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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Optimization of breeding schemes for Nile tilapia (Oreochromis niloticus) in smallholder production systems in Kenya
Omasaki, Simion Kipkemboi - \ 2017
University. Promotor(en): Hans Komen, co-promotor(en): Johan van Arendonk; A.K. Kahi. - Wageningen : Wageningen University - ISBN 9789463431064 - 167
oreochromis niloticus - tilapia - breeding programmes - selective breeding - genetic improvement - small farms - sustainability - fish culture - aquaculture - kenya - veredelingsprogramma's - selectief fokken - genetische verbetering - kleine landbouwbedrijven - duurzaamheid (sustainability) - visteelt - aquacultuur

The aim of this thesis was to develop a sustainable low cost breeding program for Nile tilapia that addresses both genetic and economic aspects of smallholder fish farmers in Kenya. First, Analytical Hierarchy Process Technique was used to define a breeding goal based on farmer’s preferences for traits. Farmers’ preferences for traits differed significantly depending on income and market orientation. Low and medium income farmers preferred harvest weight (HW) while high income farmers preferred growth (GR) and survival (S) traits. Grouping farmers according to market objective (fingerling production or fattening) showed that fingerling producers preferred GR and S while fattening farmers preferred HW and S. Consensus preference values were obtained using weighted goal programming and these values were used to derive desired gains for a breeding goal that takes into account farmers’ diverse backgrounds and preferences for traits. Secondly, the existence of genetic variation for traits of interest was investigated. Substantial additive genetic effects for HW, GR and shape traits were present that can be exploited through selection under low input production system. Heritability estimates for HW, GR and shape were 0.21 ± 0.03, 0.26 ± 0.04 and 0.12 ± 0.03 for mixed sex (nucleus) respectively. The calculation of economic values for breeding goal traits revealed that economic values for GR differed depending on the definition of the breeding goal and that selection for feed efficiency is the key factor to economic profitability of Nile tilapia breeding programs. A significant genotype by environment re-ranking was found for GR between the mixed sex nucleus and monosex production environments. Genotype by environment interaction (G x E) led to lower genetic gain for GR in production environment. Incorporating sib information from monosex production environment into the selection index resulted in a more accurate estimation of breeding values which increased genetic gain in growth. Using desired gain approach, weights for desired gains in harvest weight, growth rate and survival were derived that maximized genetic gains for these breeding goal traits. It is concluded that these results can be used to develop a sustainable centralized breeding program. However, a reliable well planned and organized decentralized strategy for dissemination of genetically improved fry of Nile tilapia to farmers is paramount.

It is time to bridge the gap between exploring and exploiting : prospects for utilizing intraspecific genetic variation to optimize arthropods for augmentative pest control – a review
Lommen, Suzanne T.E. ; Jong, Peter W. de; Pannebakker, Bart A. - \ 2017
Entomologia Experimentalis et Applicata 162 (2017)2. - ISSN 0013-8703 - p. 108 - 123.
augmentative biological control - genetic improvement - genetics - genomics - native natural enemies - offspring sex ratio - selective breeding - two-spot ladybird beetle
Intraspecific genetic variation in arthropods is often studied in the context of evolution and ecology. Such knowledge, however, can also be very usefully applied to biological pest control. Selection of genotypes with optimal trait values may be a powerful tool to develop more effective biocontrol agents. Although it has repeatedly been proposed, this approach is still hardly applied in the current commercial development of arthropod agents for pest control. In this perspective study, we call to take advantage of the increasing knowledge on the genetics underlying intraspecific variation to improve biological control agents. We argue that it is timely now because at present both the need and the technical possibilities for implementation exist, as there is (1) increased economic importance of biocontrol, (2) reduced availability of exotic biocontrol agents due to stricter legislation, and (3) increased availability of genetic information on non-model species. We present a step-by-step approach towards the exploitation of intraspecific genetic variation for biocontrol, outline that knowledge of the underlying genetic mechanisms is essential for success, and indicate how new molecular techniques can facilitate this. Finally, we exemplify this procedure by two case studies, one focussing on a target trait – offspring sex ratio – across species of hymenopteran parasitoids, and the other on a target species – the two-spot ladybird beetle – where wing length and body colouration can be optimized for aphid control. With this overview, we aim to inspire scientific researchers and biocontrol agent producers to start collaborating on the use of genetic variation for the improvement of natural enemies.
Genomic selection in egg-laying chickens
Heidaritabar, M. - \ 2016
University. Promotor(en): Martien Groenen, co-promotor(en): John Bastiaansen. - Wageningen : Wageningen University - ISBN 9789462576704 - 220 p.
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
University. Promotor(en): Johan van Arendonk, co-promotor(en): Herman Mulder; P.K. Mathur. - Wageningen University - ISBN 9789462576452 - 179 p.
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
University. Promotor(en): Roel Veerkamp; Mario Calus. - Wageningen : Wageningen University - ISBN 9789462576193 - 267 p.
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
Genomic selection for improved crossbred performance
Lopes, Marcos Soares - \ 2016
University. Promotor(en): Johan van Arendonk, co-promotor(en): Henk Bovenhuis; John Bastiaansen; E.F. Knol. - Wageningen : Wageningen University - ISBN 9789462576315 - 202 p.
pigs - crossbreds - genomics - selective breeding - performance - genetic improvement - pig breeding - varkens - kruising - genomica - selectief fokken - prestatieniveau - genetische verbetering - varkensfokkerij

