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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    Zo kies je een gezonde en sociale hond
    Ruis, M.A.W. - \ 2019
    Wageningen : Wageningen University & Research - 21 p.
    animal welfare - pets - dogs - animal behaviour - animal housing - animal health - animal nutrition - animal breeding
    Deze interactieve brochure van Platform Fairfok geeft een overzicht van beschikbare informatie, diensten of producten van organisaties die zich actief inzetten voor de gezonde en sociale hond in Nederland.
    Learn how to set up a breeding programme | WURcast
    Komen, J. - \ 2019
    Wageningen : WURcast
    animal breeding - animal breeding methods - breeding programmes
    Animal breeding: the concept of inbreeding | WURcast
    Bijma, P. - \ 2019
    Wageningen : Centre for Genetic Resources and Animal Breeding and Genomics Group, Wageningen University and Research Centre
    inbreeding - animal breeding - alleles
    Inbreeding is the result of mating two related individuals. Related individuals are more alike genetically than non-related individuals because they share alleles.
    Hoe kies je de beste stieren voor je bedrijf?
    Hoving, A.H. ; Ducro, B.J. - \ 2019
    Wageningen : Centre for Genetic Resources, the Netherlands (CGN), Wageningen University & Research
    animal breeding - dairy cattle - genetics - teaching materials - intermediate vocational training - animal welfare - animal production - animal health
    Docentenhandleiding bij lesmateriaal ‘Hoe kies je de beste stieren voor je bedrijf?’ Powerpoint ‘Hoe kies je de beste stieren voor je bedrijf?’ Excel file ‘Een selectie van de stierenkaart’.
    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.

    Milk progesterone measures to improve genomic selection for fertility in dairy cows
    Tenghe, Amabel Manyu Mefru - \ 2017
    Wageningen University. Promotor(en): R.F. Veerkamp; B. Berglund, co-promotor(en): D. J. de Koning; A.C. Bouwman. - Wageningen : Wageningen University - ISBN 9789463431330 - 179
    dairy cows - fertility - progesterone - milk - genomics - genetic improvement - heritability - genetic parameters - dairy performance - reproductive traits - animal genetics - animal breeding - dairy farming - melkkoeien - vruchtbaarheid - progesteron - melk - genomica - genetische verbetering - heritability - genetische parameters - melkresultaten - voortplantingskenmerken - diergenetica - dierveredeling - melkveehouderij

    Improved reproductive performance has a substantial benefit for the overall profitability of dairy cattle farming by decreasing insemination and veterinary treatment costs, shortening calving intervals, and lowering the rate of involuntary culling. Unfortunately, the low heritability of classical fertility traits derived from calving and insemination data makes genetic improvement by traditional animal breeding slow. Therefore, there is an interest in finding novel measures of fertility that have a higher heritability or using genomic information to aid genetic selection for fertility. The overall objective of this thesis was to explore the use of milk progesterone (P4) records and genomic information to improve selection for fertility in dairy cows. In a first step, the use of in-line milk progesterone records to define endocrine fertility traits was investigated, and genetic parameters estimated. Several defined endocrine fertility traits were heritable, and showed a reasonable repeatability. Also, the genetic correlation of milk production traits with endocrine fertility traits were considerably lower than the correlations of milk production with classical fertility traits. In the next step 17 quantitative trait loci (QTL) associated with endocrine fertility traits, were identified on Bos taurus autosomes (BTA) 2, 3, 8, 12, 15, 17, 23, and 25 in a genome-wide association study with single nucleotide polymorphisms. Further, fine-mapping of target regions on BTA 2 and 3, identified several associated variants and potential candidate genes underlying endocrine fertility traits. Subsequently, the optimal use of endocrine fertility traits in genomic evaluations was investigated; using empirical and theoretical predictions for single-trait models, I showed that endocrine fertility traits have more predictive ability than classical fertility traits. The accuracy of genomic prediction was also substantially improved when endocrine and classical fertility traits were combined in multi-trait genomic prediction. Finally, using deterministic predictions, the potential accuracy of multi-trait genomic selection when combining a cow training population measured for the endocrine trait commencement of luteal activity (C-LA), with a training population of bulls with daughter observations for a classical fertility trait was investigated. Results showed that for prediction of fertility, there is no benefit of investing in a cow training population when the breeding goal is based on classical fertility traits. However, when considering a more biological breeding goal for fertility like C-LA, accuracy is substantially improved when endocrine traits are available from a limited number of farms.

    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.

    Genetische analyse van de Stabij
    Doekes, H.P. ; Oldenbroek, J.K. ; Windig, J.J. - \ 2016
    Zeldzaam huisdier 41 (2016)1. - ISSN 0929-905X - p. 18 - 19.
    zeldzame rassen - genetische analyse - hondenrassen - friese stabij - dierveredeling - rare breeds - genetic analysis - dog breeds - frisian stabyhoun - animal breeding
    De Stabij is een van de negen oorspronkelijke Nederlandse hondenrassen die een belangrijke rol vervullen in het Fairfok-programma van de Raad van Beheer voor de Kynologie. De SZH ondersteunt dat programma door de rasverenigingen van kennis en advies te voorzien en heeft met het CGN een genetische analyse gemaakt van het Stabijras.
    Genetische analyse van het Markiesje
    Doekes, H.P. ; Oldenbroek, J.K. ; Windig, J.J. - \ 2016
    Zeldzaam huisdier 41 (2016)2. - ISSN 0929-905X - p. 20 - 21.
    hondenrassen - zeldzame rassen - genetische analyse - dierveredeling - stamboeken - dog breeds - rare breeds - genetic analysis - animal breeding - herdbooks
    Het Markiesje is een van de negen oorspronkelijke Nederlandse hondenrassen. Het vervult een belangrijke rol in het Fairfok-programma. De SZH ondersteunt dat programma door de rasverenigingen van kennis en advies te voorzien.
    Leerstoelgroep Filosofie en Dier-ethiek Wageningen; '10.000 liter per koe is onethisch'
    Gremmen, Bart - \ 2016
    animal welfare - animal ethics - animal production - dairy cattle - cattle - animal breeding - animal health

    De melkveehouderij krijgt geregeld als kritiek dat ze dieronvriendelijk en onethisch werkt. Neem de kalf-bij-de-koediscussie. Het dier wordt steeds meer vermenselijkt, met als gevolg scheve veronderstellingen over dierethiek. Wageningse professor Bart Gremmen: „Het eten van dierlijke producten gaat altijd gepaard met dierenleed.”

    ‘Inteelt zie je niet altijd, maar kost wel geld’ : onderzoeker Nauta overweegt studieclub fokkerij op te zetten
    Windig, Jack - \ 2016
    inbreeding - inbreeding depression - goat keeping - animal breeding - farm management
    Fokken, wat is dat?
    Oldenbroek, Kor - \ 2016
    animal welfare - pets - dogs - animal health - animal behaviour - animal breeding - genetics
    Genomic selection in egg-laying chickens
    Heidaritabar, M. - \ 2016
    Wageningen University. Promotor(en): Martien Groenen, co-promotor(en): John Bastiaansen. - Wageningen : Wageningen University - ISBN 9789462576704 - 220
    hens - genomics - genetic variation - selective breeding - quantitative traits - breeding value - animal genetics - animal breeding - hennen - genomica - genetische variatie - selectief fokken - kwantitatieve kenmerken - fokwaarde - diergenetica - dierveredeling

    Abstract

    Heidaritabar, M. (2016). Genomic selection in egg-laying chickens. PhD thesis, Wageningen University, the Netherlands

    In recent years, prediction of genetic values with DNA markers, or genomic selection (GS), has become a very intense field of research. Many initial studies on GS have focused on the accuracy of predicting the genetic values with different genomic prediction methods. In this thesis, I assessed several aspects of GS. I started with evaluating results of GS against results of traditional pedigree-based selection (BLUP) in data from a selection experiment that applied both methods side by side. The impact of traditional selection and GS on the overall genome variation as well as the overlap between regions selected by GS and the genomic regions predicted to affect the traits were assessed. The impact of selection on genome variation was assessed by measuring changes in allele frequencies that allowed the identification of regions in the genome where changes must be due to selection. These frequency changes were shown to be larger than what could be expected from random fluctuations, indicating that selection is really affecting the allele frequencies and that this effect is stronger in GS compared with BLUP. Next, concordance was tested between the selected regions and regions that affect the traits, as detected by a genome-wide association study. Results showed a low concordance overall between the associated regions and the selected regions. However, markers in associated regions did show larger changes in allele frequencies compared with the average changes across the genome. The selection experiment was performed using a medium density of DNA markers (60K). I subsequently explored the potential benefits of whole-genome sequence data for GS by comparing prediction accuracy from imputed sequence data with the accuracy obtained from the 60K genotypes. Before sequencing, the selection of key animals that should be sequenced to maximize imputation accuracy was assessed with the original 60K genotypes. The accuracy of genotype imputation from lower density panels using a small number of selected key animals as reference was compared with a scenario where random animals were used as the reference population. Even with a very small number of animals as reference, reasonable imputation accuracy could be obtained. Moreover, selecting key animals as reference considerably improved imputation accuracy of rare alleles compared with a set of random reference animals. While imputation from a small reference set was successful, imputation to whole-genome sequence data hardly improved genomic prediction accuracy compared with the predictions based on 60K genotypes. Using only those markers from the whole-genome sequence that are more likely to affect the phenotype was expected to remove noise from the data, but resulted in slightly lower prediction accuracy compared with the complete genome sequence. Finally, I evaluated the inclusion of dominance effects besides additive effects in GS models. The proportion of variance due to additive and dominance effects were estimated for egg production and egg quality traits of a purebred line of layers. The proportion of dominance variance to the total phenotypic variance ranged from 0 to 0.05 across traits. Also, the impact of fitting dominance besides additive effects on prediction accuracy was investigated, but was not found to improve accuracy of genomic prediction of breeding values.

    Breeding against infectious diseases in animals
    Rashidi, H. - \ 2016
    Wageningen University. Promotor(en): Johan van Arendonk, co-promotor(en): Herman Mulder; P.K. Mathur. - Wageningen University - ISBN 9789462576452 - 179
    livestock - infectious diseases - animal breeding - selective breeding - disease resistance - tolerance - genetic variation - breeding value - genetic correlation - traits - genomics - animal genetics - vee - infectieziekten - dierveredeling - selectief fokken - ziekteresistentie - tolerantie - genetische variatie - fokwaarde - genetische correlatie - kenmerken - genomica - diergenetica

    Infectious diseases in farm animals are of major concern because of animal welfare, production costs, and public health. Farms undergo huge economic losses due to infectious disease. The costs of infections in farm animals are mainly due to production losses, treatment of infected animals, and disease control strategies. Control strategies, however, are not always successful. Selective breeding for the animals that can mount a defence against infection could therefore be a promising approach. Defensive ability of an animal has two main mechanisms: resistance (ability to control the pathogen burden) and tolerance (ability to maintain performance when pathogen burden increases). When it is difficult to distinguish between resistance and tolerance, defensive ability is measured as resilience that is the ability to maintain performance during a disease outbreak regardless of pathogen burden. Studies have focused on the genetics of resistance and resilience with little known about the genetics of tolerance and its relationship with resistance and resilience. The objectives of this thesis were to: 1) estimate the genetic variation in resistance, tolerance, and resilience to infection in order to assess the amenability of these traits for selective breeding in farm animals, 2) estimate the genetic correlation between resistance, tolerance and resilience and 3) detect genomic regions associated with resistance, tolerance, and resilience.

