• Rearing calves outdoors with and without calf jackets compared with indoor housing on calf health and live-weight performance

      Earley, Bernadette; Murray, Margaret; Farrell, J.A.; Nolan, Marie-Jean (Teagasc (Agriculture and Food Development Authority), Ireland, 2004)
      The objective of this study was to compare the effects of rearing calves outdoors, with and without all-weather calf jackets, with calves reared indoors on calf immunity and animal performance. In February 1999, male Holstein calves (mean (s.e.) weight 55 (1.90) kg) were randomly assigned to one of three treatments (n=30 per treatment): 1) outdoors with jacket, (J; mean age 19 (s.e. 2.0) days); 2) outdoors without jacket (NJ; mean age 19 (s.e. 1.8) days), and 3) indoors on straw (I; mean age 19 (s.e. 1.0) days). Calves received an individual allowance of 25 kg of milk replacer dry matter during the first 42 days with ad libitum access to a concentrate ration from day 0 to 63. The jackets were removed from the calves on day 42. Live-weight gain from day 0 to day 63 of the study was not significantly different between treatments (J, 0.79; NJ, 0.80; I, 0.80 kg). Sixty percent of the J calves and 53% of the NJ calves required four or more antibiotic treatments for respiratory disease while corresponding treatments were required for 97% of the I calves. The incidence of diarrhoea was significantly higher in both outdoor treatments compared to the I treatment. There was no significant difference in white blood cell counts or in serum immunoglobulin concentrations between treatments on days 0, 21, 42 and 63 or in in vitro interferon-γ production on day 63. It is concluded that using calf jackets on calves reared outdoors had no beneficial effect on calf performance or immune status. The incidence of respiratory disease was higher and diarrhoea incidence was lower in calves reared indoors compared with calves reared outdoors. There was no significant difference in incidences of diarrhoea and respiratory disease between the two outdoor treatments.
    • Relationship between dairy cow genetic merit and profit on commercial spring calving dairy farms

      Ramsbottom, George; Cromie, A. R.; Horan, Brendan; Berry, Donagh P. (Cambridge University Press, 2011-12)
      Because not all animal factors influencing profitability can be included in total merit breeding indices for profitability, the association between animal total merit index and true profitability, taking cognisance of all factors associated with costs and revenues, is generally not known. One method to estimate such associations is at the herd level, associating herd average genetic merit with herd profitability. The objective of this study was to primarily relate herd average genetic merit for a range of traits, including the Irish total merit index, with indicators of performance, including profitability, using correlation and multiple regression analyses. Physical, genetic and financial performance data from 1131 Irish seasonal calving pasture-based dairy farms were available following edits; data on some herds were available for more than 1 year of the 3-year study period (2007 to 2009). Herd average economic breeding index (EBI) was associated with reduced herd average phenotypic milk yield but with greater milk composition, resulting in higher milk prices. Moderate positive correlations (0.26 to 0.61) existed between genetic merit for an individual trait and average herd performance for that trait (e.g. genetic merit for milk yield and average per cow milk yield). Following adjustment for year, stocking rate, herd size and quantity of purchased feed in the multiple regression analysis, average herd EBI was positively and linearly associated with net margin per cow and per litre as well as gross revenue output per cow and per litre. The change in net margin per cow per unit change in the total merit index was h1.94 (s.e.50.42), which was not different from the expectation of h2. This study, based on a large data set of commercial herds with accurate information on profitability and genetic merit, confirms that, after accounting for confounding factors, the change in herd profitability per unit change in herd genetic merit for the total merit index is within expectations.
    • Relationship between live weight and body condition score in Irish Holstein-Friesian dairy cows

      Berry, Donagh P.; Buckley, Frank; Dillon, Pat (Teagasc (Agriculture and Food Development Authority), Ireland, 2011)
      The objective of this study was to quantify the change in live weight (LWT) per unit change in body condition score (BCS) for Irish Holstein-Friesian dairy cows. Mixed model analyses were performed on 82 948 test-day records of BCS and LWT across 11 075 lactations from 7391 cows, representing 62 commercial and 4 research herds, during the years 1999 and 2000. Factors included in the mixed models were parity, stage of the inter-calving interval and the three-way interaction between herd, year and fortnight of the calendar year at calving. Interactions between the effect of BCS and either parity or stage of the inter-calving interval were included in some models to evaluate the effect of these factors on the relationship between LWT and BCS. A moderate correlation (0.49) existed between BCS and LWT in the complete dataset, but it differed significantly with parity and stage of the inter-calving interval (range 0.36 to 0.59). Analysis of the entire dataset yielded an estimate of 50 kg LWT change per unit change in BCS and this coefficient ranged from 39 kg to 66 kg, depending on parity or the stage of the inter-calving interval. Accurate values of LWT per unit BCS are important input parameters for animal or herd-level biological models designed to evaluate the energy demands of the animal or herd.
    • The relationship between various live animal scores/measurements and carcass classification for conformation and fatness with meat yield and distribution, and ultimate carcass value

