• Alum Activates the Bovine NLRP3 Inflammasome

      Harte, Ciaran; Gorman, Aoife L.; McCluskey, S.; Carty, Michael; Bowie, Andrew G.; Scott, C. J.; Meade, Kieran G; Lavelle, Ed C.; Teagasc Walsh Fellowship Programme; Science Foundation Ireland; et al. (Frontiers, 2017-11-09)
      There has been a move away from vaccines composed of whole or inactivated antigens toward subunit-based vaccines, which although safe, provide less immunological protection. As a result, the use of adjuvants to enhance and direct adaptive immune responses has become the focus of much targeted bovine vaccine research. However, the mechanisms by which adjuvants work to enhance immunological protection in many cases remains unclear, although this knowledge is critical to the rational design of effective next generation vaccines. This study aimed to investigate the mechanisms by which alum, a commonly used adjuvant in bovine vaccines, enhances IL-1β secretion in bovine peripheral blood mononuclear cells (PBMCs). Unlike the case with human PBMCs, alum promoted IL-1β secretion in a subset of bovine PBMCs without priming with a toll-like receptor agonist. This suggests that PBMCs from some cattle are primed to produce this potent inflammatory cytokine and western blotting confirmed the presence of preexisting pro-IL-1β in PBMCs from a subset of 8-month-old cattle. To address the mechanism underlying alum-induced IL-1β secretion, specific inhibitors identified that alum mediates lysosomal disruption which subsequently activates the assembly of an NLRP3, ASC, caspase-1, and potentially caspase-8 containing complex. These components form an inflammasome, which mediates alum-induced IL-1β secretion in bovine PBMCs. Given the demonstrated role of the NLRP3 inflammasome in regulating adaptive immunity in murine systems, these results will inform further targeted research into the potential of inflammasome activation for rational vaccine design in cattle.
    • Bi-directional gene set enrichment and canonical correlation analysis identify key diet-sensitive pathways and biomarkers of metabolic syndrome.

      Morine, Melissa J; McMonagle, Jolene; Toomey, Sinead; Reynolds, Clare M; Moloney, Aidan P; Gormley, Isobel C; O Gaora, Peadar; Roche, Helen M.; Department of Agriculture, Food and the Marine; Irish Research Council for Science, Engineering and Technology; et al. (Biomed Central, 2010-10-07)
      Background Currently, a number of bioinformatics methods are available to generate appropriate lists of genes from a microarray experiment. While these lists represent an accurate primary analysis of the data, fewer options exist to contextualise those lists. The development and validation of such methods is crucial to the wider application of microarray technology in the clinical setting. Two key challenges in clinical bioinformatics involve appropriate statistical modelling of dynamic transcriptomic changes, and extraction of clinically relevant meaning from very large datasets. Results Here, we apply an approach to gene set enrichment analysis that allows for detection of bi-directional enrichment within a gene set. Furthermore, we apply canonical correlation analysis and Fisher's exact test, using plasma marker data with known clinical relevance to aid identification of the most important gene and pathway changes in our transcriptomic dataset. After a 28-day dietary intervention with high-CLA beef, a range of plasma markers indicated a marked improvement in the metabolic health of genetically obese mice. Tissue transcriptomic profiles indicated that the effects were most dramatic in liver (1270 genes significantly changed; p < 0.05), followed by muscle (601 genes) and adipose (16 genes). Results from modified GSEA showed that the high-CLA beef diet affected diverse biological processes across the three tissues, and that the majority of pathway changes reached significance only with the bi-directional test. Combining the liver tissue microarray results with plasma marker data revealed 110 CLA-sensitive genes showing strong canonical correlation with one or more plasma markers of metabolic health, and 9 significantly overrepresented pathways among this set; each of these pathways was also significantly changed by the high-CLA diet. Closer inspection of two of these pathways - selenoamino acid metabolism and steroid biosynthesis - illustrated clear diet-sensitive changes in constituent genes, as well as strong correlations between gene expression and plasma markers of metabolic syndrome independent of the dietary effect. Conclusion Bi-directional gene set enrichment analysis more accurately reflects dynamic regulatory behaviour in biochemical pathways, and as such highlighted biologically relevant changes that were not detected using a traditional approach. In such cases where transcriptomic response to treatment is exceptionally large, canonical correlation analysis in conjunction with Fisher's exact test highlights the subset of pathways showing strongest correlation with the clinical markers of interest. In this case, we have identified selenoamino acid metabolism and steroid biosynthesis as key pathways mediating the observed relationship between metabolic health and high-CLA beef. These results indicate that this type of analysis has the potential to generate novel transcriptome-based biomarkers of disease.
    • Block Chain and Internet of Nano-Things for Optimizing Chemical Sensing in Smart Farming

