RSS 1.0Animal & Grassland Research & Innovation Programme
The aim of the Teagasc Animal and Grassland Research & Innovation Programme is to increase the profitability, competitiveness and sustainability of Irish livestock production through research and innovation.
Collections in this community
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Animal & Bioscience [736]
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Grassland Science [140]
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Livestock Systems [317]
Teagasc LIvestock Systems Department includes Dairy, Cattle and Sheep research. -
Pig Development [161]
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Theses - AGRIP [3]
Recent Submissions
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EUKARYOME: the rRNA gene reference database for identification of all eukaryotesMolecular identification of micro- and macroorganisms based on nuclear markers has revolutionized our understanding of their taxonomy, phylogeny and ecology. Today, research on the diversity of eukaryotes in global ecosystems heavily relies on nuclear ribosomal RNA (rRNA) markers. Here, we present the research community-curated reference database EUKARYOME for nuclear ribosomal 18S rRNA, internal transcribed spacer (ITS) and 28S rRNA markers for all eukaryotes, including metazoans (animals), protists, fungi and plants. It is particularly useful for the identification of arbuscular mycorrhizal fungi as it bridges the four commonly used molecular markers—ITS1, ITS2, 18S V4–V5 and 28S D1–D2 subregions. The key benefits of this database over other annotated reference sequence databases are that it is not restricted to certain taxonomic groups and it includes all rRNA markers. EUKARYOME also offers a number of reference long-read sequences that are derived from (meta)genomic and (meta)barcoding—a unique feature that can be used for taxonomic identification and chimera control of third-generation, long-read, high-throughput sequencing data. Taxonomic assignments of rRNA genes in the database are verified based on phylogenetic approaches. The reference datasets are available in multiple formats from the project homepage, http://www.eukaryome.org.
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Seaweed and Seaweed Bioactives for Mitigation of Enteric Methane: Challenges and OpportunitiesSeaweeds contain a myriad of nutrients and bioactives including proteins, carbohydrates and to a lesser extent lipids as well as small molecules including peptides, saponins, alkaloids and pigments. The bioactive bromoform found in the red seaweed Asparagopsis taxiformis has been identified as an agent that can reduce enteric CH4 production from livestock significantly. However, sustainable supply of this seaweed is a problem and there are some concerns over its sustainable production and potential negative environmental impacts on the ozone layer and the health impacts of bromoform. This review collates information on seaweeds and seaweed bioactives and the documented impact on CH4 emissions in vitro and in vivo as well as associated environmental, economic and health impacts.
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Annual electricity consumption prediction and future expansion analysis on dairy farms using a support vector machineThis study utilised a previously developed support vector machine (SVM) (trained using empirical data from 56 dairy farms) for predicting and analysing annual dairy farm electricity consumption to help improve the sustainability of the projected expansion of milk production in Ireland. Firstly, the capability of the SVM to predict annual electricity consumption was investigated at both a farm and catchment-level (combined consumption). Electricity consumption data were attained from 16 pasture-based, Irish dairy farms between June 2016 and May 2017 in conjunction with farm data related to herd size, milk production, infrastructural equipment and managerial tendencies, required to generate predictions using the SVM. The SVM predicted annual electricity consumption of dairy farms to within 10.4% (relative prediction error). Concurrently, catchment-level electricity consumption was predicted with an error value less than 5.0%. Secondly, an investigation was carried out to assess the impact of increasing herd size and milk production on dairy farm related electricity consumption at a catchment-level across ten hypothetical infrastructural scenarios. The dairy expansion analysis showed electricity economies of scale across all ten infrastructural scenarios. The greatest reduction in electricity consumption per litre was observed when all farms employed ground water for pre-cooling milk with two additional parlour units, reducing by 4% in 2018, relative to a base scenario (no change to infrastructural equipment). The results presented in this article demonstrate the potential effectiveness of the SVM as a macro-level simulation forecast tool for dairy farm electricity consumption that may be used to quantify the impact of milk production on electricity resources, or to offer decision support to dairy farmers.