      Drennan, Michael J; McGee, Mark; Conroy, S. B.; Keane, Michael G.; Kenny, D.A.; Berry, Donagh P. (Teagasc, 2009-12-01)
      Accordingly, the primary objectives of the following study were to: (1) determine the relationship of live animal muscular and skeletal scores, ultrasonically scanned muscle and fat depth measurements of the m. longissimus dorsi, and carcass conformation and fat scores with kill-out proportion, carcass composition and value. (2) Specifically develop and test the accuracy of prediction equations for carcass meat, fat and bone proportions, derived from carcass conformation and fat scores, and develop prediction equations for total carcass composition from hind-quarter composition.
    • Residual feed intake phenotype and gender affect the expression of key genes of the lipogenesis pathway in subcutaneous adipose tissue of beef cattle

      McKenna, Clare; Porter, Richard; Keogh, Kate; Waters, Sinead M.; McGee, Mark; Kenny, David; Teagasc Walsh Fellowship Programme (Biomed Central, 2018-09-20)
      Background Feed accounts for up to 75% of costs in beef production systems, thus any improvement in feed efficiency (FE) will benefit the profitability of this enterprise. Residual feed intake (RFI) is a measure of FE that is independent of level of production. Adipose tissue (AT) is a major endocrine organ and the primary metabolic energy reservoir. It modulates a variety of processes related to FE such as lipid metabolism and glucose homeostasis and thus measures of inter-animal variation in adiposity are frequently included in the calculation of the RFI index. The aim of this study was to determine the effect of phenotypic RFI status and gender on the expression of key candidate genes related to processes involved in energy metabolism within AT. Dry matter intake (DMI) and average daily gain (ADG) were measured over a period of 70 d for 52 purebred Simmental heifers (n = 24) and bulls (n = 28) with an initial BW±SD of 372±39.6 kg and 387±50.6 kg, respectively. Residual feed intake was calculated and animals were ranked within gender by RFI into high (inefficient; n = 9 heifers and n = 8 bulls) and low (efficient; n = 9 heifers and n = 8 bulls) groups. Results Average daily gain ±SD and daily DMI ±SD for heifers and bulls were 1.2±0.4 kg and 9.1±0.5 kg, and 1.8±0.3 kg and 9.5±1 kg respectively. High RFI heifers and bulls consumed 10% and 15% more (P < 0.05) than their low RFI counterparts, respectively. Heifers had a higher expression of all genes measured than bulls (P < 0.05). A gender × RFI interaction was detected for HMGCS2(P < 0.05) in which high RFI bulls tended to have lower expression of HMGCS2 than low RFI bulls (P < 0.1), whereas high RFI heifers had higher expression than low RFI heifers (P < 0.05) and high RFI bulls (P < 0.05). SLC2A4 expression was consistently higher in subcutaneous AT of low RFI animals across gender. Conclusion The findings of this study indicate that low RFI cattle exhibit upregulation of the molecular mechanisms governing glucose metabolism in adipose tissue, in particular, glucose clearance. The decreased expression of SLC2A4 in the inefficient cattle may result in less efficient glucose metabolism in these animals. We conclude that SLC2A4 may be a potential biomarker for RFI in cattle.
    • Response to Teladorsagia circumcincta infection in Scottish Blackface lambs with divergent phenotypes for nematode resistance

