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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    Genomic Regions Associated With Skeletal Type Traits in Beef and Dairy Cattle Are Common to Regions Associated With Carcass Traits, Feed Intake and Calving Difficulty
    Doyle, Jennifer L. ; Berry, Donagh P. ; Veerkamp, Roel F. ; Carthy, Tara R. ; Walsh, Siobhan W. ; Evans, Ross D. ; Purfield, Deirdre C. - \ 2020
    Frontiers in Genetics Livestock Genomics 11 (2020). - ISSN 1664-8021
    cattle - genome-wide association study - linear type traits - sequence - single nucleotide polymorphism - skeletal

    Linear type traits describing the skeletal characteristics of an animal are moderately to strongly genetically correlated with a range of other performance traits in cattle including feed intake, reproduction traits and carcass merit; thus, type traits could also provide useful insights into the morphological differences among animals underpinning phenotypic differences in these complex traits. The objective of the present study was to identify genomic regions associated with five subjectively scored skeletal linear traits, to determine if these associated regions are common in multiple beef and dairy breeds, and also to determine if these regions overlap with those proposed elsewhere to be associated with correlated performance traits. Analyses were carried out using linear mixed models on imputed whole genome sequence data separately in 1,444 Angus, 1,129 Hereford, 6,433 Charolais, 8,745 Limousin, 1,698 Simmental, and 4,494 Holstein-Friesian cattle, all scored for the linear type traits. There was, on average, 18 months difference in age at assessment of the beef versus the dairy animals. While the majority of the identified quantitative trait loci (QTL), and thus genes, were both trait-specific and breed-specific, a large-effect pleiotropic QTL on BTA6 containing the NCAPG and LCORL genes was associated with all skeletal traits in the Limousin population and with wither height in the Angus. Other than that, little overlap existed in detected QTLs for the skeletal type traits in the other breeds. Only two QTLs overlapped the beef and dairy breeds; both QTLs were located on BTA5 and were associated with height in both the Angus and the Holstein-Friesian, despite the difference in age at assessment. Several detected QTLs in the present study overlapped with QTLs documented elsewhere that are associated with carcass traits, feed intake, and calving difficulty. While most breeding programs select for the macro-traits like carcass weight, carcass conformation, and feed intake, the higher degree of granularity with selection on the individual linear type traits in a multi-trait index underpinning the macro-level goal traits, presents an opportunity to help resolve genetic antagonisms among morphological traits in the pursuit of the animal with optimum performance metrics.

    Genetic analysis of orotic acid predicted with Fourier transform infrared milk spectra
    Zaalberg, R.M. ; Buitenhuis, A.J. ; Sundekilde, U.K. ; Poulsen, N.A. ; Bovenhuis, H. - \ 2020
    Journal of Dairy Science 103 (2020)4. - ISSN 0022-0302 - p. 3334 - 3348.
    breed difference - cattle - orotic acid - spectroscopy

    Fourier transform infrared spectral analysis is a cheap and fast method to predict milk composition. A not very well studied milk component is orotic acid. Orotic acid is an intermediate in the biosynthesis pathway of pyrimidine nucleotides and is an indicator for the metabolic cattle disorder deficiency of uridine monophosphate synthase. The function of orotic acid in milk and its effect on calf health, health of humans consuming milk or milk products, manufacturing properties of milk, and its potential as an indicator trait are largely unknown. The aims of this study were to determine if milk orotic acid can be predicted from infrared milk spectra and to perform a large-scale phenotypic and genetic analysis of infrared-predicted milk orotic acid. An infrared prediction model for orotic acid was built using a training population of 292 Danish Holstein and 299 Danish Jersey cows, and a validation population of 381 Danish Holstein cows. Milk orotic acid concentration was determined with nuclear magnetic resonance spectroscopy. For genetic analysis of infrared orotic acid, 3 study populations were used: 3,210 Danish Holstein cows, 3,360 Danish Jersey cows, and 1,349 Dutch Holstein Friesian cows. Using partial least square regression, a prediction model for orotic acid was built with 18 latent variables. The error of the prediction for the infrared model varied from 1.0 to 3.2 mg/L, and the accuracy varied from 0.68 to 0.86. Heritability of infrared orotic acid predicted with the standardized prediction model was 0.18 for Danish Holstein, 0.09 for Danish Jersey, and 0.37 for Dutch Holstein Friesian. We conclude that milk orotic acid can be predicted with moderate to good accuracy based on infrared milk spectra and that infrared-predicted orotic acid is heritable. The availability of a cheap and fast method to predict milk orotic acid opens up possibilities to study the largely unknown functions of milk orotic acid.

