The aim of the Teagasc Animal and Grassland Research & Innovation Programme is to increase the profitability, competitiveness and sustainability of Irish livestock production through research and innovation.

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  • Heritability and impact of environmental effects during pregnancy on antral follicle count in cattle

    Walsh, S.W.; Mossa, F.; Butler, Stephen T.; Berry, Donagh P.; Scheetz, D.; Jimenez-Krassel, F.; Templeman, R.J.; Cater, F.; Lonergan, P.; Evans, A. C. O.; Ireland, J. J.; Department of Agriculture, Food and the Marine; RSF-06-328; RSF-06-328 (Elsevier for American Dairy Science Association, 2014-07)
    Previous studies have documented that ovarian antral follicle count (AFC) is positively correlated with number of healthy follicles and oocytes in ovaries (ovarian reserve), as well as ovarian function and fertility in cattle. However, environmental factors (e.g., nutrition, steroids) during pregnancy in cattle and sheep can reduce AFC in offspring. The role that genetic and environmental factors play in influencing the variability in AFC and, correspondingly, the size of the ovarian reserve, ovarian function, and fertility, are, however, poorly understood. The present study tests the hypothesis that variability in AFC in offspring is influenced not only by genetic merit but also by the dam age and lactation status (lactating cows vs. nonlactating heifers) and milk production during pregnancy. Antral follicle count was assessed by ultrasonography in 445 Irish Holstein-Friesian dairy cows and 522 US Holstein-Friesian dairy heifers. Heritability estimates for AFC (± standard error) were 0.31 ± 0.14 and 0.25 ± 0.13 in dairy cows and heifers, respectively. Association analysis between both genotypic sire data and phenotypic dam data with AFC in their daughters was performed using regression and generalized linear models. Antral follicle count was negatively associated with genetic merit for milk fat concentration. Also, AFC was greater in offspring of dams that were lactating (n = 255) compared with nonlactating dams (n = 89) during pregnancy and was positively associated with dam milk fat concentration and milk fat-to-protein ratio. In conclusion, AFC in dairy cattle is a moderately heritable genetic trait affected by age or lactation status and milk quality but not by level of dam’s milk production during pregnancy.
  • Use of different wood types as environmental enrichment to manage tail biting in docked pigs in a commercial fully-slatted system

    Chou, Jen-Yun; D'Eath, Rick B.; Sandercock, Dale A.; Waran, Natalie; Haigh, Amy; O'Driscoll, Keelin; Department of Agriculture, Food and the Marine; Teagasc Walsh Fellowship Programme; Scotland's Rural College (Elsevier, 2018-04-07)
    Provision of adequate environmental enrichment on pig farms is a legal requirement under current EU legislation and also alleviates the risk of tail biting. Wood is an organic alternative where loose bedding, which has been identified as the optimal enrichment, is not possible on fully-slatted floors since it may disrupt the slurry system. The study compared four different wood types (beech (Fagus sylvatica), larch (Larix decidua), spruce (Picea sitchensis), and Scots pine (Pinus sylvestris L.)) as enrichment, taking into account the qualities of the wood, economic considerations, and effectiveness at reducing damaging behaviours and lesions. A total of 800 tail docked finisher pigs on an Irish commercial farm were used. Eight pens were provided with each wood type (25 pigs/pen), and the study was conducted over 2 replicates in time. In each pen a single wooden post was presented to the pigs in a metal dispenser with two lateral chains during the finisher period (12–22 weeks of age). The rate of wear, moisture content, and hardness of the wood along with lesion scorings and behavioural observation on pigs were monitored. Spruce was consumed more quickly than other wood types in terms of weight loss and reduction in length (P < 0.001), resulting in a greater cost per pig. Pigs were observed interacting with the spruce more frequently than the other wood types (P < 0.05). Pigs also interacted with the wood more often than the chains in spruce allocated pens (P < 0.001). Overall the interaction with wood posts did not decline significantly across time. However, there was no difference in the frequency of harmful behaviours (tail/ear/flank-biting) observed between wood types, and also no difference in the effectiveness of the different types of wood in reducing tail or ear damage. There was a positive correlation between ear lesion and tear-staining scores (rp= 0.286, P < 0.01), and between tail lesion and tail posture scores (rp= 0.206, P < 0.05). Wood types did not affect visceral condemnation obtained in the slaughterhouse. Wood is a potentially suitable enrichment material, yet the wood species could influence its attractiveness to pigs.
  • The eating quality of beef from young dairy bulls derived from two breed types at three ages from two different production systems