    In chapter 2, we studied the variation among sows in response to porcine reproductive and respiratory syndrome (PRRS). First a statistical method was developed to detect PRRS outbreaks based on reproduction records of sows. The method showed a high sensitivity (78%) for disease phases. Then the variation of sows in response to PRRS was quantified using 2 models on the traits number of piglets born alive (NBA) and number of piglets born dead (LOSS): 1) bivariate model considering the trait in healthy and disease phases as different traits, and 2) reaction norm model modelling the response of sows as a linear regression of the trait on herd-year-week estimates of NBA. Trait correlations between healthy and disease phases deviated from unity (0.57±0.13 – 0.87±0.18). The repeatabilities ranged from 0.07±0.027 to 0.16±0.005. The reaction norm model had higher predictive ability in disease phase compared to the bivariate model.

    In chapter 3 we studied 1) the genetic variation in resistance and tolerance of sheep to gastrointestinal nematode infection and 2) the genetic correlation between resistance and tolerance. Sire models on faecal nematode egg count (FEC), IgA, and pepsinogen were used to study the genetic variation in resistance. Heritability for resistance traits ranged from 0.19±0.10 to 0.59±0.20. A random regression model was used to study the reaction norm of sheep body weight on FEC as an estimate of tolerance to nematode infection. We observed a significant genetic variance in tolerance (P<0.05). Finally a bivariate model was used to study the genetic correlation between resistance and tolerance. We observed a negative genetic correlation (-0.63±0.25) between resistance and tolerance.

    In chapter 4, we studied the response to selection in resistance and tolerance when using estimated breeding values for resilience. We used Monte Carlo simulation to generate 100 half-sib families with known breeding values for resistance (pathogen burden) and tolerance. We used selection index theory to predict response to selection for resistance and tolerance: 1) when pathogen burden is known and selection is based on true breeding values for resistance and tolerance and 2) when pathogen burden is unknown and selection is based on estimated breeding values for resilience. Using EBV for resilience in absence of records for pathogen burden resulted in favourable responses in resistance and tolerance to infections, with more emphasis on tolerance than on resistance. However, more genetic gain in resistance and tolerance could be achieved when pathogen burden was known.

    In chapter 5 we studied genomics regions associated with resistance, resilience, and tolerance to PRRS. Resistance was modelled as sire effect on area under the PRRS viremia curve up to 14 days post infection (AUC14). Resilience was modelled as sire effects on daily growth of pigs up to 28 days post infection (ADG28). Tolerance was modelled as the sire effect on the regression of ADG28 on AUC14. We identified a major genomics region on chromosome 4 associated with resistance and resilience to PRRS. We also identified genomics regions on chromosome 1 associated with tolerance to PRRS.

    In the general discussion (chapter 6) I discussed: 1) response to infection as a special case of genotype by environment interaction, 2) random regression model as a statistical tool for studying response to disease, 3) advantages and requirements of random regression models, and 4) selective breeding of farm animals for resistance, tolerance, and resilience to infections. I concluded that random regression is a powerful approach to estimate response to infection in animals. If the adequate amount of data is available random regression model could estimate breeding values of animals more accurately compared to other models. I also concluded that before including resistance and tolerance into breeding programs, breeders should make sure about the added values of including these traits on genetic progress. Selective breeding for resilience could be a pragmatic approach to simultaneously improve resistance and tolerance.

    Multi-population genomic prediction
    Wientjes, Y.C.J. - \ 2016
    Wageningen University. Promotor(en): Roel Veerkamp; Mario Calus. - Wageningen : Wageningen University - ISBN 9789462576193 - 267
    cum laude - dairy cattle - genomics - prediction - quantitative trait loci - genetic improvement - breeding value - selective breeding - animal breeding - animal genetics - melkvee - genomica - voorspelling - loci voor kwantitatief kenmerk - genetische verbetering - fokwaarde - selectief fokken - dierveredeling - diergenetica
    Cum laude graduation
    Hereditary disorders in pedigree dogs and look-a-likes
    Zeeland, C.W.M. Van; Beerda, B. - \ 2015
    Wageningen UR, Wetenschapswinkel (Rapport / Wetenschapswinkel Wageningen UR 317) - ISBN 9789461738882 - 51
    dogs - dog breeds - genetic disorders - pedigree - disease prevalence - animal breeding - animal welfare - animal health - pets - honden - hondenrassen - genetische stoornissen - stamboom - ziekteprevalentie - dierveredeling - dierenwelzijn - diergezondheid - gezelschapsdieren
    Selectie en genetische variatie in een fokprogramma
    Oldenbroek, Kor ; Maurice - Van Eijndhoven, Myrthe - \ 2015
    Zeldzaam huisdier 40 (2015)4. - ISSN 0929-905X - p. 14 - 17.
    dierveredeling - veredelingsprogramma's - genetische variatie - selectie - zeldzame rassen - heritability - inteelt - verwantschap - groninger paard - animal breeding - breeding programmes - genetic variation - selection - rare breeds - heritability - inbreeding - kinship - groningen horse
    In drie voorgaande artikelen in deze serie zijn achtereenvolgens het fokdoel, de registratie van gegevens en de basisprincipes van de erfelijkheid besproken. In dit laatste artikel wordt het belang van genetische variatie en de selectie van ouderdieren besproken. Twee belangrijke elementen in het fokprogramma van een zeldzaam ras.
    Fokkerij nieuwe strategie zonder quotum
    Veerkamp, Roel - \ 2015
    animal breeding - cattle - breeding aims - animal breeding methods - selection - mating - animal genetics
    Handboek melkveehouderij 2015/16
    Remmelink, G.J. ; Middelkoop, J.C. van; Ouweltjes, W. ; Wemmenhove, H. - \ 2015
    Wageningen : Wageningen UR Livestock Research (Handboek / Wageningen UR Livestock Research 30) - 386
    melkvee - melkveehouderij - bodemeigenschappen - bemesting - graslandbeheer - voedergrassen - voedergewassen - rundveevoeding - dierveredeling - diergezondheid - melkproductie - landbouwbedrijfsgebouwen - nederland - handboeken - dairy cattle - dairy farming - soil properties - fertilizer application - grassland management - fodder grasses - fodder crops - cattle feeding - animal breeding - animal health - milk production - farm buildings - netherlands - handbooks
    Natuurlijke antilichamen als voorspeller zieke koe
    Knaap, J. van der; Poel, J.J. van der - \ 2015
    Veeteelt 32 (2015)15. - ISSN 0168-7565 - p. 10 - 12.
    melkveehouderij - dierveredeling - natuurlijke antilichamen - diergezondheid - fokwaarde - dairy farming - animal breeding - natural antibodies - animal health - breeding value
    De aanwezigheid van natuurlijke antilichamen, de zogenaamde NAbs, kan sterk verschillen per koe. Door de erfelijkheidsgraad van NAbs is het mogelijk om erop te fokken, zo blijkt uit het project Weerbaar Vee. De uitkomsten bieden perspectief om de gezondheid te verbeteren, maar de uitvoering lijkt nog niet prakijkrijp.
    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.

    Speciation and domestication in Suiformes: a genomic perspective
    Frantz, L.A.F. - \ 2015
    Wageningen University. Promotor(en): Martien Groenen, co-promotor(en): Ole Madsen; Hendrik-Jan Megens. - Wageningen : Wageningen University - ISBN 9789462572546 - 227
    domesticatie - suiformes - soortvorming - dierveredeling - genomica - evolutie - genenstroom - dna-sequencing - moleculaire fylogenetica - domestication - suiformes - speciation - animal breeding - genomics - evolution - gene flow - dna sequencing - molecular phylogenetics

    Abstract

    Frantz, L.A.F. (2015). Speciation and Domestication in Suiformes: a genomic perspective. PhD thesis, Wageningen University, the Netherlands

    The diversity of life on earth owes its existence to the process of speciation. The concept of speciation is primordial for evolutionary biologists because it provides a framework to understand how contemporary biodiversity came to be. Moreover, not only natural phenomena can result in the differentiation of life forms. Indeed, biodiversity can also be the result of direct and indirect human influence such as domestication. In this thesis, I investigate these evolutionary processes (speciation and domestication) in the Suiformes superfamily (pigs and related species). I use complete genome sequences to illuminate many specific aspects of the speciation and domestication in Suiformes as well as to draw general conclusions on these crucial processes. In chapter 2 I show how genomes provide an essential source of information to retrieve deep taxonomic relationships among Suiformes. This allows me to describe multiple novel aspects of their early evolutionary history such as the fact that Suiformes colonised North America at least twice. In this chapter, I further highlight and discuss novel methodological limitations that are inherent to phylogenomics. In chapters 3, 4 and 5 I use genome sequences to resolve the evolutionary history of the genus Sus (domestic pigs and wild boars species). More precisely, I show that, contrary to the expectation of simple models of speciation, the evolutionary history of these species involved alternating periods of gene-flow and genetic differentiation that are tightly linked to past climatic fluctuations that took place over the last 4 million years. In addition, these chapters also provide novel insights into the process of speciation by demonstrating that genetic differentiation between species can be achieved, even when gene-flow is strong. Lastly, in chapter 6 I tested multiple models of domestication for S. scrofa. In this chapter I show that models involving reproductive isolation between wild and domestic forms are incompatible with genomic data. Moreover, this chapter demonstrates that, while domestic pigs are morphologically homogenous, they are not genetically homogenous. Together, these findings have important implications for our understanding of the process of domestication because it shows that this process was not solely the result of captivity. Together, the results of this work not only provide a comprehensive evolutionary history for the Suiformes, but also novel insights into the complex processes (speciation and domestication) that are responsible for the diversity of life on earth.