    Hittegolf kost naast melk ook voeropname en vruchtbaarheid
    Dijkstra, Jan - \ 2019
    animal welfare - animal production - dairy cattle - cattle - animal health - climate - animal housing
    Stressvrij omgaan met de koe : Wiki
    Heimensen, G. ; Ruis, M.A.W. - \ 2019
    Wageningen : Groen Kennisnet
    animal welfare - animal production - cattle - dairy cattle - animal behaviour - animal health - human-animal relationships
    Welkom bij de cursus "Stressvrij omgaan met de koe". Als je stressvrij en makkelijk met koeien werkt, ervaar je als veehouder meer plezier. Minder stress en angst zorgen ervoor dat het welzijn van de koe toeneemt. Het gevolg is een goede algemene gezondheid en klauwgezondheid. Dit kan weer leiden tot een hogere melkgift en een betere bevruchting. Dat levert een veehouder al snel duizenden euro's per jaar op.Maar hoe krijg je dit voor elkaar? Hoe zorg je voor makkelijk vee? Wat heeft de koe nodig om rustig en voorspelbaar te zijn? Waar zie je de verschillen tussen situaties, bedrijven en mensen? En wat is jouw rol hierin?In deze cursus 'Stressvrij omgaan met de koe' combineren we kennis uit de literatuur en praktijk.
    Sectorplan versnelling verduurzaming kalverhouderij
    Peet, G.F.V. van der - \ 2019
    - 26 p.
    animal welfare - animal production - cattle - calves - animal health - animal housing - animal behaviour - sustainability
    Prediction of metabolic status of dairy cows in early lactation with on-farm cow data and machine learning algorithms
    Xu, Wei ; Knegsel, Ariette T.M. van; Vervoort, Jacques J.M. ; Bruckmaier, Rupert M. ; Hoeij, Renny J. van; Kemp, Bas ; Saccenti, Edoardo - \ 2019
    Journal of Dairy Science 102 (2019)11. - ISSN 0022-0302 - p. 10186 - 10201.
    cattle - cluster analysis - energy metabolism - Random Forest

    Metabolic status of dairy cows in early lactation can be evaluated using the concentrations of plasma β-hydroxybutyrate (BHB), free fatty acids (FFA), glucose, insulin, and insulin-like growth factor 1 (IGF-1). These plasma metabolites and metabolic hormones, however, are difficult to measure on farm. Instead, easily obtained on-farm cow data, such as milk production traits, have the potential to predict metabolic status. Here we aimed (1) to investigate whether metabolic status of individual cows in early lactation could be clustered based on their plasma values and (2) to evaluate machine learning algorithms to predict metabolic status using on-farm cow data. Through lactation wk 1 to 7, plasma metabolites and metabolic hormones of 334 cows were measured weekly and used to cluster each cow into 1 of 3 clusters per week. The cluster with the greatest plasma BHB and FFA and the lowest plasma glucose, insulin, and IGF-1 was defined as poor metabolic status; the cluster with the lowest plasma BHB and FFA and the greatest plasma glucose, insulin, and IGF-1 was defined as good metabolic status; and the intermediate cluster was defined as average metabolic status. Most dairy cows were classified as having average or good metabolic status, and a limited number of cows had poor metabolic status (10–50 cows per lactation week). On-farm cow data, including dry period length, parity, milk production traits, and body weight, were used to predict good or average metabolic status with 8 machine learning algorithms. Random Forest (error rate ranging from 12.4 to 22.6%) and Support Vector Machine (SVM; error rate ranging from 12.4 to 20.9%) were the top 2 best-performing algorithms to predict metabolic status using on-farm cow data. Random Forest had a higher sensitivity (range: 67.8–82.9% during wk 1 to 7) and negative predictive value (range: 89.5–93.8%) but lower specificity (range: 76.7–88.5%) and positive predictive value (range: 58.1–78.4%) than SVM. In Random Forest, milk yield, fat yield, protein percentage, and lactose yield had important roles in prediction, but their rank of importance differed across lactation weeks. In conclusion, dairy cows could be clustered for metabolic status based on plasma metabolites and metabolic hormones. Moreover, on-farm cow data can predict cows in good or average metabolic status, with Random Forest and SVM performing best of all algorithms.

    Deciphering the patterns of genetic admixture and diversity in southern European cattle using genome-wide SNPs
    Upadhyay, Maulik ; Bortoluzzi, Chiara ; Barbato, Mario ; Ajmone-Marsan, Paolo ; Colli, Licia ; Ginja, Catarina ; Sonstegard, Tad S. ; Bosse, Mirte ; Lenstra, Johannes A. ; Groenen, Martien A.M. ; Crooijmans, Richard P.M.A. - \ 2019
    Evolutionary Applications 12 (2019)5. - ISSN 1752-4563 - p. 951 - 963.
    admixture - African taurine - cattle - genetic diversity - haplotype - indicine ancestry - SNPs - southern European

