circulating concentrations of insulin-like growth factor-I.
    • Genetic merit for fertility traits in Holstein cows: II. Ovarian follicular and corpus luteum dynamics, reproductive hormones and estrus behaviour

      Cummins, Sean B; Lonergan, P.; Evans, A.C.O.; Butler, Stephen T.; National Development Plan (Dublin, Ireland); Teagasc Walsh Fellowship Programme; Dairy Levy Research Trust (American Dairy Science Association and Elsevier Inc., 2012-07)
      The objective of this study was to characterize the estrous cycle of cows with similar proportions of Holstein genetics, similar genetic merit for milk production traits, but with good (Fert+) or poor (Fert-) genetic merit for fertility traits. A total of 37 lactating cows were enrolled on an 8-d CIDR-based protocol to synchronise estrus. 19 Fert+ and 12 Fert- cows that successfully ovulated a dominant follicle and established a corpus luteum underwent daily transrectal ultrasonography. Blood sampling was carried at 8 h intervals from d 0 to d 6 and from d 15 to ovulation, and once daily from d 7 to d 15. Blood samples were analysed for progesterone, estradiol, follicle stimulating hormone and luteinising hormone. Estrus behaviour was recorded using neck activity collars and mounting pads. Fert+ cows tended to have fewer (P = 0.07) follicular waves (2.2 vs. 2.7 waves) and had a shorter (P < 0.05) estrous cycle (21.0 vs. 25.1 d) than Fert- cows. There was no effect of genotype on day of first wave emergence or day of first wave dominant follicle peak diameter (all P > 0.05) but the peak diameter of the first wave dominant follicle tended to be larger (P = 0.08) in Fert- cows. During the first 13 d of the cycle, Fert+ cows developed a corpus luteum that was 16% larger (P = 0.08) than Fert- cows. Circulating progesterone concentrations were 34% greater (P < 0.001) in Fert+ than Fert- cows (5.15 vs. 3.84 ng/ml, respectively) from d 5 to d 13. During the final follicular wave, the interval from preovulatory follicle emergence to ovulation and the interval from preovulatory follicle dominance to ovulation were similar (P >0.05) in both genotypes. Maximum preovulatory follicle diameter was larger (P < 0.05) in Fert+ than Fert- cows (17.9 vs. 16.8 mm, respectively); however, circulating concentrations of oestradiol were not different (all P > 0.05) between genotypes. A greater proportion (P < 0.05) of Fert- cows ovulated to a silent heat than Fert+ cows (22% vs. 2%, respectively). Of cows that showed behavioural estrus Fert+ cows had 41% greater (P < 0.01) mean activity count; however, no difference (P > 0.05) was seen in mounting behaviour between genotypes. These results demonstrate for the first time that genetic merit for fertility has pronounced effects on corpus luteum development, progesterone concentration, preovulatory follicle diameter and behavioural estrus.
    • Genetic merit for fertility traits in Holstein cows: III. Hepatic expression of somatotropic axis genes during pregnancy and lactation

      Cummins, Sean B; Waters, Sinead M.; Evans, A.C.O.; Lonergan, P.; Butler, Stephen T.; National Development Plan Ireland; Dairy Levy Research Trust Ireland (American Dairy Science Association and Elsevier Inc., 2012-07)
      The objective of this study was to characterize the circulating concentrations of insulin-like growth factor-I (IGF-I) and the hepatic expression of key genes regulating the somatotropic axis in cows divergent in genetic merit for fertility traits but with similar genetic merit for milk production traits. A total of 11 cows with good genetic merit for fertility (Fert+) and 12 cows with poor genetic merit for fertility (Fert−) underwent liver biopsy by percutaneous punch technique on d 20 (± 6.7 d) prepartum and on d 2 (± 1.5 d), d 58 (± 3.7 d), d 145 (± 13 d), and d 245 (± 17.1 d) postpartum. Total RNA was isolated and the mRNA expression of growth hormone receptor (GHR 1A and GHRtot), IGF-I, janus tyrosine kinase 2 (JAK2), signal transducer and activator of transcription 5B (STAT5B), suppressor of cytokine signaling 3 (SOCS-3), acid-labile subunit (ALS), and IGF-binding proteins (IGFBP1 to IGFBP6) were measured by real-time quantitative PCR. During lactation, the circulating concentrations of IGF-I were 34% greater in Fert+ cows. The Fert+ cows had increased mean expression of IGF-I mRNA during the study; however, the difference in IGF-I mRNA abundance between Fert+ and Fert− cows was most pronounced at d 145 and 245. The expression of IGFBP3 and ALS transcript was similar in Fert+ and Fert− cows for the duration of the study. The Fert− cows, however, had greater expression of IGFBP2, IGFBP4, IGFBP5, and IGFBP6. Genotype had no effect on mRNA abundance of GHR 1A, STAT5B, JAK2, or SOCS-3. Genetic merit for fertility traits affects hepatic expression of key genes of the somatotropic axis regulating the synthesis, bioavailability, and stability of circulating IGF-I.
    • Genetic merit for fertility traits in Holstein cows: VI. Oocyte developmental competence and embryo development

