Danish Pig Research Center

Copenhagen, Denmark

Danish Pig Research Center

Copenhagen, Denmark

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Lahrmann H.P.,Danish Pig Research Center | Busch M.E.,Danish Pig Research Center | D'Eath R.B.,SRUC | Forkman B.,Copenhagen University | Hansen C.F.,Copenhagen University
Animal | Year: 2017

The vast majority of piglets reared in the European Union (EU) and worldwide is tail docked to reduce the risk of being tail bitten, even though EU animal welfare legislation bans routine tail docking. Many conventional herds experience low levels of tail biting among tail docked pigs, however it is not known, what the prevalence would have been had the pigs not been tail docked. The aim of this study was to compare the prevalence of tail lesions between docked and undocked pigs in a conventional piggery in Denmark with very low prevalence of tail biting among tail docked pigs. The study included 1922 DanAvl Duroc×(Landrace×Large White) female and castrated male pigs (962 docked and 960 undocked). Docked and undocked pigs were housed under the same conditions in the same room but in separate pens with 20 (±0.03) pigs/pen. Pigs had ad libitum access to commercial diets in a feed dispenser. Manipulable material in the form of chopped straw was provided daily on the floor (~10 g/pig per day), and each pen had two vertically placed soft wood boards. From weaning to slaughter, tail wounds (injury severity and freshness) were scored every 2nd week. No clinical signs of injured tails were observed within the tail docked group, whereas 23.0% of the undocked pigs got a tail lesion. On average, 4.0% of the pigs with undocked tails had a tail lesion on tail inspection days. More pens with tail lesions were observed among pigs weighing 30 to 60 kg (34.3%; P<0.05) than in pens with pigs weighing 7 to 30 kg (13.0%) and 60 to 90 kg (12.8%). Removal of pigs to a hospital pen was more likely in undocked pens (P<0.05, 47.7% undocked pens and 22.9% docked pens). Finally, abattoir meat inspection data revealed more tail biting remarks in undocked pigs (P<0.001). In conclusion, this study suggests that housing pigs with intact tails in conventional herds with very low prevalence of tail biting among tail docked pigs, will increase the prevalence of pigs with tail lesions considerably, and pig producers will need more hospital pens. Abattoir data indicate that tail biting remarks from meat inspection data severely underestimate on-farm prevalence of tail lesions. © The Animal Consortium 2017

Henryon M.,Danish Pig Research Center | Henryon M.,University of Western Australia | Ostersen T.,Danish Pig Research Center | Ask B.,Danish Pig Research Center | And 2 more authors.
Genetics Selection Evolution | Year: 2015

Background: We tested the hypothesis that optimum-contribution selection (OCS) with restrictions imposed during optimisation realises most of the long-term genetic gain realised by OCS without restrictions. Methods: We used stochastic simulation to estimate long-term rates of genetic gain realised by breeding schemes that applied OCS without and with restrictions imposed during optimisation, where long-term refers to generations 23 to 25 (approximately). Six restrictions were imposed. Five of these removed solutions from the solution space. The sixth removed records of selection decisions made at earlier selection times. We also simulated a conventional breeding scheme with truncation selection as a reference point. Generations overlapped, selection was for a single trait, and the trait was observed for all selection candidates prior to selection. Results: OCS with restrictions realised 67 to 99% of the additional gain realised by OCS without restrictions, where additional gain was the difference in the long-term rates of genetic gain realised by OCS without restrictions and our reference point with truncation selection. The only exceptions were those restrictions that removed all solutions near the optimum solution from the solution space and the restriction that removed records of selection decisions made at earlier selection times. Imposing these restrictions realised only -12 to 46% of the additional gain. Conclusions: Most of the long-term genetic gain realised by OCS without restrictions can be realised by OCS with restrictions imposed during optimisation, provided the restrictions do not remove all solutions near the optimum from the solution space and do not remove records of earlier selection decisions. In breeding schemes where OCS cannot be applied optimally because of biological and logistical restrictions, OCS with restrictions provides a useful alternative. Not only does it realise most of the long-term genetic gain, OCS with restrictions enables OCS to be tailored to individual breeding schemes. © 2015 Henryon et al.; licensee BioMed Central.

