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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    Wat is erfelijkheid?
    Maurice - Van Eijndhoven, M.H.T. ; Oldenbroek, Kor - \ 2015
    Zeldzaam huisdier 40 (2015)3. - ISSN 0929-905X - p. 10 - 12.
    heritability - rassen (dieren) - dierveredeling - dna - eigenschappen - spermatozoön - eicellen - bevruchting - genen - allelen - homozygoten - heterozygoten - mutaties - genetische merkers - heritability - breeds - animal breeding - dna - properties - spermatozoa - ova - fertilization - genes - alleles - homozygotes - heterozygotes - mutations - genetic markers
    Eigenschappen van dieren zijn in meer of mindere mate erfelijk. Ze gaan over van ouders op nakomelingen. Maar ervaren fokkers weten dat in de fokkerij 1+1 geen 2 is. Welke wetmatigheden en welke toevalligheden spelen een rol in de erfelijkheid? Wat heeft het DNA-onderzoek ons daar recentelijk over geleerd en wat kunnen we daarmee?
    Genetic background of claw health in dairy cattle
    Spek, D. van der - \ 2015
    Wageningen University. Promotor(en): Johan van Arendonk, co-promotor(en): Henk Bovenhuis. - Wageningen : Wageningen University - ISBN 9789462573475 - 158
    melkvee - klauwen - diergezondheid - voetziekten - genetische parameters - heritability - genomica - selectief fokken - dierveredeling - dairy cattle - claws - animal health - foot diseases - genetic parameters - heritability - genomics - selective breeding - animal breeding

    Abstract

    Van der Spek, D. (2015). Genetic background of claw health in dairy cattle. PhD thesis, Wageningen University, the Netherlands.

    Claw disorders affect cow welfare and profitability of farms and as such are important traits relevant to dairy cattle breeding. Aim of this thesis was to increase our understanding of the genetic background of claw disorders to enable selection for reduced claw disorder incidence. The claw disorders were: abscess, corkscrew claw, (inter-)digital dermatitis or heel erosion (DER), double sole (DS), hardship groove, interdigital hyperplasia (IH), interdigital phlegmon, sand crack, super-foul, sole hemorrhage (SH), sole injury, sole ulcer (SU), white line separation (WLS), and yellow discoloration of the sole. Data was collected on Holstein cows kept in dairy herds in France. Individual claw disorder frequencies ranged from 0.1% to 23.8% and more than half of the trimmed cows had at least one claw disorder in at least one hind leg between 2007 and 2012. Heritabilities were estimated for DER, DS, IH, SH, SU, and WLS, and ranged from 0.02 to 0.14. Repeatabilities ranged from 0.02 to 0.33. The need for trimming (“trimming status”) was found to be heritable as well with a heritability of 0.09. A high need for trimming the claws of cows is unfavorable and therefore trimming status is an interesting trait to include in genetic evaluation. Most claw health traits had similar heritabilities and were genetically the same trait in different parities, lactation stages and herds with different trait frequencies. Claw disorder frequency in Montbeliarde cows ranged from 9.4% to 41.1% and 73% of the cows had at least one claw disorder in at least one hind leg between 2007 and 2013. Heritabilities ranged from 0.01 to 0.09. Heritability for trimming status was 0.06, confirming that trimming status is a heritable trait.

    To identify genomic regions associated with claw disorders and trimming status, a genome wide association study was performed. In total, 11 significant and 46 suggestive SNP were detected. Three of the suggestive SNP could be validated using a dataset of genotyped bulls. The detected SNP were spread across the genome and a major gene was not found.

    In the general discussion, alternative ways of measuring claw disorders were discussed. Accuracy of progeny testing and genomic selection for claw disorders was compared and a breeding program to reduce claw disorders was simulated in order to estimate selection response. Reducing the incidence of claw disorders is achievable with selection, but at a cost of a decrease in production.