    Nian, Yingqun; Kerry, J. P.; Prendiville, Robert; Allen, Paul; Teagasc Walsh Fellowship Programme (Teagasc (Agriculture and Food Development Authority), Ireland, 2017-07-08)
    Expansion of the Irish dairy herd has led to more dairy breed male calves being available for beef production. This study investigated the physico-chemical and sensory characteristics of beef from Holstein-Friesian (HF) and Jersey × HF (JEX) young bulls fed pasture grass only or pasture grass plus 2 kg concentrate during their first grazing season and slaughtered at 15, 19 or 22 mo of age. Longissimus thoracis (LT) muscles were collected from 67 carcasses. Postmortem pH, ultimate pH (pHu), meat colour, chemical composition, collagen content and solubility were evaluated. After ageing for 21 d, Warner-Bratzler shear force and cooking loss were determined, and assessments by a trained sensory panel were conducted. Meat from older animals was darker. The pHu, moisture and ash contents decreased, while residual roast beef flavour length increased with age. However, increasing age to slaughter did not negatively influence tenderness. JEX beef had lower cooking loss, was darker and redder, in addition to having higher sensory scores for initial tenderness and fattiness than HF beef. Warner-Bratzler variables were positively correlated with cooking loss and chewiness and were negatively correlated with intramuscular fat (IMF) content, soluble collagen and initial tenderness. In summary, most young dairy bull beef samples were acceptably tender after 21 d of ageing and half of them had acceptable IMF content. Slaughter age affected beef colour, pHu, chemical composition and flavour length. The eating quality of meat from the JEX breed type was considered to be superior to that of the HF breed type. Diet during the first season had no effect on meat quality traits.
  • Scientific appraisal of the Irish grass-based milk production system as a sustainable source of premium quality milk and dairy products

    O'Brien, Bernadette; Hennessy, Deirdre (Teagasc (Agriculture and Food Development Authority), Ireland, 2017-12-29)
    The Irish dairy industry is critically important to the economy and general well-being of a large section of the Irish population. Its quality, sustainability and maintenance are the key for a vibrant rural society in the future. Two important elements for the future of this industry include (a) the quality, marketing and sale of dairy products on the export market and (b) sustainability from the perspectives of people, planet and profit. This paper provides a short review of current scientific evidence in relation to a number of topics, each of which is important in maintaining and developing dairy product quality and the sustainability of the Irish dairy industry. The topics addressed in the paper are as follows: the parameters of milk composition; milk processing; hygiene quality and safety; farm management practices and the regulations that govern such practices; animal health and welfare; environmental impacts; economic implications for farm families and rural communities; and the overall future sustainability of the family-based dairy farm structure.
  • Animal performance and economic implications of alternative production systems for dairy bulls slaughtered at 15 months of age

    Murphy, B.; Crosson, Paul; Kelly, A. K.; Prendiville, Robert; Department of Agriculture, Food and the Marine; 11/SF/322 (Teagasc (Agriculture and Food Development Authority), Ireland, 2017-10-26)
    The objectives of this experiment were to investigate (i) the influence of varying levels of concentrate supplementation during the grazing season, (ii) alternative finishing strategies for dairy bulls slaughtered at 15 mo of age and (iii) economic implications of these management strategies. Bulls were assigned to a 2 (level of concentrate supplementation during the grazing season: 1 kg [LA] and 2 kg [HA] dry matter [DM]/head daily) × 2 (finishing strategies: concentrates ad libitum group [AL] or grass silage ad libitum plus 5 kg DM of concentrates/head daily group [SC]) factorial arrangement of treatments. Average daily gain (ADG) during the grazing season was greater (P < 0.01) for HA than for LA. Consequently, HA bulls were 16 kg heavier at housing: 214 and 230 kg, respectively (P < 0.05). During the finishing period, ADG tended (P = 0.09) to be greater for LA than for HA. Carcass weight tended (P = 0.08) to be greater for HA than for LA. Fat score was greater for HA. Live weight at slaughter (P < 0.001) and carcass weight (P < 0.001) were 41 and 23 kg greater for AL than for SC, respectively. Conformation (P < 0.05) and fat score (P < 0.05) were greater for AL than for SC. The Grange Dairy Beef Systems Model simulated whole-farm system effects of the production systems. Net margin/head was greater for LA than for HA and greater for SC than for AL. Sensitivity analysis of finishing concentrate price, calf purchase price and beef price showed no re-ranking of the systems on a net margin basis. Although greater animal performance was observed from the higher plane of nutrition, overall profitability was lower.
  • The effects of stocking rate and ewe prolificacy potential on the efficiency of lamb production and grass utilisation in pasture based systems