      Vimalajeewa, Dixon; Thakur, Subhasis; Breslin, John; Berry, Donagh P.; Balasubramaniam, Sasitharan; Science Foundation Ireland; European Union; 13/1A/1977; 16/RC/3835 (2020)
      The use of Internet of Things (IoT) with the Internet of Nano Things (IoNT) can further expand decision making systems (DMS) to improve reliability as it provides a new spectrum of more granular level data to make decisions. However, growing concerns such as data security, transparency and processing capability challenge their use in real-world applications. DMS integrated with Block Chain (BC) technology can contribute immensely to overcome such challenges. The use of IoNT and IoT along with BC for making DMS has not yet been investigated. This study proposes a BC-powered IoNT (BC-IoNT) system for sensing chemicals level in the context of farm management. This is a critical application for smart farming, which aims to improve sustainable farm practices through controlled delivery of chemicals. BC-IoNT system includes a novel machine learning model formed by using the Langmuir molecular binding model and the Bayesian theory, and is used as a smart contract for sensing the level of the chemicals. A credit model is used to quantify the traceability and credibility of farms to determine if they are compliant with the chemical standards. The accuracy of detecting the chemicals of the distributed BC-IoNT approach was ≥ 90% and the centralized approach was ≤ 80%. Also, the efficiency of sensing the level of chemicals depends on the sampling frequency and variability in chemical level among farms.
    • Breed- and trait-specific associations define the genetic architecture of calving performance traits in cattle

      Purfield, Deirdre C; Evans, Ross D; Berry, Donagh; European Union; Science Foundation Ireland; 727213; 14/IA/2576); 16/RC/3835 (Oxford University Press (OUP), 2020-05-04)
      Reducing the incidence of both the degree of assistance required at calving, as well as the extent of perinatal mortality (PM) has both economic and societal benefits. The existence of heritable genetic variability in both traits signifies the presence of underlying genomic variability. The objective of the present study was to locate regions of the genome, and by extension putative genes and mutations, that are likely to be underpinning the genetic variability in direct calving difficulty (DCD), maternal calving difficulty (MCD), and PM. Imputed whole-genome single-nucleotide polymorphism (SNP) data on up to 8,304 Angus (AA), 17,175 Charolais (CH), 16,794 Limousin (LM), and 18,474 Holstein-Friesian (HF) sires representing 5,866,712 calving events from descendants were used. Several putative quantitative trait loci (QTL) regions associated with calving performance both within and across dairy and beef breeds were identified, although the majority were both breed- and trait-specific. QTL surrounding and encompassing the myostatin (MSTN) gene were associated (P < 5 × 10−8) with DCD and PM in both the CH and LM populations. The well-known Q204X mutation was the fifth strongest association with DCD in the CH population and accounted for 5.09% of the genetic variance in DCD. In contrast, none of the 259 segregating variants in MSTN were associated (P > × 10−6) with DCD in the LM population but a genomic region 617 kb downstream of MSTN was associated (P < 5 × 10−8). The genetic architecture for DCD differed in the HF population relative to the CH and LM, where two QTL encompassing ZNF613 on Bos taurus autosome (BTA)18 and PLAG1 on BTA14 were identified in the former. Pleiotropic SNP associated with all three calving performance traits were also identified in the three beef breeds; 5 SNP were pleiotropic in AA, 116 in LM, and 882 in CH but no SNP was associated with more than one trait within the HF population. The majority of these pleiotropic SNP were on BTA2 surrounding MSTN and were associated with both DCD and PM. Multiple previously reported, but also novel QTL, associated with calving performance were detected in this large study. These also included QTL regions harboring SNP with the same direction of allele substitution effect for both DCD and MCD thus contributing to a more effective simultaneous selection for both traits.
    • Candidate genes associated with the heritable humoral response to Mycobacterium avium ssp. paratuberculosis in dairy cows have factors in common with gastrointestinal diseases in humans

