Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Influence of the metabolic state during lactation on milk production in modern sows
    Costermans, N.G.J. ; Soede, N.M. ; Middelkoop, A. ; Laurenssen, B.F.A. ; Koopmanschap, R.E. ; Zak, L.J. ; Knol, E.F. ; Keijer, J. ; Teerds, K.J. ; Kemp, B. - \ 2020
    Animal (2020). - ISSN 1751-7311
    feed intake - metabolism - milk fat - milk protein - pig

    Selection for prolificacy in sows has resulted in higher metabolic demands during lactation. In addition, modern sows have an increased genetic merit for leanness. Consequently, sow metabolism during lactation has changed, possibly affecting milk production and litter weight gain. The aim of this study was to investigate the effect of lactational feed intake on milk production and relations between mobilization of body tissues (adipose tissue or skeletal muscle) and milk production in modern sows with a different lactational feed intake. A total of 36 primiparous sows were used, which were either full-fed (6.5 kg/day) or restricted-fed (3.25 kg/day) during the last 2 weeks of a 24-day lactation. Restricted-fed sows had a lower milk fat percentage at weaning and a lower litter weight gain and estimated milk fat and protein production in the last week of lactation. Next, several relations between sow body condition (loss) and milk production variables were identified. Sow BW, loin muscle depth and backfat depth at parturition were positively related to milk fat production in the last week of lactation. In addition, milk fat production was related to the backfat depth loss while milk protein production was related to the loin muscle depth loss during lactation. Backfat depth and loin muscle depth at parturition were positively related to lactational backfat depth loss or muscle depth loss, respectively. Together, results suggest that sows which have more available resources during lactation, either from a higher amount of body tissues at parturition or from an increased feed intake during lactation, direct more energy toward milk production to support a higher litter weight gain. In addition, results show that the type of milk nutrients that sows produce (i.e. milk fat or milk protein) is highly related to the type of body tissues that are mobilized during lactation. Interestingly, relations between sow body condition and milk production were all independent of feed level during lactation. Sow management strategies to increase milk production and litter growth in modern sows may focus on improving sow body condition at the start of lactation or increasing feed intake during lactation.

    Effects of nucleotides administration on growth performance and immune response of post-weaning piglets
    Perricone, Vera ; Comi, Marcello ; Bontempo, Valentino ; Lecchi, Cristina ; Ceciliani, Fabrizio ; Crestani, Maurizio ; Ferrari, Alessandra ; Savoini, Giovanni ; Agazzi, Alessandro - \ 2020
    Italian Journal of Animal Science 19 (2020)1. - ISSN 1594-4077 - p. 295 - 301.
    growth performance - immune-related genes - Nucleotides - pig - weaning

    The aim of this study was to assess the effect of nucleotides administration on growth performance and immune response in post-weaning piglets. Twenty-eight male weaned piglets, homogeneous for age and weight were randomly allocated to two experimental treatments. Treated group (T) was daily orally administered 0.8 g/head of a mixture of nucleotides suspended in 2.1 mL water solution; while control group (C) received 2.1 mL saline solution. Body weight (BW) and average daily gain (ADG) were individually recorded weekly, while feed intake (FI), and gain:feed (G:F) were recorded and calculated on pen basis. Faecal score was evaluated every seven days. On day 0, 9, 18 and 27 blood samples were collected to determine IgA, IgG and haptoglobin concentration. At day 28 all piglets were sacrificed, and tissue samples of ileal Peyer’s patches were collected for the evaluation of IL1α, IL1β, IL6, IL10, TNFα, TLR2, TLR4 and PPARγ gene expression. Nucleotides supplementation significantly increased BW (17.37 vs. 19.00 kg/pig; p = <.01), ADG (.351 vs.400 kg/d; p <.01), and FI (3.96 vs. 4.39 kg/d; p <.01), but not G:F (.61 vs.64; p =.29). Faecal consistency was not different between the experimental groups and no occurrence of diarrhoea was reported. IgA and IgG content in blood was not influenced by the treatment, as well as gene expression of inflammatory cytokines in Peyer’s patches. The present trial shows that nucleotide administration is able to improve growth performance of post-weaning piglets, with no effects on inflammatory response and the expression of immune-related genes. Highlights Nucleotides administration increased BW, ADG and FI. Nucleotides did not affect inflammatory and immune response.