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A Global Review of Monitoring, Modeling, and Analyses of Water Demand in Dairy FarmingThe production of milk must be balanced with the sustainable consumption of water resources to ensure the future sustainability of the global dairy industry. Thus, this review article aimed to collate and summarize the literature in the dairy water-usage domain. While green water use (e.g., rainfall) was found to be largest category of water use on both stall and pasture-based dairy farms, on-farm blue water (i.e., freshwater) may be much more susceptible to local water shortages due to the nature of its localized supply through rivers, lakes, or groundwater aquifers. Research related to freshwater use on dairy farms has focused on monitoring, modeling, and analyzing the parlor water use and free water intake of dairy cows. Parlor water use depends upon factors related to milk precooling, farm size, milking systems, farming systems, and washing practices. Dry matter intake is a prominent variable in explaining free water intake variability; however, due to the unavailability of accurate data, some studies have reported moving away from dry matter intake at the expense of prediction accuracy. Machine-learning algorithms have been shown to improve dairy water-prediction accuracy by 23%, which may allow for coarse model inputs without reducing accuracy. Accurate models of on-farm water use allow for an increased number of dairy farms to be used in water footprinting studies, as the need for physical metering equipment is mitigated.
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Synthetic Sequencing Standards: A Guide to Database Choice for Rumen Microbiota Amplicon Sequencing AnalysisOur understanding of complex microbial communities, such as those residing in the rumen, has drastically advanced through the use of high throughput sequencing (HTS) technologies. Indeed, with the use of barcoded amplicon sequencing, it is now cost effective and computationally feasible to identify individual rumen microbial genera associated with ruminant livestock nutrition, genetics, performance and greenhouse gas production. However, across all disciplines of microbial ecology, there is currently little reporting of the use of internal controls for validating HTS results. Furthermore, there is little consensus of the most appropriate reference database for analyzing rumen microbiota amplicon sequencing data. Therefore, in this study, a synthetic rumen-specific sequencing standard was used to assess the effects of database choice on results obtained from rumen microbial amplicon sequencing. Four DADA2 reference training sets (RDP, SILVA, GTDB, and RefSeq + RDP) were compared to assess their ability to correctly classify sequences included in the rumen-specific sequencing standard. In addition, two thresholds of phylogenetic bootstrapping, 50 and 80, were applied to investigate the effect of increasing stringency. Sequence classification differences were apparent amongst the databases. For example the classification of Clostridium differed between all databases, thus highlighting the need for a consistent approach to nomenclature amongst different reference databases. It is hoped the effect of database on taxonomic classification observed in this study, will encourage research groups across various microbial disciplines to develop and routinely use their own microbiome-specific reference standard to validate analysis pipelines and database choice.
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An investigation into the grazing efficiency of perennial ryegrass varietiesThe objective of this study was to compare the grazing efficiency of 30 perennial ryegrass varieties, differing in ploidy and heading date. Plots were grazed by lactating dairy cows and managed under a rotational grazing system with 19 grazing events occurring over two years. Pre-grazing and post-grazing compressed sward heights were measured with a rising plate meter. A mixed model was used to predict the post-grazing sward height of each variety based on year, grazing event, block and pre-grazing sward height. Residual grazed height (RGH) was derived as the difference between the actual and predicted post-grazing sward height and was used as the measure of grazing efficiency. Negative RGH values indicated that the actual herbage removed was greater than that predicted and so indicated a superior grazing efficiency. Varieties differed in their level of grazing efficiency (p < .001), with RGH values ranging from −0.38 to +0.34 cm. Tetraploid varieties exhibited significantly greater grazing efficiency performance than diploids (p < .001), with average RGH values of −0.13 and +0.13 cm respectively. A significant difference in grazing efficiency was found among recommended perennial ryegrass varieties that are not being recorded by mechanically harvested simulated grazing protocols. A variety reappraisal that included grazing efficiency could identify varieties capable of improving on-farm livestock productivity from grass.