    Earle, Elizabeth; Teagasc Walsh Fellowship Programme (2017)
    Ewe prolificacy potential (PP; predicted number of lambs born per ewe per year) and stocking 314 rate (SR; ewe per ha) are two primary drivers of output in temperate grass-based lamb 315 production systems. The aim of this thesis was to investigate and quantify the effect of ewe 316 PP, SR, and their interaction on animal performance, pasture production and utilisation and 317 the efficiency of lamb production in a grass-based production system. A 2 x 3 factorial design 318 study, consisting of two ewe PP ((medium prolificacy potential (Suffolk X ewes; 1.5 lambs 319 reared per ewe) and high prolificacy potential (Belclare X ewes; 1.7 lambs reared per ewe)) 320 and three SR: low (10 ewes per ha), medium (12 ewes per ha), and high (14 ewes per ha) was 321 conducted. Each treatment was managed in a rotational grazing system. Measurements taken 322 included; ewe body weight, ewe body condition score (BCS), number of lambs born and 323 weaned per ewe and per hectare, lamb growth rate, days to slaughter, lamb carcass traits and 324 output, ewe production efficiency (kg lamb live weight weaned: kg ewe live weight mated), 325 herbage dry matter (DM; kg) production and utilisation, sward quality and morphology, and 326 DM and energy (Unite fourrage laite per kg DM; UFL) consumption. High PP ewes produced 327 more lambs both per ewe and per hectare, with HP lambs achieving a higher average daily 328 gain (ADG) on a per hectare basis and yielded a higher lamb carcass output per hectare 329 compared to MP ewes. The total quantity of DM and UFL consumed per ewe and lamb unit 330 for the full production year did not differ by ewe PP. The HP system required a lower quantity 331 of DM and UFL to produce a kilogram of lamb carcass. The use of higher stocking rates 332 demonstrated the potential to increase lamb carcass output per hectare in a grass-based lamb 333 production, with the LSR and MSR systems achieving similar levels of performance for pre-334 weaning lamb ADG and days to slaughter. Increasing stocking rate increased herbage 335 production, utilisation and sward quality and leaf content. Limitations to increasing stocking 336 rate above 12 ewes per hectare in a grass-based lamb production system due to reductions in 337 individual animal performance and increases in DM and UFL consumption per ewe and lamb 338 unit and per kilogram of lamb carcass produced at the HSR were recorded. The findings from 339 this thesis demonstrate the potential to increase lamb output and the efficiency of lamb 340 production from a temperate grass-based lamb production system through targeted increases 341 in ewe PP and SR levels.
  • Genetics and genomics of reproductive performance in dairy and beef cattle

    Berry, Donagh P.; Wall, E.; Pryce, J. E.; Scottish Government’s Rural Affairs and the Environment Strategic Research 2011–2016.; Department of Environment and Primary Industries, Victoria, Australia; Dairy Futures Co-operative Research Council, Melbourne, Australia (Cambridge University Press, 2014-04)
    Excellent reproductive performance in both males and females is fundamental to profitable dairy and beef production systems. In this review we undertook a meta-analysis of genetic parameters for female reproductive performance across 55 dairy studies or populations and 12 beef studies or populations as well as across 28 different studies or populations for male reproductive performance. A plethora of reproductive phenotypes exist in dairy and beef cattle and a meta-analysis of the literature suggests that most of the female reproductive traits in dairy and beef cattle tend to be lowly heritable (0.02 to 0.04). Reproductive-related phenotypes in male animals (e.g. semen quality) tend to be more heritable than female reproductive phenotypes with mean heritability estimates of between 0.05 and 0.22 for semen-related traits with the exception of scrotal circumference (0.42) and field non-return rate (0.001). The low heritability of reproductive traits, in females in particular, does not however imply that genetic selection cannot alter phenotypic performance as evidenced by the decline until recently in dairy cow reproductive performance attributable in part to aggressive selection for increased milk production. Moreover, the antagonistic genetic correlations among reproductive traits and both milk (dairy cattle) and meat (beef cattle) yield is not unity thereby implying that simultaneous genetic selection for both increased (milk and meat) yield and reproductive performance is indeed possible. The required emphasis on reproductive traits within a breeding goal to halt deterioration will vary based on the underlying assumptions and is discussed using examples for Ireland, the United Kingdom and Australia as well as quantifying the impact on genetic gain for milk production. Advancements in genomic technologies can aid in increasing the accuracy of selection for especially reproductive traits and thus genetic gain. Elucidation of the underlying genomic mechanisms for reproduction could also aid in resolving genetic antagonisms. Past breeding programmes have contributed to the deterioration in reproductive performance of dairy and beef cattle. The tools now exist, however, to reverse the genetic trends in reproductive performance underlying the observed phenotypic trends.
  • Effect of early calf-hood nutrition on the transcriptomic profile of subcutaneous adipose tissue in Holstein-Friesian bulls

    English, Anne-Marie; Waters, Sineád M; Cormican, Paul; Byrne, Colin J; Fair, Seán; Kenny, David A; Department of Agriculture, Food and the Marine; Irish Research Council; 11/S/116; GOIPG/2013/1391 (Biomed Central, 2018-04-24)
    Background Adipose tissue is a major endocrine organ and is thought to play a central role in the metabolic control of reproductive function in cattle. Plane of nutrition during early life has been shown to influence the timing of puberty in both male and female cattle, though the exact biological mechanisms involved are currently unknown. The aim of this study was to investigate the effect of early calf-hood nutrition on the transcriptomic profile of subcutaneous adipose tissue in Holstein-Friesian bulls to identify possible downstream effects on reproductive physiology. Results Holstein-Friesian bull calves with a mean (±S.D.) age and bodyweight of 19 (±8.2) days and 47.5 (±5.3) kg, respectively, were assigned to either a high (n = 10) or low (n = 10) plane of nutrition. Calves were fed in order to achieve an overall growth rate of 1.08 and 0.57 kg/day for the high and low plane of nutrition treatments, respectively. At 126 days of age, the bulls were euthanized, subcutaneous adipose tissue samples were harvested and RNAseq analysis was performed. There were 674 genes differentially expressed in adipose tissue of calves on the low compared with the high plane of nutrition (P < 0.05; FDR < 0.05; fold change > 2.0). High plane of nutrition positively altered the expression of genes across an array of putative biological processes but the most dominant cellular processes affected were cellular energy production and branched chain amino acid degradation. A high plane of nutrition caused upregulation of genes such as leptin (LEP) and adiponectin (ADIPOQ), which are known to directly affect reproductive function. Conclusions These results provide an insight into the effect of augmenting the plane of nutrition of Holstein-Friesian bull calves in the prepubertal period on the transcriptome of adipose tissue.
  • Prevalence of welfare outcomes in the weaner and finisher stages of the production cycle on 31 Irish pig farms