    Textbook animal breeding : animal breeding andgenetics for BSc students
    Oldenbroek, Kor ; Waaij, Liesbeth van der - \ 2014
    Wageningen : Centre for Genetic Resources and Animal Breeding and Genomics Group, Wageningen University and Research Centre - 311
    dierveredeling - selectief fokken - huisdieren - agrarisch onderwijs - diergenetica - lesmaterialen - hoger onderwijs - animal breeding - selective breeding - domestic animals - agricultural education - animal genetics - teaching materials - higher education
    This textbook contains teaching material on animal breeding and genetics for BSc students. The text book started as an initiative of the Dutch Universities for Applied (Agricultural) Sciences. The textbook is made available by the Animal Breeding and Genomics Centre (ABGC) of Wageningen UR (University and Research Centre).
    Een onderzoek naar erfelijke gebreken bij rashonden en lookalikes
    Wageningen UR Wetenschapswinkel, - \ 2014
    Wetenschapswinkel Wageningen UR
    honden - hondenrassen - huisdieren - gezelschapsdieren - dierenwelzijn - diergezondheid - genetische stoornissen - dierveredeling - fokdoelen - dogs - dog breeds - domestic animals - pets - animal welfare - animal health - genetic disorders - animal breeding - breeding aims
    De Stichting Dier & Recht stelt op haar website dat consumenten beter een hond van een kruising uit het asiel kunnen halen, dan voor veel geld een rashond kopen. Rashonden lijken vaker een erfelijk gebrek te hebben, maar is dat echt zo en lopen rashonden dezelfde risico’s als lookalikes?
    Natuurlijke selectie van varroaresistente bijenvolken. Bijennieuws 28
    Blacquière, T. - \ 2014
    Wageningen : Bijen@wur
    apidae - wilde bijenvolken - dierveredeling - rassen (dieren) - ziekteresistentie - selectiemethoden - diergezondheid - varroa - besmetting - mijten - apidae - wild honey bee colonies - animal breeding - breeds - disease resistance - selection methods - animal health - varroa - contamination - mites
    Naar aanleiding van in het wild gevonden (Noord Amerika, Frankrijk) en via experimenten verkregen (Gotland, Zweden) min of meer resistente volken, althans natuurlijk overlevende volken, hebben wij in 2007 met een nateelt van Gotland koninginnen en in 2008 met een Nederlands mengsel van bijenvolken twee teelten van bijenvolken opgezet zonder varroa te bestrijden. Bij de 2008-serie hebben we ook een groep volken als controle meegenomen, waarin varroa twee keer per jaar wordt bestrede
    Handboek melkveehouderij 2014
    Remmelink, G.J. ; Dooren, H.J.C. van; Middelkoop, J.C. van; Ouweltjes, W. ; Wemmenhove, H. - \ 2014
    Wageningen : Wageningen UR Livestock Research (Handboek / Wageningen UR Livestock Research 29) - 385
    melkveehouderij - richtlijnen (guidelines) - naslagwerken - bemesting - graslandbeheer - ruwvoer (forage) - veevoeding - dierveredeling - gezondheid - melkproductie - landbouwbedrijfsgebouwen - bodemwater - agrarisch natuurbeheer - dairy farming - guidelines - reference works - fertilizer application - grassland management - forage - livestock feeding - animal breeding - health - milk production - farm buildings - soil water - agri-environment schemes
    Het Handboek Melkveehouderij is hét naslagwerk voor melkveehouder, agrarisch adviseur, docent en student. De opgenomen informatie is bruikbaar voor de ondersteuning van het dagelijks management én voor het management op de lange termijn.
    Eerste pups outcross Saarlooswolfhond geboren
    Eggink, M. ; Oldenbroek, J.K. - \ 2014
    Zeldzaam huisdier 39 (2014)4. - ISSN 0929-905X - p. 18 - 20.
    hondenrassen - rassen (dieren) - dierveredeling - zeldzame rassen - veredelingsmethoden - puppy's - dog breeds - breeds - animal breeding - rare breeds - breeding methods - puppies
    De Algemene Vereniging van Liefhebbers voor Saarlooswolfhonden (AVLS) heeft een plan van aanpak opgesteld met als doel de hoge onderlinge verwantschap tussen de honden op termijn te laten afnemen. Dat is hard nodig omdat anders de inteelttoename in de toekomst niet meer beheersbaar zal zijn. Gevolgen daarvan zouden zijn dat erfelijke gebreken toenemen en de vruchtbaarheid verder afneemt.
    Genetic management : from science to practice
    Windig, Jack - \ 2014
    animal genetic resources - animal breeding - dogs - kempen heath sheep - veluwe heath sheep - sheep - golden retriever - biodiversity
    The potential of genomic selection to support local breed conservation
    Calus, Mario - \ 2014
    animal breeding - genotypes - phenotypes - genetic variance - genomics - genetic correlation - irish republic - beef cows - animal genetic resources - breeds
    Blaarkopfokplan voor de toekomst : ras van het jaar
    Oldenbroek, J.K. ; Faber, J.H. ; Wieringa, R. - \ 2014
    Zeldzaam huisdier 39 (2014)4. - ISSN 0929-905X - p. 8 - 9.
    rundvee - rundveeteelt - rundveerassen - groninger blaarkop - dierveredeling - fokkerijmethoden - veredelingsprogramma - cattle - cattle farming - cattle breeds - groningen white headed - animal breeding - animal breeding methods - breeding programmes
    Eind 2013 heeft de SZH met de blaarkopbestuurders een strategiedag gehouden. Daaruit kwam onder meer naar voren dat er behoefte is aan een goed en doelgericht fokplan. Onlangs is de Landelijke (Fok)-Commissie begonnen het fokplan uit te werken.
    Fokken en scrapie resistentie bij de Toggenburger geit
    Windig, Jack - \ 2014
    goat keeping - goats - scrapie - dutch toggenburg - toggenburg - goat breeds - disease resistance - animal breeding - rare breeds
    Genetic variation of milk fatty acid composition between and within dairy cattle breeds
    Maurice - Van Eijndhoven, M.H.T. - \ 2014
    Wageningen University. Promotor(en): Johan van Arendonk; Roel Veerkamp, co-promotor(en): Mario Calus. - Wageningen : Wageningen University - ISBN 9789462571488 - 184
    dierveredeling - melkkoeien - vetzuren - melk - genetische variatie - rundveerassen - heritability - melkvet - genetische bronnen van diersoorten - melkveehouderij - animal breeding - dairy cows - fatty acids - milk - genetic variation - cattle breeds - heritability - milk fat - animal genetic resources - dairy farming

    Abstract

    Maurice – Van Eijndhoven, M.H.T. (2014). Genetic variation of milk fatty acid composition between and within dairy cattle breeds. PhD thesis, Wageningen University, the Netherlands

    Fat is one of the main components in bovine milk and comprises a large number of individual fatty acids (FA). The composition of FA in milk varies considerably due to differences in the genetics and nutrition of cows and an increasing interest in the possibilities for modifying FA composition can be noticed nowadays. In this thesis two fields of interest were combined, namely: production of milk with specific milk fat composition and conservation of native cattle breeds. Therewith, the overall objective of this thesis was to investigate the variability of detailed milk FA composition between and within different dairy cattle breeds, including the mainstream Holstein Friesian (HF) and Jersey, and the native dual purpose breeds Meuse-Rhine-Yssel (MRY), Groningen White Headed (GWH) and Dutch Friesian (DF) in the Netherlands. For this study the accuracy of mid-infrared (MIR) spectrometry was evaluated for predicting FA composition in different breeds. Differences of milk FA composition within and between breeds were investigated using MIR and Gas Chromatography (GC) information. Finally, similarities in genomic variation associated with detailed milk fat composition between the mainstream HF breed and native dual purpose breeds were studied. Results show that MIR is an accurate method for predicting FA composition among different breeds and countries. Evaluating the FA composition in different breeds, differences were found in milk FA composition among herds using different cattle breeds in the Netherlands, based on detailed milk FA measurements using GC. Evaluating the FA composition in milk between and within breeds using a large dataset that included MIR spectra of milk from cows from a range of farms using one or more breeds, in general, only minor breed differences in FA composition were found and HF showed more genetic variation in FA composition compared to MRY. Furthermore, differences were detected between the native breeds MRY, DF and GWH in genomic variations of regions that are associated with FA composition in HF, while most variation in these main regions was clearly observed in HF. Overall, it was concluded that no large differences existed in milk FA composition among the native Dutch dual purpose breeds and the mainstream HF breed. It is suggested, however, that selecting specific FA composition differences in farms using different breeds in the Netherlands can attribute to modifying the FA composition in bovine milk production.

    Gezond gebruik genetica
    Oldenbroek, Kor - \ 2014
    genetics - animal breeding - rare breeds - dogs - dog breeds - inbreeding - selection - sustainability - agricultural education
    Breeding strategies to make sheep farms resilient to uncertainty
    Rose, I.J. - \ 2014
    Wageningen University. Promotor(en): Johan van Arendonk, co-promotor(en): Herman Mulder; J. Werf. - Wageningen : Wageningen University - ISBN 9789462570900 - 188
    schapen - schapenhouderij - dierveredeling - veredelingsprogramma's - economische haalbaarheid - rentabiliteit - veerkracht - weiden - schapenvoeding - western australia - sheep - sheep farming - animal breeding - breeding programmes - economic viability - profitability - elasticity - pastures - sheep feeding - western australia

    The sheep industry in Western Australian has had many challenges over the last 20 years which have caused sheep numbers to decline. This decline is because sheep farms are not resilient to uncertain pasture growth and commodity prices. One way to improve resilience and profitability of farming systems is through breeding of sheep. Therefore, this thesis had two aims; 1. Quantify the potential to select and breed sheep that are more resilient and 2. Quantify how sheep breeding can make farming systems more resilient. To determine if sheep can be bred to be resilient to varying pasture growth I investigated if live weight change is a heritable trait. I investigated live weight change in adult Merino ewes managed in a Mediterranean climate in Katanning in Western Australia. Live weight change traits were during mating and lactation. The heritability of live weight change was low to moderate. Therefore that live weight change could be a potential indicator trait for resilience to uncertain pasture growth. To include live weight change in a breeding goal, correlations with other traits are needed. I calculated the genetic correlations between live weight change during mating, pregnancy and lactation, and reproduction traits. Most genetic correlations were not significant, but genetically gaining live weight during mating in two-year old ewes and during pregnancy for three-year-old ewes improved reproduction. Therefore, optimised selection strategies can select for live weight change and reproduction simultaneously. To investigate optimal breeding programs to make sheep farms resilient to uncertain pasture growth and prices, I modelled a sheep farm in a Mediterranean environment. The economic value of seven traits in the breeding objective were estimated. Including variation in pasture growth and commodity prices decreased average profit and increased the economic value of all breeding goal traits compared to the average scenario. Economic values increased most for traits that had increases in profit with the smallest impact on energy requirements. I also compared optimal breeding programs for across 11 years for 10 regions in Western Australia with different levels of reliability of pasture growth. I identified two potential breeding goals, one for regions with low or high pasture growth reliability and one for regions with medium reliability of pasture growth. Regions with low or high reliability of pasture growth had similar breeding goals because the relationship between economic values and reliability of pasture growth were not linear for some traits. Therefore, farmers can customise breeding goals depending on the reliability of pasture growth on their farm.



    Offspring sex ratio bias and sex related characteristics of eggs in chicken
    Aslam, M.A. - \ 2014
    Wageningen University. Promotor(en): Mari Smits; T.G.G. Groothuis, co-promotor(en): Henri Woelders. - Wageningen : Wageningen University - ISBN 9789462570757 - 192
    kippen - eieren - geslachtsverhouding - karakteristieken - nageslacht - toewijzing - polymerase-kettingreactie - hormonen - voedselbeperking - dierveredeling - fowls - eggs - sex ratio - characteristics - progeny - allocation - polymerase chain reaction - hormones - food restriction - animal breeding

    Understanding the factors influencing sex of egg and sex ratio in laying chicken may lead to finding potential solutions for the problem of killing of day old male chicks, which is the current practice in breeding of laying hens. In studies described in this thesis, it was investigated if the sex of the chicken egg can be predicted by measurable differences in male and female eggs at unincubated stage and if the female primary sex ratio can be induced in laying chicken using different experimental conditions such as feed restriction and corticosterone feeding. The method of sex determination in unincubated chicken eggs using PCR targeted to CHD1 gene was first developed. This method was subsequently used to study the primary sex ratio bias as well as relationship between egg sex and yolk hormones. No significant relationship of the sex of egg with concentrations of several hormones (testosterone, estradiol, androstenedione, progesterone, dihydrotestosterone) and glucose in yolk as well as of egg parameters (mass, width and length) was found. Effect of feed availability on sex ratio was tested in two separate studies. In one study, the rate of change of hen body mass between day of laying and day of laying minus 2 days (encompass time of meiosis completion) was a significant predictor for the sex of that egg, suggesting meiotic drive as mechanism of sex ratio bias. This relationship was not found in the later study. The difference in results could be due to the reason that hens decreased in body mass much less in the later study as compared to earlier study. Blood corticosterone concentrations were associated with sex ratio per hen in the earlier study. Effect of egg mass on egg sex was studied during the later experiment of feed restriction. The egg sex ratio per hen was negatively associated with the average egg mass per hen in the feed restriction group. Two groups of hens were selected from the feed restriction group i.e. male biased hens with low egg mass and female biased hens with high egg mass for microarray analysis of gene expression in the germinal disc of collected F1 follicle. The results did not show differential expression of genes between the groups. However, gene set enrichment analysis showed that a number of processes related to cell cycle progression, mitotic/meiotic apparatus and chromosomal movement were differently enriched between the groups, supporting meiotic drive as potential mechanisms underlying sex ratio determination. In another experiment, blood circulating levels of corticosterone in hens were increased by feeding corticosterone mixed feed under ad libitum. The blood levels of corticosterone were significantly higher in treated hens but these levels were not associated with sex ratio. Treatment did not affect the overall sex ratio, but affected the sex ratio in interaction with hen body mass. In the corticosterone group, sex ratio, laying rate, and fertility rate per hen were decreased in heavy hens. These results suggest that three parameters (sex ratio, laying rate and fertility rate) are connected at the level of ovarian physiology. Interference with meiosis have been shown to affect these three parameters, suggesting the involvement of meiotic drive as mechanism of sex ratio bias.