      Moore, Stephen G.; Cummins, Sean B; Mamo, Solomon; Lonergan, P.; Fair, Trudee; Butler, Stephen T.; National Development Plan; Dairy Levy Ireland (Elsevier, 2019-03-07)
      The hypothesis of this study was that cows with good genetic merit for fertility traits (Fert+) would produce oocytes and embryos of greater quality than cows with poor genetic merit for fertility traits (Fert−) and that mRNA expression of candidate genes would reflect the observed differences in quality. The aim of the study, therefore, was to determine the effect of genetic merit for fertility traits on morphological classification and mRNA abundance of key genes in immature oocytes and cumulus cells following ovum pick-up and in embryos following superovulation, artificial insemination (AI), and uterine flushing. In experiment 1, 17 Fert+ and 11 Fert− cows, ranging from 54 to 84 d in milk, were submitted to ovum pick-up on 4 occasions during a 2-wk period. Recovered cumulus–oocyte complexes (COC) were morphologically graded. Oocytes and cumulus cells were separated, and mRNA abundance of genes associated with oocyte developmental competence was measured. There was no effect of genotype on the distribution of COC grades or on the mRNA abundance of the candidate genes in grade 1 COC. In experiment 2, 20 Fert+ and 19 Fert− cows, ranging from 71 to 189 d in milk, were submitted to superovulation and AI. The uteri of cows that responded to the superovulation protocol (17 Fert+ and 16 Fert− cows) were nonsurgically flushed 7 d postovulation. Recovered embryos were morphologically graded, and mRNA abundance of genes associated with embryo development was measured in grade 1 blastocysts. The response to the superovulation protocol was assessed by counting the number of codominant follicles on the day of AI, which was similar for both genotypes (22.0 ± 9.7 and 19.8 ± 8.2 for Fert+ and Fert− cows, respectively). There was no effect of genotype on the proportion of transferable embryos recovered or on the mRNA abundance of the candidate genes tested in the grade 1 blastocysts. Of the total embryos classified as blastocysts, however, the Fert+ cows tended to have a greater proportion of grade 1 blastocysts compared with Fert− cows (90% vs. 64%, respectively). In conclusion, genetic merit for fertility traits had a no effect on mRNA abundance of the candidate genes that were examined in immature oocytes and cumulus cells and in embryos recovered after superovulation. The observed differences in morphological blastocyst quality following superovulation would suggest that the superior reproductive performance of Fert+ cows could arise during the later stages of embryo development from d 7 until maternal recognition of pregnancy.
    • Genetic parameters for animal mortality in pasture-based, seasonal-calving dairy and beef herds

      Ring, Siobhan C.; Evans, R. D.; Doherty, Michael L.; Berry, Donagh P.; Department of Agriculture, Food and the Marine; 14/S/801 (Elsevier, 2018-11-09)
      In the absence of informative health and welfare phenotypes, breeding for reduced animal mortality could improve overall health and welfare, provided genetic variability in animal mortality exists. The objective of the present study was to estimate genetic (and other) variance components for animal mortality in pasture-based, seasonal-calving dairy and beef herds across multiple life stages as well as to quantify the genetic relationship in mortality among life stages. National mortality records were available for all cattle born in the Republic of Ireland. Cattle were grouped into three life stages based on age (0 to 30 days, 31 to 365 days, 366 to 1095 days) whereas females with ≥1 calving event were also grouped into five life stages, based on parity number (1, 2, 3, 4, and 5), considering both the initial 60 days of lactation and a cow's entire lactation period, separately. The mean mortality prevalence ranged from 0.70 to 5.79% in young animals and from 0.53 to 3.86% in cows. Variance components and genetic correlations were estimated using linear mixed models using 21,637 to 100,993 records. Where heritability estimates were different from zero, direct heritability estimates for mortality in young animals (≤1095 days) ranged from 0.006 to 0.040, whereas the genetic standard deviation ranged from 0.015 to 0.034. The contribution of a maternal genetic effect to mortality in young animals was evident up to 30 days of age in dairy herds, but this was only the case in preliminary analysis of stillbirths in beef herds. Based on the estimated genetic standard deviation in the present study, the incidence of mortality in young animals could be reduced through breeding by up to 3.4 percentage units per generation. For cows, direct heritability estimates for mortality, where different from zero, ranged from 0.003 to 0.049. The genetic standard deviation for mortality in cows ranged from 0.005 to 0.016 during the initial 60 days of lactation and ranged from 0.011 to 0.032 during the cow's entire lactation. Genetic correlations among the age groups as well as between the age groups and cow parities had high standard errors. Genetic correlations among the cow parities were moderate to strongly positive (ranging from 0.66 to 0.99) and mostly different from zero. Results from the present study can be used to inform genetic evaluations for mortality in young animals and in cows as well as the potential genetic gain achievable.
    • Genetic parameters for milk mineral content and acidity predicted by mid-infrared spectroscopy in Holstein–Friesian cows