Hjorth M.,University of Aarhus | Cocolo G.,University of Milan | Jonassen K.,Danish Pig Research Center | Abildgaard L.,University of Aarhus | Sommer S.G.,University of Southern Denmark
Biosystems Engineering | Year: 2015

The emerging slurry acidification technology affects gaseous emissions, fertiliser value, biogas production and solid-liquid separation; however, maximising the advantages is difficult, as the effect of acidification on the slurry characteristics resulting in those observations remains unclarified. A full-scale study was therefore performed, comparing pig slurry from normal in-house slurry management with pig slurry from housing with daily in-house acidification to pH 5.5. The effect on organic, inorganic and particles was evaluated. Increasing dissolved P, Mg and Ca contents indicated mineral dissolution in acidified slurry. Acceleration of carbohydrate hydrolysis was indicated, while deceleration of microbial acidogenesis, acetogenesis, methanogenesis and sulphate reduction was indicated. The particles were larger following acidification treatment causing a lower viscosity, likely due to acidification-induced aggregation. Overall, the acidified slurry was significantly different from untreated slurry; it had higher conductivity, more dissolved inorganic components, fewer small organic compounds, more large dissolved organic compounds, and larger particles. © 2015 IAgrE.

Liu H.,University of Aarhus | Henryon M.,Danish Pig Research Center | Henryon M.,University of Western Australia | Sorensen A.C.,University of Aarhus
Animal | Year: 2016

We tested the hypothesis that mating strategies with genomic information realise lower rates of inbreeding (∆F) than with pedigree information without compromising rates of genetic gain (∆G). We used stochastic simulation to compare ∆F and ∆G realised by two mating strategies with pedigree and genomic information in five breeding schemes. The two mating strategies were minimum-coancestry mating (MC) and minimising the covariance between ancestral genetic contributions (MCAC). We also simulated random mating (RAND) as a reference point. Generations were discrete. Animals were truncation-selected for a single trait that was controlled by 2000 quantitative trait loci, and the trait was observed for all selection candidates before selection. The criterion for selection was genomic-breeding values predicted by a ridge-regression model. Our results showed that MC and MCAC with genomic information realised 6% to 22% less ∆F than MC and MCAC with pedigree information without compromising ∆G across breeding schemes. MC and MCAC realised similar ∆F and ∆G. In turn, MC and MCAC with genomic information realised 28% to 44% less ∆F and up to 14% higher ∆G than RAND. These results indicated that MC and MCAC with genomic information are more effective than with pedigree information in controlling rates of inbreeding. This implies that genomic information should be applied to more than just prediction of breeding values in breeding schemes with truncation selection. © The Animal Consortium 2016 This is an Open Access article, distributed under the terms of the Creative Commons Attribution licence (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted re-use, distribution, and reproduction in any medium, provided the original work is properly cited

PubMed | Wageningen University, University of Aarhus and Danish Pig Research Center
Type: | Journal: The Journal of heredity | Year: 2017

Under the finite-locus model in the absence of mutation, the additive genetic variation is expected to decrease when directional selection is acting on a population, according to quantitative-genetic theory. However, some theoretical studies of selection suggest that the level of additive variance can be sustained or even increased when non-additive genetic effects are present. We tested the hypothesis that finite-locus models with both additive and non-additive genetic effects maintain more additive genetic variance (V_A) and realize larger medium-to-long term genetic gains than models with only additive effects when the trait under selection is subject to truncation selection. Four genetic models that included additive, dominance, and additive-by-additive epistatic effects were simulated. The simulated genome for individuals consisted of 25 chromosomes, each with a length of 1M. One hundred bi-allelic QTL, four on each chromosome, were considered. In each generation, 100 sires and 100 dams were mated, producing five progeny per mating. The population was selected for a single trait (h

PubMed | Wageningen University, University of Aarhus and Danish Pig Research Center
Type: Journal Article | Journal: Genetics, selection, evolution : GSE | Year: 2016