    JONKOS - Rekenprogramma om opfokkosten jongvee te berekenen
    Evers, A.G. ; Haan, M.H.A. de - \ 2014
    Verantwoorde veehouderij
    rundvee - kalveren - jonge dieren - dierlijke productie - kosten - dierveredeling - berekening - cattle - calves - young animals - animal production - costs - animal breeding - calculation
    Download of open hieronder de spreadsheet van het bedrijfstype dat u door wilt rekenen door erop te klikken. Vul in de spreadsheet de gele cellen van de hoofdpagina in. Zo berekent u de kosten voor jongveeopfok van uw bedrijf.
    Milk production & greenhouse gases : integrated modeling of feeding and breeding strategies to reduce emissions
    Middelaar, C.E. van - \ 2014
    Wageningen University. Promotor(en): Imke de Boer; Jan Dijkstra, co-promotor(en): Paul Berentsen. - Wageningen : Wageningen UR - ISBN 9789461739322 - 182
    dierlijke productie - melkveehouderij - broeikasgassen - diervoedering - emissiereductie - dierveredeling - melkkoeien - animal production - dairy farming - greenhouse gases - animal feeding - emission reduction - animal breeding - dairy cows
    WU thesis no. 5779
    Actuele ontwikkelingen in de preventie en bestrijding van maagdarmwormen bij schapen : Kernpunten uit een literatuurstudie
    Bokma-Bakker, M.H. ; Antonis, A.F.G. ; Ploeger, H. ; Vellema, P. ; Verkaik, J.C. - \ 2014
    Wageningen UR/Universiteit Utrecht
    schapenhouderij - maagdarmziekten - wormen - dierparasitaire nematoden - nematodirus battus - haemonchus contortus - teladorsagia circumcincta - schapenziekten - gastheer parasiet relaties - graslandbeheer - ziektebestrijding - dierveredeling - selectief fokken - voedersupplementen - schapenvoeding - sheep farming - gastrointestinal diseases - helminths - animal parasitic nematodes - nematodirus battus - haemonchus contortus - teladorsagia circumcincta - sheep diseases - host parasite relationships - grassland management - disease control - animal breeding - selective breeding - feed supplements - sheep feeding
    De schapensector gaat de parasitaire resistentie-ontwikkeling terugdringen. Ze wil dat doen door verbetering van de preventie en de bestrijding van maagdarmwormen. Experts hebben in 2013 een literatuurstudie uitgevoerd. Hierin zijn de belangrijkste binnen- en buitenlandse innovatieve ontwikkelingen voor verlaging van de infectiedruk opgenomen en vertaald naar toepasbaarheid onder de Nederlandse omstandigheden. Bekeken zijn de gebieden fokkerij, voeding, vaccinatie, beweiding, inzet van natuurlijke middelen en diagnostiek. In deze brochure zijn de belangrijkste bevindingen samengevat.
    Unraveling the genetic background of bovine milk fat composition
    Bouwman, A.C. - \ 2014
    Wageningen University. Promotor(en): Johan van Arendonk, co-promotor(en): Henk Bovenhuis; Marleen Visker. - Wageningen : Wageningen University - ISBN 9789461739063 - 176
    dierveredeling - melkveehouderij - melkvee - melkproductie - vetzuren - genomica - loci voor kwantitatief kenmerk - animal breeding - dairy farming - dairy cattle - milk production - fatty acids - genomics - quantitative trait loci

    Identification of genomic regions, and preferably individual genes, responsible for genetic variation in bovine milk fat composition enhances the understanding of biological pathways involved in fatty acid synthesis and is expected to increase opportunities for changing bovine milk fat composition by means of selective breeding. This thesis aimed to unravel the genetic background of bovine milk fat composition by detection, confirmation and fine-mapping of quantitative trait loci (QTL) for milk fatty acids in Dutch Holstein Friesian cattle. In addition, causal relations between fatty acids were explored. For this study roughly 2,000 dairy cows were genotyped with 50,000 DNA markers and phenotyped for individual fatty acids in both winter and summer milk samples using gas chromatography. Genome-wide association studies (GWAS) showed that milk fat composition has a complex genetic background with three major QTL that explain a relatively large fraction of the genetic variation of several milk fatty acids, and many QTL that explain a relatively small fraction of the genetic variation. Results from the GWAS for summer milk fatty acids confirmed most associations that were detected in the winter milk samples. Moving from linkage analysis toward GWAS confirmed and refined the size of previously detected QTL regions and resulted in new QTL regions. Performing GWAS based on individual fatty acids resulted in additional QTL as compared to GWAS based on fat percentage or yield. This shows that refinement of complex phenotypes into underlying components results in better links between genes and phenotypes. By increasing the marker density, the QTL on BTA19 was refined to a linkage disequilibrium block that contained 2 genes: coiled-coil domain containing 57 and fatty acid synthase. A search for causal relations between fatty acids resulted in a pathway from C4:0 to C12:0, which resembled the de novo synthesis pathway. Causal relation between the QTL on BTA19 and de novo fatty acids showed that the QTL affects C4:0, C6:0, C8:0, C10:0 and C14:0 directly, while C12:0 was indirectly affected by the QTL through its effect on C10:0. The potential of GWAS based on MIR predicted fatty acids was explored but failed to detect some QTL and resulted in additional QTL that were not detected based on GC measurements. Therefore, MIR predicted phenotypes add complexity to the genotype-phenotype relationship, and renders MIR predicted phenotypes less appropriate to identify candidate genes and to infer the biological background of traits.

    Kaf van het koren scheiden
    Calus, Mario - \ 2014
    dairy farming - ai bulls - dairy bulls - animal breeding - breeding value - selective breeding - genome analysis - genomes
    ‘Speciale technieken alleen voor topfokkerij': Gary Hennip voorspelt het einde van KI als geavanceerde technieken worden gecombineerd
    Hogenkamp, W. ; Veerkamp, R.F. - \ 2014
    Boerderij 99 (2014)27. - ISSN 0006-5617 - p. 38 - 38.
    veehouderij - dierveredeling - fokwaarde - kunstmatige inseminatie - genetica - genomen - technieken - nieuwe combinatie - toekomst - livestock farming - animal breeding - breeding value - artificial insemination - genetics - genomes - techniques - new combination - future
    Gary Hennip, onderzoeker bij Penn State University (VS), denkt dat ki overbodig is bij slim combineren van technieken als ovum pick-up, ivf, genomics en sperma seksen op het bedrijf. Boerderij legt de stelling voor aan professor generieke genetcia Roel Veerkamp.
    Improvement of energy and nitrogen utilisation in pork production : genetics and growth models
    Shirali, M. - \ 2014
    Wageningen University. Promotor(en): R. Roehe; Johan van Arendonk, co-promotor(en): Egbert Kanis. - Wageningen : Wageningen University - ISBN 9789461738479 - 186
    dierveredeling - varkens - dierlijke productie - groeimodellen - genetica - stikstof - excretie - voederconversievermogen - animal breeding - pigs - animal production - growth models - genetics - nitrogen - excretion - feed conversion efficiency

    Expansion ofdemand for porkis expected to meet the nutritional requirements of an increasing world population. However, higher levels of pig production are using limited feed resources and are often associated with higher levels of environmental pollution, which provide substantial challenges for pork producers. Therefore, strategies that simultaneously improve feed efficiency and increase production with reduction of environmental pollution of pork production (e.g. per kg product) is necessary. The general aim of the current project was to investigate opportunities for improvement of energy usage and nitrogen excretion at different stages of growth in pigs, and to determine their phenotypic and genetic background in association with other performance traits as well as to provide the basis for developing strategies for improvement of these traits using biological growth models.Feed efficiency was characterised by residual energy intake (REI) as the surplus of energy intake which is not used for protein and lipid deposition along with maintenance throughout growth to 140 kg BW whereas nitrogen excretion was estimated as the difference between nitrogen intake and retention. The results of phenotypic analyses indicate that nitrogen excretion increases substantially during growth of pigs and can be reduced most effectively by improving feed efficiency and to a lesser extent through the improvement of weight gain and/or body composition. Results of genetic analyses indicate that REI as a measure of feed efficiency is highly heritable (h2= 0.44), suggesting great potential for genetic improvement. REI has different genetic background at different stages of growth, suggesting that genetic improvement of REI should consider the stage of growth. In addition, REI explains a large portion of variance in nitrogen excretion, suggesting that selection for lower REI is expected to reduce nitrogen excretion of pork production as well as improve feed efficiency. Genomic analysis showed that different genes are responsible for efficiency of feed utilisation at different stages of growth.The results further suggest that only a small proportion of the variance in REI was explained by variation in feed intake, whereas underlying factors of feed utilisation, such as metabolism and protein turnover, are likely to have great influence on REI. A biological growth model was used to characterize a crossbred population regarding feed energy and nitrogen efficiency in comparison to two purebred population selected for different performances. The results of the biological growth model can be used to developed optimal genetic, nutritional and production strategies, e.g. the impact of reduction in slaughter weight on marginal energy efficiency and nitrogen excretion was estimated. Furthermore, based on the results of the biological growth model, the influence of changes of production traits during growth on energy and nitrogen efficiency can be estimated to optimise genetic strategies. Furthermore, opportunities for further improvement of energy and nitrogen utilisation have been outlined.

    Het fokken van een gezonde rashond
    Oldenbroek, Kor - \ 2014
    animal breeding - dog breeds - animal health - dogs - domestic animals - animal welfare - inbreeding - genetic disorders - breeding aims - pets
    Quantitative genetic analysis of ascites in broilers
    Closter, A.M. - \ 2014
    Wageningen University. Promotor(en): Martien Groenen; Johan van Arendonk; Henk Bovenhuis. - Wageningen : Wageningen University - ISBN 9789461738400 - 130
    vleeskuikens - kwantitatieve genetica - ascites - genetische parameters - heritability - genetische correlatie - fenotypische correlatie - dierveredeling - genetica - kippenziekten - broilers - quantitative genetics - ascites - genetic parameters - heritability - genetic correlation - phenotypic correlation - animal breeding - genetics - fowl diseases

    Ascites, also called pulmonary hypertension syndrome, is a metabolic disorder in chickens. The tendency to develop ascites is heritable, and successful selection will benefit from understanding the genetic background of ascites. The aims of this thesis were to (i) estimate genetic parameters for ascites indicator traits using standard and novel statistical methods and (ii) to perform a genome wide association study in order to identify chromosomal regions associated with ascites. It was shown that blood gas parameters, which have been previously suggested as indicator traits for ascites susceptibility, are of limited value in the selection against ascites susceptibility. Further, it was shown that the incidence of ascites is higher in male than in female broilers and this difference affects the genetic parameters.A liability normal mixture (LNM) model can account for differences in incidence of ascites. Analyses using the LNM model showed that almost a quarter of the chickens in the analyzed population are affected by ascites. Further, this analysis showed that the ratio of right to total ventricular weight (RATIO) is genetically not the same trait in healthy and diseased chickens. Finally, the results of a genome wide association study (GWAS) showed a number of chromosomal regions associated with ascites. No regions were detected with major effects on ascites. Therefore it seems that ascites is affected by a number of genes, each with a relatively small effect.