    Prediction of nutrient digestibility in grower-finisher pigs based on faecal microbiota composition
    Verschuren, Lisanne M.G. ; Schokker, Dirkjan ; Bergsma, Rob ; Jansman, Alfons J.M. ; Molist, Francesc ; Calus, Mario P.L. - \ 2020
    Journal of Animal Breeding and Genetics 137 (2020)1. - ISSN 0931-2668 - p. 23 - 35.
    digestion - metagenomics - microbiota - pig

    Microbiota play an important role in total tract nutrient digestion, especially when fibrous diets are fed to pigs. This study aimed to use metagenomics to predict faecal nutrient digestibility in grower-finisher pigs. The study design consisted of 160 three-way crossbreed grower-finisher pigs (80 female and 80 male) which were either fed a diet based on corn/soybean meal or a more fibrous diet based on wheat/barley/by-products. On the day before slaughter, faecal samples were collected and used to determine faecal digestibility of dry matter, ash, organic matter, crude protein, crude fat, crude fibre and non-starch polysaccharides. The faecal samples were also sequenced for the 16S hypervariable region of bacteria (V3/V4) to profile the faecal microbiome. With these data, we calculated the between-animal variation in faecal nutrient digestibility associated with variation in the faecal microbiome, that is the “microbiability”. The microbiability values were significantly greater than zero for dry matter, organic matter, crude protein, crude fibre and non-starch polysaccharides, ranging from 0.58 to 0.93, as well as for crude fat with a value of 0.37, but not significantly different from zero for ash. Using leave-one-out cross-validation, we estimated the accuracy of predicting digestibility values of individual pigs based on their faecal microbiota composition. The accuracies of prediction for crude fat and ash digestibility were virtually 0, and for the other nutrients, the accuracies ranged from 0.42 to 0.63. In conclusion, the faecal microbiota composition gave high microbiability values for faecal digestibility of dry matter, organic matter, crude protein, crude fibre and non-starch polysaccharides. The accuracies of prediction are relatively low if the interest is in precisely predicting faecal nutrient digestibility of individual pigs, but are promising from the perspective of ranking animals in a genetic selection context.

    Successional Dynamics in the Gut Microbiome Determine the Success of Clostridium difficile Infection in Adult Pig Models
    Jurburg, Stephanie D. ; Cornelissen, Jan J.B.W.J. ; Boer, Paulo de; Smits, Mari A. ; Rebel, Johanna M.J. - \ 2019
    Frontiers in Cellular and Infection Microbiology 9 (2019). - ISSN 2235-2988 - 11 p.
    animal models - bacteria - Clostridium difficile - microbiome - pig

    Clostridium difficile infections (CDI) are a major cause of antibiotic-associated diarrhea. It is hypothesized that CDI develops due to the antibiotic-induced disruption of the intestinal microbial community structure, which allows C. difficile to flourish. Here, we pre-treated weaned pigs with the antibiotics Clindamycin or Ciprofloxacin for 1 day, and subsequently inoculated them with a human and pig enteropathogenic C. difficile strain 078 spores. Body temperature, clinical signs of disease, and the fecal microbiome were monitored daily for 15 days. Clindamycin had a stronger effect on the pigs than Ciprofloxacin, resulting in drastic shifts in the fecal microbiome, decreases in microbial diversity and significant increases in body temperature, even in the absence of C. difficile. Fecal shedding of C. difficile was detectable for 3 and 9 days in Ciprofloxacin and Clindamycin treated pigs inoculated with C. difficile, respectively, and in both cases decreased cell proliferation rates were detected in colon tissue. The timing of C. difficile shedding coincided with the decrease in a large cluster of Firmicutes following Clindamycin treatment, a pattern which was also independent of C. difficile inoculation. The observed community patterns suggest that successional dynamics following antibiotic treatment facilitate C. difficile establishment. The similarities between the microbiome responses observed in our study and those previously reported in CDI-infected humans further support the utility of adult pigs as models for the study of CDI.