    The divergence between indicine cattle (Bos indicus) and taurine cattle (Bos taurus) is estimated to have occurred approximately 250,000 years ago, but a small number of European cattle breeds still display shared ancestry with indicine cattle. Additionally, following the divergence of African and European taurine, the gene flow between African taurine and southern European cattle has also been proposed. However, the extent to which non-European cattle ancestry is diffused across southern European cattle has not been investigated thoroughly. Also, in recent times, many local breeds have suffered severe reductions in effective population size. Therefore, in the present study, we investigated the pattern of genetic diversity in various European cattle based on single nucleotide polymorphisms (SNP) identified from whole-genome sequencing data. Additionally, we also employed unlinked and phased SNP-based approaches on high-density SNP array data to characterize non-European cattle ancestry in several southern European cattle breeds. Using heterozygosity-based parameters, we concluded that, on average, nucleotide diversity is greater in southern European cattle than western European (British and commercial) cattle. However, an abundance of long runs of homozygosity (ROH) and the pattern of Linkage disequilibrium decay suggested recent bottlenecks in Maltese and Romagnola. High nucleotide diversity outside ROH indicated a highly diverse founder population for southern European and African taurine. We also show that Iberian cattle display shared ancestry with African cattle. Furthermore, we show that Podolica is an ancient cross-bred between Indicine zebu and European taurine. Additionally, we also inferred similar ancestry profile of non-European cattle ancestry in different Balkan and Italian cattle breeds which might be an indication of the common origin of indicine ancestry in these breeds. Finally, we discuss several plausible demographic scenarios which might account for the presence of non-European cattle ancestry in these cattle breeds.

    Short communication: Antimethanogenic effects of 3-nitrooxypropanol depend on supplementation dose, dietary fiber content, and cattle type
    Dijkstra, J. ; Bannink, A. ; France, J. ; Kebreab, E. ; Gastelen, S. van - \ 2018
    Journal of Dairy Science 101 (2018)10. - ISSN 0022-0302 - p. 9041 - 9047.
    3-nitrooxypropanol - cattle - methane

    3-Nitrooxypropanol (NOP) is a promising methane (CH4) inhibitor. Recent studies have shown major reductions in CH4 emissions from beef and dairy cattle when using NOP but with large variation in response. The objective of this study was to quantitatively evaluate the factors that explain heterogeneity in response to NOP using meta-analytical approaches. Data from 11 experiments and 38 treatment means were used. Factors considered were cattle type (dairy or beef), measurement technique (GreenFeed technique, C-Lock Inc., Rapid City, SD; sulfur hexafluoride tracer technique; and respiration chamber technique), dry matter (DM) intake, body weight, NOP dose, roughage proportion, dietary crude protein content, and dietary neutral detergent fiber (NDF) content. The mean difference (MD) in CH4 production (g/d) and CH4 yield (g/kg of DM intake) was calculated by subtracting the mean of CH4 emission for the control group from that of the NOP-supplemented group. Forest plots of standardized MD indicated variable effect sizes of NOP across studies. Compared with beef cattle, dairy cattle had a much larger feed intake (22.3 ± 4.13 vs. 7.3 ± 0.97 kg of DM/d; mean ± standard deviation) and CH4 production (351 ± 94.1 vs. 124 ± 44.8 g/d). Therefore, in further analyses across dairy and beef cattle studies, MD was expressed as a proportion (%) of observed control mean. The final mixed-effect model for relative MD in CH4 production included cattle type, NOP dose, and NDF content. When adjusted for NOP dose and NDF content, the CH4-mitigating effect of NOP was less in beef cattle (−22.2 ± 3.33%) than in dairy cattle (−39.0 ± 5.40%). An increase of 10 mg/kg of DM in NOP dose from its mean (123 mg/kg of DM) enhanced the NOP effect on CH4 production decline by 2.56 ± 0.550%. However, a greater dietary NDF content impaired the NOP effect on CH4 production by 1.64 ± 0.330% per 10 g/kg DM increase in NDF content from its mean (331 g of NDF/kg of DM). The factors included in the final mixed-effect model for CH4 yield were −17.1 ± 4.23% (beef cattle) and −38.8 ± 5.49% (dairy cattle), −2.48 ± 0.734% per 10 mg/kg DM increase in NOP dose from its mean, and 1.52 ± 0.406% per 10 g/kg DM increase in NDF content from its mean. In conclusion, the present meta-analysis indicates that a greater NOP dose enhances the NOP effect on CH4 emission, whereas an increased dietary fiber content decreases its effect. 3-Nitrooxypropanol has stronger antimethanogenic effects in dairy cattle than in beef cattle.