    Toprunderen door genomische kennis
    Veerkamp, R.F. ; Calus, M.P.L. ; Roos, S. de; Geus, B. de - \ 2014
    V-focus 2014 (2014)1. - ISSN 1574-1575 - p. 30 - 31.
    rundveehouderij - dierveredeling - dierenwelzijn - duurzame veehouderij - duurzame ontwikkeling - bedrijfsresultaten in de landbouw - dna - genotypen - dierlijke productie - tracking en tracing - cattle husbandry - animal breeding - animal welfare - sustainable animal husbandry - sustainable development - farm results - dna - genotypes - animal production - tracking and tracing
    Met de introductie van genomics is het mogelijk om op basis van DNA-testen te voorspellen wat de genetische waarde van een dier in de populatie is. Breed4Food, een samenwerking van vier private partijen en Wageningen UR, wil de kennis over genomische informatie versnellen en samen delen. Dit artikel beschrijft de activiteiten, die worden opgepakt voor de rundveehouderij.
    Fokkerij geeft antwoord op vragen maatschappij
    Greef, K.H. de; Hiemstra, S.J. ; Kool, E. - \ 2014
    V-focus 2014 (2014)1. - ISSN 1574-1575 - p. 28 - 29.
    varkenshouderij - dierenwelzijn - varkens - dierveredeling - staartbijten - varkensfokkerij - diergenetica - genotypische variatie - duurzame veehouderij - pig farming - animal welfare - pigs - animal breeding - tail biting - pig breeding - animal genetics - genetic variance - sustainable animal husbandry
    De fokkerij kan een belangrijke bijdrage leveren aan het oplossen van een probleem als berengeur en het begrijpen van staartbijten. Naast deze twee maatschappelijke vraagstukken zijn er veel meer vragen waarop het samenwerkingsverband Breed4Food antwoord wil geven. Dit artikel beschrijft doorbraken, die Breed- 4Food wil realiseren in de varkensfokkerij om daarmee bij te dragen aan een economisch en maatschappelijk duurzame houderij.
    Consensus methods for breeding low methane emitting : Breeding ruminants that emit less methane - development of consensus methods for measurements of methane (white paper)
    Pickering, N.K. ; Haas, Y. de; Basarab, J. ; Cammack, K. ; Hayes, B. ; Hegarty, R. ; Lassen, J. ; McEwan, J. ; Miller, S. ; Pinares-Patino, C. ; Shackell, G. ; Vercoe, P. ; Oddy, Hutton - \ 2013
    ASGGN - 57
    animal breeding - selection - animal genetics - genomics - methane - sheep - cattle - agriculture and environment - dierveredeling - selectie - diergenetica - genomica - methaan - schapen - rundvee - landbouw en milieu
    This report was prepared by a working group of the Animal Selection, Genetics and Genomics Network (ASGGN) of the Global Research Alliance for reducing greenhouse gases from agriculture. It is a summary of published and yet to be published work. The purpose is to evaluate methods that are potentially useful for measuring CH4 emissions in individual animals so as to estimate genetic parameters and subsequently screen animals for use in selective breeding programs including its use in the development of genomic selection.
    Erfelijke verbetering van bijen : "Kunt u mij de weg naar Hamelen vertellen, meneer?"
    Brascamp, E.W. - \ 2013
    Bijenhouden 7 (2013)6. - ISSN 1877-9786 - p. 25 - 26.
    honingbijen - rassen (dieren) - dierveredeling - professionele bijenhouderij - genetische bronnen van diersoorten - imkers - diergezondheid - kennis - resistentie van variëteiten - honey bees - breeds - animal breeding - commercial beekeeping - animal genetic resources - beekeepers - animal health - knowledge - varietal resistance
    Er is toenemende belangstelling voor de erfelijke verbetering van de bijenpopulatie. Dat komt grotendeels doordat telkens weer tijdig varroa bestrijden tegen gaat staan en erfelijke varroaresistentie dus heel wat waard is. In dit artikel worden ervaringsfeiten met betrekking tot veredeling van landbouwhuisdieren vertaald in zeven vuistregels die voor alle selectie gelden, inclusief die bij de honingbij.
    Handboek melkveehouderij 2013
    Remmelink, G.J. ; Dooren, H.J.C. van; Middelkoop, J.C. van; Ouweltjes, W. ; Wemmenhove, H. - \ 2013
    Lelystad : Wageningen UR Livestock Research [etc.] (Handboek / Wageningen UR Livestock Research 26) - 392
    melkveehouderij - agrarische bedrijfsvoering - graslandbeheer - bemesting - rundveevoeding - dierveredeling - diergezondheid - melk- en zuivelapparatuur - huisvesting van koeien - landbouwwerktuigen - bedrijfsontwikkeling in de landbouw - handboeken - dairy farming - farm management - grassland management - fertilizer application - cattle feeding - animal breeding - animal health - dairy equipment - cow housing - farm machinery - farm development - handbooks
    Het digitale Handboek Melkveehouderij 2013 is geactualiseerd met de laatste ontwikkelingen in de melkveehouderij, zoals in de hoofdstukken: - Bemesting; - Grasland en voedergewassen; - Voederwinning; - Rundveeverbetering; - Gezondheid; - Melkwinning; - Bedrijfsgebouwen; - Mechanisatie.
    Hoe gaat het met de zeldzame landbouwhuisdierrassen in Nederland. Deel 1: De diersoorten rund, paard, schaap en geit.
    Jansen, H. ; Hoving-Bolink, A.H. ; Hiemstra, S.J. - \ 2013
    Zeldzaam huisdier 37 (2013). - ISSN 0929-905X - p. 6 - 8.
    zeldzame rassen - rundveerassen - paardenrassen - schapenrassen - geitenrassen - dierveredeling - genetische bronnen van diersoorten - stamboeken - schapenstamboeken - paardenstamboeken - rare breeds - cattle breeds - horse breeds - sheep breeds - goat breeds - animal breeding - animal genetic resources - herdbooks - flockbooks - studbooks
    Het Centrum voor Genetische Bronnen Nederland (CGN) inventariseert regelmatig in nauwe samenwerking met de Stichting Zeldzame Huisdierrassen (SZH), de rasverenigingen en stamboeken de gegevens over het aantal vrouwelijke en mannelijke fokdieren van de zeldzame landbouwhuisdierrassen. Aan de hand van deze gegevens worden de rassen in een risicocategorie geplaatst. In dit nummer staan de gegevens voor de runderen, paarden, schapen en geiten. In het volgende nummer worden de gegevens voor de soorten kip, gans, eend, duif, hond, konijn en varken gepresenteerd.
    Vier boeren werken samen aan beter melkschaap (interview met H. Sulkers)
    Engelen, J. ; Sulkers, H. - \ 2013
    Het Schaap 22 (2013)10/11. - ISSN 0165-3156 - p. 14 - 16.
    zeeuws melkschaap - fries melkschaap - rammen - kunstmatige inseminatie - genetische bronnen van diersoorten - zeldzame rassen - dierveredeling - zeeland milk sheep - frisian milk sheep - rams - artificial insemination - animal genetic resources - rare breeds - animal breeding
    Het aantal Friese en Zeeuwse melkschapen in ons land is klein. Voor professionele melkers wordt het steeds lastiger om goed verervende rammen te vinden die ook nog eens niet te veel inteelt geven. Vier boeren doen daarom samen een fokkerijproef, ondersteund door het Centrum voor Genetische Bronnen en Stichting Zeldzame Huisdierrassen.
    Optimizing genomic selection for scarcely recorded traits
    Pszczola, M.J. - \ 2013
    Wageningen University. Promotor(en): Johan van Arendonk, co-promotor(en): Mario Calus; T. Strabel. - Wageningen : Wageningen UR - ISBN 9789461737663 - 158
    melkvee - genomen - selectief fokken - genetische verbetering - fokwaarde - fenotypen - genotypen - kenmerken - voeropname - dierveredeling - dairy cattle - genomes - selective breeding - genetic improvement - breeding value - phenotypes - genotypes - traits - feed intake - animal breeding

    Animal breeding aims to genetically improve animal populations by selecting the best individuals as parents of the next generation. New traits are being introduced to breeding goals to satisfy new demands faced by livestock production. Selecting for novel traits is especially challenging when recording is laborious and expensive and large scale recording is not possible. Genetic improvement of novel traits may be thus limited due to the small number of observations. New breeding tools, such as genomic selection, are therefore needed to enable the genetic improvement of novel traits. Using the limited available data optimally may, however, require alternative approaches and methodologies than currently used for conventional breeding goal traits. The overall objective of this thesis was to investigate different options for optimizing genomic selection for scarcely recorded novel traits. The investigated options were: (1) genotype imputation for ungenotyped but phenotyped animals to be used to enlarge the reference population; (2) optimization of the design of the reference population with respect to the relationships among the animals included in it; (3) prioritizing genotyping of the reference population or the selection candidates; and (4) using easily recordable predictor traits to improve the accuracy of breeding values for scarcely recorded traits. Results showed that: (1) including ungenotyped animals to the reference population can lead to a limited increase in the breeding values accuracy; (2) the reference population is designed optimally when the relationship within the reference are minimized and between reference population and potential selection candidates maximized; (3) the main gain in accuracy when moving from traditional to genomic selection is due to genotyping the selection candidates, but preferably both reference population and selection candidates should be genotyped; and (4) including the predictor traits in the analysis when it is recorded on both reference population and selection candidates can lead to a significant increase in the selection accuracy. The key factors for successful implementation of selection for a novel trait in a breeding scheme are: (1) maximizing accuracy of genotype prediction for ungenotyped animals to be used for updating the reference population; (2) optimizing the design of the reference population; (3) determining easy to record indicator traits that are also available on the selection candidates (4) developing large scale phenotyping techniques; and (5) establishing strategies and policies for increasing the engagement of farmers in the recording of novel traits.

    Advies voor genetisch beheer van de Bonte Bentheimen populatie in Nederland
    Windig, J.J. ; Hoving, A.H. - \ 2013
    Wageningen : Centre for genetic resources (CGN) (CGN rapport 28) - 16
    varkens - beren (varkens) - kunstmatige inseminatie - fokkerijmethoden - dierveredeling - populatiegenetica - genetische bronnen van diersoorten - varkensrassen - zeldzame rassen - pigs - boars - artificial insemination - animal breeding methods - animal breeding - population genetics - animal genetic resources - pig breeds - rare breeds
    De Bonte Bentheimer heeft in Nederland een kleine populatieomvang. In kleine rassen kan inteelt voor grote problemen zorgen en dus is een goed fokbeleid nodig om een te sterke inteelttoename te voorkomen.
    Behoud en duurzaam gebruik van diversiteit in landbouwhuisdieren
    Centrum voor genetische bronnen (CGN) in Nederland- -, - \ 2013
    Lelystad : Centrum voor Genetische Bronnen
    huisdieren - agrobiodiversiteit - genetische bronnen van diersoorten - veehouderij - dierlijke productie - dierveredeling - domestic animals - agro-biodiversity - animal genetic resources - livestock farming - animal production - animal breeding
    Genetische diversiteit staat aan het begin van de landbouw. De fokkerij van landbouwhuisdieren is onmogelijk zonder genetische diversiteit. Deze diversiteit is niet alleen essentieel voor de verbetering van onze landbouwproductie, maar is tegelijkertijd onderdeel van ons cultureel erfgoed.
    Winning en opslag van sperma van zeldzame Nederlandse schapen- en geitenrassen in de genenbank (2001-2012)
    Hoving, A.H. ; Sulkers, H. ; Zuidberg, C.A. ; Hulsegge, B. ; Woelders, H. ; Wit, A.A.C. de; Hiemstra, S.J. - \ 2013
    Lelystad : Centrum voor Genetische Bronnen Wageningen UR (CGN rapport / Centrum voor Genetische Bronnen Nederland 29) - 30
    schapenrassen - geitenrassen - zeldzame rassen - schapenhouderij - geitenhouderij - spermaconservering - genetische bronnen van diersoorten - dierveredeling - genenbanken - sheep breeds - goat breeds - rare breeds - sheep farming - goat keeping - semen preservation - animal genetic resources - animal breeding - gene banks
    In de periode 2001-2012 is in een aantal acties genetisch materiaal van Nederlandse schapen- en geitenrassen opgenomen in de genenbank voor landbouwhuisdieren. In totaal zijn er ruim 34.000 doses rammen- en bokkensperma van 12 rassen opgeslagen in de genenbank. In dit rapport wordt beschreven welke activiteiten het Centrum voor Genetische Bronnen Nederland in de periode 2001-2012 heeft ondernomen om genetisch materiaal van schapen- en geitenrassen veiliig te stellen in de genenbank. De eerste actie vond plaats in 2001-2002, net na de MKZ-crisis, die duidelijk maakte dat er een reëel gevaar is dat een groot deel van de heideschapen bij een dergelijke dierziekte kan verdwijnen. Na deze eerste actie is het aantal doses sperma van diverse schapen- en geitenrassen verder uitgebreid in de periode 2003-2012. Naast de heideschaaprassen zijn het Melkschaap, de Zwartbles, de Blauwe Texelaar, de Nederlandse Landgeit en de Nederlandse Bonte en Witte geit toegevoegd aan de genenbank.
    Immunogenetic analysis of natural antibody isotypes in laying hens
    Sun, Y. - \ 2013
    Wageningen University. Promotor(en): Johan van Arendonk, co-promotor(en): Jan van der Poel; Henk Parmentier. - S.l. : s.n. - ISBN 9789461736796 - 192
    hennen - pluimvee - immunogenetica - genetische analyse - antilichamen - isotopen - overleving - genetische parameters - verenpikken - dierveredeling - hens - poultry - immunogenetics - genetic analysis - antibodies - isotopes - survival - genetic parameters - feather pecking - animal breeding