      McRae, Kathryn M.; Good, Barbara; Hanrahan, James P; Glynn, Assumpta; O'Connell, Mary J.; Keane, Orla M (Elsevier, 2014-10-24)
      The objective of this study was to identify Scottish Blackface lambs that were at the extremes of the spectrum of resistance to gastrointestinal nematodes and characterise their response to an experimental nematode challenge. Lambs (n = 90) were monitored for faecal egg count (FEC) (2 samples from each of 2 independent natural infections). The most resistant (n = 10) and susceptible (n = 10) individuals were selected and challenged with 30,000 Teladorsagia circumcincta larvae (L3) at 9 months of age. Response to infection was monitored by measuring FEC, plasma pepsinogen, serum antibodies against nematode larval antigens and haematology profile, until necropsy at 71 days post infection. Worm burden, worm fecundity and the level of anti-nematode antibodies in abomasal mucosa were determined at necropsy. FEC was consistently higher in susceptible animals (P < 0.05), validating the selection method. Worm fecundity was significantly reduced in resistant animals (P = 0.03). There was also a significant correlation (r = 0.88; P < 0.001) between the number of adult worms and FEC at slaughter. There was no effect of phenotype (resistance/susceptibility) on plasma pepsinogen or on haematology profile. Phenotype had a significant effect on the level of anti-nematode IgA antibodies in serum (P < 0.01), reflecting a higher peak in resistant animals at day 7 post infection. It is concluded that significant variation in the response to gastrointestinal nematode challenge exists within the Scottish Blackface population with resistant animals displaying significantly lower FEC, lower worm fecundity and higher concentration of anti-nematode IgA antibodies in serum.
    • Responses of North American and New Zealand strains of Holstein–Friesian dairy cattle to homeostatic challenges during early and mid-lactation

      Patton, Joe; Murphy, J.J.; O'Mara, Frank P.; Butler, Stephen T. (Cambridge University Press, 2009-02)
      This study investigated the physiological basis of differences in nutrient partitioning between the North American (NA) and New Zealand (NZ) strains of Holstein Friesian cattle by determining the responses to homeostatic challenges at two stages of lactation. Glucose tolerance tests, epinephrine challenges, and insulin challenges were carried out on consecutive days commencing on day 32 ± 0.48 (mean ± s.e.m) of lactation (T1) and again commencing on day 137 ± 2.44 of lactation (T2). The insulin and non-esterified fatty acid (NEFA) responses to glucose infusion did not differ between the strains. The NZ strain had a greater clearance rate (CR) of glucose (2.04 vs. 1.66 % / min) and tended to have a shorter (34.4 vs. 41.1 min) glucose half-life (t½) at T2 when infused with glucose. The NA cows had a greater glucose response to epinephrine infusion across T1 and T2, and tended to have a greater insulin response to epinephrine infusion. Plasma NEFA concentration declined to similar nadir concentrations for both strains at T1 in response to insulin, though from a higher basal concentration in NA cows, resulting in a greater (-2.29 vs. -1.38) NEFA area under the response curve (AUC) for NA cows. Glucose response to insulin varied with time, tending to be greater for NA at T1, but tending to be lower for NA at T2. The results indicated that NA cows had a greater glycogenolytic response to epinephrine, but both strains had similar lipolytic responses. The results also imply that higher basal circulating NEFA concentrations in the NA strain in early lactation were not due to diminished adipose tissue responsiveness to insulin. There were indications that glucose clearance rate was greater in NZ cows in mid-lactation, and may form the basis of increased body tissue accretion during mid- to late-lactation in this strain.
    • Review of studies on flukicide residues in cows’ milk and their transfer to dairy products

      Power, C.; Sayers, Riona; O'Brien, Bernadette; Furey, A.; Danaher, Martin; Kieran, Jordan; Teagasc Walsh Fellowship Programme (Teagasc (Agriculture and Food Development Authority), Ireland, 2013)
      Flukicides are widely used to treat infestations of liver fluke in dairy cattle. This could result in flukicide residues in milk if animals are improperly treated or if withdrawal periods are not properly observed. The purpose of this review is to summarise the results of studies on depletion of flukicides from milk and the transfer of flukicide residues to dairy products, if present in the milk. As the depletion of flukicide residues from milk of animals treated during lactation was relatively slow, the studies support the view that the dry period (when milk is not being used for human consumption) is the most suitable time for flukicide treatment. Migration of residues to product occurred at different rates, depending on the drug in question. Generally, concentration of flukicides occurred in cheese, butter and skim milk powder. Pasteurisation or heat treatment during spray drying had no impact in reducing residues.
    • Risk factors associated with detailed reproductive phenotypes in dairy and beef cows