    A bead-based suspension array for the detection of Salmonella antibodies in pig sera
    Wal, F.J. van der; Achterberg, R.P. ; Maassen, Catharina B.M. - \ 2018
    Wageningen University & Research
    Salmonella - serology - pig - swine - bead-based suspension array - LPS - triazine chemistry
    Background Slaughter pigs are monitored for the presence of the zoonotic pathogen Salmonella, using both serology and bacteriology. ELISAs used to investigate pig herds are based on the detection of antibodies against components of the Salmonella cell envelope. Nearly all Salmonella isolates in food-producing animals are serovars of Salmonella enterica subspecies enterica, distributed over various serogroups as determined by the composition of their lipopolysaccharide (LPS). ELISAs for Salmonella serology are usually based on serogroup B and C1 LPS, often combined with serogroup D or E LPS. Although C2 LPS may improve serology, use of C2 LPS in a broad ELISA was never achieved. Results To enable detection of serum antibodies against Salmonella in pigs, a bead-based suspension array was developed with five LPS variants (B, 2Ă— C1, C2, D1), each conjugated to a different bead set using triazine chemistry. Reactivity of the beads was confirmed with rabbit agglutination sera and with experimental pig sera. With a mixture of bead sets, 175 sera from slaughter pigs were investigated for the presence of antibodies against Salmonella. With a combination of ROC analysis (B and D LPS) and a prevalence estimation based on historic data (C LPS), individual cut-offs were defined for each LPS-conjugated bead set, and assay performance was evaluated. Results of the suspension array (BC1C1C2D) suggest that more pigs are seroconverted than indicated by a commercial BC1D1-ELISA, and that most of these extra seropositive samples give a signal on one of the beads with C LPS. These results show that expansion of a standard panel with more C LPS variants improves antibody detection. Conclusions A suspension array for Salmonella serology in pigs was developed, that detects more seropositive sera than ELISA, which is achieved by expanding the panel of Salmonella LPS variants, including C2 LPS. The results demonstrate that bead-based suspension arrays allow for testing of pig sera, with the advantage of being able to set cut-offs per antigen. Ultimately, this type of assay can be applied in routine veterinary serology to test for antibodies against multiple Salmonella serovars (or other pathogens) in one single serum sample, using up-to-date antigen panels.
    Data from: Genome-wide SNP data unveils the globalization of domesticated pigs
    Yang, Bin ; Cui, Leilei ; Pérez-Enciso, M. ; Traspov, Aleksei ; Crooijmans, R.P.M.A. ; Zinovieva, Natalia ; Schook, Lawrence B. ; Gatphayak, Kesinee ; Knorr, Christophe ; Triantafyllidis, Alex ; Alexandri, Panoraia ; Semiadi, Gono ; Hanotte, Olivier ; Dias, Deodália ; Dovč, Peter ; Uimari, Pekka ; Iacolina, Laura ; Scandura, Massimo ; Groenen, M. ; Huang, L. ; Megens, H.J.W.C. - \ 2017
    National Key Laboratory for Pig Genetic Improvement and Production Technology
    pig - domestication - genome - selection
    Background: Pigs were domesticated independently in Eastern and Western Eurasia early during the agricultural revolution, and have since been transported and traded across the globe. Here, we present a worldwide survey on 60K genome-wide single nucleotide polymorphism (SNP) data for 2093 pigs, including 1839 domestic pigs representing 122 local and commercial breeds, 215 wild boars, and 39 out-group suids, from Asia, Europe, America, Oceania and Africa. The aim of this study was to infer global patterns in pig domestication and diversity related to demography, migration, and selection. Results: A deep phylogeographic division reflects the dichotomy between early domestication centers. In the core Eastern and Western domestication regions, Chinese pigs show differentiation between breeds due to geographic isolation, whereas this is less pronounced in European pigs. The inferred European origin of pigs in the Americas, Africa, and Australia reflects European expansion during the sixteenth to nineteenth centuries. Human-mediated introgression, which is due, in particular, to importing Chinese pigs into the UK during the eighteenth and nineteenth centuries, played an important role in the formation of modern pig breeds. Inbreeding levels vary markedly between populations, from almost no runs of homozygosity (ROH) in a number of Asian wild boar populations, to up to 20% of the genome covered by ROH in a number of Southern European breeds. Commercial populations show moderate ROH statistics. For domesticated pigs and wild boars in Asia and Europe, we identified highly differentiated loci that include candidate genes related to muscle and body development, central nervous system, reproduction, and energy balance, which are putatively under artificial selection. Conclusions: Key events related to domestication, dispersal, and mixing of pigs from different regions are reflected in the 60K SNP data, including the globalization that has recently become full circle since Chinese pig breeders in the past decades started selecting Western breeds to improve local Chinese pigs. Furthermore, signatures of ongoing and past selection, acting at different times and on different genetic backgrounds, enhance our insight in the mechanism of domestication and selection. The global diversity statistics presented here highlight concerns for maintaining agrodiversity, but also provide a necessary framework for directing genetic conservation.