In pig breeding, selection is usually carried out in purebred populations, although the final goal is to improve crossbred performance. Genomic selection can be used to select purebred parental lines for crossbred performance. Dominance is the likely genetic basis of heterosis and explicitly including dominance in the genomic selection model may be an advantage when selecting purebreds for crossbred performance. Our objectives were two-fold: (1) to compare the predictive ability of genomic prediction models with additive or additive plus dominance effects, when the validation criterion is crossbred performance; and (2) to compare the use of two pure line reference populations to a single combined reference population.We used data on litter size in the first parity from two pure pig lines (Landrace and Yorkshire) and their reciprocal crosses. Training was performed (1) separately on pure Landrace (2085) and Yorkshire (2145) sows and (2) the two combined pure lines (4230), which were genotyped for 38k single nucleotide polymorphisms (SNPs). Prediction accuracy was measured as the correlation between genomic estimated breeding values (GEBV) of pure line boars and mean corrected crossbred-progeny performance, divided by the average accuracy of mean-progeny performance. We evaluated a model with additive effects only (MA) and a model with both additive and dominance effects (MAD). Two types of GEBV were computed: GEBV for purebred performance (GEBV) based on either the MA or MAD models, and GEBV for crossbred performance (GEBV-C) based on the MAD. GEBV-C were calculated based on SNP allele frequencies of genotyped animals in the opposite line.Compared to MA, MAD improved prediction accuracy for both lines. For MAD, GEBV-C improved prediction accuracy compared to GEBV. For Landrace (Yorkshire) boars, prediction accuracies were equal to 0.11 (0.32) for GEBV based on MA, and 0.13 (0.34) and 0.14 (0.36) for GEBV and GEBV-C based on MAD, respectively. Combining animals from both lines into a single reference population yielded higher accuracies than training on each pure line separately. In conclusion, the use of a dominance model increased the accuracy of genomic predictions of crossbred performance based on purebred data.

PubMed | The Danish AgriFish Agency, University of Aarhus and Danish Pig Research Center
Type: | Journal: Research in veterinary science | Year: 2016

According to Danish legislation, sick or injured pigs must be housed in hospital pens with specific requirements. During recent years the majority of cases of non-compliance with legislation have been related to management of these animals. Hence, we hypothesized that 1) pig farmers generally find a requirement for hospital pens reasonable, but do not know the specific requirements; 2) pig farmers do not find the specific requirements for hospital pens meaningful compared with their perception of what sick pigs need; and 3) pig farmers often omit to move sick pigs to hospital pens due to lack of time or labour. An on-line questionnaire regarding farmers attitudes towards and knowledge about legal requirements for hospital pens was constructed and e-mailed to 2348 pig farmers. In total, 508 farmers answered the questionnaire. Overall, 66% of the respondents found that the requirements for hospital pens made good sense, and more than 90% found that it made at least partial sense. Even though almost all respondents thought they knew the legal requirements for specific facilities in hospital pens, in fact 20% of them did not. The majority of respondents found all specific requirements in accordance with the needs of sick pigs, with the exception of cooling (only 17% agreed that cooling was needed). Unexpectedly, lack of time or labour wasnt reported to be a major obstacle to the use of hospital pens. Possibly, different thresholds for defining a pig as sick enough to need housing in a hospital pen may exist between farmers and authorities.

PubMed | University of Aarhus, Danish Pig Research Center and China Agricultural University
Type: Journal Article | Journal: Genetics, selection, evolution : GSE | Year: 2016

Dominance and imprinting genetic effects have been shown to contribute to genetic variance for certain traits but are usually ignored in genomic prediction of complex traits in livestock. The objectives of this study were to estimate variances of additive, dominance and imprinting genetic effects and to evaluate predictions of genetic merit based on genomic data for average daily gain (DG) and backfat thickness (BF) in Danish Duroc pigs.Corrected phenotypes of 8113 genotyped pigs from breeding and multiplier herds were used. Four Bayesian mixture models that differed in the type of genetic effects included: (A) additive genetic effects, (AD) additive and dominance genetic effects, (AI) additive and imprinting genetic effects, and (ADI) additive, dominance and imprinting genetic effects were compared using Bayes factors. The ability of the models to predict genetic merit was compared with regard to prediction reliability and bias.Based on model ADI, narrow-sense heritabilities of 0.18 and 0.31 were estimated for DG and BF, respectively. Dominance and imprinting genetic effects accounted for 4.0to4.6 and 1.3to1.4% of phenotypic variance, respectively, which were statistically significant. Across the four models, reliabilities of the predicted total genetic values (GTV, sum of all genetic effects) ranged from 16.1 (AI) to 18.4% (AD) for DG and from 30.1 (AI) to 31.4% (ADI) for BF. The least biased predictions of GTV were obtained with model AD, with regression coefficients of corrected phenotypes on GTV equal to 0.824 (DG) and 0.738 (BF). Reliabilities of genomic estimated breeding values (GBV, additive genetic effects) did not differ significantly among models for DG (between 16.5 and 16.7%); however, for BF, model AD provided a significantly higher reliability (31.3%) than model A (30.7%). The least biased predictions of GBV were obtained with model AD with regression coefficients of 0.872 for DG and 0.764 for BF.Dominance and genomic imprinting effects contribute significantly to the genetic variation of BF and DG in Danish Duroc pigs. Genomic prediction models that include dominance genetic effects can improve accuracy and reduce bias of genomic predictions of genetic merit.