      Carthy, T. R.; Berry, Donagh P.; Fitzgerald, A.; McParland, Sinead; Williams, E. J.; Butler, Stephen T.; Cromie, A. R.; Ryan, D. (Cambridge University PRess, 2014-04-17)
      The objective of this study was to identify detailed fertility traits in dairy and beef cattle from transrectal ultrasonography records and quantify the associated risk factors. Data were available on 148 947 ultrasound observations of the reproductive tract from 75 949 cows in 843 Irish dairy and beef herds between March 2008 and October 2012. Traits generated included (1) cycling at time of examination, (2) cystic structures, (3) early ovulation, (4) embryo death and (5) uterine score; the latter was measured on a scale of 1 (good) to 4 (poor) characterising the tone of the uterine wall and fluid present in the uterus. After editing, 72 773 records from 44 415 dairy and beef cows in 643 herds remained. Factors associated with the logit of the probability of a positive outcome for each of the binary fertility traits were determined using generalised estimating equations; linear mixed model analysis was used for the analysis of uterine score. The prevalence of cycling, cystic structures, early ovulation and embryo death was 84.75%, 3.87%, 7.47% and 3.84%, respectively. The occurrence of the uterine heath score of 1, 2, 3 and 4 was 70.63%, 19.75%, 8.36% and 1.26%, respectively. Cows in beef herds had a 0.51 odds (95% CI = 0.41 to 0.63, P<0.001) of cycling at the time of examination compared with cows in dairy herds; stage of lactation at the time of examination was the same in both herd types. Furthermore, cows in dairy herds had an inferior uterine score (indicating poorer tone and a greater quantity of uterine fluid present) compared with cows in beef herds. The likelihood of cycling at the time of examination increased with parity and stage of lactation, but was reduced in cows that had experienced dystocia in the previous calving. The presence of cystic structures on the ovaries increased with parity and stage of lactation. The likelihood of embryo/foetal death increased with parity and stage of lactation. Dystocia was not associated with the presence of cystic structures or embryo death. Uterine score improved with parity and stage of lactation, while cows that experienced dystocia in the previous calving had an inferior uterine score. Heterosis was the only factor associated with increased likelihood of early ovulation. The fertility traits identified, and the associated risk factors, provide useful information on the reproductive status of dairy and beef cows.
    • Risk factors associated with lambing traits

      McHugh, Noirin; Berry, Donagh P.; Pabiou, T. (Cambridge University Press, 2015-08-12)
      The objective of this study was to establish the risk factors associated with both lambing difficulty and lamb mortality in the Irish sheep multibreed population. A total of 135 470 lambing events from 42 675 ewes in 839 Irish crossbred and purebred flocks were available. Risk factors associated with producer-scored ewe lambing difficulty score (scale of one (no difficulty) to four (severe difficulty)) were determined using linear mixed models. Risk factors associated with the logit of the probability of lamb mortality at birth (i.e. binary trait) were determined using generalised estimating equations. For each dependent variable, a series of simple regression models were developed as well as a multiple regression model. In the simple regression models, greater lambing difficulty was associated with quadruplet bearing, younger ewes, of terminal breed origin, lambing in February; for example, first parity ewes experienced greater (P<0.001) lambing difficulty (1.56±0.02) than older ewes. The association between lambing difficulty and all factors persisted in the multiple regression model, and the trend in fixed effects level solutions did not differ from the trend observed in the simple regression models. In the simple regression analyses, a greater odds of lamb mortality was associated with male lambs (1.31 times more likely of death than females), lambs of very light (2 to 3 kg) and very heavy (>7.0 kg) birth weights, quadruplet born lambs and lambs that experienced a more difficult lambing (predicted probability of death for lambs that required severe and veterinary assistance of 0.15 and 0.32, respectively); lambs from dual-purpose breeds and born to younger ewes were also at greater risk of mortality. In the multiple regression model, the association between ewe parity, age at first lambing, year of lambing and lamb mortality no longer persisted. The trend in solutions of the levels of each fixed effect that remained associated with lamb mortality in the multiple regression model, did not differ from the trends observed in the simple regression models although the differential in relative risk between the different lambing difficulty scores was greater in the multiple regression model. Results from this study show that many common flock- and animal-level factors are associated with both lambing difficulty and lamb mortality and management of different risk category groups (e.g. scanned litter sizes, ewe age groups) can be used to appropriately manage the flock at lambing to reduce their incidence.
    • Risk factors for the introduction and within-herd transmission of Mycobacterium avium subspecies paratuberculosis (MAP) infection on 59 Irish dairy herds

