• Inter- and intra-reproducibility of genotypes from sheep technical replicates on Illumina and Affymetrix platforms

      Berry, Donagh; O'Brien, Aine; Wall, E.; McDermott, Kevin; Randles, Shane; Flynn, Paul; Park, Stephen D. E.; Grose, Jenny; Weld, Rebecca; McHugh, Noirin; et al. (Biomed Central, 2016-11-10)
      Background Accurate genomic analyses are predicated upon access to accurate genotype input data. The objective of this study was to quantify the reproducibility of genotype data that are generated from the same genotype platform and from different genotyping platforms. Methods Genotypes based on 51,121 single nucleotide polymorphisms (SNPs) for 84 animals that were each genotyped on Illumina and Affymetrix platforms and for another 25 animals that were each genotyped twice on the same Illumina platform were compared. Genotypes based on 11,323 SNPs for an additional 21 animals that were genotyped on two different Illumina platforms by two different service providers were also compared. Reproducibility of the results was measured as the correlation between allele counts and as genotype and allele concordance rates. Results A mean within-animal correlation of 0.9996 was found between allele counts in the 25 duplicate samples that were genotyped on the same Illumina platform and varied from 0.9963 to 1.0000 per animal. The mean (minimum, maximum) genotype and allele concordance rates per animal between the 25 duplicate samples were equal to 0.9996 (0.9968, 1.0000) and 0.9993 (0.9937, 1.0000), respectively. The concordance rate between the two different Illumina platforms was also near 1. A mean within-animal correlation of 0.9738 was found between genotypes that were generated on the Illumina and Affymetrix platforms and varied from 0.9505 to 0.9812 per animal. The mean (minimum, maximum) within-animal genotype and allele concordance rates between the Illumina and Affymetrix platforms were equal to 0.9711 (0.9418, 0.9798) and 0.9845 (0.9695, 0.9889), respectively. The genotype concordance rate across all genotypes increased from 0.9711 to 0.9949 when the SNPs used were restricted to those with three high-resolution genotype clusters which represented 75.2% of the called genotypes. Conclusions and implications Our results suggest that, regardless of the genotype platform or service provider, high genotype concordance rates are achieved especially if they are restricted to high-quality extracted DNA and SNPs that result in high-quality genotypes.
    • Inter-relationships among alternative definitions of feed efficiency in grazing lactating dairy cows

      Hurley, A. M.; Lopez-Villalobos, N.; McParland, Sinead; Kennedy, Emer; Lewis, Eva; O'Donovan, Michael; Burke, Jennifer L.; Berry, Donagh; Department of Agriculture, Food and the Marine; Marie Curie project (Elsevier for American Dairy Science Association, 2015-11-14)
      International interest in feed efficiency, and in particular energy intake and residual energy intake (REI), is intensifying due to a greater global demand for animal-derived protein and energy sources. Feed efficiency is a trait of economic importance, and yet is overlooked in national dairy cow breeding goals. This is due primarily to a lack of accurate data on commercial animals, but also a lack of clarity on the most appropriate definition of the feed intake and utilization complex. The objective of the present study was to derive alternative definitions of energetic efficiency in grazing lactating dairy cows and to quantify the inter-relationships among these alternative definitions. Net energy intake (NEI) from pasture and concentrate intake was estimated up to 8 times per lactation for 2,693 lactations from 1,412 Holstein-Friesian cows. Energy values of feed were based on the French Net Energy system where 1 UFL is the net energy requirements for lactation equivalent of 1 kg of air-dry barley. A total of 8,183 individual feed intake measurements were available. Energy balance was defined as the difference between NEI and energy expenditure. Efficiency traits were either ratio-based or residual-based; the latter were derived from least squares regression models. Residual energy intake was defined as NEI minus predicted energy to fulfill the requirements for the various energy sinks. The energy sinks (e.g., NEL, metabolic live weight) and additional contributors to energy kinetics (e.g., live weight loss) combined, explained 59% of the variation in NEI, implying that REI represented 41% of the variance in total NEI. The most efficient 10% of test-day records, as defined by REI (n = 709), on average were associated with a 7.59 UFL/d less NEI (average NEI of the entire population was 16.23 UFL/d) than the least efficient 10% of test-day records based on REI (n = 709). Additionally, the most efficient 10% of test-day records, as defined by REI, were associated with superior energy conversion efficiency (ECE, i.e., NEL divided by NEI; ECE = 0.55) compared with the least efficient 10% of test-day records (ECE = 0.33). Moreover, REI was positively correlated with energy balance, implying that more negative REI animals (i.e., deemed more efficient) are expected to be, on average, in greater negative energy balance. Many of the correlations among the 14 defined efficiency traits differed from unity, implying that each trait is measuring a different aspect of efficiency.
    • International genetic evaluations for feed intake in dairy cattle through the collation of data from multiple sources