Lopes, M.S. (2016). Genomic selection for improved crossbred performance. PhD thesis, Wageningen University, the Netherlands

With the implementation of genomic selection in pig breeding, the genetic progress in purebred populations is expected to increase up to 55% compared to traditional selection based on pedigree information. However, as most of the animals in the pork production system are crossbreds, the increase in genetic progress in purebreds will only be observed on production farms if this progress is expressed in the performance of crossbreds. The main aim of this thesis was to evaluate different models based on genomic information which can be applied to improve performance of crossbred animals. Another aim was to gain insight into genetic architecture of (complex) traits and to investigate how selection history has influenced haplotype patterns of current commercial pigs. This thesis shows that by going beyond traditional genomic selection models, phenotypes can be predicted more accurately. Therefore, these improved models should be considered to improve crossbred performance. Further, this thesis provides important insights into the genetic architecture of the evaluated (complex) traits and also shows evidence that human-driven introgression and selection have shaped the genome of current commercial pig breeds. The research presented in this thesis was performed using data from pigs and the discussion on the practical application of results was focused on pig breeding. The results are relevant for all livestock species where crossbreeding is applied.

Linkage disequilibrium and genomic selection in pigs
Veroneze, R. - \ 2015
University. Promotor(en): Johan van Arendonk; S.E.F. Guimarães, co-promotor(en): John Bastiaansen. - Wageningen : Wageningen University - ISBN 9789462574151 - 142
varkens - verstoord koppelingsevenwicht - loci voor kwantitatief kenmerk - genomica - populaties - kruising - inteeltlijnen - fokwaarde - selectief fokken - genetica - pigs - linkage disequilibrium - quantitative trait loci - genomics - populations - crossbreds - inbred lines - breeding value - selective breeding - genetics

Securing a sufficiently large set of genotypes and phenotypes can be a limiting factor when implementing genomic selection. This limitation may be overcome by combining data from multiple populations or by using information of crossbred animals. The research described in this thesis characterized linkage disequilibrium (LD) patterns in different pig populations and evaluated whether the consistency of LD between populations allows us to make predictions about the performance of genomic selection when multiple populations are included in the prediction and/or validation datasets.

In chapter 2 I evaluated the persistence of LD and patterns of LD decay of pure and crossbred pig populations using real data that was representative of the crossbreeding structure of pig production. The persistence of phase between the crosses and their parental populations was high, indicating that similar marker effects might be expected across these populations. Across the purebred populations the persistence of phase was low therefore higher density panels should be used to have the same marker-QTL associations across these populations.

In chapter 3, the well-known nonlinear model developed by Sved (1971) was compared against a an alternative, loess regression, to describe LD decay. The loess regression model was found to be less influenced by the lack of residual normality, independence and homogeneity of variance than the nonlinear regression model. The loess regression model resulted in more reliable LD predictions and can be used to formally compare the LD decay curves between populations.

Chapter 4 showed the utility of different reference sets (across- and multi-population) for the prediction of genomic breeding values, as well as the potential of using crossbred performance in genomic prediction. None of the accuracies obtained using across-population, or multi-population genomic prediction, nor the accuracies obtained using crossbred data, followed the expectations based on LD that was described in chapter 2. I showed that across-population prediction accuracy was negligible even when the populations had common breeds in their genetic background. The variable accuracies of multi-population prediction and moderate accuracy of prediction of crossbred performance appeared to be a result of the differences in genetic architecture between pure populations and between purebred and crossbred animals.

In chapter 5, a methodology that uses information from genome wide association analyses in the genomic predictions was developed and evaluated. The aim in chapter 5 was to let the genomic prediction model use information from the genetic architecture in single- and multi-population genomic prediction. I showed that using weights based on GWAS results from a combined population did result in higher accuracies of GBLUP in single- as well as in multi-population predictions.