    Performance of human observers and an automatic 3-dimensional computer-vision-based locomotion scoring method to detect lameness and hoof lesions in dairy cows
    Schlageter-Tello, Andrés ; Hertem, Tom Van; Bokkers, Eddie A.M. ; Viazzi, Stefano ; Bahr, Claudia ; Lokhorst, Kees - \ 2018
    Journal of Dairy Science 101 (2018)7. - ISSN 0022-0302 - p. 6322 - 6335.
    automatic detection - cattle - hoof lesion - lameness - locomotion score
    The objective of this study was to determine if a 3-dimensional computer vision automatic locomotion scoring (3D-ALS) method was able to outperform human observers for classifying cows as lame or nonlame and for detecting cows affected and nonaffected by specific type(s) of hoof lesion. Data collection was carried out in 2 experimental sessions (5 mo apart). In every session all cows were assessed for (1) locomotion by 2 observers (Obs1 and Obs2) and by a 3D-ALS; and (2) identification of different types of hoof lesions during hoof trimming (i.e., skin and horn lesions and combinations of skin/horn lesions and skin/hyperplasia). Performances of observers and 3D-ALS for classifying cows as lame or nonlame and for detecting cows affected or nonaffected by types of lesion were estimated using the percentage of agreement (PA), kappa coefficient (κ), sensitivity (SEN), and specificity (SPE). Observers and 3D-ALS showed similar SENlame values for classifying lame cows as lame (SENlame comparison Obs1-Obs2 = 74.2%; comparison observers-3D-ALS = 73.9–71.8%). Specificity values for classifying nonlame cows as nonlame were lower for 3D-ALS when compared with observers (SPEnonlame comparison Obs1-Obs2 = 88.5%; comparison observers-3D-ALS = 65.3–67.8%). Accordingly, overall performance of 3D-ALS for classifying cows as lame and nonlame was lower than observers (Obs1-Obs2 comparison PAlame/nonlame = 84.2% and κlame/nonlame = 0.63; observers-3D-ALS comparisons PAlame/nonlame = 67.7–69.2% and κlame/nonlame = 0.33–0.36). Similarly, observers and 3D-ALS had comparable and moderate SENlesion values for detecting horn (SENlesion Obs1 = 68.6%; Obs2 = 71.4%; 3D-ALS = 75.0%) and combinations of skin/horn lesions (SENlesion Obs1 = 51.1%; Obs2 = 64.5%; 3D-ALS = 53.3%). The SPEnonlesion values for detecting cows without lesions when classified as nonlame were lower for 3D-ALS than for observers (SPEnonlesion Obs1 = 83.9%; Obs2 = 80.2%; 3D-ALS = 60.2%). This was translated into a poor overall performance of 3D-ALS for detecting cows affected and nonaffected by horn lesions (PAlesion/nonlesion Obs1 = 80.6%; Obs2 = 78.3%; 3D-ALS = 63.5% and κlesion/nonlesion Obs1 = 0.48; Obs2 = 0.44; 3D-ALS = 0.25) and skin/horn lesions (PAlesion/nonlesion Obs1 = 75.1%; Obs2 = 75.9%; 3D-ALS = 58.6% and κlesion/nonlesion Obs1 = 0.35; Obs2 = 0.42; 3D-ALS = 0.10), when compared with observers. Performance of observers and 3D-ALS for detecting skin lesions was poor (SENlesion for Obs1, Obs2, and 3D-ALS <40%). Comparable SENlame and SENlesion values for observers and 3D-ALS are explained by an overestimation of lameness by 3D-ALS when compared with observers. Thus, comparable SENlame and SENlesion were reached at the expense high number of false positives and low SPEnonlame and SPEnonlesion. Considering that observers and 3D-ALS showed similar performance for classifying cows as lame and for detecting horn and combinations of skin/horn lesions, the 3D-ALS could be a useful tool for supporting dairy farmers in their hoof health management.
    Traditional ecological knowledge underlying herding decisions of pastoralists
    Tamou, C. ; Boer, I.J.M. De; Ripoll-Bosch, R. ; Oosting, S.J. - \ 2018
    Animal 12 (2018)4. - ISSN 1751-7311 - p. 831 - 843.
    cattle - forage quality - grazing lands - pastoralism - soils
    Pastoralists have traditional ecological knowledge (TEK), which is important for their livelihoods and for policies and interventions. Pastoralism is under pressure, however, which may result in a decline of pastoral lifestyle and its related TEK. We, therefore, addressed the following objectives (i) to inventorise and assess how pastoralists characterise and value soils and forages in their environment, (ii) to analyse how soil, forage and livestock (i.e. cattle) characteristics relate to herding decisions and (iii) to determine whether TEK underlying herding decisions differs across generations. Data were collected through focus groups and individual interviews with 72 pastoralists, belonging to three generations and to three agro-ecological zones. Using a three-point scale (high, medium, low), four grasses and three tree forages were assessed in terms of nutritional quality for milk, meat, health and strength. Using their own visual criteria, pastoralists identified five different soils, which they selected for herding at different times of the year. Pastoralists stated that Pokuri was the best soil because of its low moisture content, whereas Karaal was the worst because forage hardly grows on it. They stated that perennials, such as Andropogon gayanus and Loxoderra ledermannii, were of high nutritional quality, whereas annuals such as Andropogon pseudapricus and Hyparrhenia involucrata were of low nutritional quality. Afzelia africana was perceived of high quality for milk production, whereas Khaya senegalensis had the highest quality for meat, health and strength. Pastoralists first used soil, then forage and finally livestock characteristics in their herding decisions. Pastoralists' TEK was not associated with their generations, but with their agro-ecological zones. This study suggests that pastoralists had common and detailed TEK about soils, forages and livestock characteristics, underlying their herding decisions. To conclude, pastoralists use a holistic approach, combining soil, vegetation and livestock TEK in herding decisions. Such TEK can guide restoration or improvement of grazing lands, and land use planning.
    8 gamechangers voor een duurzame productie van gezond en veilig voedsel
    Vogelezang, J.V.M. ; Angelino, Steven ; Dubbeldam, Ria - \ 2017
    Topsector Agri & Food - 13 p.
    animal welfare - animal production - cattle - pigs - poultry - animal ethics - animal housing
    Exploiting whole genome sequence variants in cattle breeding : Unraveling the distribution of genetic variants and role of rare variants in genomic evaluation
    Zhang, Qianqian - \ 2017
    Wageningen University. Promotor(en): H. Bovenhuis; M.S. Lund, co-promotor(en): G. Sahana; M. Calus; B. Guldbrandtsen. - Wageningen : Wageningen University - ISBN 9788793643147 - 249
    cattle - genomes - genetic variation - inbreeding - homozygosity - longevity - quantitative traits - animal breeding - animal genetics - rundvee - genomen - genetische variatie - inteelt - homozygotie - gebruiksduur - kwantitatieve kenmerken - dierveredeling - diergenetica