    van Staaveren, Nienke; Calderón Díaz, Julia A; Garcia Manzanilla, Edgar; Hanlon, Alison; Boyle, Laura A; Department of Agriculture, Food and the Marine; 11/S/107 (Biomed Central, 2018-03-27)
    Background Knowledge on the most prevalent welfare problems for pigs in different production stages is required to improve herd management plans. Thirty-one farrow-to-finish pig farms were visited between July and November 2015 to assess the welfare of pigs using the multicriteria approach of the Welfare Quality® protocol. On each farm, 6 pens were selected using proportionate stratified sampling in the first weaner (S1, 4 to 8 wks), second weaner (S2, 8 to 13 wks) and finisher stage (S3, 13 to 23 wks), excluding hospital pens. Each pen was observed for 10 min and the number of pigs affected by different welfare outcomes was recorded. The percentage of pigs affected was calculated and ranked to identify the most prevalent outcomes within each production stage. Differences between production stages were analysed using generalised linear mixed models for binomial data with pen within stage and farm as a random effect. Results Tail and ear lesions showed the highest prevalence; however, large variation was observed between farms. In S1 the most prevalent welfare outcomes (presented as median prevalence) were poor body condition (4.4%), lethargic pigs (1.5%), scouring (20.3% of pens) and huddling (3.7%). In S2 and S3 outcomes related to injurious behaviour (tail lesions: 5.9% [S2] and 10.5% [S3], ear lesions: 9.1% [S2] and 3.3% [S3], and flank lesions: 0.4% [S2] and 1.3% [S3]), lameness (0.8% [S2] and 1.1% [S3]), bursitis (3.9% [S2] and 7.5% [S3]) and hernias (1.6% [S2] and 1.8% [S3]) were more prevalent. Conclusions A large variation was observed for the recorded welfare outcomes corresponding to the different challenges pigs experience during the different stages of production on commercial pig farms. The prevalence of pigs affected by lesions caused by injurious behavior is a cause for concern and requires a collaborative approach to identify appropriate intervention strategies. This information could be used to further investigate appropriate benchmark values for different welfare outcomes that would assist the pig industry to develop appropriate health and welfare management plans to minimise welfare problems. At herd level such plans should include information on aspects of intervention, treatment, and the management of hospital pens as well as euthanasia.
  • Effect of pre-milking teat disinfection on new mastitis infection rates of dairy cows

    Gleeson, David; Flynn, Jimmy; O'Brien, Bernadette (Biomed Central, 2018-04-18)
    Background The practise of teat disinfection prior to cluster attachment for milking is being adopted by farmers in Ireland, particularly where there are herd issues with new infection rates. Pre-milking teat disinfection has been shown to reduce bacterial numbers on teat skin and to be most effective against environmental bacteria such as Escherichia coli and Streptococcus uberis. A split udder design experiment was undertaken on two research herds (A = 96 cows: B = 168 cows) to test the benefit of pre-milking teat disinfection on new mastitis infection levels. The disinfectant was applied to the left front and right hind teats of all cows in each herd and the right front and left hind teats received no disinfectant treatment prior to milking over a complete lactation. Individual quarter foremilk samples were taken on 5 occasions during the lactation and all clinical cases were recorded. The presence and number of staphylococcus and streptococcus bacteria on teat skin of a random sample of experimental cows (n = 20) was measured on 3 occasions during lactation (April, June, and October). Results Pre-milking teat disinfection had no significant impact on quarter SCC and new infection rates (P > 0.05). The median SCC was 169 (95% CI = 144–198) × 103 cells/mL and 170 (95% CI = 145–199) × 103 cells/mL for disinfected teats and non-disinfected teats, respectively. There were no differences in SCC observed between herds (A = 161 (95% CI = 127–205) × 103 cells/mL; B = 169 (95% CI = 144–198) × 103 cells/mL) over the complete lactation. Bacterial levels on teat skin were reduced significantly with pre-milking teat disinfection compared to teats receiving no disinfectant (P < 0.001). Total infections (clinical and sub-clinical) were similar for disinfected teats (n = 36) and not disinfected teats (n = 40), respectively. Staphylococcus aureus (n = 47) and Strep. uberis (n = 9) were identified as the predominant bacteria in quarter foremilk samples with both clinical and sub-clinical infections. Conclusion SCC and new infection rates were similar in non-disinfected teats and disinfected (pre-milking) teats. The routine application of pre-milking teat disinfectant in pasture-grazed herds is unlikely to be of benefit where herd SCC is below 200 × 103 cells/mL.
  • Imputation of ungenotyped parental genotypes in dairy and beef cattle from progeny genotypes