    Pig behaviour linked to sanitary conditions and diets
    Meer, Y. van der; Gerrits, W.J.J. ; Jansman, A.J.M. ; Kemp, B. ; Bolhuis, J.E. - \ 2017
    Pig Progress
    pigs - pig - feed - abnormal behaviour - health - research - housing systems - tail biting
    There is a connection between damaging behaviour in pigs, sanitary conditions and diet formulations. How exactly, was presented by Dutch researchers recently.
    Effects of environmental enrichment and regrouping on natural autoantibodies-binding danger and neural antigens in healthy pigs with different individual characteristics
    Luo, L. ; Geers, R. ; Reimert, I. ; Kemp, B. ; Parmentier, H.K. ; Bolhuis, J.E. - \ 2017
    Animal 11 (2017)11. - ISSN 1751-7311 - p. 2019 - 2026.
    environmental enrichment - immunity - natural autoantibody - pig - stress
    Pigs living in commercial husbandry systems may experience both acute stress due to standard management procedures and chronic stress through limitations in their barren housing environment. This might influence their immune status, including antibody responses to neural and danger autoantigens. Levels of natural autoantibody (NAAb)-binding phosphorylcholine-conjugated bovine serum albumin (PC-BSA) and myelin basic protein (MBP) were measured over time in pigs that were kept in environmental enriched v. barren housing, and that underwent a regrouping test. In total, 480 pigs were housed in 80 pens in either barren or straw-enriched pens from 4 through 23 weeks of age. Blood samples were taken from pigs before (week 8), and 3 days after a 24 h regrouping test (week 9), and at 22 weeks of age. Phosphorylcholine-conjugated bovine serum albumin (PC-BSA) and MBP antibody titres in serum were measured using ELISA. Enriched-housed pigs had higher levels of IgM-binding MBP, and tended to have higher levels of IgG-binding MBP and IgA-binding PC-BSA than barren-housed pigs. Each NAAb measured in this study was affected by gender and litter. These results suggest that enriched housing conditions, as well as acute regrouping stress, have an influence on levels of serum NAAb-binding danger and neural antigens in pigs.
    Standardising the assessment of environmental enrichment and tail-docking legal requirements for finishing pigs in Europe
    Hothersall, B. ; Whistance, L.K. ; Zedlacher, H. ; Algers, B. ; Andersson, E. ; Bracke, M.B.M. ; Courboulay, V. ; Ferrari, P. ; Leeb, C. ; Mullan, S. ; Nowicki, J. ; Meunier-Salaün, M.C. ; Schwarz, T. ; Stadig, L. ; Main, D. - \ 2016
    Animal Welfare 25 (2016)4. - ISSN 0962-7286 - p. 499 - 515.
    animal welfare - enrichment - inspector - legislation - pig - tail-docking - animal welfare - enrichment - inspector - legisation - pig - tail-docking
    An online training package providing a concise synthesis of the scientific data underpinning EU legislation on enrichment and tail-docking of pigs was produced in seven languages, with the aim of improving consistency of professional judgements regarding legislation compliance on farms. In total, 158 participants who were official inspectors, certification scheme assessors and advisors from 16 EU countries completed an initial test and an online training package. Control group participants completed a second identical test before, and Training group participants after, viewing the training. In Section 1 of the test participants rated the importance of modifying environmental enrichment defined in nine scenarios from 1 (not important) to 10 (very important). Training significantly increased participants' overall perception of the need for change. Participants then rated nine risk factors for tail-biting from 1 (no risk) to 10 (high risk). After training scores were better correlated with risk rankings already described by scientists. Scenarios relating to tail-docking and management were then described. Training significantly increased the proportion of respondents correctly identifying that a farm without tail lesions should stop tail-docking. Finally, participants rated the importance of modifying enrichment in three further scenarios. Training increased ratings in all three. The pattern of results indicated that participants' roles influenced scores but overall the training improved: i) recognition of enrichments that, by virtue of their type or use by pigs, may be insufficient to achieve legislation compliance; ii) knowledge on risk factors for tail-biting; and iii) recognition of when routine tail-docking was occurring.