    The availability of whole genome sequence data enables to better explore the genetic mechanisms underlying different quantitative traits that are targeted in animal breeding. This thesis presents different strategies and perspectives on utilization of whole genome sequence variants in cattle breeding. Using whole genome sequence variants, I show the genetic variation, recent and ancient inbreeding, and genome-wide pattern of introgression across the demographic and breeding history in different cattle populations. Using the latest genomic tools, I demonstrate that recent inbreeding can accurately be estimated by runs of homozygosity (ROH). This can further be utilized in breeding programs to control inbreeding in breeding programs. In chapter 2 and 4, by in-depth genomic analysis on whole genome sequence data, I demonstrate that the distribution of functional genetic variants in ROH regions and introgressed haplotypes was shaped by recent selective breeding in cattle populations. The contribution of whole genome sequence variants to the phenotypic variation partly depends on their allele frequencies. Common variants associated with different traits have been identified and explain a considerable proportion of the genetic variance. For example, common variants from whole genome sequence associated with longevity have been identified in chapter 5. However, the identified common variants cannot explain the full genetic variance, and rare variants might play an important role here. Rare variants may account for a large proportion of the whole genome sequence variants, but are often ignored in genomic evaluation, partly because of difficulty to identify associations between rare variants and phenotypes. I compared the powers of different gene-based association mapping methods that combine the rare variants within a gene using a simulation study. Those gene- based methods had a higher power for mapping rare variants compared with mixed linear models applying single marker tests that are commonly used for common variants. Moreover, I explored the role of rare and low-frequency variants in the variation of different complex traits and their impact on genomic prediction reliability. Rare and low-frequency variants contributed relatively more to variation for health-related traits than production traits, reflecting the potential of improving prediction reliability using rare and low-frequency variants for health-related traits. However, in practice, only marginal improvement was observed using selected rare and low-frequency variants when combined with 50k SNP genotype data on the reliability of genomic prediction for fertility, longevity and health traits. A simulation study did show that reliability of genomic prediction could be improved provided that causal rare and low-frequency variants affecting a trait are known.

    Rabies in Ethiopia: modelling the burden and the effectiveness of control
    Beyene, Tariku Jibat - \ 2017
    Wageningen University. Promotor(en): H. Hogeveen, co-promotor(en): M.C.M. Mourits. - Wageningen : Wageningen University - ISBN 9789463432177 - 194
    cattle - dogs - rabies - farmers - cattle farming - vaccination - business economics - cost effectiveness analysis - ethiopia - east africa - rundvee - honden - hondsdolheid - boeren - rundveeteelt - vaccinatie - bedrijfseconomie - cost effective analysis - ethiopië - oost-afrika

    Rabies claims the lives of more than 24,000 people in Africa annually, but efforts to control the disease are still lacking, particularly in sub-Saharan Africa such as Ethiopia. The overall objective of this study was to support the design of an appropriate cost-effective rabies control policy in Ethiopia by providing insights in the health burden of the disease and its economic impacts, as well as an understanding of the relationship between intervention levels, implementation costs and potential returns.

    As most human rabies cases result from the bite of domestic dogs, the disease can be eliminated by mass canine rabies vaccination. An extensive literature review on mass canine vaccination programs in Africa indicated that most dogs in Africa are owned and therefore accessible for vaccination, but vaccination coverages strongly depend on the implemented cost schemes. Canine vaccination in Ethiopia is voluntarily based, i.e. “owner-charged”, resulting in one of the lowest coverages in the world.

    To assess the current burden of rabies in Ethiopia a retrospective study was conducted by collecting data on human rabies exposure over the period of one year through extensive bite case searching in three representative districts of Ethiopia. Extrapolation of the results to national level indicated an annual average of 3,000 human deaths and 97,000 rabies-exposed persons treated at an average costs of 21 USD per case, causing 2 million USD on treatment costs per year and a health loss of about 93,000 DALYs. About 77% of the exposure cases visited a health centre, while only 57% received sufficient doses of post exposure treatment. Important factors that influenced victim’s medical treatment seeking behaviour were ownership status of the biting dog, severity of the bite, body part bitten, monthly spending and distance to the nearest health centre whereas the likelihood of receiving sufficient doses of treatment were determined by monthly spending and distance to health centre. The district in which victims lived appeared to have a relevant influence on the likelihood of seeking medical treatment but not on the likelihood of treatment compliance. By means of a structured questionnaire administered to cattle-owning households the economic impact of rabies in livestock was assessed. Herd-level incidence rates appeared higher in the mixed crop-livestock system (21%) than in the pastoral system (11%). Average economic losses per herd due to rabies were estimated at 49 USD per year for the mixed-crop livestock system, and at 52 USD per year for the pastoral system.