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Skin Temperature of Slaughter Pigs With Tail LesionsThe aim of this study was to assess the effect of tail lesion severity on skin temperature of slaughter pigs measured at the base of the tail and the ear by infrared thermography camera and to evaluate the association between the temperature measurements. Pigs were randomly selected in the lairage, containing ~200 pigs/pen. Tail lesions were scored according to severity, using a 0-4 scale. Tail lesion scores 0 and 1 were summed as it was difficult to distinguish healed lesions from mild lesions due to animal dirtiness. In total, 269 study pigs were imaged at the two locations. The effect of tail lesion score and sex of the pig on the highest temperature of the infrared image areas were analyzed using linear mixed models. Association between the tail base and ear base temperatures was evaluated using Pearson correlation. Skin temperature measured at the base of the tail was significantly lower for tails scored 0–1 than for all other tail lesion scores (P < 0.05). Pigs with tail lesion scored 2 had significantly lower skin temperatures at the base of the tail than pigs with tail lesion scored 3 or 4 (P < 0.05) while there was no difference in skin temperature at the base of the tail between pigs with tail lesion scored 3 and 4 (P > 0.05). Skin temperature measured at the ear base was significantly lower for pigs with tail lesion scored 0–1 than pigs of all other tail lesion scores (P < 0.05) with no difference between the other scores (P > 0.05). Furthermore, there was an association between the two measurements (r = 0.50; P < 0.001). The findings suggest that even pigs with moderate tail lesions (score 2) may have general inflammation and infection, evidenced by the elevated systemic temperature compared to pigs with none or mild tail lesion (score 0–1).
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Replacing Barley and Soybean Meal With By-products, in a Pasture Based Diet, Alters Daily Methane Output and the Rumen Microbial Community in vitro Using the Rumen Simulation Technique (RUSITEC)Plant based by-products (BP) produced from food and bioethanol industries are human inedible, but can be recycled into the global food chain by ruminant livestock. However, limited data is available on the methanogenesis potential associated with supplementing a solely BP formulated concentrate to a pastoral based diet. Therefore the objective of this in vitro study was to investigate the effects of BP inclusion rate (in a formulated concentrate) to a pasture based diet on dietary digestibility, rumen fermentation patterns, methane production and the prokaryotic microbial community composition. Diets consisted of perennial ryegrass and one of two supplementary concentrates, formulated to be isonitrogenous (16% CP) and isoenergetic (12.0 MJ/ME/kg), containing either 35% BP, barley and soybean meal (BP35) or 95% BP (BP95) offered on a 50:50 basis, however, starch, NDF and fat content varied. The BPs, included in equal proportions on a DM basis, were soyhulls, palm kernel expeller and maize dried distillers grains. The BP35 diet had greater (P < 0.05) digestibility of the chemical constituents DM, OM, CP, NDF, ADF. Greater total VFA production was seen in the BP35 diet (P < 0.05). Daily methane production (mmol/day; +22.7%) and methane output per unit of total organic matter digested (MPOMD; +20.8%) were greatest in the BP35 diet (P < 0.01). Dietary treatment influenced microbial composition (PERMANOVA; P = 0.023) with a greater relative abundance of Firmicutes (adj P < 0.01) observed in the BP35. The Firmicutes:Bacteroidetes ratio was significantly reduced in the BP95 diet (P < 0.01). The relative proportions of Proteobacteria (adj P < 0.01), Succinivibrionaceae (adj P < 0.03) and Succinivibrio (adj P = 0.053) increased in the BP95 diet. The abundance of Proteobacteria was found to be negatively associated with daily methane production (rs, −0.71; P < 0.01) and MPOMD (rs, −0.65; P < 0.01). Within Proteobacteria, the relationship of methane production was maintained with the mean abundance of Succinivibrio (rs, −0.69; P < 0.01). The abundance of the Firmicutes phyla was found to be positively correlated with both daily methane production (rs, 0.79; P < 0.001) and MPOMD (rs, 0.75; P < 0.01). Based on in vitro rumen simulation data, supplementation of an exclusively BP formulated concentrate was shown to reduce daily methane output by promoting a favorable alteration to the rumen prokaryotic community.