    Oligosaccharides in Urine, Blood, and Feces of Piglets Fed Milk Replacer Containing Galacto-oligosaccharides
    Difilippo, Elisabetta ; Bettonvil, Monique ; Willems, Rianne ; Braber, Saskia ; Fink-Gremmels, Johanna ; Jeurink, Prescilla V. ; Schoterman, Margriet H.C. ; Gruppen, Harry ; Schols, Henk A. - \ 2015
    Journal of Agricultural and Food Chemistry 63 (2015)50. - ISSN 0021-8561 - p. 10862 - 10872.
    absorption - capillary electrophoresis - creatinine - fermentation - GOS - intestine - liquid chromatography - mass spectrometry - pig - prebiotics

    Human milk oligosaccharides (HMOs) are absorbed into the blood (about 1% of the HMO intake) and subsequently excreted in urine, where they may protect the infant from pathogen infection. As dietary galacto-oligosaccharides (GOS) have partial structural similarities with HMOs, this study investigated the presence of GOS and oligosaccharides originating from milk replacer in blood serum, urine, and cecal and fecal samples of piglets, as a model for human infants. Using liquid chromatography-mass spectrometry and capillary electrophoresis with fluorescence detection, oligosaccharides originating from piglet diet including 3′-sialyllactose and specific GOS ranging from degree of polymerization 3 to 6 were detected in blood serum and in urine of piglets. In blood serum, GOS levels ranged from 16 to 23 μg/mL, representing about 0.1% of the GOS daily intake. In urine, approximately 0.85 g of GOS/g of creatinine was found. Cecum digesta and feces contained low amounts of oligosaccharides, suggesting an extensive GOS intestinal fermentation in piglets.

    Potential of extensification of European agriculture for a more sustainable food system; the case for nitrogen and livestock
    Grinsven, J.J.M. van; Erisman, J.W. ; Vries, W. de; Westhoek, H. - \ 2015
    Environmental Research Letters 10 (2015)2. - ISSN 1748-9326 - 10 p.
    dairy farms - management - intensification - welfare - trends - impact - costs - meat - pig
    Most global strategies for future food security focus on sustainable intensification of production of food and involve increased use of nitrogen fertilizer and manure. The external costs of current high nitrogen (N) losses from agriculture in the European Union, are 0.3–1.9% of gross domestic product (GDP) in 2008. We explore the potential of sustainable extensification for agriculture in the EU and The Netherlands by analysing cases and scenario studies focusing on reducing N inputs and livestock densities. Benefits of extensification are higher local biodiversity and less environmental pollution and therefore less external costs for society. Extensification also has risks such as a reduction of yields and therewith a decrease of the GDP and farm income and a smaller contribution to the global food production, and potentially an i0ncrease of global demand for land. We demonstrate favourable examples of extensification. Reducing the N fertilization rate for winter wheat in Northwest Europe to 25–30% below current N recommendations accounts for the external N cost, but requires action to compensate for a reduction in crop yield by 10–20%. Dutch dairy and pig farmers changing to less intensive production maintain or even improve farm income by price premiums on their products, and/or by savings on external inputs. A scenario reducing the Dutch pig and poultry sector by 50%, the dairy sector by 20% and synthetic N fertilizer use by 40% lowers annual N pollution costs by 0.2–2.2 billion euro (40%). This benefit compensates for the loss of GDP in the primary sector but not in the supply and processing chain. A 2030 scenario for the EU27 reducing consumption and production of animal products by 50% (demitarean diet) reduces N pollution by 10% and benefits human health. This diet allows the EU27 to become a food exporter, while reducing land demand outside Europe in 2030 by more than 100 million hectares (2%), which more than compensates increased land demand when changing to organic farming. We conclude that in Europe extensification of agriculture is sustainable when combined with adjusted diets and externalization of environmental costs to food prices.
    Evaluation of the sustainability of contrasted pig farming systems : Economy
    Ilari-Antoine, E. ; Bonneau, M. ; Klauke, T.N. ; Gonzàlez, J. ; Dourmad, J.Y. ; Greef, K. De; Houwers, H.W.J. ; Fabrega, E. ; Zimmer, C. ; Hviid, M. ; Oever, B. Van Der; Edwards, S.A. - \ 2014
    Animal 8 (2014)12. - ISSN 1751-7311 - p. 2047 - 2057.
    economy - evaluation - farming system - pig - sustainability

    The aim of this paper is to present an efficient tool for evaluating the economy part of the sustainability of pig farming systems. The selected tool IDEA was tested on a sample of farms from 15 contrasted systems in Europe. A statistical analysis was carried out to check the capacity of the indicators to illustrate the variability of the population and to analyze which of these indicators contributed the most towards it. The scores obtained for the farms were consistent with the reality of pig production; the variable distribution showed an important variability of the sample. The principal component analysis and cluster analysis separated the sample into five subgroups, in which the six main indicators significantly differed, which underlines the robustness of the tool. The IDEA method was proven to be easily comprehensible, requiring few initial variables and with an efficient benchmarking system; all six indicators contributed to fully describe a varied and contrasted population.