    Inteelt-scanner voor rashonden
    Windig, Jack - \ 2015
    breeds - animal genetics - kinship - animal breeding - dogs - animal health - animal welfare - genetic disorders - pets
    Non-genetic variance in pigs: genetic analysis of reproduction and production traits
    Sell-Kubiak, E.B. - \ 2015
    Wageningen University. Promotor(en): Johan van Arendonk, co-promotor(en): Piter Bijma; Herman Mulder. - Wageningen : Wageningen University - ISBN 9789462573291 - 186
    varkens - dierveredeling - voortplanting - dierlijke productie - genetische analyse - genotypische variatie - genomica - fenotypische variatie - pigs - animal breeding - reproduction - animal production - genetic analysis - genetic variance - genomics - phenotypic variation

    Abstract

    Sell-Kubiak, E. (2015). Non-genetic variance in pigs: genetic analysis of reproduction and production traits. PhD thesis, Wageningen University, The Netherlands

    The main objective of this thesis was to study the origin of random variance in reproduction and production traits of pigs. In pig breeding for many traits it is important not only to improve the reproduction and production trait itself, but also its variation. The variance of traits can be used to improve pigs’ productivity, and potentially also to improve uniformity of traits. Results presented in Chapters 2 and 3 show that the proposed approach to explore the origin of common litter variance was not successful. The impact of various sow features on growth rate and feed intake of grow-finish pigs was very small. More importantly, sow features did not explain the phenotypic variance due to common litter effects found in production traits of pigs. In Chapters 4 and 5 the residual variance of birth weight and litter size were found to have a genetic component. The genetic coefficient of variation at residual standard deviation level (GCVSDe) was proposed as a measure of expressing the potential response to selection (Chapter 4). For both traits the estimated GCVSDe was about 10%, indicating sufficient potential for response to selection. In Chapter 4 it was shown that analyzing variation in traits with Double Hierarchical Generalized Linear model (DHGLM) was highly comparable with the conventional analysis of standard deviation of a trait. The correlation between the additive genetic effects for birth weight and the residual variance was 0.6 (Chapter 4), whereas for litter size (TNB) and its residual variance (varTNB) this correlation was 0.5 (Chapter 5). Those moderate correlations are an important indication of the direction of correlated selection response in the mean of those traits. In Chapter 5 in a genome-wide association study for litter size variation, the significant SNPs explained 0.83% of total genetic variance in TNB and 1.44% in varTNB. The most significant SNP explained 0.4% of genetic variance in TNB (chromosome 11) and 0.5% in varTNB (chromosome 7). One of the possible candidate genes for varTNB on chromosome 7 is heat shock protein (HSPCB). Studying the residual variance of traits with DHGLM has a great potential to serve as an alternative to conventional analysis to study and to select for improved uniformity of various traits. Lastly, Chapter 6 focuses on discussion of the findings of this thesis and their overall importance for pig breeding, as well as highly relevant topics for breeding uniform and robust pigs (macro-micro sensitivity analysis and application of genomic selection).

    Genetic improvement in indigenous chicken of Ethiopia
    Woldegiorgiss, W.E. - \ 2015
    Wageningen University. Promotor(en): Johan van Arendonk, co-promotor(en): Liesbeth van der Waaij; T. Dessie. - Wageningen : Wageningen University - ISBN 9789462573161 - 130
    kippen - pluimvee - inheems vee - genetische verbetering - houding van boeren - perceptie - kippenrassen - prestatieniveau - dierveredeling - ethiopië - fowls - poultry - native livestock - genetic improvement - farmers' attitudes - perception - fowl breeds - performance - animal breeding - ethiopia

    Abstract

    Wondmeneh Esatu Woldegiorgiss (2015). Genetic improvement in indigenous chicken of Ethiopia. PhD thesis, Wageningen University, the Netherlands