      Berry, Donagh; Coffey, Mike P.; Pryce, J. E.; de Haas, Y.; Lovendahl, P.; Krattenmacher, N.; Crowley, J.J.; Wang, Z.; Spurlock, D.; Weigel, K.; et al. (Elsevier for American Dairy Science Association, 2014-04-13)
      Feed represents a large proportion of the variable costs in dairy production systems. The omission of feed intake measures explicitly from national dairy cow breeding objectives is predominantly due to a lack of information from which to make selection decisions. However, individual cow feed intake data are available in different countries, mostly from research or nucleus herds. None of these data sets are sufficiently large enough on their own to generate accurate genetic evaluations. In the current study, we collate data from 10 populations in 9 countries and estimate genetic parameters for dry matter intake (DMI). A total of 224,174 test-day records from 10,068 parity 1 to 5 records of 6,957 cows were available, as well as records from 1,784 growing heifers. Random regression models were fit to the lactating cow test-day records and predicted feed intake at 70 d postcalving was extracted from these fitted profiles. The random regression model included a fixed polynomial regression for each lactation separately, as well as herd-year-season of calving and experimental treatment as fixed effects; random effects fit in the model included individual animal deviation from the fixed regression for each parity as well as mean herd-specific deviations from the fixed regression. Predicted DMI at 70 d postcalving was used as the phenotype for the subsequent genetic analyses undertaken using an animal repeatability model. Heritability estimates of predicted cow feed intake 70 d postcalving was 0.34 across the entire data set and varied, within population, from 0.08 to 0.52. Repeatability of feed intake across lactations was 0.66. Heritability of feed intake in the growing heifers was 0.20 to 0.34 in the 2 populations with heifer data. The genetic correlation between feed intake in lactating cows and growing heifers was 0.67. A combined pedigree and genomic relationship matrix was used to improve linkages between populations for the estimation of genetic correlations of DMI in lactating cows; genotype information was available on 5,429 of the animals. Populations were categorized as North America, grazing, other low input, and high input European Union. Albeit associated with large standard errors, genetic correlation estimates for DMI between populations varied from 0.14 to 0.84 but were stronger (0.76 to 0.84) between the populations representative of high-input production systems. Genetic correlations with the grazing populations were weak to moderate, varying from 0.14 to 0.57. Genetic evaluations for DMI can be undertaken using data collated from international populations; however, genotype-by-environment interactions with grazing production systems need to be considered.
    • Intestinal microbiota profiles associated with low and high residual feed intake in chickens across two geographical locations

      Siegerstetter, Sina-Catherine; Schmitz-Esser, Stephan; Magowan, Elizabeth; Wetzels, Stefanie Urimare; Zebeli, Qendrim; Lawlor, Peadar G; O'Connell, Niamh E.; Metzler-Zebeli, Barbara U.; European Union; 311794 (PLOS, 2017-11-15)
      Intestinal microbe-host interactions can affect the feed efficiency (FE) of chickens. As inconsistent findings for FE-associated bacterial taxa were reported across studies, the present objective was to identify whether bacterial profiles and predicted metabolic functions that were associated with residual feed intake (RFI) and performance traits in female and male chickens were consistent across two different geographical locations. At six weeks of life, the microbiota in ileal, cecal and fecal samples of low (n = 34) and high (n = 35) RFI chickens were investigated by sequencing the V3-5 region of the 16S rRNA gene. Location-associated differences in α-diversity and relative abundances of several phyla and genera were detected. RFI-associated bacterial abundances were found at the phylum and genus level, but differed among the three intestinal sites and between males and females. Correlation analysis confirmed that, of the taxonomically classifiable bacteria, Lactobacillus (5% relative abundance) and two Lactobacillus crispatus-OTUs in feces were indicative for high RFI in females (P < 0.05). In males, Ruminococcus in cecal digesta (3.1% relative abundance) and Dorea in feces (<0.1% relative abundance) were best indicative for low RFI, whereas Acinetobacter in feces (<1.5% relative abundance) related to high RFI (P < 0.05). Predicted metabolic functions in feces of males confirmed compositional relationships as functions related to amino acid, fatty acid and vitamin metabolism correlated with low RFI, whereas an increasing abundance of bacterial signaling and interaction (i.e. cellular antigens) genes correlated with high RFI (P < 0.05). In conclusion, RFI-associated bacterial profiles could be identified across different geographical locations. Results indicated that consortia of low- abundance taxa in the ileum, ceca and feces may play a role for FE in chickens, whereby only bacterial FE-associations found in ileal and cecal digesta may serve as useful targets for dietary strategies.
    • Intra-Group Lethal Gang Aggression in Domestic Pigs (Sus scrofa domesticus)