    Evaluation of the sustainability of contrasted pig farming systems: The procedure, the evaluated systems and the evaluation tools
    Bonneau, M. ; Greef, K. De; Brinkman, D. ; Cinar, M.U. ; Dourmad, J.Y. ; Edge, H.L. ; Fàbrega, E. ; Gonzàlez, J. ; Houwers, H.W.J. ; Hviid, M. ; Ilari-Antoine, E. ; Klauke, T.N. ; Phatsara, C. ; Rydhmer, L. ; Oever, B. Van Der; Zimmer, C. ; Edwards, S.A. - \ 2014
    Animal 8 (2014)12. - ISSN 1751-7311 - p. 2011 - 2015.
    assessment - farming system - pig - sustainable

    Although a few studies consider the sustainability of animal farming systems along the three classical main pillars (economy, environment and society), most studies on pig farming systems address only one of these pillars. The present paper is the introduction to a series of companion papers presenting the results of a study undertaken within the EU-supported project Q-PorkChains, aiming at building a comprehensive tool for the evaluation of pig farming systems, which is robust to accommodate the large variability of systems existing in Europe. The tool is mostly based on questions to farmers and comprises a total of 37 dimensions distributed along eight themes: Animal Welfare, Animal Health, Breeding Programmes, Environmental Sustainability, Meat Safety, Market Conformity, Economy and Working Conditions. The paper describes the procedure that was used for building the tool, using it on 15 contrasted pig farming systems and analysing the results. The evaluated systems are briefly described and a short overview of the dimensions is provided. Detailed descriptions of the theme-wise tools and results, as well as the results of an integrated evaluation, are available in the companion papers.

    Genomic relationships computed from either next- generation sequence or array SNP data
    Perez Enciso, M. - \ 2014
    Journal of Animal Breeding and Genetics 131 (2014)2. - ISSN 0931-2668 - p. 85 - 96.
    genetic-variation - complex traits - selection - pig - predictions - genotype - samples - cattle
    The use of sequence data in genomic prediction models is a topic of high interest, given the decreasing prices of current next'-generation sequencing technologies (NGS) and the theoretical possibility of directly interrogating the genomes for all causal mutations. Here, we compare by simulation how well genetic relationships (G) could be estimated using either NGS or ascertained SNP arrays. DNA sequences were simulated using the coalescence according to two scenarios: a cattle' scenario that consisted of a bottleneck followed by a split in two breeds without migration, and a pig' model where Chinese introgression into international pig breeds was simulated. We found that introgression results in a large amount of variability across the genome and between individuals, both in differentiation and in diversity. In general, NGS data allowed the most accurate estimates of G, provided enough sequencing depth was available, because shallow NGS (4x) may result in highly distorted estimates of G elements, especially if not standardized by allele frequency. However, high-density genotyping can also result in accurate estimates of G. Given that genotyping is much less noisy than NGS data, it is suggested that specific high-density arrays (similar to 3M SNPs) that minimize the effects of ascertainment could be developed in the population of interest by sequencing the most influential animals and rely on those arrays for implementing genomic selection.
    Signatures of Diversifying Selection in European Pig Breeds
    Wilkinson, S. ; Lu, Z.H. ; Megens, H.J.W.C. ; Archibald, A.L. ; Haley, C. ; Jackson, I.J. ; Groenen, M. ; Crooijmans, R.P.M.A. ; Ogden, R. ; Wiener, P. - \ 2013
    Wageningen UR
    pig - porcine - selection - domestication - introgression - breed development
    Following domestication, livestock breeds have experienced intense selection pressures for the development of desirable traits. This has resulted in a large diversity of breeds that display variation in many phenotypic traits, such as coat colour, muscle composition, early maturity, growth rate, body size, reproduction, and behaviour. To better understand the relationship between genomic composition and phenotypic diversity arising from breed development, the genomes of 13 traditional and commercial European pig breeds were scanned for signatures of diversifying selection using the Porcine60K SNP chip, applying a between-population (differentiation) approach. Signatures of diversifying selection between breeds were found in genomic regions associated with traits related to breed standard criteria, such as coat colour and ear morphology. Amino acid differences in the EDNRB gene appear to be associated with one of these signatures, and variation in the KITLG gene may be associated with another. Other selection signals were found in genomic regions including QTLs and genes associated with production traits such as reproduction, growth, and fat deposition. Some selection signatures were associated with regions showing evidence of introgression from Asian breeds. When the European breeds were compared with wild boar, genomic regions with high levels of differentiation harboured genes related to bone formation, growth, and fat deposition.