    This thesis considered various approaches to study the potential for improvement of village poultry production system using improved indigenous chicken. The approaches were structured survey questionnaire, village poultry simulation model (VIPOSIM), Heckman two-step model (econometric model), and experiments involving laboratory and field. First factors that determine the probability and intensity of adoption of exotic chickens were assessed. The probability of adopting exotic chickens was found to be positively affected by access to an off-farm income and negatively by livestock income. The intensity of adoption was negatively affected by being male household head, having a larger farm size, and having livestock income. Then, perceptions of farmers towards village poultry and impacts of interventions on flock and economic performance were assessed. Farmers’ perceptions affected their decisions about implementation of interventions, and interventions increased productivity but only in a few cases the increased revenues outweighed the additional costs. Subsequently, the evaluation of the breeds was conducted by comparing the natural antibody and productivity of improved indigenous chicken with crossbred, commercial and unimproved indigenous chickens. The results revealed that not only the NAb levels but also the effect of NAbs on survival differ between indigenous and improved breeds. NAb levels are associated with survival in commercial layer breed, but reduced survival in indigenous chickens placed in confinement. Improved indigenous chickens showed higher performance than unimproved one for all traits measured on-station, but remains lighter and developed more into a laying type than meat through the short-term selective breeding program. Overall, the present studies indicate that interventions need to be tailored towards the local situation to ensure that they lead not only to improved productivity but also to improved income.

    Breeding program for indigenous chicken in Kenya
    Ngeno, K. - \ 2015
    Wageningen University. Promotor(en): Johan van Arendonk, co-promotor(en): Liesbeth van der Waaij; A.K. Kahi. - Wageningen : Wageningen University - ISBN 9789462572775 - 154
    kippen - pluimvee - inheems vee - dierveredeling - veredelingsprogramma's - genetische diversiteit - ecotypen - genomen - genetische verbetering - kenya - fowls - poultry - native livestock - animal breeding - breeding programmes - genetic diversity - ecotypes - genomes - genetic improvement - kenya

    Abstract

    Ngeno, K. (2015). Breeding program for indigenous chicken in Kenya. Analysis of diversity in indigenous chicken populations. PhD thesis, Wageningen University, the Netherlands

    The objective of this research was to generate knowledge required for the development of an indigenous chicken (IC) breeding program for enhanced productivity and improved human livelihood in Kenya. The initial step was to review five questions; what, why and how should we conserve IC in an effective and sustainable way, who are the stakeholders and what are their roles in the IC breeding program. The next step of the research focused on detecting distinctive IC ecotypes through morphological and genomic characterization. Indigenous chicken ecotypes were found to be populations with huge variability in the morphological features. Molecular characterization was carried out using microsatellite markers and whole genome re-sequenced data. The studied IC ecotypes are genetically distinct groups. The MHC-linked microsatellite markers divided the eight IC ecotypes studied into three mixed clusters, composing of individuals from the different ecotypes whereas non-MHC markers grouped ICs into two groups. Analysis revealed high genetic variation within the ecotype with highly diverse MHC-linked alleles which are known to be involved in disease resistance. Whole genome re-sequencing revealed genomic variability, regions affected by selection, candidate genes and mutations that can explain partially the phenotypic divergence between IC and commercial layers. Unlike commercial chickens, IC preserved a high genomic variability that may be important in addressing present and future challenges associated with environmental adaptation and farmers’ breeding goals. Lastly, this study showed that there is an opportunity to improve IC through selection within the population. Genetic improvement utilizing within IC selection requires setting up a breeding program. The study described the systematic and logical steps in designing a breeding program by focusing on farmers’ need, how to improve IC to fit the farming conditions, and management regimes.