PubMed | University of Aarhus and Danish Pig Research Center
Type: | Journal: BMC genetics | Year: 2016

In animal breeding, genetic variance for complex traits is often estimated using linear mixed models that incorporate information from single nucleotide polymorphism (SNP) markers using a realized genomic relationship matrix. In such models, individual genetic markers are weighted equally and genomic variation is treated as a black box. This approach is useful for selecting animals with high genetic potential, but it does not generate or utilise knowledge of the biological mechanisms underlying trait variation. Here we propose a linear mixed-model approach that can evaluate the collective effects of sets of SNPs and thereby open the black box. The described genomic feature best linear unbiased prediction (GFBLUP) model has two components that are defined by genomic features.We analysed data on average daily gain, feed efficiency, and lean meat percentage from 3,085 Duroc boars, along with genotypes from a 60 K SNP chip. In addition information on known quantitative trait loci (QTL) from the animal QTL database was integrated in the GFBLUP as a genomic feature. Our results showed that the most significant QTL categories were indeed biologically meaningful. Additionally, for high heritability traits, prediction accuracy was improved by the incorporation of biological knowledge in prediction models. A simulation study using the real genotypes and simulated phenotypes demonstrated challenges regarding detection of causal variants in low to medium heritability traits.The GFBLUP model showed increased predictive ability when enough causal variants were included in the genomic feature to explain over 10 % of the genomic variance, and when dilution by non-causal markers was minimal. In the observed data set, predictive ability was increased by the inclusion of prior QTL information obtained outside the training data set, but only for the trait with highest heritability.

Kongsted H.,Danish Pig Research Center | Kongsted H.,Copenhagen University | Stege H.,Copenhagen University | Toft N.,Technical University of Denmark | Nielsen J.P.,Copenhagen University
BMC Veterinary Research | Year: 2014

Background: The study evaluated the effect of New Neonatal Porcine Diarrhoea Syndrome (NNPDS) on average daily gain (ADG) and mortality and described the clinical manifestations in four herds suffering from the syndrome. NNPDS is a diarrhoeic syndrome affecting piglets within the first week of life, which is not caused by enterotoxigenic Escherichia coli (ETEC), Clostridium perfringens (C. perfringens) type A/C, Clostridium difficile (C. difficile), rotavirus A, coronavirus, Cystoisospora suis, Strongyloides ransomi, Giardia spp or Cryptosporidium spp.Results: Piglets were estimated to have a negative ADG of 9 and 14 g when diarrhoeic for 1 day and >1 day respectively. However, if only diarrhoeic on the day of birth, no negative effect on ADG was seen. Piglets originating from severely affected litters were estimated to have a reduced ADG of 38 g. The study did not show an overall effect of diarrhoea on mortality, but herd of origin, sow parity, birth weight, and gender were significantly associated with mortality. In one of the herds, approximately 25% of the diarrhoeic piglets vs. 6% of the non-diarrhoeic piglets died, and 74% of necropsied piglets were diagnosed with enteritis. These findings indicate that the high mortality seen in this herd was due to diarrhoea.Conclusions: NNPDS negatively affected ADG in piglets, and even piglets that were diarrhoeic for one day only experienced a reduction in ADG. However, the study showed that diarrhoea restricted to the day of birth did not affect ADG and suggested this phenomenon to be unrelated to the syndrome. Since the diarrhoeal status of the litter had important effects on ADG, future research on NNPDS probably ought to focus on piglets from severely affected litters.The study showed important dissimilarities in the course of diarrhoea between the herds, and one herd was considerably more affected than the others. Within this herd, NNPDS seemed to be associated with a higher mortality, whereas in general the study did not show lethal effects of NNPDS. © 2014 Kongsted et al.; licensee BioMed Central Ltd.

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