    Data from: Porcine colonization of the Americas: a 60k SNP story
    Burgos-Paz, W. ; Souza, C. ; Megens, Hendrik-Jan ; Ramayo-Caldas, Y. ; Crooijmans, Richard ; Groenen, Martien - \ 2012
    Autonomous University of Barcelona
    Americas - SNP - Creole - arrays - Sus scrofa - pig - adaptation
    The pig, Sus scrofa, is a foreign species to the American continent. Although pigs originally introduced in the Americas should be related to those from the Iberian Peninsula and Canary islands, the phylogeny of current creole pigs that now populate the continent is likely to be very complex. Because of the extreme climates that America harbours, these populations also provide a unique example of a fast evolutionary phenomenon of adaptation. Here, we provide a genome wide study of these issues by genotyping, with a 60k SNP chip, 206 village pigs sampled across 14 countries and 183 pigs from outgroup breeds that are potential founders of the American populations, including wild boar, Iberian, international and Chinese breeds. Results show that American village pigs are primarily of European ancestry, although the observed genetic landscape is that of a complex conglomerate. There was no correlation between genetic and geographical distances, neither continent wide nor when analysing specific areas. Most populations showed a clear admixed structure where the Iberian pig was not necessarily the main component, illustrating how international breeds, but also Chinese pigs, have contributed to extant genetic composition of American village pigs. We also observe that many genes related to the cardiovascular system show an increased differentiation between altiplano and genetically related pigs living near sea level.
    Effect of excessive, hormonally induced intrauterine crowding in the gilt on fetal development on day 40 of pregnancy
    Waaij, E.H. van der; Hazeleger, W. ; Soede, N.M. ; Laurenssen, B.F.A. ; Kemp, B. - \ 2010
    Journal of Animal Science 88 (2010)8. - ISSN 0021-8812 - p. 2611 - 2619.
    ovulation rate - litter size - swine - survival - number - sows - pig - fertilization - embryogenesis - responses
    Selection for litter size may result in an increase in uterine crowding due to a faster increase in ovulation rate than in litter size. Increased ovulation rate does not result in a proportionally increased number of piglets born alive. In this study, the effect of ovulation rate on vitality characteristics of fetal-placental units at d 40 of pregnancy was investigated. For this, 43 Large White gilts were treated with hormones to induce superovulation. Average ovulation rate was 45.16 ± 13.22; average number of vital fetuses at d 40 of pregnancy was 17.09 ± 3.61 that weighed 11.26 ± 1.99 g; their placenta weighed 31.88 ± 14.79 g; and they occupied 11.69 ± 4.90 cm of the uterus. Loss in oocytes (i.e., that did not result in a vital fetus at d 40) increased with increasing ovulation rate and occurred before (early mortality; P = 0.0003) and after implantation (late mortality, i.e., traces visible at d 40; P <0.0001). With respect to the vital fetuses, increased ovulation rate resulted in decreased fetal (P = 0.0008) and placental weight (P = 0.0008) and decreased length of the area in the uterus that was occupied by the placenta (P = 0.0011). Strong correlations existed between placental and fetal weight [0.68; 95% confidence interval (CI) = 0.64 to 0.72], and placental weight and length (0.78; 95% CI = 0.74 to 0.82). Fetal-placental characteristics were weakly correlated to distance to the implantation sites of neighboring fetuses, a measure of crowdedness [-0.002 (95% CI = -0.042 to 0.038) with fetal weight to 0.16 (95% CI = 0.12 to 0.20) with placental length]. Increased ovulation rates, but more specifically increased late mortality rates, have negative effects on the remaining vital fetuses with respect to the fetal (P = 0.0085) and placental weight (P <0.0001) and length of the implantation site (P = 0.0016). The most extreme effect was on placental weight, in which a uterus with 18 cases of late mortality (P <0.0001). Furthermore, increased ovulation rates resulted in decreased within litter variation for fetal (P = 0.0018) and placental weight (P = 0.0084). At increased ovulation rates, the number of live fetuses remained similar, but placental development is impaired and the growth of the fetus is retarded compared with reduced ovulation rate, with effects likely lasting into adult life.