      McGovern, S. P.; Purfield, Deirdre C; Ring, Siobhan C.; Carthy, Tara; Graham, David A.; Berry, Donagh; Department of Agriculture, Food and the Marine; Science Foundation Ireland; 14/IA/2576; 16/RC/3835 (Elsevier, 2019-03-07)
      Infection of cattle with bovine paratuberculosis (i.e., Johne's disease) is caused by Mycobacterium avium ssp. paratuberculosis (MAP) and results in a chronic incurable gastroenteritis. This disease, which has economic ramifications for the cattle industry, is increasing in detected prevalence globally; subclinically infected animals can silently shed the bacterium into the environment for years, exposing contemporaries and hampering disease-control programs. The objective of the present study was to first quantify the genetic parameters for humoral response to MAP in dairy cattle. This was followed by a genome-based association analysis and subsequent downstream bioinformatic analyses from imputed whole genome sequence SNP data. After edits, ELISA test records were available on 136,767 cows; analyses were also undertaken on a subset of 33,818 of these animals from herds with at least 5 MAP ELISA-positive cows, with at least 1 of those positive cows being homebred. Variance components were estimated using univariate animal and sire linear mixed models. The heritability calculated from the animal model for humoral response to MAP using alternative phenotype definitions varied from 0.02 (standard error = 0.003) to 0.05 (standard error = 0.008). The genome-based associations were undertaken within a mixed model framework using weighted deregressed estimated breeding values as a dependent variable on 1,883 phenotyped animals that were ≥87.5% Holstein-Friesian. Putative susceptibility quantitative trait loci (QTL) were identified on Bos taurus autosome 1, 3, 5, 6, 8, 9, 10, 11, 13, 14, 18, 21, 23, 25, 26, 27, and 29; mapping the most significant SNP to genes within and overlapping these QTL revealed that the most significant associations were with the 10 functional candidate genes KALRN, ZBTB20, LPP, SLA2, FI3A1, LRCH3, DNAJC6, ZDHHC14, SNX1, and HAS2. Pathway analysis failed to reveal significantly enriched biological pathways, when both bovine-specific pathway data and human ortholog data were taken into account. The existence of genetic variation for MAP susceptibility in a large data set of dairy cows signifies the potential of breeding programs for reducing MAP susceptibility. Furthermore, the identification of susceptible QTL facilitates greater biological understanding of bovine paratuberculosis and potential therapeutic targets for future investigation. The novel molecular similarities identified between bovine paratuberculosis and human inflammatory bowel disease suggest potential for human therapeutic interventions to be translated to veterinary medicine and vice versa.
    • Carcass characteristics of cattle differing in Jersey proportion

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

      Magee, David A; Berkowicz, Erik W; Sikora, Klaudia M; Berry, Donagh; Park, Stephen D. E.; Kelly, Alan K; Sweeney, Torres; Kenny, David A.; Evans, R. D.; Wickham, Brian W.; et al. (Cambridge University Press, 2010-06)
      Genetic (or ‘genomic’) imprinting, a feature of approximately 100 mammalian genes, results in monoallelic expression from one of the two parentally inherited chromosomes. To date, most studies have been directed on imprinted genes in murine or human models; however, there is burgeoning interest in the effects of imprinted genes in domestic livestock species. In particular, attention has focused on imprinted genes that influence foetal growth and development and that are associated with several economically important production traits in cattle, sheep and pigs. We have re-sequenced regions in 20 candidate bovine imprinted genes in order to validate single nucleotide polymorphisms (SNPs) that may influence important production traits in cattle. Putative SNPs detected via re-sequencing were subsequently re-formatted for high-throughput SNP genotyping in 185 cattle samples comprising 138 performance-tested European Bos taurus (all Limousin bulls), 29 African B. taurus and 18 Indian B. indicus samples. Analysis of the resulting genotypic data identified 117 validated SNPs. Preliminary genotype–phenotype association analyses using 83 SNPs that were polymorphic in the Limousin samples with minor allele frequencies >0.05 revealed significant associations between two candidate bovine imprinted genes and a range of important beef production traits: average daily gain, average feed intake, live weight, feed conversion ratio, residual feed intake and residual gain. These genes were the Ras proteinspecific guanine nucleotide releasing factor gene ( RASGRF1) and the zinc finger, imprinted 2 gene ( ZIM2). Despite the relatively small sample size used in these analyses, the observed associations with production traits are supported by the purported biological function of the RASGRF1 and ZIM2 gene products. These results support the hypothesis that imprinted genes contribute significantly to important complex production traits in cattle. Furthermore, these SNPs may be usefully incorporated into future marker-assisted and genomic selection breeding schemes.
    • Cattle stratified on genetic merit segregate on carcass characteristics, but there is scope for improvement