      Toffanin, V.; Penasa, M.; McParland, Sinead; Berry, Donagh P.; Cassandro, M.; de Marchi, M. (Cambridge University PRess, 2015-01-13)
      The aim of the present study was to estimate genetic parameters for calcium (Ca), phosphorus (P) and titratable acidity (TA) in bovine milk predicted by mid-IR spectroscopy (MIRS). Data consisted of 2458 Italian Holstein−Friesian cows sampled once in 220 farms. Information per sample on protein and fat percentage, pH and somatic cell count, as well as test-day milk yield, was also available. (Co)variance components were estimated using univariate and bivariate animal linear mixed models. Fixed effects considered in the analyses were herd of sampling, parity, lactation stage and a two-way interaction between parity and lactation stage; an additive genetic and residual term were included in the models as random effects. Estimates of heritability for Ca, P and TA were 0.10, 0.12 and 0.26, respectively. Positive moderate to strong phenotypic correlations (0.33 to 0.82) existed between Ca, P and TA, whereas phenotypic weak to moderate correlations (0.00 to 0.45) existed between these traits with both milk quality and yield. Moderate to strong genetic correlations (0.28 to 0.92) existed between Ca, P and TA, and between these predicted traits with both fat and protein percentage (0.35 to 0.91). The existence of heritable genetic variation for Ca, P and TA, coupled with the potential to predict these components for routine cow milk testing, imply that genetic gain in these traits is indeed possible.
    • Genetic parameters of dairy cow energy intake and body energy status predicted using mid-infrared spectrometry of milk

      McParland, Sinead; Kennedy, Emer; Lewis, Eva; Moore, Stephen G.; McCarthy, B.; O'Donovan, Michael; Berry, Donagh P.; Department of Agriculture, Food and the Marine, Ireland; European Commission; Marie Curie project International Research Staff Exchange Scheme SEQSEL; et al. (Elsevier for American Dairy Science Association, 2014-12)
      Energy balance (EB) and energy intake (EI) are heritable traits of economic importance. Despite this, neither trait is explicitly included in national dairy cow breeding goals due to a lack of routinely available data from which to compute reliable breeding values. Mid-infrared (MIR) spectrometry, which is performed during routine milk recording, is an accurate predictor of both EB and EI. The objective of this study was to estimate genetic parameters of EB and EI predicted using MIR spectrometry. Measured EI and EB were available for 1,102 Irish Holstein-Friesian cows based on actual feed intake and energy sink data. A subset of these data (1,270 test-day records) was used to develop equations to predict EI, EB, and daily change in body condition score (ΔBCS) and body weight (ΔBW) using the MIR spectrum with or without milk yield also as a predictor variable. Accuracy of cross-validation of the prediction equations was 0.75, 0.73, 0.77, and 0.70 for EI, EB, ΔBCS, and ΔBW, respectively. Prediction equations were applied to additional spectral data, yielding up to 94,653 records of MIR-predicted EI, EB, ΔBCS, and ΔBW available for variance component estimation. Variance components were estimated using repeatability animal linear mixed models. Heritabilities of MIR-predicted EI, EB, ΔBCS, and ΔBW were 0.20, 0.10, 0.07, and 0.06, respectively; heritability estimates of the respective measured traits were 0.35, 0.16, 0.07, and 0.08, respectively. The genetic correlation between measured and MIR-predicted EI was 0.84 and between measured and MIR-predicted EB was 0.54, indicating that selection based on MIR-predicted EI or EB would improve true EI or EB. Genetic and phenotypic associations between EI and both the milk production and body-change traits were generally in agreement, regardless of whether measured EI or MIR-predicted EI was considered. Higher-yielding animals of higher body weight had greater EI. Predicted EB was negatively genetically correlated with milk yield (genetic correlation = −0.29) and positively genetically correlated with both milk fat and protein percent (genetic correlation = 0.17 and 0.16, respectively). Least squares means phenotypic EI of 198 animals stratified as low, average, and high estimated breeding values for MIR-predicted EI (animal phenotypes were not included in the genetic evaluation) were 154.3, 156.0, and 163.3 MJ/d, corroborating that selection on MIR-predicted EI will, on average, result in differences in phenotypic true EI.
    • Genetic parameters of ovarian and uterine reproductive traits in dairy cows