    Transcriptomics of enterotoxigenic Escherichia coli infection. Individual variation in intestinal gene expression correlates with intestinal function
    Niewold, T.A. ; Meulen, J. van der; Kerstens, H.H.D. ; Smits, M.A. ; Hulst, M.M. - \ 2010
    Veterinary Microbiology 141 (2010)1-2. - ISSN 0378-1135 - p. 110 - 114.
    up-regulation - epithelium - disease - pig
    Acute secretory diarrhea is a major cause of morbidity and mortality in young animals and humans. Deaths result from excessive fluid and electrolyte losses. The disease is caused by non-invasive bacteria such as Vibrio cholerae and Escherichia coli which produce enterotoxins, however, much less is known about the role of individual host responses. Here we report the response of intact porcine small intestinal mucosa to infection with enterotoxigenic E. coli (ETEC). Jejunal segments in four piglets were infused with or without ETEC, and perfused for 8 h, and net absorption measured. Microarray analysis at 8 h post-infection showed significant differential regulation of on average fifteen transcripts in mucosa, with considerable individual variation. Differential net absorption varied between animals, and correlated negatively with the number of up regulated genes, and with one individual gene (THO complex 4). This shows that quantitative differences in gene regulation can be functionally linked to the physiological response in these four animals.
    Mapping markers linked to porcine salmonellosis susceptibility
    Galina-Pantoja, L. ; Siggens, K. ; Schriek, M.G.M. van; Heuven, H.C.M. - \ 2009
    Animal Genetics 40 (2009)6. - ISSN 0268-9146 - p. 795 - 803.
    quantitative trait loci - differential gene-expression - population-structure - natural-resistance - linkage map - aflp - choleraesuis - infection - pig - polymorphisms
    The goal of this study was to identify pig chromosomal regions associated with susceptibility to salmonellosis. Genomic DNA from pig reference populations with differences in susceptibility to Salmonella enterica serovar Choleraesuis as quantified by spleen and liver bacterial colonization at day 7 post-infection (dpi; Van Diemen et al. 2002) was used. These samples belonged to the offspring of a sire thought to be heterozygous for genes involved in susceptibility to salmonellosis. Amplified fragment length polymorphism (AFLP) markers were created and used to determine associations with spleen or bacterial counts at 7 dpi. To position linked markers, two mapping populations, the Roslin and Uppsala PiGMaP pedigrees were used to create an integrated map which included the AFLP markers associated with salmonellosis. Twenty-six AFLP markers located in 14 different chromosomal regions in the porcine genome were found to be significantly associated with susceptibility (Chi-square P <0.05). More than one linked marker was found on chromosomes 1, 7, 13, 14 and 18. It is likely that these regions contain genes involved in Salmonella susceptibility. Regions on chromosomes 1, 7 and 14 were significantly associated with Salmonella counts in the liver and regions on chromosomes 11, 13 and 18 with counts in spleen. The identification of these chromosomal regions highlights specific areas to search for candidate genes that may be involved in innate or adaptive immunity. Further investigation into these chromosomal regions would be useful to improve our understanding of host responses to infection with this widespread pathogen.
    Overview of European and Netherlands' regulations on airborne emissions from intensive livestock production with a focus on the application of air scrubbers
    Melse, R.W. ; Ogink, N.W.M. ; Rulkens, W.H. - \ 2009
    Biosystems Engineering 104 (2009)3. - ISSN 1537-5110 - p. 289 - 298.
    ammonia - odor - reduction - pig
    Intensive livestock production is of major importance to the economies of many countries but is also connected with a number of environmental effects, including airborne emissions. Currently emission standards are becoming increasingly stringent in European countries and the livestock industry is challenged to comply with them. One of the available techniques for emission reduction is the application of air scrubbing for end-of-pipe treatment of animal house exhaust air. In this paper, international and national Netherlands' emission regulations and targets are summarised for ammonia, odour and particulate matter (PM). Secondly, specific regulations on end-of-pipe air treatment technology are discussed in more detail. Finally the role of air scrubbing techniques in relation to Best Available Technique (BAT) is discussed. Currently air treatment systems are not considered as BATs in European Union (EU) legislation because of economic (high running costs), ecologic (high energy consumption, chemical use, discharge water), and technical reasons (unstable performance of bioscrubbers). Although we think that this rebuff is appropriate for bioscrubbers, it might be advisable to reconsider the status of acid scrubbers with regard to BAT
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