    The hybrid nature of pig genomes : unraveling the mosaic haplotype structure in wild and commercial Sus scrofa populations
    Bosse, M. - \ 2015
    Wageningen University. Promotor(en): Martien Groenen, co-promotor(en): Hendrik-Jan Megens; Ole Madsen. - Wageningen : Wageningen University - ISBN 9789462573000 - 253
    dieren - varkens - dierveredeling - genomen - hybridisatie - sus scrofa - haplotypen - genomica - populaties - genetische variatie - animals - pigs - animal breeding - genomes - hybridization - sus scrofa - haplotypes - genomics - populations - genetic variation - cum laude
    cum laude graduation
    Zeldzame Nederlandse konijnenrassen in de genenbank
    Hoving, A.H. ; Renes, J. ; Taks, A. - \ 2015
    Zeldzaam huisdier 40 (2015)2. - ISSN 0929-905X - p. 20 - 21.
    rassen (dieren) - genetische bronnen van diersoorten - genenbanken - konijnen - zeldzame rassen - dierveredeling - bevruchtingsvermogen - sperma - ingevroren sperma - breeds - animal genetic resources - gene banks - rabbits - rare breeds - animal breeding - fertilizing ability - semen - frozen semen
    In 2014 is van de meeste zeldzame Nederlandse konijnenrassen sperma ingevroren en opgeslagen in de genenbank. Dit kon gerealiseerd worden dankzij samenwerking tussen konijnenfokkers, het Centrum voor Genetische Bronnen Nederland van Wageningen UR (CGN), Kleindier Liefhebbers Nederland (KLN) en de Stichting Zeldzame Huisdierrassen (SZH).
    Leerboek fokkerij en genetica voor het HBO
    Oldenbroek, Kor - \ 2015
    teaching materials - animal breeding - animal genetics - animal breeding methods - livestock farming - professional education - animal welfare - animal health - animal production - pets - dogs - cats - dairy cattle - pigs - poultry - horses
    'Maak risicoanalyse voor het sperma'
    Hoefman, R. ; Veerkamp, R.F. - \ 2015
    Boerderij 100 (2015)28. - ISSN 0006-5617 - p. 44 - 44.
    rundveehouderij - ki stieren - melkveestieren - dierveredeling - genomica - sperma - cattle husbandry - ai bulls - dairy bulls - animal breeding - genomics - semen
    Van het Holstein-sperma is in Nederland ongeveer 50 procent afkomstig van jonge genomicstieren. In Frankrijk is dat 67 procent, in Duitsland 70 procent en in de Scandinavië zelfs 95 procent. Professor numerieke genetica Roel Veer- kamp is bang dat Nederlandse veehouders niet optimaal gebruik maken van de mogelijkheden en kansen laten liggen.
    GReIS en Elda als registratiesystemen voor geitenrassen
    Oldenbroek, J.K. ; Eijndhoven, M.H.T. - \ 2015
    Zeldzaam huisdier 40 (2015)2. - ISSN 0929-905X - p. 16 - 17.
    dierveredeling - rassen (dieren) - zeldzame rassen - geitenrassen - registratie - melkcontrole - computer software - stamboeken - bedrijfsinformatiesystemen - toggenburgergeit - fokwaarde - animal breeding - breeds - rare breeds - goat breeds - registration - milk recording - computer software - herdbooks - management information systems - toggenburg - breeding value
    In een serie artikelen worden de mogelijkheden van registratiesystemen voor zeldzame rassen toegelicht. In dit tweede artikel komt eerst GReIS (GeitenRegistratie- en InformatieSysteem) aan de orde en daarna het Elda-systeem.
    Registreren: meten is weten!
    Maurice - Van Eijndhoven, M.H.T. ; Oldenbroek, J.K. - \ 2015
    Zeldzaam huisdier 40 (2015)2. - ISSN 0929-905X - p. 10 - 11.
    rassen (dieren) - dierveredeling - selectie - registratie - selectief fokken - fenotypen - fokdoelen - stamboeken - databanken - breeds - animal breeding - selection - registration - selective breeding - phenotypes - breeding aims - herdbooks - databases
    Om te kunnen selecteren op bepaalde kenmerken moeten deze ‘meetbaar’
    zijn en worden geregistreerd. Pas dan wordt zichtbaar of er echte
    verbeteringen richting fokdoel worden bereikt in volgende generaties.
    In dit tweede artikel lichten we toe waarom het belangrijk is om goed
    te registeren en hoe een gedegen registratiesysteem eruitziet.
    Erfelijke problemen bij honden los je met fokkerijmaatregelen op!
    Oldenbroek, Kor - \ 2015
    animal welfare - animal health - pets - domestic animals - dogs - animal behaviour - animal breeding - education - genetic disorders - hereditary diseases - dog breeds
    Fokwaarde voeropname : introductie van fokwaarde voor voeropname in Nederland
    Haas, Y. de; Veerkamp, R.F. - \ 2015
    Wageningen : Wageningen UR Livestock Research (Livestock Research rapport 837) - 17
    fokwaarde - melkveehouderij - melkproductie - voeropname - dierveredeling - rundveehouderij - rundveevoeding - breeding value - dairy farming - milk production - feed intake - animal breeding - cattle husbandry - cattle feeding