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

      Berry, Donagh P.; Buckley, Frank; Dillon, Pat; Evans, R. D.; Veerkamp, Roel F.; Allied Irish Bank; AI Managers Association; Holstein-Friesian Society of Great Britain and Ireland (Teagasc (Agriculture and Food Development Authority), Ireland, 2004)
      Phenotypic and genetic (co)variances among type traits, milk yield, body weight, fertility and somatic cell count were estimated. The data analysed included 3,058 primiparous spring-calving Holstein-Friesian cows from 80 farms throughout the south of Ireland. Heritability estimates for the type traits varied from 0.11 to 0.43. Genetic correlations among some type traits were very strong and may indicate the possibility of reducing the number of traits assessed on each animal; the genetic correlation between angularity and body condition score was –0.84. Genetic correlations between all type traits (except body condition score, udder depth and teat length) and milk yield were positive and ranged from 0.08 to 0.69. The possibility of selecting for body weight may be achievable within a national progeny-testing programme using type traits within a selection index. Moderate to strong genetic correlations existed between some type traits and the various fertility measures and somatic cell count indicating the opportunity of indirect selection for improved fertility and health of animals using type traits within a selection index; however, the standard errors of some of the genetic correlations were large and should thus be treated with caution. Genetically taller, wider, deeper, more angular cows with tighter, stronger, shallower udders were predisposed to have inferior pregnancy rates to first service and require more services.
    • Genetic relationships between carcass cut weights predicted from video image analysis and other performance traits in cattle

      Pabiou, Thierry; Fikse, W. F.; Amer, P. R.; Cromie, A. R.; Nasholm, A.; Berry, Donagh P. (Cambridge University Press, 2012-04)
      The objective of this study was to quantify the genetic associations between a range of carcass-related traits including wholesale cut weights predicted from video image analysis (VIA) technology, and a range of pre-slaughter performance traits in commercial Irish cattle. Predicted carcass cut weights comprised of cut weights based on retail value: lower value cuts (LVC), medium value cuts (MVC), high value cuts (HVC) and very high value cuts (VHVC), as well as total meat, fat and bone weights. Four main sources of data were used in the genetic analyses: price data of live animals collected from livestock auctions, live-weight data and linear type collected from both commercial and pedigree farms as well as from livestock auctions and weanling quality recorded on-farm. Heritability of carcass cut weights ranged from 0.21 to 0.39. Genetic correlations between the cut traits and the other performance traits were estimated using a series of bivariate sire linear mixed models where carcass cut weights were phenotypically adjusted to a constant carcass weight. Strongest positive genetic correlations were obtained between predicted carcass cut weights and carcass value (min rg(MVC)50.35; max rg(VHVC)50.69), and animal price at both weaning (min rg(MVC)50.37; max rg(VHVC)50.66) and post weaning (min rg(MVC)50.50; max rg(VHVC)50.67). Moderate genetic correlations were obtained between carcass cut weights and calf price (min rg(HVC)50.34; max rg(LVC)50.45), weanling quality (min rg(MVC)50.12; max rg(VHVC)50.49), linear scores for muscularity at both weaning (hindquarter development: min rg(MVC)520.06; max rg(VHVC)50.46), post weaning (hindquarter development: min rg(MVC)50.23; max rg(VHVC)50.44). The genetic correlations between total meat weight were consistent with those observed with the predicted wholesale cut weights. Total fat and total bone weights were generally negatively correlated with carcass value, auction prices and weanling quality. Total bone weight was, however, positively correlated with skeletal scores at weaning and post weaning. These results indicate that some traits collected early in life are moderate-to-strongly correlated with carcass cut weights predicted from VIA technology. This information can be used to improve the accuracy of selection for carcass cut weights in national genetic evaluations.
    • Genetic relationships between detailed reproductive traits and performance traits in Holstein-Friesian dairy cattle