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Impact of birth and rearing type, as well as inaccuracy of recording, on pre-weaning lamb phenotypic and genetic merit for live weight1The objective of the present study was to quantify the impact of the systematic environmental effects of both birth and rearing type on pre-weaning lamb live weight, and to evaluate the repercussions of inaccurate recording of birth and rearing type on subsequent genetic evaluations. A total of 32,548 birth weight records, 35,770 forty-day weight records and 32,548 records for average daily gain (ADG) between birth and 40-day weight from the Irish national sheep database were used. For each lamb, a new variable, birth-rearing type, reflecting both the birth and rearing type of a lamb was generated by concatenating both parameters. The association between birth-rearing type and birth weight, 40-day weight, and ADG was estimated using linear mixed models. The repercussions of inaccurate recording of birth type were determined by quantifying the impact on sire estimated breeding value (EBV; with an accuracy of ≥ 35%), where one of the lambs born in a selection of twin litter births was assumed to have died at birth but the farmer recorded the birth and rearing type as a singleton. The heaviest mean birth weight was associated with lambs born and subsequently reared as singles (5.47 kg); the lightest mean birth weight was associated with lambs born and reared as triplets (4.10 kg). The association between birth-rearing type and 40-day weight differed by dam parity (P < 0.001). Lambs reared by first parity dams as singles, irrespective of birth type were, on average, heavier at 40-day weighing than lambs reared as multiples, but as parity number increased, single-born lambs reared as twins outperformed triplet-born lambs reared as singles. Irrespective of the trait evaluated, the correlation between sire EBV estimated from the accurately recorded data and sire EBV estimated from the data with recording errors was strong ranging from 0.93 (birth weight) to 0.97 (ADG). The EBV for sires with progeny data manipulated were 0.14 kg, 0.34 kg and 5.56 g/d less for birth weight, 40-day weight and ADG, respectively, compared to their equivalent EBV calculated using accurately recorded data. Results from this study highlight the importance of precise recording of birth-rearing type by producers for the generation of accurate genetic evaluations.
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Is TB Testing Associated With Increased Blood Interferon-Gamma Levels?The Republic of Ireland reports a relatively low prevalence of Johne’s disease (JD) compared to international counterparts. Postulated reasons for this include a lower average herd size and a grass-based production system. Ireland also engages in high levels of bovine tuberculosis (bTB) testing. As interferon-gamma (IFN-γ) is believed to play a key role in protecting against JD, it is our hypothesis that administration of purified protein derivative (PPD), as part of the bTB test, is associated with a systemic increase in IFN-γ production, which may potentially limit clinical progression of the disease. We studied 265 cows (202 Friesian and 63 “Non-Friesian,” e.g., JerseyX, Norwegian Red) to assess IFN-γ levels and Mycobacterium avium subspecies paratuberculosis (MAP) antibody response before and after the bTB test. As part of the compulsory annual bTB test, avian and bovine PPD were administered at two separate cervical sites. To assess IFN-γ production, blood samples were taken before and 72 h after PPD administration. MAP antibody response was assessed before and 10 days post-PPD administration. A significant increase in MAP antibody response was identified post-bTB compared to pre-bTB response (p < 0.001). Additionally, IFN-γ production significantly increased at the post-bTB time point (p < 0.001) compared to the pre-bTB test readings. This may indicate a beneficial effect of bTB testing in controlling JD.