    Worldwide, especially in Europe, poultry industry is undergoing important changes including ban of the battery housing system and prohibition of beak trimming. The former can facilitate more spread of infectious diseases, and the latter will contribute to higher mortality because of severe feather pecking. Furthermore, given the growing social concern about food safety and human health, abundant use of antibiotics will either be prohibited or restricted. These changes further emphasize the importance of implementing general disease resistance in layers breeding goals next to maintaining high production. The aim of this thesis was to find proper traits which are associated with laying hens survival, and reveal genetic architecture and background underlying the traits. Natural antibody (NAb), which are the antibodies present in normal healthy animals in the absence of a deliberate antigen exposure are an important humoral part of innate immunity. The relationships between survival and NAb isotype titers were firstly investigated by the logistic regression analysis in a population of laying hens from 12 purebred lines. The results indicated that NAb, especially the IgM isotype titers at young age was predictive for survival of a laying period. Genetic parameters of NAb isotypes IgM and IgG titers were estimated in the same population. The estimation showed that both NAb isotypes are moderate to high heritable traits which were possible to breed for. An association study revealed different QTL or SNP markers for NAb isotypes titers. The majority of the commercial laying hens are crossbred. Therefore, the relationships between NAb isotype titers and survival were further investigated in crossbred laying hens. However, a consistent relationship as in the purebred was not found. This confirmed the speculation that non-health-related causes of mortality (severe feather pecking) overruled the anticipated relationships between NAb isotype titers and survival in birds with intact beaks. Overall, the present studies indicate that it is possible to implement NAb especially the IgM isotype titers into the breeding goals of laying hens to improve the health-related survival.

    De vererving van het witrikpatroon en de variatie daaarin
    Schoon, M. ; Oldenbroek, J.K. ; Oijen, M. van - \ 2013
    Zeldzaam huisdier 38 (2013)3. - ISSN 0929-905X - p. 18 - 19.
    witrik - rundveerassen - zeldzame rassen - diergenetica - dierveredeling - kleur - overerving - coloursides white back - cattle breeds - rare breeds - animal genetics - animal breeding - colour - inheritance
    In een afstudeeropdracht voor van Hall Larenstein is de vererving van de witrikkleur bij runderen bestudeerd en is de vraag beantwoord waarom er zoveel kleurpatronen zijn binnen deze kleurslag.
    De Hollandse Herder: verwantschap en inteelt
    Oldenbroek, J.K. ; Windig, J.J. ; Scholten, I. - \ 2013
    Zeldzaam huisdier 38 (2013)3. - ISSN 0929-905X - p. 8 - 9.
    hollandse herder - hondenrassen - dierveredeling - genetische bronnen van diersoorten - zeldzame rassen - dutch shepherd - dog breeds - animal breeding - animal genetic resources - rare breeds
    De SZH heeft de Hollandse Herder tot ras van het jaar 2013 gekozen. Een van de redenen is dat er binnen dit oorspronkelijke Nederlandse hondenras in de fokkerij veel aandacht aan het voorkomen van inteelt wordt besteed. De resultaten van dit beleid zijn door het Centrum voor Genetische Bronnen Nederland (CGN) geanalyseerd.
    Fokken op welzijn
    Hoving-Bolink, Rita - \ 2013
    animal breeding - animal welfare - animal health - animal production - breeding aims - animal breeding methods - sheep farming - poultry farming
    Optimisation of selective breeding program for Nile tilapia (Oreochromis niloticus)
    Trong, T.Q. - \ 2013
    Wageningen University. Promotor(en): Johan van Arendonk, co-promotor(en): Hans Komen. - S.l. : s.n. - ISBN 9789461735447 - 176
    oreochromis niloticus - selectief fokken - veredelingsprogramma's - genetische parameters - voortplantingskenmerken - kuitschieten - voortplantingspotentieel - vruchtbaarheid - heritability - genotype-milieu interactie - groeitempo - dierveredeling - visteelt - aquacultuur - oreochromis niloticus - selective breeding - breeding programmes - genetic parameters - reproductive traits - spawning - fecundity - fertility - heritability - genotype environment interaction - growth rate - animal breeding - fish culture - aquaculture

    The aim of this thesis was to optimise the selective breeding program for Nile tilapia in the Mekong Delta region of Vietnam. Two breeding schemes, the “classic” BLUP scheme following the GIFT method (with pair mating) and a rotational mating scheme with own performance selection and natural group spawning, were investigated. In the latter scheme, the aim was to mimic natural spawning conditions of Nile tilapia to reduce the time for family production; however reconstruction of pedigrees using DNA markers to monitor inbreeding is required. Parental assignment using microsatellites and SNPs showed that exclusion- and likelihood-based methods are equally good for parental assignment, provided that good marker sets with high exclusion power, such as SNPs, are available and that all parents are sampled. Prolonged family production is problematic in BLUP breeding value estimation and could be a consequence of selection for harvest weight in Nile tilapia. Using a natural mating design with single males mated to multiple females in groups, 85% of the successful spawns were collected within 20 days. Genetic correlations between harvest weight and spawning success ranged from 0.48 to 0.52, provided that the mating period is limited to 20-32 days. We conclude that Nile tilapia favour mating in groups, and that selection for harvest weight in GIFT should improve spawning success of Nile tilapia. Moreover, harvest weight and body weight at spawning have favourable genetic correlations with number of eggs, relative fecundity, and number of swim-up fry, which are the desired characteristics for Nile tilapia seed production. High-input cages and low-input ponds are the dominant production systems for tilapia in the Mekong Delta. We show that selection in nucleus ponds will produce desired correlated responses in Nile tilapia grown in river-cages. Moreover, they are expected to develop a more rotund and thicker body shape at the same length compared to fish grown in ponds. In conclusion, we recommend the use of the ‘single male, multiple females’ mating as this will reduce the generation interval by 2 months, thereby increasing genetic gain by about 20%. A rotational mating scheme, with at least 4 cohorts, can be incorporated into the GIFT selection scheme to further reduce inbreeding, to estimate pond effects and to secure the breeding material. Finally, a reliable multiplier system is important to sustain the current Nile tilapia breeding program, which can provide sufficient improved fry (>50 million per year) for the whole Mekong Delta Nile tilapia production.

    Genomics in de fokkerij: in tien jaar van topwetenschap naar big business
    Arendonk, J.A.M. van; Groenen, M. - \ 2013
    Kennis Online 10 (2013)mei. - p. 7 - 8.
    dierveredeling - genomica - fokkerijmethoden - moleculaire technieken - single nucleotide polymorphism - selectiemethoden - melkvee - varkens - genomen - animal breeding - genomics - animal breeding methods - molecular techniques - single nucleotide polymorphism - selection methods - dairy cattle - pigs - genomes
    Genomics was tien jaar geleden topwetenschap die alleen bedreven werd in dure laboratoria van universiteiten en onderzoeksinstituten. Nu gebruiken fokbedrijven DNA-chips om al op jonge leeftijd te kunnen voorspellen welke stier het beste sperma levert, en om te zien of berengeur bij varkens door een slim fokprogramma kan worden voorkomen.
    Zestig jaar kippenfokker in hart en nieren
    Oldenbroek, J.K. ; Boks, A. - \ 2013
    Zeldzaam huisdier 38 (2013)2. - ISSN 0929-905X - p. 14 - 15.
    kippenrassen - zeldzame rassen - dierveredeling - fowl breeds - rare breeds - animal breeding
    Dit najaar treedt Ad Boks terug als vice-voorzitter van de SZH na zestien jaar bestuurslid te zijn geweest. In december 2012 werd hij erelid van de plaatselijke vereniging van pluimveefokkers omdat hij zestig jaar lid was. In dit interview proberen we deze in 1964 afgestudeerde agrarische socioloog wat van zijn grote kennis en ervaring in de pluimveefokkerij te ontfutselen.
    Op zoek naar de ideale hen
    Leenstra, F.R. ; Bestman, M.W.P. - \ 2013
    In: Biologisch ondernemen : legpluimvee / Janmaat, L., Driebergen : Louis Bolk Instituut - p. 12 - 13.
    dierveredeling - biologische landbouw - pluimveehouderij - hennen - selectief fokken - selectie - eigenschappen - animal breeding - organic farming - poultry farming - hens - selective breeding - selection - properties
    Heeft de biologische pluimveehouderij een ander type hen nodig dan de reguliere houderijsystemen? Is zo’n hen beschikbaar of moet die nog worden gefokt? Wat wordt verstaan onder ‘de’ biologische pluimveehouderij? Zijn dat bedrijven met 18.000 hennen die alleen mengvoer voeren of zijn dat bedrijven met eigen voer verbouw of met een koppeltje van 100-200 dieren die de restjes op het gemengd bedrijf moeten opeten?
    'Gewanhoopt heb ik niet, wel af en toe slecht geslapen' : Martien Groenen over twintig jaar varkensgenen
    Groenen, Martien - \ 2013
    pig farming - animal breeding - genetics - pig breeding - genomes - scientific research
    One size fits all? : optimization of rainbow trout breeding program under diverse preferences and genotype-by-environment interaction
    Sae-Lim, P. - \ 2013
    Wageningen University. Promotor(en): Johan van Arendonk, co-promotor(en): Hans Komen; A. Kause. - S.l. : s.n. - ISBN 9789461734648 - 200
    regenboogforel - dierveredeling - veredelingsprogramma's - genotype-milieu interactie - optimalisatie - kenmerken - genetische winst - selectief fokken - simulatie - visteelt - aquacultuur - rainbow trout - animal breeding - breeding programmes - genotype environment interaction - optimization - traits - genetic gain - selective breeding - simulation - fish culture - aquaculture

    Global fish breeders distribute improved animal material to several continents to be farmed under diverse environments, and for very different market conditions. When establishing a global breeding program, there is a need to assess whether or not a single breeding objective satisfies the markets across different countries. It may be challenging to develop a single fish stock that performs well across all environments due to genotype-by-environment interaction (GxE). GxE is a phenomenon describing the possibility that different genotypes have a different sensitivity to changes in an environment. The objective of this thesis was to develop an optimized global breeding program for rainbow trout (Oncorhynchus mykiss) in terms of a balanced breeding goal that satisfies preferences of trout producers and maximized genetic gains across environments in the presence of GxE in production traits. Analytic hierarchy process (AHP) was used to estimate preferences, which can be aggregated to consensus preference values using weighted goal programming (WGP). The analysis revealed that the 6 most important traits were thermal growth coefficient (TGC), survival (Surv), feed conversion ratio (FCR), condition factor (CF), fillet percentage (FIL%), and late maturation (LMat). Individual trait preferences are different for farmers having different farming environments and producing different end-products. Calculating consensus preference values resulted in consensus desired genetic gains. To satisfy most farmers, consensus desired genetic gains can be taken into account in a global breeding strategy. Strong genotype re-ranking was found for all growth traits across environments. Based on simulation, re-location of breeding program led to highest total genetic gain for body weight at harvest. Alternatively, including sib performance into selection index increased genetic gain in all environments. Finally, environment-specific program can be used, but this is costly. There is a possibility of a conflict between 2 profits: from a breeding company and fish farmers and an optimum solution for that conflict can be found by using macroeconomics and cost-benefit analysis.