      Berry, Donagh; Pabiou, Thierry; Brennan, Denis; Hegarthy, Patrick J; Judge, Michelle M; Science Foundation Ireland; Department of Agriculture, Food and the Marine; European Union; 16/ RC/3835 (Oxford University Press (OUP), 2019-05-03)
      The study objective was to quantify the ability of genetic merit for a generated carcass index to differentiate animals on primal carcass cut weights using data from 1,446 herds on 9,414 heifers and 22,413 steers with weights for 14 different primal carcass cuts (plus 3 generated groups of cuts). The carcass genetic merit index was compromised of carcass weight (positive weight), conformation (positive weight), and fat score (negative weight), each equally weighted within the index. The association analyses were undertaken using linear mixed models; models were run with or without carcass weight as a covariate. In a further series of analyses, carcass weight and carcass fat score were both included as covariates in the models. Whether the association between primal cut yield and carcass weight differed by genetic merit stratum was also investigated. Genetic merit was associated (P < 0.001) with the weight of all cuts evaluated even when adjusted to a common carcass weight (P < 0.01); when simultaneously adjusted to a common carcass weight and fat score, genetic merit was not associated with the weight of the cuberoll or the group cuts termed minced-meat. The weight of the different primal cuts increased almost linearly within increasing genetic merit, with the exception of the rump and bavette. The difference in mean primal cut weight between the very low and very high genetic merit strata, as a proportion of the overall mean weight of that cut in the entire data set, varied from 0.05 (bavette) to 0.28 (eye of round); the average was 0.17. Following adjustment for differences in carcass weight, there was no difference in cut weight between the very low and very high strata for the rump, chuck tender, and mince cut group; the remaining cuts were heavier in the higher index animals with the exception of the cuberoll and bavette, which were lighter in the very high index animals. The association between carcass weight and the weight of each of the evaluated primal cuts differed (P < 0.05) by genetic merit stratum for all cuts evaluated with the exception of the rump, striploin, and brisket as well as the group cuts of frying and mincing. With the exception of these 5 primal (group) cuts, the regression coefficients of primal cut weight on carcass weight increased consistently for all traits with increasing genetic merit stratum, other than for the fillet, cuberoll, bavette, chuck and neck, and heel and shank.
    • Cervico-vaginal mucus (CVM) – an accessible source of immunologically informative biomolecules

      Adnane, Mounir; Meade, Kieran G; O’Farrelly, Cliona; Science Foundation Ireland; Health Research Board; Department of Agriculture, Food and the Marine; 12/Ia/1667; HRA_POR/2012/37; FIRM/ RSF/CoFoRD 2013–2016: ENRICH; FIRM/RSF/CoFoRD 2011-2015 (Springer Science and Business Media LLC, 2018-08-16)
      Cervico-vaginal mucus (CVM), the product of epithelial cells lining the uterus, cervix and vagina, is secreted to facilitate uterine lubrication and microbial clearance. Predominantly composed of water and mucins, CVM also contains high levels of immuno-active proteins such as immunoglobulin A (IgA), lactoferrin and lysozyme which protect against infection by blocking adhesion and mediating microbial killing. The repertoire of cytokines, chemokines and antimicrobial peptides is predominantly generated by the secretions of endometrial epithelial cells into the uterine lumen and concentrated in the CVM. The quantity and relative proportions of these inflammatory biomarkers are affected by diverse factors including the estrus cycle and health status of the animal and therefore potentially provide important diagnostic and prognostic indicators. We propose that measuring molecular signatures in bovine CVM could be a useful approach to identifying and monitoring genital tract pathologies in beef and dairy cows.
    • Choice of artificial insemination beef bulls used to mate with female dairy cattle

      Berry, Donagh; Ring, S.C.; Twomey, A.J.; Evans, R.D.; Science Foundation Ireland; Department of Agriculture, Food and the Marine; 16/RC/3835 (Elsevier for American Dairy Science Association, 2020-02)
      Understanding the preferences of dairy cattle producers when selecting beef bulls for mating can help inform beef breeding programs as well as provide default parameters in mating advice systems. The objective of the present study was to characterize the genetic merit of beef artificial insemination (AI) bulls used in dairy herds, with particular reference to traits associated with both calving performance and carcass merit. The characteristics of the beef AI bulls used were compared with those of the dairy AI bulls used on the same farms. A total of 2,733,524 AI records from 928,437 females in 5,967 Irish dairy herds were used. Sire predicted transmitting ability (PTA) values and associated reliability values for calving performance and carcass traits based on national genetic evaluations from prior to the insemination were used. Fixed effects models were used to relate both genetic merit and the associated reliability of the dairy and beef bulls used on the farm with herd size, the extent of Holstein-Friesian × Jersey crossbreeding adopted by the herd, whether the herd used a technician insemination service or do-ityourself, and the parity of the female mated. The mean direct calving difficulty PTA of the beef bulls used was 1.85 units higher than that of the dairy bulls but with over 3 times greater variability in the beef bulls. This 1.85 units equates biologically to an expectation of 1.85 more dystocia events per 100 dairy cows mated in the beef × dairy matings. The mean calving difficulty PTA of the dairy AI bulls used reduced with increasing herd size, whereas the mean calving difficulty PTA of the beef AI bulls used increased as herd size increased from 75 cows or fewer to 155 cows; the largest herds (>155 cows) used notably easier-calving beef bulls, albeit the calving difficulty PTA of the beef bulls was 3.33 units versus 1.67 units for the dairy bulls used in these herds. Although we found a general tendency for larger herds to use dairy AI bulls with lower reliability, this trend was not obvious in the beef AI bulls used. Irrespective of whether dairy or beef AI bulls were considered, herds that operated more extensive Holstein-Friesian × Jersey crossbreeding (i.e., more than 50% crossbred cows) used, on average, easier calving, shorter gestationlength bulls with lighter expected progeny carcasses of poorer conformation. Mean calving difficulty PTA of dairy bulls used increased from 1.39 in heifers to 1.79 in first-parity cows and to 1.82 in second-parity cows, remaining relatively constant thereafter. In contrast, the mean calving difficulty PTA of the beef bulls used increased consistently with cow parity. Results from the present study demonstrate a clear difference in the mean acceptable genetic merit of beef AI bulls relative to dairy AI bulls but also indicates that these acceptable limits vary by herd characteristics.
    • Concordance rate between copy number variants detected using either high- or medium-density single nucleotide polymorphism genotype panels and the potential of imputing copy number variants from flanking high density single nucleotide polymorphism haplotypes in cattle