      Cashman, W.; Buckley, J.; Quigley, T.; Fanning, S.; More, S.; Egan, J.; Berry, Donagh P.; Grant, I.; O'Farrell, K. (Biomed Central, 2008)
      Since 1994, Irish cattle have been exposed to greater risks of acquiring Mycobacterium avium subspecies paratuberculosis (MAP) infection as a consequence of the importation of over 70,000 animals from continental Europe. In recent years, there has been an increase in the number of reported clinical cases of paratuberculosis in Ireland. This study examines the prevalence of factors that promote the introduction and within-herd transmission of Mycobacterium avium subspecies paratuberculosis (MAP) on selected Irish dairy farms in the Cork region, and the association between these factors and the results of MAP screening tests on milk sock filter residue (MFR). A total of 59 dairy farms, selected using non-random methods but apparently free of endemic paratuberculosis, were enrolled into the study. A questionnaire was used to collect data about risk factors for MAP introduction and transmission. The MFR was assessed on six occasions over 24 months for the presence of MAP, using culture and immunomagnetic separation prior to polymerase chain reaction (IMS-PCR). Furthermore, blood samples from all entire male and female animals over one year of age in 20 herds were tested by ELISA. Eighteen (31%) farms had operated as closed herds since 1994, 28 (47%) had purchased from multiple sources and 14 (24%) had either direct or indirect (progeny) contact with imported animals. Milk and colostrum were mixed on 51% of farms, while 88% of farms fed pooled milk. Thirty (51%) herds tested negative to MFR culture and IMS-PCR, 12 (20%) were MFR culture positive, 26 (44%) were IMS-PCR positive and seven (12%) were both culture and IMS-PCR positive. The probability of a positive MFR culture was significantly associated with reduced attendance at calving, and with increased use of individual calf pens and increased (but not significantly) if mulitiple suckling was practised. There was poor agreement between MFR culture and MFR IMS-PCR results, but moderate agreement between MFR culture and ELISA test results. This study highlights a lack of awareness among Irish dairy farmers about the effect of inadequate biosecurity on MAP introduction. Furthermore, within-herd transmission will be facilitated by traditional calf rearing and waste management practices. The findings of viable MAP in the presence of known transmission factors in non-clinically affected herds could be a prelude to long-term problems for the Irish cattle and agri-business generally.
    • RNA-seq analysis of differential gene expression in liver from lactating dairy cows divergent in negative energy balance

      McCabe, Matthew; Waters, Sinead M.; Morris, Dermot G.; Kenny, David J; Lynn, David J; Creevey, Christopher J. (Biomed Central, 2012-05-20)
      Background: The liver is central to most economically important metabolic processes in cattle. However, the changes in expression of genes that drive these processes remain incompletely characterised. RNA-seq is the new gold standard for whole transcriptome analysis but so far there are no reports of its application to analysis of differential gene expression in cattle liver. We used RNA-seq to study differences in expression profiles of hepatic genes and their associated pathways in individual cattle in either mild negative energy balance (MNEB) or severe negative energy balance (SNEB). NEB is an imbalance between energy intake and energy requirements for lactation and body maintenance. This aberrant metabolic state affects high-yielding dairy cows after calving and is of considerable economic importance because of its negative impact on fertility and health in dairy herds. Analysis of changes in hepatic gene expression in SNEB animals will increase our understanding of NEB and contribute to the development of strategies to circumvent it. Results: RNA-seq analysis was carried out on total RNA from liver from early post partum Holstein Friesian cows in MNEB (n = 5) and SNEB (n = 6). 12,833 genes were deemed to be expressed (>4 reads per gene per animal), 413 of which were shown to be statistically significantly differentially expressed (SDE) at a false discovery rate (FDR) of 0.1% and 200 of which were SDE (FDR of 0.1%) with a ≥2-fold change between MNEB and SNEB animals. GOseq/KEGG pathway analysis showed that SDE genes with ≥2- fold change were associated (P <0.05) with 9 KEGG pathways. Seven of these pathways were related to fatty acid metabolism and unexpectedly included ‘Steroid hormone biosynthesis’, a process which mainly occurs in the reproductive organs rather than the liver. Conclusions: RNA-seq analysis showed that the major changes at the level of transcription in the liver of SNEB cows were related to fat metabolism. 'Steroid hormone biosynthesis', a process that normally occurs in reproductive tissue, was significantly associated with changes in gene expression in the liver of SNEB cows. Changes in gene expression were found in this pathway that have not been previously been identified in SNEB cows.
    • The Roles of Whole-Genome and Small-Scale Duplications in the Functional Specialization of Saccharomyces cerevisiae Genes