      Camerlink, Irene; Chou, Jen-Yun; Turner, Simon P.; European Cooperation in Science and Technology; Scottish Government Strategic Research (MDPI AG, 2020-07-28)
      Intraspecific coalitional aggression is rare among all species, especially within stable social groups. We report here numerous cases of intraspecific lethal gang aggression within stable groups of domestic pigs. The objective was to describe this extreme aggression and to identify potential causes. Management data were collected from farms with (n = 23) and without (n = 19) gang aggression. From one farm, 91 victims were assessed for skin injuries and body condition score. Lethal gang aggression was significantly associated with deep straw bedding, which may be related to various other factors. Gang aggression tended to occur more in winter, and was unrelated to genetic line, breeding company, group size or feed type. It occurred equally in female-only and mixed sex groups (male-only groups were not represented), from around eight weeks of age. Injuries typically covered the whole body and were more severe on the front of the body. Victims who survived had a lower body condition score and fewer injuries than victims found dead. There are still many unknowns as to why this abnormal social behaviour occurs and it deserves further research attention, both for its applied relevance to animal welfare as for the evolutionary background of lethal gang aggression.
    • Investigating early life microbial and host transcriptomic dynamics in the bovine gastrointestinal tract

      O'Hara, Eoin (Department of Agriculture, Food, and Nutritional Science - University of Alberta, 2019)
      There is increasing concern surrounding the ability of livestock industries to meet the needs of the rising global population. The gastrointestinal microbiota of ruminants plays a critical role in feed degradation, host energy supply, but is also a substantial source of anthropogenic greenhouse gas emissions. It is proposed that dietary intervention during the first weeks of life may offer an opportunity to permanently manipulate microbial colonisation patterns of the rumen, with a view to enhancing host performance whilst mitigating climatic impacts. However, the optimum window for intervention remains to be elucidated. Despite the close relationship between the rumen and its microbes, understanding of the molecular controls of rumen development during early life is limited. In mature animals, microbial fermentation in the rumen is the principle host energy source, but the hindgut and its microbiome may play of increased importance while the rumen develops during early life. However, little is known of the hindgut microbiota and its contribution to animal growth. Study 1 investigated the temporal dynamics of the rumen microbiota in beef calves during early life using 16S rRNA sequencing, to characterise the patterns of microbial establishment in the rumen and identify the most favourable timeframe for dietary manipulation. The microbial community displayed an ordered pattern of succession during the first 3 weeks of life, but settled by day 21, indicating that this may be the limit of any timeframe for early life manipulation. Study 1 also revealed a substantial farm effect on the colonisation of certain microbial groups, including Methanobrevibacter smithii (P<0.05) and Dialister (P<0.05). Such an effect has not been reported previously and may have substantial implications in future manipulation efforts. Study 2 characterised the transcriptomic profile of rumen tissue from birth to post weaning, revealing significant enrichment in immune related genes (e.g. TLR5, LAP, TAP) and processes following birth (P<0.05). This was not associated with any depression in known tight junction genes (P>0.05), indicating that rumen permeability was not compromised. Further exploring the relationship between microbial colonisation and rumen immune function may offer an opportunity to manipulate the establishment of certain taxa. Solid feed allocation was associated with enhanced expression of genes involved in Volatile Fatty Acid (VFA) absorption (MCT1; P<0.05) and metabolism (BDH1, ACAT; P<0.05). Understanding the mechanistic control of VFA absorption and how it changes during the life-cycle of the animal will be key for the design of optimal calf nutrition strategies. Study 3 characterised the hindgut microbiota of young ruminants, and its response to fortification of milk replacer with sodium butyrate (SB). The trophic effect of butyrate on calf growth and feed efficiency (P<0.1) was associated with increased concentrations of total VFA, propionate and acetate (P<0.05) in the hindgut. Native butyrogenic bacteria Butyrivibrio and Shuttleworthia were decreased by SB (P<0.05), while the proportion of the propionate producer Phascolarctobacterium was higher (P<0.05). Mogibacterium is associated with impaired gut health and was reduced in the cecum of SB calves (P<0.05). These data show that the beneficial effects of SB on growth and performance occur in tandem with changes in the abundance of important SCFA producing and health-associated bacteria in the hindgut in milk-fed calves, and that SB supplementation may suppress butyrate biosynthesis in the gut. Therefore, efforts to improve animal performance via early life manipulation should also consider the hindgut compartments, as this may offer a method to improve animal performance during the milk-feeding period. In summary, the data presented in this thesis contributes to understanding of rumen microbial composition and molecular development during early life and shows that enhanced activity of the hindgut microbiota may contribute to early life calf growth.
    • Investigating the role of stocking rate and prolificacy potential on profitability of grass based sheep production systems