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

      O' Connor, A.H.; Bokkers, E.A.M.; de Boer, I.J.M.; Hogeveen, H; Sayers, Riona; Byrne, Nicky; Ruelle, Elodie; Engel, E; Shalloo, Laurence; Department of Agriculture, Food and the Marine; et al. (Elsevier, 2020-06-24)
      Lameness in dairy cows is an area of concern from an economic, environmental and animal welfare point of view. While the potential risk factors associated with suboptimal mobility in non-pasture-based systems are evident throughout the literature, the same information is less abundant for pasture-based systems specifically those coupled with seasonal calving, like those in Ireland. Therefore, the objective of this study was to determine the potential risk factors associated with specific mobility scores (0 = good, 1 = imperfect, 2 = impaired, and 3 = severely impaired mobility) for pasture-based dairy cows. Various cow and herd-level potential risk factors from Irish pasture-based systems were collected and analyzed for their association with suboptimal mobility, whereby a mobility score of 0 refers to cows with optimal mobility and a mobility score ≥ 1 refers to a cow with some form of suboptimal mobility. Combined cow and herd-level statistical models were used to determine the increased or decreased risk for mobility score 1, 2, and 3 (any form of suboptimal mobility) compared to the risk for mobility score 0 (optimal mobility), as the outcome variable and the various potential risk factors at both the cow and herd-level were included as predictor type variables. Cow-level variables included body condition score, milk yield, genetic predicted transmitting ability for ‘lameness’, somatic cell score, calving month and cow breed. Herd-level variables included various environmental and management practices on farm. These analyses have identified several cow-level potential risk factors (including low body condition score, high milk yield, elevated somatic cell count, stage of lactation, calving month, and certain breed types), as well as various herd-level potential risk factors (including the amount of time taken to complete the milking process, claw trimmer training, farm layout factors and foot bathing practices) which are associated with suboptimal mobility. The results of this study should be considered by farm advisors when advising and implementing a cow/herd health program for dairy cows in pasture-based systems.
    • Differences in the bovine milk whey proteome between early pregnancy and the estrous cycle

      Johnston, Dayle; Malo Estepa, Irene; Ebhardt, H. A.; Crowe, Mark A.; Diskin, Michael G.; Science Foundation Ireland; 13/IA/2025 (Elsevier, 2018-04-12)
      Current bovine pregnancy detection methods are not reliable until at least day 28 post artificial insemination (AI). The bovine estrous cycle is approximately 21 days; consequently, producers miss an opportunity to rebreed at the next estrous event. Therefore, commercial interest exists for the discovery of novel biomarkers of pregnancy which could reliably detect pregnancy status at or before day 21 of pregnancy. The objective of the present study was to use liquid chromatography tandem mass spectrometry (LC-MS/MS) to perform a global, label-free, proteomics study on (i) milk whey and (ii) extracellular vesicle (EV) enriched milk whey samples, from day 21 of pregnancy, compared with day 21 of the estrous cycle, in order to identify potential protein biomarkers of early pregnancy. The estrous cycles of 10 dairy cows were synchronized, they went through one (control) estrous cycle and these cows were artificially inseminated during the following estrus. These cows were confirmed pregnant by ultrasound scanning. Milk whey samples were collected on day 21 of the estrous cycle and on day 21 post AI. Milk whey samples and EV enriched milk whey samples were analyzed by LC-MS/MS and subsequent analyzes of the label-free quantitative data was performed in MaxQuant and Perseus. Four proteins (APOB, SPADH1, PLIN2 and LPO) were differentially expressed between the proteomes of milk whey from day 21 of pregnancy and day 21 of the estrous cycle (P < 0.05). Ten proteins (PIGR, PGD, QSOX1, MUC1, SRPRA, MD2, GAPDH, FOLR1, GPRC5B and HHIPL2) were differentially expressed between the proteomes of EV enriched milk whey from day 21 of pregnancy and day 21 of the estrous cycle (P < 0.05). These proteins are potential milk whey biomarkers of early pregnancy.
    • Differences in the bovine milk whey proteome between early pregnancy and the estrous cycle