      Carthy, T. R.; Ryan, Dan P.; Fitzgerald, A. M.; Evans, R. D.; Berry, Donagh P.; Department of Agriculture, Food and the Marine; European Union; RSF 11/S/133 (Elsevier for American Dairy Science Association, 2015-12-17)
      The objective of the study was to estimate the genetic relationships between detailed reproductive traits derived from ultrasound examination of the reproductive tract and a range of performance traits in Holstein-Friesian dairy cows. The performance traits investigated included calving performance, milk production, somatic cell score (i.e., logarithm transformation of somatic cell count), carcass traits, and body-related linear type traits. Detailed reproductive traits included (1) resumed cyclicity at the time of examination, (2) multiple ovulations, (3) early ovulation, (4) heat detection, (5) ovarian cystic structures, (6) embryo loss, and (7) uterine score, measured on a 1 (little or no fluid with normal tone) to 4 (large quantity of fluid with a flaccid tone) scale, based on the tone of the uterine wall and the quantity of fluid present in the uterus. (Co)variance components were estimated using a repeatability animal linear mixed model. Genetic merit for greater milk, fat, and protein yield was associated with a reduced ability to resume cyclicity postpartum (genetic correlations ranged from −0.25 to −0.15). Higher genetic merit for milk yield was also associated with a greater genetic susceptibility to multiple ovulations. Genetic predisposition to elevated somatic cell score was associated with a decreased likelihood of cyclicity postpartum (genetic correlation of −0.32) and a greater risk of both multiple ovulations (genetic correlation of 0.25) and embryo loss (genetic correlation of 0.32). Greater body condition score was genetically associated with an increased likelihood of resumption of cyclicity postpartum (genetic correlation of 0.52). Genetically heavier, fatter carcasses with better conformation were also associated with an increased likelihood of resumed cyclicity by the time of examination (genetic correlations ranged from 0.24 to 0.41). Genetically heavier carcasses were associated with an inferior uterine score as well as a greater predisposition to embryo loss. Despite the overall antagonistic relationship between reproductive performance and both milk and carcass traits, not all detailed aspects of reproduction performance exhibited an antagonistic relationship.
    • Genetic selection for hoof health traits and cow mobility scores can accelerate the rate of genetic gain in producer-scored lameness in dairy cows

      Ring, Siobhan C.; Twomey, Alan J.; Byrne, Nicky; Kelleher, Margaret M.; Pabiou, Thierry; Doherty, Michael L.; Berry, Donagh P.; Department of Agriculture, Food and the Marine (American Dairy Science Association, 2018-09-13)
      Cattle breeding programs that strive to reduce the animal-level incidence of lameness are often hindered by the availability of informative phenotypes. As a result, indicator traits of lameness (i.e., hoof health and morphological conformation scores) can be used to improve the accuracy of selection and subsequent genetic gain. Therefore, the objectives of the present study were to estimate the variance components for hoof health traits using various phenotypes collected from a representative sample of Irish dairy cows. Also of interest to the present study was the genetic relationship between both hoof health traits and conformation traits with producer-scored lameness. Producer-recorded lameness events and linear conformation scores from 307,657 and 117,859 Irish dairy cows, respectively, were used. Data on hoof health (i.e., overgrown sole, white line disease, and sole hemorrhage), mobility scores, and body condition scores were also available from a research study on up to 11,282 Irish commercial dairy cows. Linear mixed models were used to quantify variance components for each trait and to estimate genetic correlations among traits. The estimated genetic parameters for hoof health traits in the present study were greater (i.e., heritability range: 0.005 to 0.27) than previously reported in dairy cows. With the exception of analyses that considered hoof health traits in repeatability models, little difference in estimated variance components existed among the various hoof-health phenotypes. Results also suggest that producer-recorded lameness is correlated with both hoof health (i.e., genetic correlation up to 0.48) and cow mobility (i.e., genetic correlation = 0.64). Moreover, cows that genetically tend to have rear feet that appear more parallel when viewed from the rear are also genetically more predisposed to lameness (genetic correlation = 0.39); genetic correlations between lameness and other feet and leg type traits, as well as between lameness and frame type traits, were not different from zero. Results suggest that if the population breeding goal was to reduce lameness incidence, improve hoof health, or improve cow mobility, genetic selection for either of these traits should indirectly benefit the other traits. Results were used to quantify the genetic gains achievable for lameness when alternative phenotypes are available.
    • Genetic variability in the humoral immune response to bovine herpesvirus-1 infection in dairy cattle and genetic correlations with performance traits

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