    Use of genetic markers in pig breeding programs
    Coster, A. - \ 2013
    Wageningen University. Promotor(en): Johan van Arendonk, co-promotor(en): Henk Bovenhuis; Henri Heuven. - S.l. : s.n. - ISBN 9789461734426 - 152
    varkens - dierveredeling - varkensfokkerij - genetische merkers - marker assisted breeding - stamboom - genomica - loci voor kwantitatief kenmerk - worpgrootte - pigs - animal breeding - pig breeding - genetic markers - marker assisted breeding - pedigree - genomics - quantitative trait loci - litter size

    The objective of this thesis was to investigate the use of genetic markers in commercial pig breeding, with a special emphasis on genomically imprinted genes. For the latter purpose, an association study was undertaken to identify genomically imprinted QTL related to sow fertility traits in two commercial pig populations. Furthermore, several simulation studies were performed to evaluate methods to estimate breeding values with marker data. Finally, a new method was designed to estimate the parental origin of marker alleles in crossed populations when the pedigree is unknown.

    The association study involved approximately sows from two commercial pig populations. The sows were genotyped for SNP markers, of which were finally used. The results revealed one SNP with a significant imprinting effect on the trait litter size in one population. The imprinting effect of this SNP was not significant in the other population but its effect was similar. The SNP was located close to the gene DIO3, which has a known imprinting status. Furthermore, several SNP with significant additive and dominance effects were found in both populations.

    The simulation studies were designed to evaluate the effect of the number of genes and the relative importance of these genes on the trait on performance of distinct methods to estimate breeding values with markers. Results of the first study showed that the performance of these methods is affected by gene number and size. Results of the second study continued on these results and showed that genetic gain achievable by selecting on breeding values estimated by these methods strongly depends on the number of genes and their relative size.

    Knowledge of parental origin of marker or gene alleles is of crucial importance to study genomically imprinted genes. A method based on the Dirichlet Process was designed to estimate the parental origin of SNP alleles in crossed populations. The method performed better than methods that did not account crossbreeding, and the performance of the method was strongly improved when some genotypes of some parental individuals were available in the data.

    The last chapter evaluated the influence of genomic imprinting on genetic parameters of genes. An important conclusion of this chapter is that genomically imprinted genes have less variance compared to similar, non-imprinted genes. This lower variance leads to lower power of statistical methods to detect these genes and lower genetic gain achievable in breeding programs. On the other hand, however, genomically imprinted genes could be effectively used in crossbreeding programs.

    Animal genetic resources: conservation-breeding-regulatory framework
    Hiemstra, Sipke Joost - \ 2012
    livestock farming - agro-biodiversity - genetic diversity - animal genetic resources - genetic improvement - animal breeding - sustainable animal husbandry - gene banks - breeds - distribution
    Quickscan van de gegevensverzameling voor duurzaamheid in de veehouderij
    Napel, J. ten; Engelsma, K.A. - \ 2012
    Lelystad : Wageningen UR Livestock Research (Rapport / Wageningen UR Livestock Research 715) - 35
    dierveredeling - duurzaamheid (sustainability) - veehouderij - fokdoelen - dierenwelzijn - diergezondheid - rundvee - varkens - hennen - gegevens verzamelen - animal breeding - sustainability - livestock farming - breeding aims - animal welfare - animal health - cattle - pigs - hens - data collection
    Utilising monitoring for sustainability in breeding of farm animals.
    Stand van zaken fokprogramma voor kortere staarten bij drie schapenrassen met een ontheffing op het coupeerverbod
    Windig, J.J. ; Napel, J. ten; Hoving, A.H. - \ 2012
    Lelystad : Wageningen UR Livestock Research (Rapport / Wageningen UR Livestock Research 656) - 13
    schapen - dierenwelzijn - couperen van de staart - schapenhouderij - schapenrassen - dierveredeling - selectief fokken - fokwaarde - fokdoelen - sheep - animal welfare - docking - sheep farming - sheep breeds - animal breeding - selective breeding - breeding value - breeding aims
    Three sheep breeds exempted from the ban on tail docking have set up breeding value estimation for shorter tails. Their breeding policy needs to be extended further in order to realise shorter tails in practice.
    Naar een probleemloos afkalvende dikbilkoe = Towards an easy-calving double-muscled cow
    Napel, J. ten; Hoving, A.H. ; Bohte-Wilhelmus, D.I. ; Hannewijk, P. - \ 2012
    Lelystad : Wageningen UR Livestock Research (Rapport / Wageningen UR Livestock Research 648) - 40
    rundveehouderij - vleesvee - dierenwelzijn - keizersnede - dierveredeling - selectief fokken - geboorte - dierlijke productie - diergezondheid - vleesveerassen - cattle husbandry - beef cattle - animal welfare - caesarean section - animal breeding - selective breeding - birth - animal production - animal health - beef breeds
    A measuring and breeding programme has been developed for easy calving doublemuscled beef cattle.
    Berigheid is een spel van factoren
    Ginneken, R. van; Soede, N.M. ; Hoving, L.L. ; Wientjes, J.G.M. ; Hazeleger, W. - \ 2012
    Varkensbedrijf: onafhankelijk maandblad voor de Varkenshouderij 10 (2012)Nov 2012. - ISSN 0777-5091 - p. 14 - 17.
    varkenshouderij - zeugen - bronststimulatie - vrouwelijke vruchtbaarheid - fokkerijmethoden - dierveredeling - pig farming - sows - teasing - female fertility - animal breeding methods - animal breeding
    In het streven naar een beperking van het aantal verliesdagen is het interval spenen-dekken een belangrijk ijkpunt. De bronst van een zeug lijkt prima gestimuleerd te kunnen worden, zo hebben meerdere onderzoeken bewezen. Dat betekent echter niet altijd dat het inseminatieresultaat steeds beter is. De kwaliteit van de eicel is immers afhankelijk van het management in de kraamstal.
    Pluimvee met Smaak – De rol van fokkerij in duurzamere vleeskuikenhouderij
    Janssen, Arni - \ 2012
    poultry farming - animal breeding - broilers - sustainability - animal welfare - animal health - poultry meat - animal production - chicken housing - poultry
    Insect bite hypersensitivity in horses: genetic and epidemiological analysis
    Schurink, A. - \ 2012
    Wageningen University. Promotor(en): Johan van Arendonk, co-promotor(en): Bart Ducro; Klaas Frankena. - S.l. : s.n. - ISBN 9789461733566 - 168
    dierveredeling - overgevoeligheid - paarden - genetische analyse - epidemiologie - insectenbeten - nederland - fries (paardenras) - shetland pony - animal breeding - hypersensitivity - horses - genetic analysis - epidemiology - insect bites - netherlands - frisian (horse breed) - shetland pony

    Insect bite hypersensitivity (IBH) is the most common allergic skin disease in horses and is caused by bites of Culicoides spp. IBH reduces welfare of affected horses and at present no effective preventive measure or cure exists. Aim of our research was to increase knowledge of the genetic background of IBH in horse populations and to explore opportunities to reduce IBH prevalence through selection and breeding.

    Data on Shetland pony and Friesian horse mares were gathered at obligatory inspections. IBH prevalence was 7.5% in Shetland pony mares and 18.2% in Friesian horse mares. Data were analyzed to identify risk factors. Combined effect of month and year of IBH scoring, region within the Netherlands and inspector were associated with IBH in both breeds. IBH prevalence significantly differed with coat colour and withers height category in Shetland pony mares. Moreover, prevalence was higher in Shetland pony mares with high body condition score (9.4%).

    Quantitative genetic analyses revealed substantial genetic variation for IBH in both breeds. Heritability on the observed scale and on the underlying scale was 0.08 and 0.24 respectively in Shetland pony mares, 0.07 and 0.16 respectively in Friesian horse mares. Therefore, IBH is a heritable phenotype in both breeds. Repeatability was 0.30 in Shetland pony mares and 0.89 in Friesian horse mares. Maternal effect (0.17) was estimated in Friesian horse mares only.

    To identify genomic regions contributing to the genetic variance, Shetland pony mares and Icelandic horses were selected according to a matched case-control design. Odds ratios of allele substitution effects of the unfavourable allele were between 1.94 and 5.95. Also, 13 and 28% of genetic variance was explained by all SNPs in respectively Shetland pony mares and Icelandic horses. Significant associated genomic regions across breeds suggest interesting candidate regions on ECA3, 7, 11, 20 and 23 contributing to genetic variance. Results support that ELA class II region on ECA20 is involved in IBH etiology, although follow-up studies are needed to confirm this and to identify genes in the other regions.

    The general discussion explored possibilities to reduce IBH prevalence through breeding and discussed implications of using clinical symptoms or diagnostic test results. Simulated selection was based on EBV, which included own performance, progeny performance or genomic data. Selection on IBH clinical symptoms should be based on testing at least 10 but preferably more progeny, accompanying strict selection in sires to achieve reasonable genetic gain. Expected genetic gain per year in genomic selection outperformed other strategies, although implementation of genomic selection requires a considerable investment in a reference population. A diagnostic test for IBH (yet unfeasible to perform on a large sample) has the potential to increase genetic gain

    Genomica in de melkveehouderij : de praktische toepassingen
    Haas, Yvette de - \ 2012
    dairy farming - dairy cattle - animal breeding - genomics - dna - milk
    Use of SNP markers to conserve genome-wide genetic diversity in livestock
    Engelsma, K.A. - \ 2012
    Wageningen University. Promotor(en): Johan van Arendonk, co-promotor(en): Jack Windig. - S.l. : s.n. - ISBN 9789461733863 - 178
    dierveredeling - rundvee - single nucleotide polymorphism - genetische diversiteit - genomen - genomica - conservering - animal breeding - cattle - single nucleotide polymorphism - genetic diversity - genomes - genomics - conservation

    Conservation of genetic diversity in livestock breeds is important since it is, both within and between breeds, under threat. The availability of large numbers of SNP markers has resulted in new opportunities to estimate genetic diversity in more detail, and to improve prioritization of animals for conservation of genetic diversity. The aim of this thesis was to further explore the potential of SNP markers for estimation and conservation of genetic diversity within livestock breeds. This was evaluated analyzing Holstein cattle populations, genotyped with a commonly used 50k SNP chip. Genetic diversity was estimated with SNP markers and compared to genetic diversity estimated with pedigree information. Both methods could detect differences in overall genetic diversity, even between two closely related populations. With SNP markers, differences in genetic diversity at the chromosomal level could be identified as well. Subsequently, SNP markers and pedigree information were used to prioritize animals for conservation in a gene bank using optimal contributions. SNP based prioritization was slightly more effective than pedigree based information, both over the whole genome and at specific regions of the genome. We extended the optimal contribution method to simultaneously conserve a single allele at a specific frequency and maximize the overall genetic diversity conserved in a gene bank. The loss of overall genetic diversity was larger when the target frequency for animals conserved in the gene bank differed more from the original frequency in the population. It can be concluded that dense SNP data form a powerful tool for estimation and conservation of genetic diversity in livestock breeds. Although pedigree information gives a good representation of the overall genetic diversity, SNP markers can provide more detailed information about the genetic diversity over the genome. Especially for small populations, SNP markers can play an important role in conservation of unique alleles, while simultaneously minimizing the loss of genetic diversity at the rest of the genome.