    In light of policy support for rabies control, an evaluation of the cost-effectiveness of control strategies was performed by the use of a dynamic epidemiological model coupled with an economic analysis to predict the human health impact and economic benefit (reducing human treatment costs and livestock rabies-related losses) across a range of vaccination scenarios. Human exposures, human deaths, and rabies-related livestock losses decreased monotonically with increasing vaccination coverage. In the evaluated urban and rural districts, 50% coverage was identified as most likely scenario to provide the greatest net health benefits at the WHO-recommended willingness-to-pay threshold over a time frame of 10 years. The additional economic benefit from rabies control in livestock justified the additional costs of vaccination campaigns with higher coverages than would have been efficient from a strict human health perspective, highlighting the importance of applying a broad perspective with regard to the evaluation of vaccination benefits.

    Forest-grassland transitions : How livestock and fire shape grassy biomes
    Bernardi, Rafael E. - \ 2017
    Wageningen University. Promotor(en): M. Scheffer, co-promotor(en): M. Holmgren; Matías Arim. - Wageningen : Wageningen University - ISBN 9789463436212 - 129
    forests - grasslands - fire - cattle - livestock - subtropics - south america - trees - bossen - graslanden - brand - rundvee - vee - subtropen - zuid-amerika - bomen

    Plant associations are determined by complex interactions with their environment depending on resource availability, landscape features, and periodic disturbances that shape the structure and functions of these communities. Forests, savannas and grasslands extend across the global land surface, contribute to planetary processes and provide ecosystems services sustaining local production. However, the factors that explain the distribution of trees and determine these biomes are still not well understood. In this thesis, long-standing questions about the origins and distribution of these ecosystems are discussed in light of new evidence suggesting that a feedback of fire and grasses may maintain forests, savannas and grasslands as alternative tree cover states. I also address how anthropogenic land use, including the introduction of livestock, may be affecting these dynamics, particularly in the neotropics, with consequences in terms of potential transitions in tree cover regimes.

    I analyze the distribution of trees in the grasslands of subtropical South America, looking at what may determine current tree cover and change dynamics (Chapters 2 & 3). The results suggest that, in non-cultivated areas, the expansion of trees into grasslands is likely limited by fire, livestock and precipitation, and that livestock likely reduces fire frequency (Chapter 2). The analyses also suggest that in the Uruguayan Campos of southeastern South America, where fire frequency is low and livestock densities are high, a release in livestock density may cause a moderate expansion of forests into grasslands (Chapter 3). To understand the consequences of a potential transition to higher tree cover by increasing precipitation, I looked at the effects of tree cover in subtropical rangelands (Chapter 5). The results indicated that isolated trees can improve the forage quality and abundance of these rangelands, with potential benefits in terms of biodiversity and ecosystem services. Lastly, I analyzed correlational patterns relating livestock density to vegetation structure across the global tropics and subtropics (Chapter 4), in an attempt to generalize the findings of Chapter 2. The results indicate that extensive livestock systems reduce fire frequency and impact vegetation structure, maintaining savannas and grasslands with low tree cover, low fire frequency and a higher presence of shrubs and dwarf trees.

    Stalboekje Vleeskalveren 2016 : handboek voor natuurlijke diergezondheidzorg met kruiden en andere natuurproducten
    Groot, Maria ; Asseldonk, Tedje van - \ 2017
    IJmuiden : RIKILT Wageningen UR (RIKILT-uitgave 2016.702) - 128
    rundvee - dierenwelzijn - diergezondheid - diervoeding - geneeskrachtige kruiden - dierlijke productie - biologische landbouw - cattle - animal welfare - animal health - animal nutrition - herbal drugs - animal production - organic farming
    Deze uitgave van ‘Stalboekje vleeskalveren’ is bedoeld om kalverhouders te helpen bij het vinden van de juiste toepassing van kruiden en andere natuurproducten. Kruiden en andere natuurproducten kunnen ter ondersteuning van gezonde dieren bij stress en ter ondersteuning van therapeutische maatregelen worden ingezet. Grootste meerwaarde is dat problemen voorkomen worden en dieren weerbaar gemaakt worden. Deze gids geeft een leidraad welke kruiden en natuurproducten op basis van beschikbare kennis een effect kunnen hebben bij verschillende gezondheidsproblemen. De ontwikkelingen op dit gebied gaan snel en daarom zal dit boekje regelmatig herzien en aangevuld moeten worden.
    Monitoring integraal duurzame stallen : peildatum 1 januari 2017
    Peet, G.F.V. van der; Meer, R.W. van der; Docters van Leeuwen, H. - \ 2017
    Wageningen : Wageningen UR Livestock Research (Wageningen Livestock Research rapport 1027) - 19
    huisvesting, dieren - stallen - monitoring - dierlijke productie - dierenwelzijn - rundvee - melkvee - pluimvee - duurzaamheid (sustainability) - animal housing - stalls - monitoring - animal production - animal welfare - cattle - dairy cattle - poultry - sustainability
    De overheid ambieert een integraal duurzame veehouderij in 2023. Daarom wordt jaarlijks een nieuw doel gesteld. Voor eind 2016 (peildatum 1 januari 2017) noemt het ministerie als ambitie dat minimaal 14% van de rundvee-, varkens- en pluimveestallen integraal duurzaam is. Deze studie laat zien dat op 1 januari 2017 in Nederland 13,6 % van alle stallen integraal duurzaam is.
    Prospects of whole-genome sequence data in animal and plant breeding
    Binsbergen, Rianne van - \ 2017
    Wageningen University. Promotor(en): R.F. Veerkamp; F.A. Eeuwijk, co-promotor(en): M.P.L. Calus. - Wageningen : Wageningen University - ISBN 9789463431903 - 220
    next generation sequencing - dna sequencing - quantitative trait loci - cattle - genomics - solanum lycopersicum - animal breeding - plant breeding - next generation sequencing - dna-sequencing - loci voor kwantitatief kenmerk - rundvee - genomica - solanum lycopersicum - dierveredeling - plantenveredeling