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Genomic identification, expression profiling, and functional characterization of CatSper channels in the bovine†Cation channels of sperm (CatSper) are sperm-specific calcium channels with identified roles in the regulation of sperm function in humans, mice, and horses. We sought to employ a comparative genomics approach to identify conserved CATSPER genes in the bovine genome, and profile their expression in reproductive tissue. We hypothesized that CATSPER proteins expressed in bull testicular tissue mediates sperm hyperactivation and their rheotactic response in the reproductive tract of the cow. Bioinformatic analysis identified all four known CATSPER genes (CATSPER 1–4) in the bovine genome, and profiling by quantitative real-time polymerase chain reaction identified site-specific variation in messenger ribonucleic acid (mRNA) expression for all four genes along the reproductive tract of the bull. Using a novel antibody against CATSPER 1, protein expression was confirmed and localized to the principal piece of bull sperm, in agreement with what has been reported in other species. Subsequent treatment of bull sperm with either the calcium chelator ethylene glycol tetraacetic acid; mibefradil, a specific blocker of CatSper channels in human sperm; or CATSPER1 antibody all significantly inhibited caffeine-induced hyperactivation and the rheotactic response, supporting the concept that the calcium influx occurs via CatSper channels. Taken together, the work here provides novel insights into expression and function of CatSper channels in bull testicular tissue and in the function of ejaculated sperm.
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The creation and evaluation of a model to simulate the probability of conception in seasonal-calving pasture-based dairy heifersBackground: Herd fertility in pasture-based dairy farms is a key driver of farm economics. Models for predicting nulliparous reproductive outcomes are rare, but age, genetics, weight, and BCS have been identified as factors influencing heifer conception. The aim of this study was to create a simulation model of heifer conception to service with thorough evaluation. Methods: Artificial Insemination service records from two research herds and ten commercial herds were provided to build and evaluate the models. All were managed as spring-calving pasture-based systems. The factors studied were related to age, genetics, and time of service. The data were split into training and testing sets and bootstrapping was used to train the models. Logistic regression (with and without random effects) and generalised additive modelling were selected as the model-building techniques. Two types of evaluation were used to test the predictive ability of the models: discrimination and calibration. Discrimination, which includes sensitivity, specificity, accuracy and ROC analysis, measures a model’s ability to distinguish between positive and negative outcomes. Calibration measures the accuracy of the predicted probabilities with the Hosmer-Lemeshow goodness-of-fit, calibration plot and calibration error. Results: After data cleaning and the removal of services with missing values, 1396 services remained to train the models and 597 were left for testing. Age, breed, genetic predicted transmitting ability for calving interval, month and year were significant in the multivariate models. The regression models also included an interaction between age and month. Year within herd was a random effect in the mixed regression model. Overall prediction accuracy was between 77.1% and 78.9%. All three models had very high sensitivity, but low specificity. The two regression models were very well-calibrated. The mean absolute calibration errors were all below 4%. Conclusion: Because the models were not adept at identifying unsuccessful services, they are not suggested for use in predicting the outcome of individual heifer services. Instead, they are useful for the comparison of services with different covariate values or as sub-models in whole-farm simulations. The mixed regression model was identified as the best model for prediction, as the random effects can be ignored and the other variables can be easily obtained or simulated.
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Rapid Communication: Large exploitable genetic variability exists to shorten age at slaughter in cattleApprehension among consumers is mounting on the efficiency by which cattle convert feedstuffs into human edible protein and energy as well as the consequential effects on the environment. Most (genetic) studies that attempt to address these issues have generally focused on efficiency metrics defined over a certain time period of an animal’s life cycle, predominantly the period representing the linear phase of growth. The age at which an animal reaches the carcass specifications for slaughter, however, is also known to vary between breeds; less is known on the extent of the within-breed variability in age at slaughter. Therefore, the objective of the present study was to quantify the phenotypic and genetic variability in the age at which cattle reach a predefined carcass weight and subcutaneous fat cover. A novel trait, labeled here as the deviation in age at slaughter (DAGE), was represented by the unexplained variability from a statistical model, with age at slaughter as the dependent variable and with the fixed effects, among others, of carcass weight and fat score (scale 1 to 15 scored by video image analysis of the carcass at slaughter). Variance components for DAGE were estimated using either a 2-step approach (i.e., the DAGE phenotype derived first and then variance components estimated) or a 1-step approach (i.e., variance components for age at slaughter estimated directly in a mixed model that included the fixed effects of, among others, carcass weight and carcass fat score as well as a random direct additive genetic effect). The raw phenotypic SD in DAGE was 44.2 d. The genetic SD and heritability for DAGE estimated using the 1-step or 2-step models varied from 14.2 to 15.1 d and from 0.23 to 0.26 (SE 0.02), respectively. Assuming the (genetic) variability in the number of days from birth to reaching a desired carcass specifications can be exploited without any associated unfavorable repercussions, considerable potential exists to improve not only the (feed) efficiency of the animal and farm system but also the environmental footprint of the system. The beauty of the approach proposed, relative to strategies that select directly for the feed intake complex and enteric methane emissions, is that data on age at slaughter are generally readily available. Of course, faster gains may potentially be achieved if a dual objective of improving animal efficiency per day coupled with reduced days to slaughter was embarked on.