    Berry, Donagh P.; McParland, Sinead; Kearney, J.F.; Sargolzaei, M.; Mullen, Michael P.; Department of Agriculture, Food and Marine; Science Foundation Ireland; European Union; RSF-06-0353; RSF-06-0428; 1/SF/311; 09/IN.1/B2642 (Cambridge University Press, 2014-04-09)
    The objective of this study was to quantify the accuracy of imputing the genotype of parents using information on the genotype of their progeny and a family-based and population-based imputation algorithm. Two separate data sets were used, one containing both dairy and beef animals (n = 3122) with high-density genotypes (735 151 single nucleotide polymorphisms (SNPs)) and the other containing just dairy animals (n = 5489) with medium-density genotypes (51 602 SNPs). Imputation accuracy of three different genotype density panels were evaluated representing low (i.e. 6501 SNPs), medium and high density. The full genotypes of sires with genotyped half-sib progeny were masked and subsequently imputed. Genotyped half-sib progeny group sizes were altered from 4 up to 12 and the impact on imputation accuracy was quantified. Up to 157 and 258 sires were used to test the accuracy of imputation in the dairy plus beef data set and the dairy-only data set, respectively. The efficiency and accuracy of imputation was quantified as the proportion of genotypes that could not be imputed, and as both the genotype concordance rate and allele concordance rate. The median proportion of genotypes per animal that could not be imputed in the imputation process decreased as the number of genotyped half-sib progeny increased; values for the medium-density panel ranged from a median of 0.015 with a half-sib progeny group size of 4 to a median of 0.0014 to 0.0015 with a half-sib progeny group size of 8. The accuracy of imputation across different paternal half-sib progeny group sizes was similar in both data sets. Concordance rates increased considerably as the number of genotyped half-sib progeny increased from four (mean animal allele concordance rate of 0.94 in both data sets for the medium-density genotype panel) to five (mean animal allele concordance rate of 0.96 in both data sets for the medium-density genotype panel) after which it was relatively stable up to a half-sib progeny group size of eight. In the data set with dairy-only animals, sufficient sires with paternal half-sib progeny groups up to 12 were available and the withinanimal mean genotype concordance rates continued to increase up to this group size. The accuracy of imputation was worst for the low-density genotypes, especially with smaller half-sib progeny group sizes but the difference in imputation accuracy between density panels diminished as progeny group size increased; the difference between high and medium-density genotype panels was relatively small across all half-sib progeny group sizes. Where biological material or genotypes are not available on individual animals, at least five progeny can be genotyped (on either a medium or high-density genotyping platform) and the parental alleles imputed with, on average, ⩾96% accuracy.
  • A comparison of 4 predictive models of calving assistance and difficulty in dairy heifers and cows

    Fenlon, Caroline; O'Grady, Luke; Mee, John F; Butler, Stephen T.; Doherty, Michael L.; Dunnion, John; Dairy Research Ireland (Elsevier, 21/09/2017)
    The aim of this study was to build and compare predictive models of calving difficulty in dairy heifers and cows for the purpose of decision support and simulation modeling. Models to predict 3 levels of calving difficulty (unassisted, slight assistance, and considerable or veterinary assistance) were created using 4 machine learning techniques: multinomial regression, decision trees, random forests, and neural networks. The data used were sourced from 2,076 calving records in 10 Irish dairy herds. In total, 19.9 and 5.9% of calving events required slight assistance and considerable or veterinary assistance, respectively. Variables related to parity, genetics, BCS, breed, previous calving, and reproductive events and the calf were included in the analysis. Based on a stepwise regression modeling process, the variables included in the models were the dam's direct and maternal calving difficulty predicted transmitting abilities (PTA), BCS at calving, parity; calving assistance or difficulty at the previous calving; proportion of Holstein breed; sire breed; sire direct calving difficulty PTA; twinning; and 2-way interactions between calving BCS and previous calving difficulty and the direct calving difficulty PTA of dam and sire. The models were built using bootstrapping procedures on 70% of the data set. The held-back 30% of the data was used to evaluate the predictive performance of the models in terms of discrimination and calibration. The decision tree and random forest models omitted the effect of twinning and included only subsets of sire breeds. Only multinomial regression and neural networks explicitly included the modeled interactions. Calving BCS, calving difficulty PTA, and previous calving assistance ranked as highly important variables for all 4 models. The area under the receiver operating characteristic curve (ranging from 0.64 to 0.79) indicates that all of the models had good overall discriminatory power. The neural network and multinomial regression models performed best, correctly classifying 75% of calving cases and showing superior calibration, with an average error in predicted probability of 3.7 and 4.5%, respectively. The neural network and multinomial regression models developed are both suitable for use in decision-support and simulation modeling.
  • Do weaner pigs need in-feed antibiotics to ensure good health and welfare?