      Bohan, A.; Creighton, Philip; Boland, T.M.; Shalloo, Laurence; Earle, Elizabeth; McHugh, Noirin; Department of Agriculture, Food and the Marine; 15/S/696 (Elsevier BV, 2018-02-21)
      The objective of this study was to simulate and compare the profitability of a grass based sheep production system under three stocking rates and two prolificacy rates. Analysis was conducted using the Teagasc Lamb Production Model (TLPM), a stochastic budgetary simulation model of a sheep farm. Experimental data from the Teagasc Athenry Research Demonstration Flock was used to parameterise the model at three stocking rates (10, 12 and 14 ewes/ha) and two prolificacy potentials (1.5 and 1.8 lambs weaned per ewe joined to the ram). The TLPM assessed the performance of the key factors affecting profitability and was also used to evaluate the spread in profitability associated with some stochastic variables included in the analysis. The number of lambs weaned per hectare increased with stocking rate and prolificacy potential from 16 lambs/ha to 27 lambs/ha resulting in carcass weight produced per hectare ranging from 272 kg/ha to 474 kg/ha. Increasing stocking rates resulted in lower individual lamb performance from grass and milk, thereby increasing the proportion of lambs which required concentrate for finishing, which resulted in higher input costs on a per animal basis. As the number of lambs weaned per hectare increased, net profit increased from €361/ha to €802/ha. Across all stocking rates, increasing weaning rate from 1.5 to 1.8 lambs weaned per ewe joined increased net profit, on average, by €336/ha. Increasing stocking rate, at 1.5 lambs weaned per ewe joined, increased net profit on average by €15/ha while increasing stocking rate, at 1.8 lambs weaned per ewe joined increased net profit on average by €87/ha. Risk analysis showed that across all stocking rates the high prolificacy scenarios achieved greater profits across the variation in input variables. Results from this study indicate that lambs weaned per hectare linked with grass growth and utilisations are the key drivers of profitability on Irish grass based sheep production systems.
    • An investigation into the factors associated with ewe colostrum production

      Campion, Frank P.; Crosby, Thomas F.; Creighton, Philip; Fahey, Alan G.; Boland, Tommy M.; Teagasc Walsh Fellowship Programme (Elsevier BV, 2019-09)
      The majority of lamb mortality which occurs during the first 24 h post-partum is preventable through providing the lamb with sufficient quantities of high quality colostrum during this time. Data from seven late gestation nutrition experiments carried out at this institute between 2002 and 2014 were collated into a single data set comprising of 415 twin bearing ewes. Analysis was carried out to investigate the key drivers of ewe colostrum production excluding nutrient intake, namely body reserve mobilisation, ewe breed type, ewe age, gestation length and lamb birth weight. The volume of colostrum produced at 1 and 18 h post-partum was significantly lower than the volume recorded at 10 h post-partum (P = 0.01). Multivariate regression analysis indicated that colostrum volume during the first 18 h post-partum was influenced by lamb birth weight (P = 0.01), ewe age (P = 0.01), breed type (P = 0. 01) and gestation length (P = 0.06). Live weight change (P = 0.05) also had a significant influence on the volume of colostrum produced but BCS change did not affect colostrum production (P = 0.25). Further multivariate regression analysis indicated that IgG yield was influenced ewe breed type (P = 0.01), lamb birth weight (P = 0.02), gestation length (P = 0.05) and BCS change (P = 0.04). Live weight change (P = 0.12) and ewe age (P = 0.62) did not influence the quantity of IgG produced. Leicester ewes produced less colostrum per kg lamb birth weight at 1 h post-partum compared to all other ewe breed types (P = 0.01) and less than Suffolk ewes at 10 h post-partum (P = 0.01). The result of this analysis shows the key factors excluding ewe nutrition that drive colostrum production. Ewe breed type in particular appears to play an important role in the ability of the ewe to produce sufficient quantities of adequate quality colostrum. In conclusion the result of this analysis highlights the important factors associated with ewe colostrum volume and IgG yield excluding nutrition. In particular the overall structure of the flock such as breed type and ewe age is important when considering the ability of the flock to meet colostrum demands and hence reduce lamb mortality.
    • Investigation of molecular mechanisms underlying tetracycline resistance in thermophilic Campylobacter spp. suggests that previous reports of tet(A)-mediated resistance in these bacteria are premature