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Limitation of Grassland Productivity by Low Temperature and Seasonality of GrowthThe productivity of temperate grassland is limited by the response of plants to low temperature, affecting winter persistence and seasonal growth rates. During the winter, the growth of perennial grasses is restricted by a combination of low temperature and the lack of available light, but during early spring low ground temperature is the main limiting factor. Once temperature increases, growth is stimulated, resulting in a peak in growth in spring before growth rates decline later in the season. Growth is not primarily limited by the ability to photosynthesize, but controlled by active regulatory processes that, e.g., enable plants to restrict growth and conserve resources for cold acclimation and winter survival. An insufficient ability to cold acclimate can affect winter persistence, thereby also reducing grassland productivity. While some mechanistic knowledge is available that explains how low temperature limits plant growth, the seasonal mechanisms that promote growth in response to increasing spring temperatures but restrict growth later in the season are only partially understood. Here, we assess the available knowledge of the physiological and signaling processes that determine growth, including hormonal effects, on cellular growth and on carbohydrate metabolism. Using data for grass growth in Ireland, we identify environmental factors that limit growth at different times of the year. Ideas are proposed how developmental factors, e.g., epigenetic changes, can lead to seasonality of the growth response to temperature. We also discuss perspectives for modeling grass growth and breeding to improve grassland productivity in a changing climate.
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An ultra-high density genetic linkage map of perennial ryegrass (Lolium perenne) using genotyping by sequencing (GBS) based on a reference shotgun genome assemblyBackground and aims: High density genetic linkage maps that are extensively anchored to assembled genome sequences of the organism in question are extremely useful in gene discovery. To facilitate this process in perennial ryegrass (Lolium perenne L.), a high density single nucleotide polymorphism (SNP)- and presence/absence variant (PAV)-based genetic linkage map has been developed in an F2 mapping population that has been used as a reference population in numerous studies. To provide a reference sequence to which to align genotyping by sequencing (GBS) reads, a shotgun assembly of one of the grandparents of the population, a tenth-generation inbred line, was created using Illumina-based sequencing. Methods: The assembly was based on paired-end Illumina reads, scaffolded by mate pair and long jumping distance reads in the range of 3-40 kb, with >200-fold initial genome coverage. A total of 169 individuals from an F2 mapping population were used to construct PstI-based GBS libraries tagged with unique 4-9 nucleotide barcodes, resulting in 284 million reads, with approx. 1·6 million reads per individual. A bioinformatics pipeline was employed to identify both SNPs and PAVs. A core genetic map was generated using high confidence SNPs, to which lower confidence SNPs and PAVs were subsequently fitted in a straightforward binning approach. Key results: The assembly comprises 424 750 scaffolds, covering 1·11 Gbp of the 2·5 Gbp perennial ryegrass genome, with a scaffold N50 of 25 212 bp and a contig N50 of 3790 bp. It is available for download, and access to a genome browser has been provided. Comparison of the assembly with available transcript and gene model data sets for perennial ryegrass indicates that approx. 570 Mbp of the gene-rich portion of the genome has been captured. An ultra-high density genetic linkage map with 3092 SNPs and 7260 PAVs was developed, anchoring just over 200 Mb of the reference assembly. Conclusions: The combined genetic map and assembly, combined with another recently released genome assembly, represent a significant resource for the perennial ryegrass genetics community.