      Fares, Mario A; Keane, Orla M; Toft, Christina; Carretero-Paulet, Lorenzo; Jones, Gary W (PLoS, 2013-01-03)
      Researchers have long been enthralled with the idea that gene duplication can generate novel functions, crediting this process with great evolutionary importance. Empirical data shows that whole-genome duplications (WGDs) are more likely to be retained than small-scale duplications (SSDs), though their relative contribution to the functional fate of duplicates remains unexplored. Using the map of genetic interactions and the re-sequencing of 27 Saccharomyces cerevisiae genomes evolving for 2,200 generations we show that SSD-duplicates lead to neo-functionalization while WGD-duplicates partition ancestral functions. This conclusion is supported by: (a) SSD-duplicates establish more genetic interactions than singletons and WGD-duplicates; (b) SSD-duplicates copies share more interaction-partners than WGD-duplicates copies; (c) WGDduplicates interaction partners are more functionally related than SSD-duplicates partners; (d) SSD-duplicates gene copies are more functionally divergent from one another, while keeping more overlapping functions, and diverge in their subcellular locations more than WGD-duplicates copies; and (e) SSD-duplicates complement their functions to a greater extent than WGD–duplicates. We propose a novel model that uncovers the complexity of evolution after gene duplication
    • Rumen fluke in Irish sheep: prevalence, risk factors and molecular identification of two paramphistome species

      Martinez-Ibeas, Ana M; Munita, Maria P; Lawlor, Kim; Sekiya, Mary; Mulcahy, Grace; Sayers, Riona (Biomed Central, 2016-07-18)
      Background Rumen flukes are trematode parasites found globally; in tropical and sub-tropical climates, infection can result in paramphistomosis, which can have a deleterious impact on livestock. In Europe, rumen fluke is not regarded as a clinically significant parasite, recently however, the prevalence of rumen fluke has sharply increased and several outbreaks of clinical paramphistomosis have been reported. Gaining a better understanding of rumen fluke transmission and identification of risk factors is crucial to improve the control of this parasitic disease. In this regard, a national prevalence study of rumen fluke infection and an investigation of associated risk factors were conducted in Irish sheep flocks between November 2014 and January 2015. In addition, a molecular identification of the rumen fluke species present in Ireland was carried out using an isolation method of individual eggs from faecal material coupled with a PCR. After the DNA extraction of 54 individual eggs, the nuclear fragment ITS-2 was amplified and sequenced using the same primers. Results An apparent herd prevalence of 77.3 % was determined. Several risk factors were identified including type of pasture grazed, regional variation, and sharing of the paddocks with other livestock species. A novel relationship between the Suffolk breed and higher FEC was reported for the first time. The predominant rumen fluke species found was C. daubneyi. Nevertheless, P. leydeni was unexpectedly identified infecting sheep in Ireland for the first time. Conclusions An exceptionally high prevalence of rumen fluke among Irish sheep flocks has been highlighted in this study and a more thorough investigation is necessary to analyse its economic impact. The isolation of individual eggs coupled with the PCR technique used here has proven a reliable tool for discrimination of Paramphistomum spp. This technique may facilitate forthcoming studies of the effects of paramphistomosis on livestock production. The most noteworthy finding was the identification of P. leydeni affecting sheep in Ireland, however further studies are required to clarify its implications. Also, a significant relationship between Suffolk breed and a heavier infection was found, which can be used as a starting point for future research on control strategies of rumen fluke infection.
    • Runs of homozygosity and population history in cattle

      Purfield, Deirdre C; Berry, Donagh P.; McParland, Sinead; Bradley, Daniel G (Biomed Central, 2012-08-14)
      Background: Runs of homozygosity (ROH) are contiguous lengths of homozygous genotypes that are present in an individual due to parents transmitting identical haplotypes to their offspring. The extent and frequency of ROHs may inform on the ancestry of an individual and its population. Here we use high density (n = 777,962) bi-allelic SNPs in a range of cattle breed samples to correlate ROH with the pedigree-based inbreeding coefficients and to validate subsequent analyses using 54,001 SNP genotypes. This study provides a first testing of the inference drawn from ROH through comparison with estimates of inbreeding from calculations based on the detailed pedigree data available for several breeds. Results: All animals genotyped on the HD panel displayed at least one ROH that was between 1–5 Mb in length with certain regions of the genome more likely to be involved in a ROH than others. Strong correlations (r = 0.75, p < 0.0001) existed between the pedigree-based inbreeding coefficient and a statistic based on sum of ROH of length > 0.5 KB and suggests that in the absence of an animal’s pedigree data, the extent of a genome under ROH may be used to infer aspects of recent population history even from relatively few samples. Conclusions: Our findings suggest that ROH are frequent across all breeds but differing patterns of ROH length and burden illustrate variations in breed origins and recent management.
    • Short Communication: The effect of dry period duration and dietary energy density on the rennet gelation properties of milk in early lactation