      Lynch, Caoimhe; Hawkins, Kayleigh; Lynch, Helen; Egan, John; Bolton, Declan; Coffey, Aidan; Lucey, Brigid; Department of Agriculture, Food and the Marine; Teagasc Walsh Fellowship Programme; Ref. 15/F/641; et al. (Springer Science and Business Media LLC, 2019-11-09)
      The true prevalence of tet(A), which codes for a tetracycline efflux pump, in thermophilic Camplyobacter spp. requires clarification after reports emerged in Iran (2014) and Kenya (2016) of the novel detection of tet(A) in Campylobacter. During our investigation of antibiotic resistance mechanisms in a sample of Irish thermophilic Campylobacter broiler isolates, it was determined that 100% of tetracycline-resistant isolates (n = 119) harboured tet(O). Accessory tetracycline-resistance mechanisms were considered as tetracycline minimum inhibitory concentrations ranged from 4 to ≥ 64 mg/L. Primers previously reported for the detection of tet(A) in Campylobacter failed to produce an amplicon using a positive control strain (Escherichia coli K12 SK1592 containing the pBR322 plasmid) and a selection of Campylobacter isolates. Accordingly, we designed new tet(A)-targeting primers on SnapGene2.3.2 that successfully generated a 407 bp product from the positive control strain only. Further in silico analysis using BLASTn and SnapGene2.3.2 revealed that previously reported Campylobacter tet(A) sequences deposited on GenBank shared 100% homology with Campylobacter tet(O). We postulate that this gave rise to the erroneous report of a high tet(A) prevalence among a pool of Kenyan broiler Campylobacter isolates that were tested using primers designed based on these apparent tet(A) sequences. In conclusion, further work would be required to determine whether the homology between tet(A) potentially present in Campylobacter and known tet(A) genes would be sufficient to allow amplification using the primers designed in our study. Finally, the existence of tet(A) in thermophilic Campylobacter spp. remains to be demonstrated.
    • Investigation of Prolific Sheep from UK and Ireland for Evidence on Origin of the Mutations in BMP15 (FecXG, FecXB) and GDF9 (FecGH) in Belclare and Cambridge Sheep

      Mullen, Michael P.; Hanrahan, James P; Dawn, J. Howard; Powell, Richard; Teagasc Walsh Fellowship Programme; Genesis Faraday SPARK award; Science Foundation Ireland; 07/SRC/B1156 (PLoS, 2013-01-02)
      This paper concerns the likely origin of three mutations with large effects on ovulation rate identified in the Belclare and Cambridge sheep breeds; two in the BMP15 gene (FecXG and FecXB) and the third (FecGH) in GDF9. All three mutations segregate in Belclare sheep while one, FecXB, has not been found in the Cambridge. Both Belclare and Cambridge breeds are relatively recently developed composites that have common ancestry through the use of genetic material from the Finnish Landrace and Lleyn breeds. The development of both composites also involved major contributions from exceptionally prolific ewes screened from flocks in Ireland (Belclare) and Britain (Cambridge) during the 1960s. The objective of the current study was to establish the likely origin of the mutations (FecXG, FecXB and FecGH) through analysis of DNA from Finnish Landrace and Lleyn sheep, and Galway and Texel breeds which contributed to the development of the Belclare breed. Ewes with exceptionally high prolificacy (hyper-prolific ewes) in current flocks on Irish farms were identified to simulate the screening of ewes from Irish flocks in the 1960s. DNA was obtained from: prolific ewes in extant flocks of Lleyn sheep (n = 44) on the Lleyn peninsula in Wales; hyper-prolific ewes (n = 41); prolific Galway (n = 41) ewes; Finnish Landrace (n = 124) and Texel (n = 19) ewes. The FecXG mutation was identified in Lleyn but not in Finnish Landrace, Galway or Texel sheep; FecXB was only found among the hyper-prolific ewes. The FecGH mutation was identified in the sample of Lleyn sheep. It was concluded from these findings that the Lleyn breed was the most likely source of the FecXG and FecGH mutations in Belclare and Cambridge sheep and that the FecXB mutation came from the High Fertility line that was developed using prolific ewes selected from commercial flocks in Ireland in the 1960′s and subsequently used in the genesis of the Belclare.
    • Investigations and implications of associations between mycobacterial purified protein derivative hypersensitivity and MAP-antibody ELISA in Irish dairy cows