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Study on the Association between Tail Lesion Score, Cold Carcass Weight, and Viscera Condemnations in Slaughter PigsThe aim of this study was to assess the relationship between tail lesions, cold carcass weight, and viscera condemnations in an Irish abattoir. The following data were collected at the evisceration point from every third pig slaughtered over 7 days: farm identification, sex, tail lesion score, viscera inspection outcome, and cold carcass weight. Tail lesions were scored according to a 5-point scale. Disease lesions responsible for lung (pleurisy, pneumonia, and abscess), heart (pericarditis), and liver (ascariasis) condemnation were recorded based on the decision of the veterinary inspector (VI). Data on 3,143 pigs from 61 batches were available. The relationship between disease lesions, tail lesion score, and cold carcass weight was studied at individual carcass level, while the relationship between disease lesions and tail lesion score was studied at both carcass and batch level. Tail lesions (score ≥1) were found in 72% of the study population, with 2.3% affected by severe tail lesions (scores ≥3). Pleurisy (13.7%) followed by pneumonia (10.4%) showed the highest prevalence, whereas the prevalence of ascariasis showed the greatest variation between batches (0–75%). Tail lesion score, pleurisy, pleuropneumonia, and pericarditis were associated with reductions in carcass cold weight (P ≤ 0.05) ranging from 3 to 6.6 kg. Tail lesion score was associated with condemnations for pleurisy, pneumonia, and pleuropneumonia (P ≤ 0.05) at a batch level. VI shift was associated with condemnations for pneumonia, pleuropneumonia, and pericarditis (P ≤ 0.05) at a carcass level and with pneumonia at a batch level. Sex was not associated with viscera condemnations but males were more likely to be affected by tail lesions. The relationship between overall tail lesion score and the lung diseases at batch level supports the relationship between poor health and poor welfare of pigs on farms. The inclusion of tail lesion scores at post-mortem meat inspection should be considered as a health and welfare diagnostic tool.
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Responses in lactose yield, lactose percentage and protein-to-protein-plus-lactose ratio from index selection in New Zealand dairy cattleThe breeding goal of the New Zealand dairy industry is to improve the genetic capability of cows to convert pasture-based feed into farmer profit. The New Zealand dairy industry exports over 95% of milk produced and the most significant product by export volume is whole milk powder (WMP). The current selection objective, breeding worth (BW), will increase yields of protein and fat, potentially shifting milk composition further from the ideal composition for making WMP. This study aimed to investigate the correlated responses in lactose yield (LY), lactose percentage (LP) and protein-to-protein-plus-lactose ratio (P:P + L) from selection for BW, BW plus LY, BW plus LP and BW plus P:P + L. Selection for BW is predicted to have per-cow responses of 54.92 kg milk/year, 2.22 kg fat/year, 1.78 kg protein/year and 2.84 kg lactose/year. When lactose was included in the selection objective in the form of LY, LP or P:P + L, genetic responses ranged from −59.98 kg to 61.08 kg milk/year and from −2.67 kg to 3.70 kg lactose/year. The industry could reduce imported lactose requirements per tonne of WMP by 6%–11% by including lactose into the selection objective, compared with selection on BW alone.