    Diana, Alessia; Manzanilla, Edgar G.; Calderon Diaz, Julia A.; Leonard, Finola C.; Boyle, Laura A. (PLOS, 2017-10-05)
    Antibiotics (AB) are used in intensive pig production systems to control infectious diseases and they are suspected to be a major source of antibiotic resistance. Following the ban on AB use as growth promoters in the EU, their prophylactic use in-feed is now under review. The aim of this study was to evaluate the effect of removing prophylactic in-feed AB on pig health and welfare indicators. Every Monday for six weeks, a subset of 70 pigs were weaned, tagged and sorted into two groups of 35 pigs according to weight (9.2 ± 0.6 kg). AB were removed from the diet of one group (NO, n=6) and maintained in the other group (AB, n=6) for nine weeks. Ten focal pigs were chosen per group. After c. five weeks each group was split into two pens of c.17 pigs for the following 4 weeks. Data were recorded weekly. Skin, tail, ear, flank and limb lesions of focal pigs were scored according to severity. The number of animals per group affected by health deviations was also recorded. The number of fights and harmful behaviours (ear, tail bites) per group was counted during 3×5min observations once per week. Data were analysed using mixed model equations and binomial logistic regression. At group level, AB pigs were more likely to have tail (OR=1.70; P=0.05) but less likely to have ear lesions than NO pigs (OR=0.46; P<0.05). The number of ear bites (21.4±2.15 vs. 17.3±1.61; P<0.05) and fights (6.91±0.91 vs. 5.58±0.72; P=0.09) was higher in AB than in NO pigs. There was no effect of treatment on health deviations and the frequency of these was low. Removing AB from the feed of weaner pigs had minimal effects on health and welfare indicators.
  • Finishing pigs that are divergent in feed efficiency show small differences in intestinal functionality and structure

    Metzler-Zebeli, Barbara U.; Lawlor, Peadar G; Magowan, Elizabeth; McCormack, Ursula M.; Curiao, Tania; Hollmann, Manfred; Ertl, Reinhardt; Aschenbach, Jorg R.; Zebeli, Qendrim (PLOS, 2017-04-05)
    Controversial information is available regarding the feed efficiency-related variation in intestinal size, structure and functionality in pigs. The present objective was therefore to investigate the differences in visceral organ size, intestinal morphology, mucosal enzyme activity, intestinal integrity and related gene expression in low and high RFI pigs which were reared at three different geographical locations (Austria, AT; Northern Ireland, NI; Republic of Ireland, ROI) using similar protocols. Pigs (n = 369) were ranked for their RFI between days 42 and 91 postweaning and low and high RFI pigs (n = 16 from AT, n = 24 from NI, and n = 60 from ROI) were selected. Pigs were sacrificed and sampled on ~day 110 of life. In general, RFI-related variation in intestinal size, structure and function was small. Some energy saving mechanisms and enhanced digestive and absorptive capacity were indicated in low versus high RFI pigs by shorter crypts, higher duodenal lactase and maltase activity and greater mucosal permeability (P < 0.05), but differences were mainly seen in pigs from AT and to a lesser degree in pigs from ROI. Additionally, low RFI pigs from AT had more goblet cells in duodenum but fewer in jejunum compared to high RFI pigs (P < 0.05). Together with the lower expression of TLR4 and TNFA in low versus high RFI pigs from AT and ROI (P < 0.05), these results might indicate differences in the innate immune response between low and high RFI pigs. Results demonstrated that the variation in the size of visceral organs and intestinal structure and functionality was greater between geographic location (local environmental factors) than between RFI ranks of pigs. In conclusion, present results support previous findings that the intestinal size, structure and functionality do not significantly contribute to variation in RFI of pigs.
  • The bovine paranasal sinuses: Bacterial flora, epithelial expression of nitric oxide and potential role in the in-herd persistence of respiratory disease pathogens

    Murray, Gerard M.; O'Neill, Ronan G.; Lee, Alison M.; McElroy, Maire; More, Simon J.; Monagle, Aisling; Earley, Bernadette; Cassidy, Joseph P. (PLOS, 2017-03-10)
    The bovine paranasal sinuses are a group of complex cavernous air-filled spaces, lined by respiratory epithelium, the exact function of which is unclear. While lesions affecting these sinuses are occasionally reported in cattle, their microbial flora has not been defined. Furthermore, given that the various bacterial and viral pathogens causing bovine respiratory disease (BRD) persist within herds, we speculated that the paranasal sinuses may serve as a refuge for such infectious agents. The paranasal sinuses of clinically normal cattle (n = 99) and of cattle submitted for post-mortem examination (PME: n = 34) were examined by microbial culture, PCR and serology to include bacterial and viral pathogens typically associated with BRD: Mycoplasma bovis, Histophilus somni, Mannheimia haemolytica and Pasteurella multocida, bovine respiratory syncytial virus (BRSV) and bovine parainfluenza-3 virus (BPIV-3). Overall, the paranasal sinuses were either predominantly sterile or did not contain detectable microbes (83.5%: 94.9% of clinically normal and 50.0% of cattle submitted for PME). Bacteria, including BRD causing pathogens, were identified in relatively small numbers of cattle (<10%). While serology indicated widespread exposure of both clinically normal and cattle submitted for PME to BPIV-3 and BRSV (seroprevalences of 91.6% and 84.7%, respectively), PCR identified BPIV-3 in only one animal. To further explore these findings we investigated the potential role of the antimicrobial molecule nitric oxide (NO) within paranasal sinus epithelium using immunohistochemistry. Expression of the enzyme responsible for NO synthesis, inducible nitric oxide synthase (iNOS), was detected to varying degrees in 76.5% of a sub-sample of animals suggesting production of this compound plays a similar protective role in the bovine sinus as it does in humans.
  • Genome-wide association analysis and functional annotation of positional candidate genes for feed conversion efficiency and growth rate in pigs