      Butler, Stephen T.; de Feu, M.A.; O'Brien, Bernadette; Guinee, Timothy P.; Murphy, J.J. (American Dairy Science Association and Elsevier Inc., 2010-02)
      This study was carried out to examine the effects of decreasing dry period duration (DP) and altering the energy density of the diet during early lactation on the rheological characteristics of milk. Forty mature Holstein-Friesian cows were used in a completely randomized design with a 2 × 2 factorial arrangement of treatments. Cows were randomly assigned to one of two dry period treatments and one of two nutritional treatments. The dry period treatments were continuous milking (CM) or an 8-week standard dry period (SDP), and the nutritional treatments were a standard energy diet (SE) or a high energy diet (HE). Actual dry period lengths were 6.3 ± 1.7 days and 62.1 ± 1.9 days for cows for the CM and SDP treatments, respectively. Milk samples were collected at 2, 6 and 10 weeks postpartum. The concentration of fat, protein and lactose was determined in each sample. The rennet gelation properties were measured at 31 ° C using dynamic low-amplitude strain oscillatory rheometry. The following parameters were obtained from the resultant elastic shear modulus (G′): gelation time (GT), maximum curd firming rate (CFRmax) and gel strength (GS). Reducing dry period duration from 62 to 6 days resulted in increases in milk protein concentration (31.8 vs. 34.7 g/kg; P < 0.001), CFRmax (2.58 vs. 3.60 Pa/min; P < 0.001) and GS (69.4 vs. 90.5 Pa; P = 0.003). Raising the dietary energy density decreased percentage milk fat (43.1 vs. 37.7 g/kg; P < 0.001) but otherwise had no effect. GS was correlated with CFRmax (r = 0.98; P < 0.001), and both variables were correlated with milk protein concentration (r = 0.71; P < 0.001, and r = 0.73; P < 0.001, respectively). The results indicate that decreasing the duration of DP increased milk protein concentration and improved the rennet gelation properties of milk, but that dietary energy density had little effect.
    • Single nucleotide polymorphisms at the imprinted bovine insulin-like growth factor 2 (IGF2) locus are associated with dairy performance in Irish Holstein-Friesian cattle

      Berkowicz, Erik W; Magee, David A; Sikora, Klaudia M.; Berry, Donagh P.; Howard, Dawn J.; Mullen, Michael Paul; Evans, Ross D.; Spillane, Charles; MacHugh, David E (Cambridge University Press: Published for the Institute of Food Research and the Hannah Research Institute, 2010-09)
      The imprinted insulin-like growth factor 2 gene (IGF2) encodes a fetal mitogenic hormone protein (IGF-II) and has previously been shown to be associated with performance in dairy cattle. In this study we assessed genotype-phenotype associations between four single nucleotide polymorphisms (SNPs) located within the bovine IGF2 locus on chromosome 29 and a range of performance traits related to milk production, animal growth and body size, fertility and progeny survival in 848 progeny-tested Irish Holstein-Friesian sires. Two of the four SNPs (rs42196909 and IGF2.g-3815A>G), which were in strong linkage disequilibrium (r 2=0.995), were associated with milk yield (Pf0.01) and milk protein yield (Pf0.05); the rs42196901 SNP was also associated (Pf0.05) with milk fat yield. Associations (Pf0.05) with milk fat percentage and milk protein percentage were observed at the rs42196901 and IGF2.g-3815A>G SNPs, respectively. The rs42196909 and IGF2.g-3815A>G SNPs were also associated with progeny carcass conformation (Pf0.05), while an association (Pf0.01) with progeny carcass weight was observed at the rs42194733 SNP locus. None of the four SNPs were associated with body size, fertility and progeny survival. These findings support previous work which suggests that the IGF2 locus is an important biological regulator of milk production in dairy cattle and add to an accumulating body of research showing that imprinted genes influence many complex performance traits in cattle.
    • Single nucleotide polymorphisms in the insulin-like growth factor 1 (IGF-1) gene are associated with performance in Holstein-Friesian dairy cattle