    The rapid decrease in costs of DNA sequencing implies that whole-genome sequence data will be widely available in the coming few years. Whole-genome sequence data includes all base-pairs on the genome that show variation in the sequenced population. Consequently, it is assumed that the causal mutations (e.g. quantitative trait loci; QTL) are included, which allows testing a given trait directly for association with a QTL, and might lead to discovery of new QTL or higher accuracies in genomic predictions compared to currently available marker panels. The main aim of this thesis was to investigate the benefits of using whole-genome sequence data in breeding of animals and plants compared to currently available marker panels. First the potential and benefits of using whole-genome sequence data were studied in (dairy) cattle. Accuracy of genotype imputation to whole-genome sequence data was generally high, depending on the used marker panel. In contrast to the expectations, genomic prediction showed no advantage of using whole-genome sequence data compared to a high density marker panel. Thereafter, the use of whole-genome sequence data for QTL detection in tomato (S. Lycopersicum) was studied. In a recombinant inbred line (RIL) population, more QTL were found when using sequence data compared to a marker panel, while increasing marker density was not expected to provide additional power to detect QTL. Next to the RIL population, also in an association panel it was shown that, even with limited imputation accuracy, the power of a genome-wide association study can be improved by using whole-genome sequence data. For successful application of whole-genome sequence data in animals or plants, genotype imputation will remain important to obtain accurate sequence data for all individuals in a cost effective way. Sequence data will increase the power of QTL detection in RIL populations, association panels or outbred populations. Added value of whole-genome sequence data in genomic prediction will be limited, unless more information is known about the biological background of traits and functional annotations of DNA. Also statistical models that incorporate this information and that can efficiently handle large datasets have to be developed.

    Rekenregels rundvee voor de Landbouwtelling : verantwoording van het gebruik van het Identificatie & Registratiesysteem
    Os, J. van; Bartholomeus, M.G.T.M. ; Jeurissen, L.J.J. ; Reenen, C.G. van - \ 2017
    Wageningen : Wettelijke Onderzoekstaken Natuur & Milieu (WOt-technical report 91) - 68
    rundveehouderij - rundvee - landbouwtellingen - emissie - registratie - identificatie - bedrijfsstructuur in de landbouw - nederland - cattle husbandry - cattle - agricultural censuses - emission - registration - identification - farm structure - netherlands
    Om te voldoen aan statistische verplichtingen voor veehouderij en bedrijfsstructuur en voor de registratievan emissies is informatie nodig over de rundveehouderij in Nederland. Daartoe vraagt de Rijksoverheid bijveehouders op hoeveel rundvee aanwezig is, uitgesplitst in verschillende diergroepen; dit is een onderdeelvan de jaarlijkse landbouwtelling. De Rijksoverheid streeft naar beperking van administratieve lastendruk bijondernemers. Wageningen Environmental Research heeft op verzoek van het ministerie van EconomischeZaken onderzocht in welke mate het mogelijk is om de benodigde gegevens af te leiden uit het bestaandeIdentificatie & Registratiesysteem (I&R) Rundveehouderij (een systeem voor identificatie en registratie vandieren voor dier- en volksgezondheid). Dat blijkt grotendeels goed haalbaar; voor de meeste bedrijvenkunnen alle diergroepen automatisch uit I&R bepaald worden. Voor sommige bedrijven is een aanvullendeverdeling van diergroepen over productiedoelen nodig. Deze nieuwe werkwijze leidt niet alleen tot lagereadministratieve lasten, maar ook tot een kwaliteitsverbetering van de rundveegegevens.---Information on cattle farming in the Netherlands is needed for the national statistics on beef and dairy farmsand farm structure. To obtain this information the national government asks farmers to submit informationon the number of cattle on their farms, divided into the various animal classes, as part of the annualagricultural census. The government also wants to minimise the administrative burden on farmers. At therequest of the Ministry of Economic Affairs, Wageningen Environmental Research has studied to what extentit would possible to derive the required information from the existing identification and registration system(I&R) for beef and dairy farms (a system for identifying and registering livestock for animal and humanhealth purposes). The results show that this is largely possible: for most farms all the animal classes can beautomatically derived from the I&R. For some farms it is necessary to make an additional division of animalclasses by product category. This new way of working will not only reduce the administrative burden, but itwill also lead to better quality data on beef and dairy cattle.
    Genetic improvement of feed intake and methane emissions of cattle
    Manzanilla Pech, Coralia I.V. - \ 2017
    Wageningen University. Promotor(en): Roel Veerkamp, co-promotor(en): Yvette de Haas. - Wageningen : Wageningen University - ISBN 9789463430692 - 199
    cattle - feed intake - methane production - genetic improvement - genetic parameters - conformation - breeding value - animal genetics - rundvee - voeropname - methaanproductie - genetische verbetering - genetische parameters - bouw (dier) - fokwaarde - diergenetica