      Kennedy, Aideen E.; Byrne, Nicky; O'Mahony, John; Sayers, Riona (Elsevier, 2017-01-21)
      Intradermal testing, involving administration of purified protein derivative (PPD), to elicit a delayed hypersensitivity (DTH) response, is used as a diagnostic tool for bovine tuberculosis (bTB) and to aid in the identification of exposure to Mycobacterium avium subspecies paratuberculosis (MAP), the causative agent of Johne's disease (JD). Further research is required to increase the diagnostic value of skin testing for MAP. The aim of this study was to investigate if animals showing DTH reactions to PPD had an associated increase in MAP ELISA response, thereby identifying potential cases of sub-clinical JD. A 139-cow dairy herd was recruited to the study. During the mandatory annual bTB test, skin thickness measurements (mm) were recorded at the site of avian and bovine PPD administration. Cows were categorised based on recording no DTH, DTH at both PPD administration sites and DTH at one PPD site only. Blood samples were collected pre and post bTB testing, and ELISA tested. Generalised estimating equations were performed to identify associations between DTH responses and MAP ELISA results. Significant associations were identified between PPD DTH responses and MAP ELISA readings. Animals with DTH at both avian and bovine PPD sites were most likely to test ELISA positive in the post-PPD period relative to other categories. Further research is required to identify whether skin thickness increases post-PPD and associated increase in ELISA response, identifies animals previously exposed to MAP, or if results are due to cross reactivity.
    • Invited review: Cattle lameness detection with accelerometers

      O'Leary, N.W.; Byrne, D.T.; O'Connor, A.H.; Shalloo, Laurence; Science Foundation Ireland; 13/IA/1977 (American Dairy Science Association, 2020-05)
      Locomotion scoring is time consuming and is not commonly completed on farms. Farmers also underestimate their herds' lameness prevalence, a knowledge gap that impedes lameness management. Automation of lameness detection could address this knowledge gap and facilitate improved lameness management. The literature pertinent to adding lameness detection to accelerometers is reviewed in this paper. Options for lameness detection systems are examined including the choice of sensor, raw data collected, variables extracted, and statistical classification methods used. Two categories of variables derived from accelerometer-based systems are examined. These categories are behavior measures such as lying and measures of gait. For example, one measure of gait is the time a leg is swinging during a gait cycle. Some behavior-focused studies have reported accuracy levels of greater than 80%. Cow gait measures have been investigated to a lesser extent than behavior. However, classification accuracies as high as 91% using gait measures have been reported with hardware likely to be practical for commercial farms. The need for even higher accuracy and potential barriers to adoption are discussed. Significant progress is still required to realize a system with sufficient specificity and sensitivity. Lameness detection systems using 1 accelerometer per cow and a resolution lower than 100 Hz with gait measurement functions are suggested to balance cost and data requirements. However, gait measurement using accelerometers is rather underdeveloped. Therefore, a high priority should be given to the development of novel gait measures and testing their ability to differentiate lame from nonlame cows.
    • Invited review: Milk lactose—Current status and future challenges in dairy cattle

      Costa, Angela; Lopez-Villalobos, N.; Sneddon, N.W.; Shalloo, Laurence; Franzoi, Marco; de Marchi, M.; Penasa, M.; University of Padova, Italy; DOR1721792/17 (Elsevier, 2019-05-10)
      Lactose is the main carbohydrate in mammals' milk, and it is responsible for the osmotic equilibrium between blood and alveolar lumen in the mammary gland. It is the major bovine milk solid, and its synthesis and concentration in milk are affected mainly by udder health and the cow's energy balance and metabolism. Because this milk compound is related to several biological and physiological factors, information on milk lactose in the literature varies from chemical properties to heritability and genetic associations with health traits that may be exploited for breeding purposes. Moreover, lactose contributes to the energy value of milk and is an important ingredient for the food and pharmaceutical industries. Despite this, lactose has seldom been included in milk payment systems, and it has never been used as an indicator trait in selection indices. The interest in lactose has increased in recent years, and a summary of existing information about lactose in the dairy sector would be beneficial for the scientific community and the dairy industry. The present review collects and summarizes knowledge about lactose by covering and linking several aspects of this trait in bovine milk. Finally, perspectives on the use of milk lactose in dairy cattle, especially for selection purposes, are outlined.
    • Invited review: Nitrogen in ruminant nutrition: A review of measurement techniques