    Horodyska, Justyna; Hamill, Ruth M.; Varley, Patrick F.; Wimmers, Klaus (PLOS, 2017-06-12)
    Feed conversion efficiency is a measure of how well an animal converts feed into live weight and it is typically expressed as feed conversion ratio (FCR). FCR and related traits like growth rate (e.g. days to 110 kg—D110) are of high interest for animal breeders, farmers and society due to implications on animal performance, feeding costs and environmental sustainability. The objective of this study was to identify genomic regions associated with FCR and D110 in pigs. A total of 952 terminal line boars, showing an individual variation in FCR, were genotyped using 60K SNP-Chips. Markers were tested for associations with estimated breeding values (EBV) for FCR and D110. For FCR, the largest number of associated SNPs was located on chromosomes 4 (30 SNPs), 1 (25 SNPs), X (15 SNPs) and 6 (12 SNPs). The most prominent genomic regions for D110 were identified on chromosomes 15 (10 SNPs), 1 and 4 (both 9 SNPs). The most significantly associated SNPs for FCR and D110 mapped 129.8 Kb from METTL11B (chromosome 4) and 32Kb from MBD5 (chromosome 15), respectively. A list of positional genes, closest to significantly associated SNPs, was used to identify enriched pathways and biological functions related to the QTL for both traits. A number of candidate genes were significantly overrepresented in pathways of immune cell trafficking, lymphoid tissue structure, organ morphology, endocrine system function, lipid metabolism, and energy production. After resequencing the coding region of selected positional and functional candidate genes, six SNPs were genotyped in a subset of boars. SNPs in PRKDC, SELL, NR2E1 and AKRIC3 showed significant associations with EBVs for FCR/D110. The study revealed a number of chromosomal regions and candidate genes affecting FCR/D110 and pointed to corresponding biological pathways related to lipid metabolism, olfactory reception, and also immunological status.
  • Illumina MiSeq Phylogenetic Amplicon Sequencing Shows a Large Reduction of an Uncharacterised Succinivibrionaceae and an Increase of the Methanobrevibacter gottschalkii Clade in Feed Restricted Cattle

    McCabe, Matthew Sean; Cormican, Paul; Keogh, Kate; O'Connor, Aaron; O'Hara, Eoin; Palladino, Rafael Alejandro; Kenny, David A.; Waters, Sinead M. (PLOS, 2015-07-30)
    Periodic feed restriction is used in cattle production to reduce feed costs. When normal feed levels are resumed, cattle catch up to a normal weight by an acceleration of normal growth rate, known as compensatory growth, which is not yet fully understood. Illumina Miseq Phylogenetic marker amplicon sequencing of DNA extracted from rumen contents of 55 bulls showed that restriction of feed (70% concentrate, 30% grass silage) for 125 days, to levels that caused a 60% reduction of growth rate, resulted in a large increase of relative abundance of Methanobrevibacter gottschalkii clade (designated as OTU-M7), and a large reduction of an uncharacterised Succinivibrionaceae species (designated as OTU-S3004). There was a strong negative Spearman correlation (ρ = -0.72, P = <1x10-20) between relative abundances of OTU-3004 and OTU-M7 in the liquid rumen fraction. There was also a significant increase in acetate:propionate ratio (A:P) in feed restricted animals that showed a negative Spearman correlation (ρ = -0.69, P = <1x10-20) with the relative abundance of OTU-S3004 in the rumen liquid fraction but not the solid fraction, and a strong positive Spearman correlation with OTU-M7 in the rumen liquid (ρ = 0.74, P = <1x10-20) and solid (ρ = 0.69, P = <1x10-20) fractions. Reduced A:P ratios in the rumen are associated with increased feed efficiency and reduced production of methane which has a global warming potential (GWP 100 years) of 28. Succinivibrionaceae growth in the rumen was previously suggested to reduce methane emissions as some members of this family utilise hydrogen, which is also utilised by methanogens for methanogenesis, to generate succinate which is converted to propionate. Relative abundance of OTU-S3004 showed a positive Spearman correlation with propionate (ρ = 0.41, P = <0.01) but not acetate in the liquid rumen fraction.
  • The distribution of runs of homozygosity and selection signatures in six commercial meat sheep breeds