    Het fokken van rashonden : omgaan met verwantschap en inteelt
    Oldenbroek, J.K. ; Windig, J.J. - \ 2012
    Amsterdam : Raad van Beheer op Kynologische Gebied in Nederland - ISBN 9789071101007 - 144
    honden - hondenrassen - gezelschapsdieren - huisdieren - dierenwelzijn - diergezondheid - dierveredeling - fokkerijmethoden - dogs - dog breeds - pets - domestic animals - animal welfare - animal health - animal breeding - animal breeding methods
    Het boek beschrijft de kennis van dit moment over de fokkerij van dieren en in het bijzonder die over het fokken met rashonden. Het boek gaat vooral in op de effecten van verwantschap en inteelt en het verminderen van de kans op erfelijke aandoeningen. Het boek is vooral geschreven voor bestuursleden van rasverenigingen en voor leden van foktechnische commissies. Hiermee kunnen zij binnen hun vereniging samen met de fokkers maatregelen treffen die nodig zijn om tot gezonde rashondenpups te komen.
    All in good time : dynamics of the bovine estrous cycle investigated with a mathematical model
    Boer, H.M.T. - \ 2012
    Wageningen University. Promotor(en): Roel Veerkamp; Bas Kemp, co-promotor(en): Henri Woelders. - S.l. : s.n. - ISBN 9789461733559 - 192
    rundvee - dierveredeling - voortplanting - geslachtscyclus - wiskundige modellen - vruchtbaarheid - genomica - systeembiologie - cattle - animal breeding - reproduction - oestrous cycle - mathematical models - fertility - genomics - systems biology

    Bovine fertility is subject of extensive research in animal sciences, especially since a decline in dairy cow fertility has been observed during the last decades. One factor is reduced expression of estrous behavior. Fertility is a complex process, regulated by interactions between brain and reproductive organs. The objective of this thesis was to improve insight in the regulation of dairy cow fertility by developing and using a mechanistic mathematical model of the bovine estrous cycle. The model that was developed describes the dynamics of the bovine estrous cycle on individual cow level. It simulates follicle and CL development and the periodic changes in hormone levels that control these processes by a set of linked differential equations. The model captures a number of key physiological processes of the bovine estrous cycle, and serves as a starting point for further simulation studies, model validation, and extended models. The model was used to find candidate mechanisms that regulate follicular development. A normal estrous cycle contains 2 or 3 waves of follicular development, but why some cycles consist of 3 and others of 2 waves is unknown. Results showed that variation of (combinations of) model parameters regulating follicle growth rate or time point of CL regression can change the model output from 3 to 2 waves of follicular growth in a cycle. Several factors may perturb the regular oscillatory behavior of a normal estrous cycle. Such perturbations are likely the effect of simultaneous changes in multiple parameters. It was investigated how multiple parameter perturbation changes the behavior of the estrous cycle model, so as to identify biological mechanisms that could play a role in the development of cystic ovaries, a common reason for reproductive failure in dairy cows. Simulation results indicated that CL functioning, luteolytic signals, and GnRH synthesis are likely involved in the development of cystic ovaries. Empirical data of individual cows was used to identify mechanisms that explain individual differences in cycle characteristics by fitting the model to the data. Finding specific parameter configurations for individual cows shows the capability of the model to simulate ‘real’ data. Certain combinations of estimated parameter values induced a clear qualitative shift in model behavior (e.g. a different number of follicular waves), suggesting possible routes how environmental or genetic influences could affect estrous cycle characteristics. Experimental data to verify simulation results are not always available, but hypotheses based on the model predictions could be investigated in future animal experimen

    Animal breeding for food security : opportunities in the genome sequencing era
    Veerkamp, R.F. - \ 2012
    Wageningen : Wageningen University, Wageningen UR - ISBN 9789461733245 - 23
    dierveredeling - genomica - genoomanalyse - dna-sequencing - fokkerijmethoden - animal breeding - genomics - genome analysis - dna sequencing - animal breeding methods
    Inaugural lecture upon taking up the position of Special Professor of Numerical Genetics and Genomics at Wageningen University.
    Natuurlijke geboorte extreme vleesrassen
    Napel, J. ten - \ 2012
    V-focus 9 (2012)5a. - ISSN 1574-1575 - p. 15 - 17.
    rundveehouderij - vleesvee - verbeterd roodbont - belgisch witblauw - dierveredeling - fokwaarde - geboorte - dierenwelzijn - dierlijke productie - cattle husbandry - beef cattle - improved red pied - belgian blue - animal breeding - breeding value - birth - animal welfare - animal production
    Dikbilkoeien die probleemloos natuurlijk afkalven is geen utopie. Na drie jaar voorbereidend onderzoek en vier jaar onderzoek in de praktijk binnen het project Natuurlijke Luxe is duidelijk hoe dat moet. Het belangrijkste is om met fokkerij de ruimte in het geboortekanaal te vergroten. Of dat ook gebeurt, is nu een kwestie van willen en doen.
    Genetic control and variation in turkey: molecular insights in selection
    Aslam, M.L. - \ 2012
    Wageningen University. Promotor(en): Martien Groenen, co-promotor(en): John Bastiaansen; Richard Crooijmans. - S.l. : s.n. - ISBN 9789461733092 - 184
    meleagris - kalkoenen - genetische variatie - moleculaire veredeling - selectie - genetische kartering - loci voor kwantitatief kenmerk - moleculaire technieken - dierveredeling - meleagris - turkeys - genetic variation - molecular breeding - selection - genetic mapping - quantitative trait loci - molecular techniques - animal breeding


    The turkey (Meleagris gallopavo) is an important agricultural species that is largely used as a meat type bird as egg production of this species is very low. Turkey is the second largest contributor to the world’s poultry meat production after chicken. Understanding the etiology and biology underlying production and health traits is very important for the genetic improvement of these traits in the desired direction and to avoid undesired side-effects. The aim of the research described in this thesis was to interrogate the genetics of turkey traits related to meat production and to investigate the genetic diversity of commercial and heritage turkey populations.
    Different analyses were performed that included the estimation of genetic and (common) environmental variances for growth (body weight as well as growth curve traits), breast meat yield and meat quality traits in turkeys. I describe the construction of a single nucleotide polymorphism (SNP) based linkage map of turkey and its comparison with the physical map of chicken to investigate genome structural differences between these highly important poultry production species. Two inter-, and 57 intra-chromosomal rearrangements between these two species were confirmed or discovered which is a low number in comparison to mammals and lead to the conclusion that turkey and chicken have highly conserved genomic structure. I used the linkage map of turkey together with individual phenotypes to map quantitative trait loci (QTL) in the same population for the traits described above. Results showed quantitative trait loci on 21 of the 27 turkey chromosomes covered by the linkage map. Forty-five quantitative trait loci were detected across all traits and these were found in 29 different regions on the 21 chromosomes. The next step, after the analyses on the reference population was to investigate the genomic variation in turkeys Next generation sequencing was used to investigate genome variation and the discovery of genome-wide signatures of selection in the turkey respectively. Sequencing was performed on 32 individuals from eleven different turkey populations (seven commercial, three heritage and a South Mexican wild population). Analysis of next generation sequencing data resulted in the detection of 5.49 million putative SNPs compared to the reference genome. The average frequency of heterozygous nucleotide positions in individual turkeys was 1.07 Kb-1 which is substantially lower than in chicken and pigs. The SNPs were subsequently used for the analysis of genetic diversity between the different populations. Genetic diversity analysis using pairwise Nei’s genetic distance among all the individuals from the 11 turkey populations showed that all of the commercial lines branched from a single node relative to the heritage varieties and the ancestral turkey population, indicating that commercial lines appear to share a common origin.
    After assessing genome wide variation and diversity between breeds, the SNP data from ten of the turkey populations (29 individuals) was used to detect selective sweep regions. Across the turkey populations, 54 genomic regions with significant evidence for a selective sweep were detected. These sweeps were distributed over 14 different chromosomes. This study has investigated the genetics i.e. analysis of variances and QTL mapping related to economically important traits in turkey production and the genomic variation of turkey. Furthermore, this study has also created resources e.g. millions of discovered SNPs for subsequent genomic work in the turkey such as to discover variant (s) for both minor and major effects on traits of economic importance, and a high-resolution linkage map can be developed.


    Genetic aspects of somatic cell count and udder health in the Italian Valle del Belice dairy sheep
    Riggio, V. - \ 2012
    Wageningen University. Promotor(en): Johan van Arendonk, co-promotor(en): Henk Bovenhuis; B. Portolano. - [S.l. : s.n. - ISBN 9789461732460 - 137
    ovis - schapen - schapenziekten - uiers - mastitis - celgetal - genetica - melkveehouderij - dierveredeling - italië - ovis - sheep - sheep diseases - udders - mastitis - somatic cell count - genetics - dairy farming - animal breeding - italy

    Mastitis is an inflammation of the udder, which leads to economic loss, mainly consisting of discarded milk, reduced milk production and quality, and increased health costs. Somatic cell count (SCC), and therefore somatic cell score (SCS), is widely used as indicator of mastitis. In this thesis, I focus on the genetic parameters of SCS as indicator of mastitis, and on the possibilities of using this trait for selection for mastitis resistance in the Valle del Belice dairy sheep.

    In Chapter 1, mastitis and SCS are defined and introduced. Chapter 2 deals with the estimation of genetic parameters for SCS and milk production traits in primiparous Valle del Belice ewes. Heritability estimates ranged from 0.09 to 0.14 for milk, fat and protein yields and contents. For SCS, the heritability of 0.14 was relatively high. SCS was genetically positively correlated to milk, fat and protein yields and contents. However, correlations were not extreme, so simultaneous improvement for milk yield and SCS seems possible. In Chapter 3, the level of SCC is included in a survival analysis to evaluate the effect of SCC on functional longevity. Results showed that an increase in SCC was associated with an increase in culling rate.Elevated SCC, therefore, play an indirect role in the culling decisions of Valle del Belice dairy sheep farmers, although, at present, farmers do not directly select for reduced SCC. In Chapter 4, the genetic parameters of the infection status and SCS, according to whether the samples were bacteria negative or positive are reported. Moreover, the impact of imperfect sensitivity and specificity on variance component estimates was investigated. The heritability was 0.10 for bacteria negative SCS, 0.03 for bacteria positive SCS, and 0.09 for infection status, on the liability scale. The genetic correlation between bacteria negative and bacteria positive SCS (0.62) suggests that they may be genetically different traits, confirming that SCSfrom healthy and infected animals should be analyzed separately. Moreover, a positive genetic correlation between bacteria negative SCS and liability to mastitis was found, suggesting that the approach of selecting animals for decreased SCS will help to reduce the prevalence of mastitis. The results also showed that the imperfect diagnosis of infection has an impact on estimated genetic parameters,which may reduce the efficiency of selection strategies aiming at distinguishing between bacteria negative and bacteria positive SCS. In Chapter 5, the diagnostic ability of SCCand California Mastitis Test (CMT) to detect intramammary infectionswas evaluated by using the Receiver-Operating Characteristic(ROC) curves, in order to identify a SCCthreshold that better discriminated healthy from infected udders. The results indicate that the CMT can only discriminate the udders infected from major pathogens. Nevertheless, in general SCS was the best indirect test for the bacteriological status of the udder.

    The final chapter explores and discusses the opportunities to use SCS as indicator of mastitis in a selection scheme to improve mastitis resistance for the Valle del Belice dairy sheep breed.

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