      Hristov, A.N.; Bannink, A.; Crompton, L.A.; Huhtanen, P.; Kreuzer, M.; McGee, Mark; Nozière, P.; Reynolds, C.K.; Bayat, A.R.; Yáñez-Ruiz, D.R.; et al. (American Dairy Science Association, 2019-04-25)
      Nitrogen is a component of essential nutrients critical for the productivity of ruminants. If excreted in excess, N is also an important environmental pollutant contributing to acid deposition, eutrophication, human respiratory problems, and climate change. The complex microbial metabolic activity in the rumen and the effect on subsequent processes in the intestines and body tissues make the study of N metabolism in ruminants challenging compared with nonruminants. Therefore, using accurate and precise measurement techniques is imperative for obtaining reliable experimental results on N utilization by ruminants and evaluating the environmental impacts of N emission mitigation techniques. Changeover design experiments are as suitable as continuous ones for studying protein metabolism in ruminant animals, except when changes in body weight or carryover effects due to treatment are expected. Adaptation following a dietary change should be allowed for at least 2 (preferably 3) wk, and extended adaptation periods may be required if body pools can temporarily supply the nutrients studied. Dietary protein degradability in the rumen and intestines are feed characteristics determining the primary AA available to the host animal. They can be estimated using in situ, in vitro, or in vivo techniques with each having inherent advantages and disadvantages. Accurate, precise, and inexpensive laboratory assays for feed protein availability are still needed. Techniques used for direct determination of rumen microbial protein synthesis are laborious and expensive, and data variability can be unacceptably large; indirect approaches have not shown the level of accuracy required for widespread adoption. Techniques for studying postruminal digestion and absorption of nitrogenous compounds, urea recycling, and mammary AA metabolism are also laborious, expensive (especially the methods that use isotopes), and results can be variable, especially the methods based on measurements of digesta or blood flow. Volatile loss of N from feces and particularly urine can be substantial during collection, processing, and analysis of excreta, compromising the accuracy of measurements of total-tract N digestion and body N balance. In studying ruminant N metabolism, nutritionists should consider the longer term fate of manure N as well. Various techniques used to determine the effects of animal nutrition on total N, ammonia- or nitrous oxide-emitting potentials, as well as plant fertilizer value, of manure are available. Overall, methods to study ruminant N metabolism have been developed over 150 yr of animal nutrition research, but many of them are laborious and impractical for application on a large number of animals. The increasing environmental concerns associated with livestock production systems necessitate more accurate and reliable methods to determine manure N emissions in the context of feed composition and ruminant N metabolism.
    • Iodine concentrations in milk

      O'Brien, Bernadette; Gleeson, David E; Jordan, Kieran; Irish Dairy Levy Research Trust (Teagasc (Agriculture and Food Development Authority), Ireland, 2013)
      Iodine tends to be supplemented at farm level in the expectation of increasing cow health and fertility. There is concern that such practices may result in high milk iodine, which could affect ingredients for infant formula and, thus, dairy export markets. The objective of this study was to quantify the effect of iodine fortified feed and teat disinfection practices of dairy cows on milk iodine concentration. Thirty lactating cows were fed 7 kg, 3 kg (10 mg iodine/kg) and 0 kg of concentrate feed during 3 periods of 35 days each. During the first 14 days of each period, cows were on dietary iodine treatments only; during days 15–21, one of three teat disinfection treatments (n = 10) was applied (in addition to the dietary iodine treatments): non-iodine (chlorhexidine) post-milking spray; 0.5% iodine spray post-milking; 0.5% iodine spray pre- and post-milking. Cow milk yield was 21.3 kg/day. Individual cow milk samples were analysed for iodine concentration on 2 days at the end of each treatment period. Dietary supplementation of iodine at both 30 mg and 70 mg/day, when compared to the diet with no supplement, increased milk iodine concentrations significantly (P < 0.001) from 449 to 1034 and 915 μg/kg, respectively. Teat disinfection both pre- and post-milking increased milk iodine concentration at each of the dietary supplementation levels of 0, 30 and 70 mg/day compared with a non-iodine teat disinfectant (P < 0.001). In conclusion, both dietary iodine supplementation and teat disinfection iodine increased milk iodine concentrations in an additive manner, exceeding common target values of 250 μg/kg. As both iodine treatments can occur simultaneously on farm, supplementation strategies should be monitored.
    • Irish pig farmer's perceptions and experiences of tail and ear biting.