      Johnston, Dayle; Malo Estepa, Irene; Ebhardt, H. Alexander; Crowe, Mark; Diskin, Michael G.; Science Foundation Ireland; 13/IA/2025 (Elsevier, 2018-04-12)
      Current bovine pregnancy detection methods are not reliable until at least day 28 post artificial insemination (AI). The bovine estrous cycle is approximately 21 days; consequently, producers miss an opportunity to rebreed at the next estrous event. Therefore, commercial interest exists for the discovery of novel biomarkers of pregnancy which could reliably detect pregnancy status at or before day 21 of pregnancy. The objective of the present study was to use liquid chromatography tandem mass spectrometry (LC-MS/MS) to perform a global, label-free, proteomics study on (i) milk whey and (ii) extracellular vesicle (EV) enriched milk whey samples, from day 21 of pregnancy, compared with day 21 of the estrous cycle, in order to identify potential protein biomarkers of early pregnancy. The estrous cycles of 10 dairy cows were synchronized, they went through one (control) estrous cycle and these cows were artificially inseminated during the following estrus. These cows were confirmed pregnant by ultrasound scanning. Milk whey samples were collected on day 21 of the estrous cycle and on day 21 post AI. Milk whey samples and EV enriched milk whey samples were analyzed by LC-MS/MS and subsequent analyzes of the label-free quantitative data was performed in MaxQuant and Perseus. Four proteins (APOB, SPADH1, PLIN2 and LPO) were differentially expressed between the proteomes of milk whey from day 21 of pregnancy and day 21 of the estrous cycle (P < 0.05). Ten proteins (PIGR, PGD, QSOX1, MUC1, SRPRA, MD2, GAPDH, FOLR1, GPRC5B and HHIPL2) were differentially expressed between the proteomes of EV enriched milk whey from day 21 of pregnancy and day 21 of the estrous cycle (P < 0.05). These proteins are potential milk whey biomarkers of early pregnancy.
    • DNA sequence polymorphisms in a panel of eight candidate bovine imprinted genes and their association with performance traits in Irish Holstein-Friesian cattle

      Magee, David A; Sikora, Klaudia M; Berkowicz, Erik W; Berry, Donagh; Howard, Dawn J.; Mullen, Michael P.; Evans, R. D.; Spillane, Charles; MacHugh, David E; Department of Agriculture, Food and the Marine; et al. (Biomed Central, 2010-10-13)
      Background: Studies in mice and humans have shown that imprinted genes, whereby expression from one of the two parentally inherited alleles is attenuated or completely silenced, have a major effect on mammalian growth, metabolism and physiology. More recently, investigations in livestock species indicate that genes subject to this type of epigenetic regulation contribute to, or are associated with, several performance traits, most notably muscle mass and fat deposition. In the present study, a candidate gene approach was adopted to assess 17 validated single nucleotide polymorphisms (SNPs) and their association with a range of performance traits in 848 progeny-tested Irish Holstein-Friesian artificial insemination sires. These SNPs are located proximal to, or within, the bovine orthologs of eight genes (CALCR, GRB10, PEG3, PHLDA2, RASGRF1, TSPAN32, ZIM2 and ZNF215) that have been shown to be imprinted in cattle or in at least one other mammalian species (i.e. human/mouse/pig/sheep). Results: Heterozygosities for all SNPs analysed ranged from 0.09 to 0.46 and significant deviations from Hardy-Weinberg proportions (P ≤ 0.01) were observed at four loci. Phenotypic associations (P ≤ 0.05) were observed between nine SNPs proximal to, or within, six of the eight analysed genes and a number of performance traits evaluated, including milk protein percentage, somatic cell count, culled cow and progeny carcass weight, angularity, body conditioning score, progeny carcass conformation, body depth, rump angle, rump width, animal stature, calving difficulty, gestation length and calf perinatal mortality. Notably, SNPs within the imprinted paternally expressed gene 3 (PEG3) gene cluster were associated (P ≤ 0.05) with calving, calf performance and fertility traits, while a single SNP in the zinc finger protein 215 gene (ZNF215) was associated with milk protein percentage (P ≤ 0.05), progeny carcass weight (P ≤ 0.05), culled cow carcass weight (P ≤ 0.01), angularity (P ≤ 0.01), body depth (P ≤ 0.01), rump width (P ≤ 0.01) and animal stature (P ≤ 0.01). Conclusions: Of the eight candidate bovine imprinted genes assessed, DNA sequence polymorphisms in six of these genes (CALCR, GRB10, PEG3, RASGRF1, ZIM2 and ZNF215) displayed associations with several of the phenotypes included for analyses. The genotype-phenotype associations detected here are further supported by the biological function of these six genes, each of which plays important roles in mammalian growth, development and physiology. The associations between SNPs within the imprinted PEG3 gene cluster and traits related to calving, calf performance and gestation length suggest that this domain on chromosome 18 may play a role regulating pre-natal growth and development and fertility. SNPs within the bovine ZNF215 gene were associated with bovine growth and body conformation traits and studies in humans have revealed that the human ZNF215 ortholog belongs to the imprinted gene cluster associated with Beckwith-Wiedemann syndrome--a genetic disorder characterised by growth abnormalities. Similarly, the data presented here suggest that the ZNF215 gene may have an important role in regulating bovine growth. Collectively, our results support previous work showing that (candidate) imprinted genes/loci contribute to heritable variation in bovine performance traits and suggest that DNA sequence polymorphisms within these genes/loci represents an important reservoir of genomic markers for future genetic improvement of dairy and beef cattle populations.
    • Economic impact of different strategies to use sex-sorted sperm for reproductive management in seasonal-calving, pasture-based dairy herds