    Feed costs represent above 50% of the total costs of dairy production, so reducing costs by improving dairy cow feed efficiency is a way to increase profitability. Therefore it is important to improve efficiency of that dairy cattle population. This project has shown that it is possible to breed for more efficient animals, resulting in permanent and cumulative changes in the genetic merit of dairy cows. The breeding value for feed intake is currently integrated in the Better Life Efficiency index for all sires of CRV, and it is under discussing if it will be included in the national index (published by GES) for all bulls in the Netherlands and Flanders.
    Studium Generale “Fairfok the Dog” : oplossing erfelijke rashondenproblematiek; van theorie naar praktijk
    Hopster, Hans - \ 2015
    animal welfare - pets - animal health - animal breeding - education - domestic animals - dogs - dog breeds - hereditary diseases - genetic disorders - animal behaviour
    Vaak scrapieresistentie bij Nederlandse Toggenburgers
    Hoving-Bolink, A.H. ; Windig, J.J. ; Koekoek, A. ; Hoekstra, H. ; Oldenbroek, J.K. ; Langeveld, J. - \ 2015
    Zeldzaam huisdier 40 (2015)1. - ISSN 0929-905X - p. 20 - 21.
    rassen (dieren) - geitenrassen - zeldzame rassen - genetische variatie - scrapie - ziekteresistentie - nederlandse toggenburgergeit - geitenziekten - dierveredeling - toegepast onderzoek - breeds - goat breeds - rare breeds - genetic variation - scrapie - disease resistance - dutch toggenburg - goat diseases - animal breeding - applied research
    Zeldzame Nederlandse rassen zijn niet alleen onderdeel van ons cultureel erfgoed, maar hebben soms ook een verrassende genetische variant. Zo is sinds een paar jaar bekend dat er een allel bestaat dat bescherming biedt tegen scrapie. In onderzoek van Wageningen UR met de geitensector blijkt dat het relatief kleine ras de Nederlandse Toggenburger veel dieren kent met het scrapieresistentie allel.
    ZooEasy als registratiesysteem voor zeldzame rassen
    Oldenbroek, J.K. ; Eijndhoven, M.H.T. - \ 2015
    Zeldzaam huisdier 40 (2015)1. - ISSN 0929-905X - p. 16 - 17.
    dierveredeling - identificatie - zeldzame rassen - rassen (dieren) - hondenrassen - vogels - stamboom - stamboeken - geitenrassen - fokken van kleine dieren - computer software - internet - animal breeding - identification - rare breeds - breeds - dog breeds - birds - pedigree - herdbooks - goat breeds - small animal rearing - computer software - internet
    Nauwkeurige registratie is een vereiste voor een verantwoorde en
    succesvolle fokkerij. Niet alleen speelt afstamming bij zeldzame rassen
    een cruciale rol, fokkers willen ook gegevens over het exterieur
    en de prestaties van de dieren overzichtelijk vastleggen. In deze
    serie worden de mogelijkheden van een aantal systemen toegelicht.
    Het hoe en waarom van een fokprogramma
    Eijndhoven, M.H.T. ; Oldenbroek, J.K. - \ 2015
    Zeldzaam huisdier 40 (2015)1. - ISSN 0929-905X - p. 10 - 11.
    kenmerken - dierveredeling - rassen (dieren) - fokwaarde - fokdoelen - selectiecriteria - traits - animal breeding - breeds - breeding value - breeding aims - selection criteria
    Voor velen van u zal het herkenbaar zijn: verknocht zijn aan een dier om zijn of haar uiterlijk en gedrag. Juist deze kenmerken die horen bij een bepaald ras, wilt u behouden en optimaliseren wanneer u gaat fokken. Verstandig fokken binnen een ras vraagt naast enige kennis van erfelijkheidsleer om het systematisch nalopen van een aantal foktechnische stappen. Deze stappen, die samen het fokprogramma bepalen, komen vanaf dit nummer van Zeldzaam Huisdier in 2015 aan bod.
    Fokkerij op ziekteresistentie van Japanse oesters
    Kamermans, P. ; Engelsma, M.Y. ; Peene, F. ; Blonk, R.J.W. - \ 2015
    Yerseke : IMARES (Rapport / IMARES Wageningen UR C025/15) - 28
    ziekteresistentie - dierveredeling - oesters - nederland - oesterteelt - schaal- en schelpdierenteelt - disease resistance - animal breeding - oysters - netherlands - oyster culture - shellfish culture
    Het oesterherpesvirus OsHV-1 µvar veroorzaakt hoge sterfte onder Japanse oesters in de Nederlandse kweekgebieden. De oestersector ondervindt problemen van deze sterfte. In deze studie is geïnventariseerd of een fokprogramma waarbij oesters geselecteerd worden op resistentie tegen het oesterherpesvirus en vervolgens worden voortgeplant in een hatchery uitkomst kan geven voor deze problematiek. Ook is bekeken of een fokprogramma gebruikt kan worden ter verbetering van groei en conditie van oesters.
    Structural variations in pig genomes
    Paudel, Y. - \ 2015
    Wageningen University. Promotor(en): Martien Groenen, co-promotor(en): Ole Madsen; Hendrik-Jan Megens. - Wageningen : Wageningen University - ISBN 9789462572171 - 204
    varkens - dierveredeling - genomen - genomica - single nucleotide polymorphism - dna-sequencing - fenotypische variatie - chromosoomafwijkingen - evolutie - soortvorming - pigs - animal breeding - genomes - genomics - single nucleotide polymorphism - dna sequencing - phenotypic variation - chromosome aberrations - evolution - speciation