    Feed costs represent half of the total costs of dairy production. One way to increase profitability of dairy production is to reduce feed costs by improving feed efficiency. As DMI is a trait that varies significantly during and across lactations, it is imperative to understand the underlying genetic architecture of DMI across lactation. Moreover, phenotypes of DMI are scarce, due to the difficulty of recording them (expensive and labor-intensive). Some predictor traits have been suggested to predict DMI. Examples of these predictor traits are those related to production (milk yield (MY) or milk content) or to the maintenance of the cow (body weight (BW) or conformation traits). The ability to determine when predictor traits ideally should be measured in order to achieve an accurate prediction of DMI throughout the whole lactation period is thus important. Recently, with the use of information of single nucleotide polymorphism (SNP) markers, together with phenotypic data and pedigree, genomically estimated breeding values (GEBV) of scarcely recorded traits, such as DMI, have become easier to accurately predict. This approach, combined with predictor traits, could contribute to an increased accuracy of predictions of GEBV of DMI. Methane (CH4) is the second important greenhouse gas, and enteric CH4 is the largest source of anthropogenic CH4, representing 17% of global CH4 emissions. Furthermore, methane emissions represent 2-12% of feed energy losses. Selecting for lower CH4 emitting animals and more feed-efficient animals would aid in mitigating global CH4 emissions. To identify the impact on CH4 emissions of selecting for lower DMI animals, it is important to determine the correlations between DMI and CH4 and to identify whether the same genes that control DMI affect CH4. Therefore, the general objectives of this thesis were to (1) explore the genetic architecture of DMI during lactation, (2) study the relationship of DMI to conformation, production and other related traits, (3) investigate the correlations between DMI and methane traits, and determine the SNP in common between DMI and CH4 through a genome-wide association study (GWAS), and (4) investigate the accuracy of predictions of DMI using predictor traits combined with genomic data.

    Selection for pure- and crossbred performance in Charolais
    Vallée-Dassonneville, Amélie - \ 2017
    Wageningen University. Promotor(en): Johan van Arendonk; Henk Bovenhuis. - Wageningen : Wageningen University - ISBN 9789463430180 - 151
    charolais - cattle - animal breeding - crossbreeding - crossbreds - selection - beef cattle - genomes - genetic parameters - charolais - rundvee - dierveredeling - kruisingsfokkerij - kruising - selectie - vleesvee - genomen - genetische parameters

    Two categories of beef production exist; i.e. (i) purebred animals from a beef sire and a beef dam and (ii) crossbred animals from a beef sire and a dairy dam.

    For the purebred beef production, there is a growing interest to include behavior and type traits in the breeding goal. Heritabilities for behavior traits, estimated using subjective data scored by farmers, range from 0.02 to 0.19. Heritabilities for type traits range from 0.02 to 0.35. Results show that there are good opportunities to implement selection for behavior traits using a simple on-farm recording system to allow collection of large data set, and for type traits in Charolais. A genome-wide association study detected 16 genomic regions with small effect on behavior and type traits. This suggests that behavior and type traits are influenced by many genes each explaining a small part of the genetic variance.

    The two main dairy breeds mated to Charolais sires for crossbred beef production in France are Montbéliard and Holstein. The genetic correlation between the same trait measured on Montbéliard x Charolais and on Holstein x Charolais was 0.99 for muscular development, 0.96 for birth weight; and 0.91 for calving difficulty, 0.80 for height, and 0.70 for bone thinness. Thus, for these last three traits, results show evidence for re-ranking of Charolais sires depending on whether they are mated to Montbéliard or Holstein cows. When using genomic prediction, the Montbéliard x Charolais and Holstein x Charolais populations could be combined into a single reference population to increase size and accuracy of genomic prediction. Results indicate that the higher the genetic correlation is between the two crossbred populations, the higher the gain in accuracy is achieved when combining the two populations into a single reference.

    The selection of Charolais sires to produce purebred or crossbred animals is made through distinct breeding programs. An alternative could be to combine selection into one breeding program. Decision for combining or keeping breeding programs separate is determined by the correlation between the breeding objectives, the selection intensity, the difference in level of genetic merit, the accuracy of selection, and the recent implementation of genomic evaluation. Considering all parameters and based on estimations for selection on birth weight, I recommend combining both breeding programs because this will lead to higher genetic gain, and might simplify operating organization and reduce associated costs.

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