      Mullen, Michael Paul; Berry, Donagh P.; Howard, Dawn J.; Diskin, Michael G.; Lynch, Ciaran O.; Giblin, Linda; Kenny, David A.; Magee, David A; Meade, Kieran G; Waters, Sinead M.; Science Foundation Ireland; Department of Agriculture, Food and the Marine; 07/SRC/B1156; RSF-06-0353; RSF-06-0409; Irish Dairy Levy Research Trust (Frontiers Media SA, 16/02/2011)
      Insulin-like growth factor 1 (IGF-1) has been shown to be associated with fertility, growth, and development in cattle. The aim of this study was to (1) identify novel single nucleotide polymorphisms (SNPs) in the bovine IGF-1 gene and alongside previously identified SNPs (2) determine their association with traits of economic importance in Holstein-Friesian dairy cattle. Nine novel SNPs were identified across a panel of 22 beef and dairy cattle by sequence analysis of the 5′ promoter, intronic, and 3′ regulatory regions, encompassing ∼5 kb of IGF-1. Genotyping and associations with daughter performance for milk production, fertility, survival, and measures of body size were undertaken on 848 Holstein-Friesian AI sires. Using multiple regression analysis nominal associations (P < 0.05) were identified between six SNPs (four novel and two previously identified) and milk composition, survival, body condition score, and body size. The C allele of AF017143 a previously published SNP (C-512T) in the promoter region of IGF-1 predicted to introduce binding sites for transcription factors HSF1 and ZNF217 was associated (P < 0.05) with increased cow carcass weight (i.e., an indicator of mature cow size). Novel SNPs were identified in the 3′ region of IGF-1 were associated (P < 0.05) with functional survival and chest width. The remaining four SNPs, all located within introns of IGF-1 were associated (P < 0.05) with milk protein yield, milk fat yield, milk fat concentration, somatic cell score, carcass conformation, and carcass fat. Results of this study further demonstrate the multifaceted influences of IGF-1 on milk production and growth related traits in cattle.
    • Snpdat: Easy and rapid annotation of results from de novo snp discovery projects for model and non-model organisms

      Doran, Anthony G; Creevey, Christopher J. (Biomed Central, 2013-02-08)
      Background: Single nucleotide polymorphisms (SNPs) are the most abundant genetic variant found in vertebrates and invertebrates. SNP discovery has become a highly automated, robust and relatively inexpensive process allowing the identification of many thousands of mutations for model and non-model organisms. Annotating large numbers of SNPs can be a difficult and complex process. Many tools available are optimised for use with organisms densely sampled for SNPs, such as humans. There are currently few tools available that are species non-specific or support non-model organism data. Results: Here we present SNPdat, a high throughput analysis tool that can provide a comprehensive annotation of both novel and known SNPs for any organism with a draft sequence and annotation. Using a dataset of 4,566 SNPs identified in cattle using high-throughput DNA sequencing we demonstrate the annotations performed and the statistics that can be generated by SNPdat. Conclusions: SNPdat provides users with a simple tool for annotation of genomes that are either not supported by other tools or have a small number of annotated SNPs available. SNPdat can also be used to analyse datasets from organisms which are densely sampled for SNPs. As a command line tool it can easily be incorporated into existing SNP discovery pipelines and fills a niche for analyses involving non-model organisms that are not supported by many available SNP annotation tools. SNPdat will be of great interest to scientists involved in SNP discovery and analysis projects, particularly those with limited bioinformatics experience.
    • Snpdat: Easy and rapid annotation of results from de novo snp discovery projects for model and non-model organisms

      Doran, Anthony G; Creevey, Christopher J. (Biomed Central, 2013-02-08)
      Background: Single nucleotide polymorphisms (SNPs) are the most abundant genetic variant found in vertebrates and invertebrates. SNP discovery has become a highly automated, robust and relatively inexpensive process allowing the identification of many thousands of mutations for model and non-model organisms. Annotating large numbers of SNPs can be a difficult and complex process. Many tools available are optimised for use with organisms densely sampled for SNPs, such as humans. There are currently few tools available that are species non-specific or support non-model organism data. Results: Here we present SNPdat, a high throughput analysis tool that can provide a comprehensive annotation of both novel and known SNPs for any organism with a draft sequence and annotation. Using a dataset of 4,566 SNPs identified in cattle using high-throughput DNA sequencing we demonstrate the annotations performed and the statistics that can be generated by SNPdat. Conclusions: SNPdat provides users with a simple tool for annotation of genomes that are either not supported by other tools or have a small number of annotated SNPs available. SNPdat can also be used to analyse datasets from organisms which are densely sampled for SNPs. As a command line tool it can easily be incorporated into existing SNP discovery pipelines and fills a niche for analyses involving non-model organisms that are not supported by many available SNP annotation tools. SNPdat will be of great interest to scientists involved in SNP discovery and analysis projects, particularly those with limited bioinformatics experience.