    Purfield, Deirdre C; McParland, Sinead; Wall, Eamon; Berry, Donagh P.; Department of Agriculture, Food and the Marine; 11/S/112; 14/S/849 (PLOS, 2017-05-02)
    Domestication and the subsequent selection of animals for either economic or morphological features can leave a variety of imprints on the genome of a population. Genomic regions subjected to high selective pressures often show reduced genetic diversity and frequent runs of homozygosity (ROH). Therefore, the objective of the present study was to use 42,182 autosomal SNPs to identify genomic regions in 3,191 sheep from six commercial breeds subjected to selection pressure and to quantify the genetic diversity within each breed using ROH. In addition, the historical effective population size of each breed was also estimated and, in conjunction with ROH, was used to elucidate the demographic history of the six breeds. ROH were common in the autosomes of animals in the present study, but the observed breed differences in patterns of ROH length and burden suggested differences in breed effective population size and recent management. ROH provided a sufficient predictor of the pedigree inbreeding coefficient, with an estimated correlation between both measures of 0.62. Genomic regions under putative selection were identified using two complementary algorithms; the fixation index and hapFLK. The identified regions under putative selection included candidate genes associated with skin pigmentation, body size and muscle formation; such characteristics are often sought after in modern-day breeding programs. These regions of selection frequently overlapped with high ROH regions both within and across breeds. Multiple yet uncharacterised genes also resided within putative regions of selection. This further substantiates the need for a more comprehensive annotation of the sheep genome as these uncharacterised genes may contribute to traits of interest in the animal sciences. Despite this, the regions identified as under putative selection in the current study provide an insight into the mechanisms leading to breed differentiation and genetic variation in meat production.
  • Effect of dietary restriction and subsequent re-alimentation on the transcriptional profile of bovine ruminal epithelium

    Keogh, Kate; Waters, Sinead M.; Cormican, Paul; Kelly, Alan K.; O'Shea, Emma; Kenny, David A. (PLOS, 2017-05-17)
    Compensatory growth (CG) is utilised worldwide in beef production systems as a management approach to reduce feed costs. However the underlying biology regulating the expression of CG remains to be fully elucidated. The objective of this study was to examine the effect of dietary restriction and subsequent re-alimentation induced CG on the global gene expression profile of ruminal epithelial papillae. Holstein Friesian bulls (n = 60) were assigned to one of two groups: restricted feed allowance (RES; n = 30) for 125 days (Period 1) followed by ad libitum access to feed for 55 days (Period 2) or (ii) ad libitum access to feed throughout (ADLIB; n = 30). At the end of each period, 15 animals from each treatment were slaughtered and rumen papillae harvested. mRNA was isolated from all papillae samples collected. cDNA libraries were then prepared and sequenced. Resultant reads were subsequently analysed bioinformatically and differentially expressed genes (DEGs) are defined as having a Benjamini-Hochberg P value of <0.05. During re-alimentation in Period 2, RES animals displayed CG, growing at 1.8 times the rate of their ADLIB contemporary animals in Period 2 (P < 0.001). At the end of Period 1, 64 DEGs were identified between RES and ADLIB, with only one DEG identified at the end of Period 2. When analysed within RES treatment (RES, Period 2 v Period 1), 411 DEGs were evident. Genes identified as differentially expressed in response to both dietary restriction and subsequent CG included those involved in processes such as cellular interactions and transport, protein folding and gene expression, as well as immune response. This study provides an insight into the molecular mechanisms underlying the expression of CG in rumen papillae of cattle; however the results suggest that the role of the ruminal epithelium in supporting overall animal CG may have declined by day 55 of re-alimentation.
  • Novel Graphical Analyses of Runs of Homozygosity among Species and Livestock Breeds

    Iacolina, Laura; Stronen, Astrid V.; Pertoldi, Cino; Tokarska, Małgorzata; Norgaard, Louise S.; Munoz, Joaquin; Kjaersgaard, Anders; Ruiz-Gonzalez, Aritz; Kaminski, Stanislaw; Purfield, Deirdre C (Hindawi, 2016)
    Runs of homozygosity (ROH), uninterrupted stretches of homozygous genotypes resulting from parents transmitting identical haplotypes to their offspring, have emerged as informative genome-wide estimates of autozygosity (inbreeding). We used genomic profiles based on 698 K single nucleotide polymorphisms (SNPs) from nine breeds of domestic cattle (Bos taurus) and the European bison (Bison bonasus) to investigate how ROH distributions can be compared within and among species. We focused on two length classes: 0.5–15 Mb to investigate ancient events and >15 Mb to address recent events (approximately three generations). For each length class, we chose a few chromosomes with a high number of ROH, calculated the percentage of times a SNP appeared in a ROH, and plotted the results. We selected areas with distinct patterns including regions where (1) all groups revealed an increase or decrease of ROH, (2) bison differed from cattle, (3) one cattle breed or groups of breeds differed (e.g., dairy versus meat cattle). Examination of these regions in the cattle genome showed genes potentially important for natural and human-induced selection, concerning, for example, meat and milk quality, metabolism, growth, and immune function. The comparative methodology presented here permits visual identification of regions of interest for selection, breeding programs, and conservation.

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