    Abstract

    Paudel, Y. (2015). Structural variations in pig genomes. PhD thesis, Wageningen University, the Netherlands

    Structural variations are chromosomal rearrangements such as insertions-deletions (INDELs), duplications, inversions, translocations, and copy number variations (CNVs). It has been shown that structural variations are as important as single nucleotide polymorphisms (SNPs) in regards to phenotypic variations. The general aim of this thesis was to use next generation sequencing data to improve our understanding of the evolution of structural variations such as CNVs, and INDELs in pigs. We found that: 1) the frequency of copy number variable regions did not change during pig domestications but rather reflected the demographic history of pigs. 2) CNV of olfactory receptor genes seems to play a role in the on-going speciation of the genus Sus. 3) Variation in copy number of olfactory receptor genes in pigs (Sus scrofa) seems to be shaped by a combination of selection and genetic drift, where the clustering of ORs in the genome is the major source of variation in copy number. 4) Analysis on short INDELs in the pig genome shows that the level of purifying selection of INDELs positively correlates with the functional importance of a genomic region, i.e. strongest purifying selection was observed in gene coding regions. This thesis provides a highly valuable resource for copy number variable regions, INDELs, and SNPs, for future pig genetics and breeding research. Furthermore, this thesis discusses the limitations and improvements of the available tools to conduct structural variation analysis and insights into the future trends in the detection of structural variations.

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