      Ruelle, E.; Shalloo, L.; Butler, S.T.; Department of Agriculture, Food and the Marine; Science Foundation Ireland; Irish Dairy Levy; 15/5/696; 16/RC/3835 (Elsevier, 2021)
      To maximize efficiency, profitability, and societal acceptance of modern dairy production, it is important to minimize the production of male dairy calves with poor beef merit. One solution involves using sex-sorted sperm (SS) to generate dairy replacements and breeding all other cows to an easy-calving, short-gestation bull with good beef merit. We used the Pasture Based Herd Dynamic Milk Model to investigate the effect of herd fertility and use of SS on farm net profit in a herd of 100 cows. This was completed by simulating herds with differing fertility performance (good, average, poor), and differing farm reproductive management [conventional semen (CONV) or SS with varying pregnancy per artificial insemination (P/AI) relative to CONV (i.e., relative P/AI 100%, 85%, and 70%)]. As an additional consideration, the method of allocating SS to cows was also examined. The first option used SS on random heifers and cows (S). The second option used SS on heifers and targeted high-fertility cows (SSel). The final option was similar to SSel, but used a fixed-time artificial insemination (AI) protocol to facilitate AI on the farm mating start date (SSync). For CONV, dairy breed semen was used for AI until 50 animals were pregnant (50% chance of a female calf), whereas for S, SSel, or SSync the target number of animals successfully conceiving with SS was set at 28 (based on assumed 90% chance of a female calf from pregnancies derived from SS). Beef breed semen was used on all other dams. The results indicated that the biggest effect on farm net profit was not based on whether or not SS was used, but instead was most affected by the overall fertility performance of the herd. Total farm profit decreased by 10% between the good and average fertility herds, and decreased by a further 12% between the average and poor fertility herds. In almost all situations, when the relative P/AI with SS was 85%, use of SS led to an overall increase of the farm net profit. There was an economic benefit of using either SSel or SSync compared with S for the average and poor fertility herds but not for the good fertility herd, highlighting an interaction between SS P/AI and overall herd fertility as well as management practices. If the relative P/AI with SS was <70%, the use of SS led to a decrease in profitability in all simulations except for SSync, highlighting the importance of a good management strategy for use of SS. The findings in this study indicated that SS has significant potential to help facilitate greater integration between the dairy and beef production sectors, as well as increase farm profitability when used appropriately.
    • The Effect of Compositional Changes Due to Seasonal Variation on Milk Density and the Determination of Season-Based Density Conversion Factors for Use in the Dairy Industry

      Parmar, Puneet; Lopez-Villalobos, Nicolas; Tobin, John T.; Murphy, Eoin; McDonagh, Arleen; Crowley, Shane V.; Kelly, Alan L.; Shalloo, Laurence; Enterprise Ireland; Science Foundation Ireland; et al. (MDPI AG, 2020-07-27)
      The objective of this study was to determine the effect of seasonal variation on milk composition and establish an algorithm to predict density based on milk composition to enable the calculation of season-based density conversion calculations. A total of 1035 raw whole milk samples were collected from morning and evening milking of 60 spring-calving individual cows of different genetic groups, namely Jersey, Elite HF (Holstein–Friesian) and National Average HF, once every two weeks for a period of 9 months (March–November, 2018). The average mean and standard deviation for milk compositional traits were 4.72 ± 1.30% fat, 3.85 ± 0.61% protein and 4.69 ± 0.30% lactose and density was estimated at 1.0308 ± 0.002 g/cm3 . The density of the milk samples was evaluated using three methods: a portable density meter, DMA 35; a standard desktop version, DMA 4500M; and an Association of Official Agricultural Chemists (AOAC) method using 100-mL glass pycnometers. Statistical analysis using a linear mixed model showed a significant difference in density of milk samples (p < 0.05) across seasonal and compositional variations adjusted for the effects of days in milk, parity, the feeding treatment, the genetic group and the measurement technique. The mean density values and standard error of mean estimated for milk samples in each season, i.e., spring, summer and autumn were 1.0304 ± 0.00008 g/cm3 , 1.0314 ± 0.00005 g/cm3 and 1.0309 ± 0.00007 g/cm3 , respectively.
    • Effect of dietary restriction and subsequent re-alimentation on the transcriptional profile of bovine jejunal epithelium