      Haigh, Amy; O'Driscoll, Keelin; Department of Agriculture, Food and the Marine (Biomed Central, 2019-01-01)
      Abnormal behaviours such as ear and tail biting of pigs is of significant welfare and economic concern. Currently, pig welfare legislation is under renewed focus by the EU commission and is likely to be enforced more thoroughly. The legislation prohibits routine tail docking and requires adequate enrichment to be provided. In Ireland, tail-docking is still the most utilised control mechanism to combat tail biting, but biting is still widespread even in tail-docked pigs. In addition, as pig farms are almost all fully slatted, bedding type material cannot be provided. Thus, the opinions, and practices of farmers in countries like Ireland, which may need to make significant adaptations to typical pig management systems soon, need to be considered and addressed. We carried out a survey of pig farmers during 2015 in order to gain a greater understanding of the extent of biting on Irish farms, perception on the most important preventive measures, current enrichment use and actions following outbreaks. Fifty-eight farmers from 21 Counties responded with an average herd size of 710 ± 597 sows (range 90–3000 sows). Only two farms had experienced no biting in the last year. Of the farms that had experienced tail biting (88%), 86% had also experienced ear biting. The most common concerns relating to biting were condemnation and reduced productivity of bitten pigs with both receiving an average score of 4 (most serious). Ear biting occurred most commonly in the 2nd stage (approximately 47–81 days from weaning) weaner and tail biting in the finishing stage. The most important preventive measures were felt to be taking care of animal health, restricting density, maintaining an even quality of feed/content and maintaining good air movement. Sixty-five percent of respondents added additional enrichment following an outbreak. Chains were the most common form of enrichment currently used (83%). Those not using chains favoured wood, toys and rope (17%). Identification of the most effective and accessible control and prevention measures both for the animals and for the farming community is thus essential. Improved understanding of the concerns and practices of producers, which this survey contributes to, is a first step towards this aim.
    • Labour efficiency on-farm

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

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

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

      Vimalajeewa, Dixon; Balasubramaniam, Sasitharan; O'Brien, Bernadette; Kulatunga, Chamil; Berry, Donagh P.; Science Foundation Ireland; Department of Agriculture, Food and the Marine; European Union; 13/1A/1977; 16/RC/3835; et al. (Institute of Electrical and Electronics Engineers (IEEE), 2019-04)
      Social network analysis (SNA) is a technique to study behavioral dynamics within a social group. In SNA, it is an open question whether it is possible to characterize animal-level behaviors by using group-level information. Also, it was believed that the combined use of SNA would provide a more comprehensive understanding of social dynamics. In light of these two factors, here we explain an approach to evaluate animal importance to a group by considering the variability in group-level structural information, which is computed by joining the animal- and group-level SNA measures node centrality and network entropy, respectively. Moreover, two other metrics, animal social interaction range and nearest-neighbor frequency matrix, which represent a social affiliation of each animal within the group, are computed to help address the general challenges in graph-based SNA and, thereby, improve the precision of animal importance measures. Finally, we derive the joint distribution of animal importance of the group in detecting atypical social behaviors. The approach is tested using tracking data of dairy cows. The reliability of the derived animal importance was superior to the already existing animal importance measures. To illustrate the usability of the animal importance metric, a simulation study was conducted to identify sick and estrus animals in a group. The social affiliation of sick cows was less when compared to healthy cows. Also, their individual distributions of animal importance were shifted toward the left of the mean of the animal importance distributions of healthy cows. Consequently, the joint distribution of animal importance of the group exhibited a bimodal distribution with a left tailored shape. The behavior of cows in estrus was opposite to that of sick cows. Moreover, with the increasing number of sick and estrus cows in the group, respectively, the group entropy decreased with larger variance and slightly increased with less variance. Therefore, the entropy-based animal importance metric has superior performances when evaluating animal importance to the group compared to the existing metrics. It can be used for generating alerts for the early detection of atypical social behaviors associated with, for instance, animal health, veterinary, and welfare.