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Sperm-Coating Beta-Defensin 126 Is a Dissociation-Resistant Dimer Produced by Epididymal Epithelium in the Bovine Reproductive TractBeta-defensins are innate immune molecules, often described as antimicrobial peptides because of their bactericidal activity and are now known to have diverse additional functions, including cell signaling, chemoattraction, immunoregulation, and reproduction. In humans and primates, beta-defensin 126 has been shown to regulate the ability of sperm to swim through cervical mucus and to protect sperm from attack by the female immune system during transit toward the oviduct. Bovine beta-defensin 126 (BBD126) is the ortholog of human defensin 126, and computational analysis here revealed significant conservation between BBD126 and other mammalian orthologs at the N-terminus, although extensive sequence differences were detected at the C-terminus, implying possible species-specific roles for this beta-defensin in reproduction. We had previously demonstrated preferential expression of this and related beta-defensin genes in the bovine male reproductive tract, but no studies of bovine beta-defensin proteins have been performed to date. Here, we analyzed BBD126 protein using a monoclonal antibody (a-BBD126) generated against a 14 amino acid peptide sequence from the secreted fragment of BBD126. The specificity of a-BBD126 was validated by testing against the native form of the peptide recovered from bovine caudal epididymal fluid and recombinant BBD126 generated using a prokaryotic expression system. Western blot analysis of the native and recombinant forms showed that BBD126 exists as a dimer that was highly resistant to standard methods of dissociation. Immunohistochemical staining using a-BBD126 demonstrated BBD126 protein expression by epithelial cells of the caudal epididymis and vas deferens from both mature and immature bulls. BBD126 could also be seen (by confocal microscopy) to coat caudal sperm, with staining concentrated on the tail of the sperm cells. This study is the first to demonstrate beta-defensin 126 protein expression in the bovine reproductive tract and on bull sperm. Its dissociation-resistant dimeric structure is likely to have important functional implications for the role of BBD126 in bovine reproduction.
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Contextual Hub Analysis Tool (CHAT): A Cytoscape app for identifying contextually relevant hubs in biological networksHighly connected nodes (hubs) in biological networks are topologically important to the structure of the network and have also been shown to be preferentially associated with a range of phenotypes of interest. The relative importance of a hub node, however, can change depending on the biological context. Here, we report a Cytoscape app, the Contextual Hub Analysis Tool (CHAT), which enables users to easily construct and visualize a network of interactions from a gene or protein list of interest, integrate contextual information, such as gene expression or mass spectrometry data, and identify hub nodes that are more highly connected to contextual nodes (e.g. genes or proteins that are differentially expressed) than expected by chance. In a case study, we use CHAT to construct a network of genes that are differentially expressed in Dengue fever, a viral infection. CHAT was used to identify and compare contextual and degree-based hubs in this network. The top 20 degree-based hubs were enriched in pathways related to the cell cycle and cancer, which is likely due to the fact that proteins involved in these processes tend to be highly connected in general. In comparison, the top 20 contextual hubs were enriched in pathways commonly observed in a viral infection including pathways related to the immune response to viral infection. This analysis shows that such contextual hubs are considerably more biologically relevant than degree-based hubs and that analyses which rely on the identification of hubs solely based on their connectivity may be biased towards nodes that are highly connected in general rather than in the specific context of interest.
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Effect of Freezing Conditions on Fecal Bacterial Composition in PigsSample preservation and recovery of intact DNA from gut samples may affect the inferred gut microbiota composition in pigs. This study aimed to evaluate the effect of the freezing process and storage temperature prior to DNA extraction on DNA recovery and bacterial community composition in pig feces using quantitative PCR. Fresh fecal samples from six growing pigs were collected and five aliquots of each prepared: (1) total DNA extracted immediately; (2) stored at −20 °C; (3) snap frozen and stored at −20 °C; (4) stored at −80 °C; and (5) snap frozen and stored at −80 °C. Results showed that DNA yields from fresh fecal samples were, on average, 25 to 30 ng higher than those from the various stored samples. The DNA extracted from fresh samples had more gene copies of total bacteria and all targeted bacterial groups per gram feces compared to DNA extraction from frozen samples. Data presentation also modified the observed effect of freeze storage; as results for Lactobacillus group, Enterococcus spp., Streptococcus spp., Clostridium cluster IV, Bacteroides-Prevotella-Porphyromonas and Enterobacteriaceae showed the opposite effect when expressed as relative abundance, by being greater in freeze stored feces than in fresh feces. Snap freezing increased the relative proportion of Clostridium cluster IV by 24%. In conclusion, the freezing process affected DNA yield and bacterial abundances, whereas snap freezing and storage temperature had only little influence on abundances of bacterial populations in pig feces.