      Keogh, Kate; Waters, Sinead M.; Cormican, Paul; Kelly, Alan K.; Kenny, David A.; Science Foundation Ireland; 09/RFP/GEN2447 (Public Library of Science (PLoS), 2018-03-19)
      Compensatory growth (CG), an accelerated growth phenomenon which occurs following a period of dietary restriction is utilised worldwide in animal production systems as a management practise to lower feed costs. The objective of this study was to evaluate the contribution of jejunal epithelial to CG in cattle through transcriptional profiling following a period of dietary restriction as well as subsequent re-alimentation induced CG. Sixty Holstein Friesian bulls were separated into two groups; RES and ADLIB, with 30 animals in each. RES animals were offered a restricted diet for 125 days (Period 1) followed by ad libitum feeding for 55 days (Period 2). ADLIB animals had ad libitum access to feed across both periods 1 and 2. At the end of each period, 15 animals from each treatment group were slaughtered, jejunal epithelium collected and RNAseq analysis performed. Animals that were previously diet restricted underwent CG, gaining 1.8 times the rate of their non-restricted counterparts. Twenty-four genes were differentially expressed in RES compared to ADLIB animals at the end of Period 1, with only one gene, GSTA1, differentially expressed between the two groups at the end of Period 2. When analysed within treatment (RES, Period 2 v Period 1), 31 genes were differentially expressed between diet restricted and animals undergoing CG. Dietary restriction and subsequent re-alimentation were associated with altered expression of genes involved in digestion and metabolism as well as those involved in cellular division and growth. Compensatory growth was also associated with greater expression of genes involved in cellular protection and detoxification in jejunal epithelium. This study highlights some of the molecular mechanisms regulating the response to dietary restriction and subsequent re-alimentation induced CG in cattle; however the gene expression results suggest that most of the CG in jejunal epithelium had occurred by day 55 of re-alimentation.
    • Effect of dietary restriction and subsequent re-alimentation on the transcriptional profile of bovine jejunal epithelium

      Keogh, Kate; Waters, Sinead M.; Cormican, Paul; Kelly, Alan K.; Kenny, David A.; Science Foundation Ireland; 09/ RFP/GEN2447 (Public Library of Science (PLoS), 2018-03-19)
      Compensatory growth (CG), an accelerated growth phenomenon which occurs following a period of dietary restriction is utilised worldwide in animal production systems as a management practise to lower feed costs. The objective of this study was to evaluate the contribution of jejunal epithelial to CG in cattle through transcriptional profiling following a period of dietary restriction as well as subsequent re-alimentation induced CG. Sixty Holstein Friesian bulls were separated into two groups; RES and ADLIB, with 30 animals in each. RES animals were offered a restricted diet for 125 days (Period 1) followed by ad libitum feeding for 55 days (Period 2). ADLIB animals had ad libitum access to feed across both periods 1 and 2. At the end of each period, 15 animals from each treatment group were slaughtered, jejunal epithelium collected and RNAseq analysis performed. Animals that were previously diet restricted underwent CG, gaining 1.8 times the rate of their non-restricted counterparts. Twenty-four genes were differentially expressed in RES compared to ADLIB animals at the end of Period 1, with only one gene, GSTA1, differentially expressed between the two groups at the end of Period 2. When analysed within treatment (RES, Period 2 v Period 1), 31 genes were differentially expressed between diet restricted and animals undergoing CG. Dietary restriction and subsequent re-alimentation were associated with altered expression of genes involved in digestion and metabolism as well as those involved in cellular division and growth. Compensatory growth was also associated with greater expression of genes involved in cellular protection and detoxification in jejunal epithelium. This study highlights some of the molecular mechanisms regulating the response to dietary restriction and subsequent re-alimentation induced CG in cattle; however the gene expression results suggest that most of the CG in jejunal epithelium had occurred by day 55 of re-alimentation.
    • 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.; Science Foundation Ireland; RFP/GEN2447 (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.