In chapter 6 I placed my results in a broader context. I discussed about the theoretical and practical aspects of linkage disequilibrium in breeding and in the estimation of effective population size. I also discussed the application of genomic selection in a small population and in practical pig breeding, including the prospects of using whole genome sequence for genomic prediction.

Genetic background of claw health in dairy cattle
Spek, D. van der - \ 2015
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 - 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.

Indirect genetic effects for group-housed animals
Alemu, S.W. - \ 2015
University. Promotor(en): Johan van Arendonk, co-promotor(en): L.G. Janss; Piter Bijma; P. Berg. - Wageningen : Wageningen University - ISBN 9788793176713 - 228
nerts - pluimvee - groepshuisvesting - genetische effecten - sociaal gedrag - agressief gedrag - interacties - heritability - veredelingsprogramma's - statistische analyse - genetische parameters - selectief fokken - mink - poultry - group housing - genetic effects - social behaviour - aggressive behaviour - interactions - breeding programmes - statistical analysis - genetic parameters - selective breeding

ABSTRACT

Alemu, SW(2015) Indirect Genetic effects for Group-housed Animals. Joint PhD thesis between Aarhus University, Denmark and Wageningen University, the Netherlands.

Social interactions among individuals are common both in plants and animals. With social interactions, the trait value of an individual may be influenced by the genes of its interacting partners, a phenomenon known as indirect genetic effects (IGE). An IGE is heritable effect of an individual on trait values of another individual. A large body of literature has shown that social interactions can create addition heritable variation in both plants and animals, for both behavioural and production traits.

When IGE are estimated it is usually assumed that an individual interacts equally with all its group mates, irrespective of genetic relatedness. This assumption may not be true in mixed groups of kin and non-kin, where an individual may interact systematically different with kin and non-kin. Current IGE models ignore such systematically different interactions between kin and non-kin. Thus, the main aim of this thesis was to develop and apply statistical methods to estimate IGE when interactions differ between kin and non-kin.

Social interactions are important in mink that are kept in groups for the production of fur. Group housing of mink increases aggression behaviours, which is reflected by an increase in the number of bite marks on the pelts, and reduces the welfare of the animals. We estimated the genetic parameter for bite mark traits in group-housed mink, to investigate the prospects for genetic improvement of bite mark traits. We found that there are good prospects to produce mink that have a low level of biting. Finally, we further concluded that genetic parameter estimation for bite mark score should take into account systematic interactions due to sex or kin.

In this thesis we also investigated genomic selection for socially affected traits, considering survival time in two lines of brown egg layers showing cannibalistic behaviour. Despite the limited reference population of ~234 progeny tested sires, the accuracy of estimated breeding values (EBV) was ~35% higher for genomic selection compared with the parent average-EBV. We found that the response to genomic selection per year for line B1 was substantially higher than for the traditional breeding scheme, whereas for line BD response was slightly higher than for the traditional breeding scheme. In conclusion, genetic selection with IGE combined with marker information can substantially reduce detrimental social behaviours such as cannibalism in layers and biting in group-housed mink.

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.
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).
Sociable swine : indirect genetic effects on growth rate and their effect on behaviour and production of pigs in different environments
Camerlink, I. - \ 2014
University. Promotor(en): Johan van Arendonk; Bas Kemp, co-promotor(en): Liesbeth Bolhuis; Piter Bijma. - Wageningen : Wageningen University - ISBN 9789461739551 - 231
varkens - sociaal gedrag - genetische effecten - groeitempo - diergedrag - agressief gedrag - sociaal milieu - dierlijke productie - selectief fokken - varkenshouderij - pigs - social behaviour - genetic effects - growth rate - animal behaviour - aggressive behaviour - social environment - animal production - selective breeding - pig farming

Social interactions between pigs can influence their health, welfare, and productivity. The effects of social interactions on individuals are partly genetic, and this genetic effect is known as an Indirect Genetic Effect. IGEs are thus the heritable effects of an individual on the trait values of its social partners, e.g. group mates. Previous research has identified IGE for production traits, which suggests that selection for IGE may contribute to selection response. However, validation through selection experiments is required.

The objectives of this thesis were a) to determine the consequences of selection for ‘IGE on growth rate’ (IGEg) for production traits and behaviour of pigs, and b) to study possible mechanisms underlying IGEg in pigs. First, the relationship between pig behaviour and growth rate was studied in several trials. This showed that oral manipulative behaviours directed at pen mates, such as tail- and ear biting and chewing, can reduce growth rate of the victims, whereas receiving social nosing may enhance growth rate. Second, a one-generation selection experiment was conducted in pigs. Sires (n= 24) and dams (n= 64) were selected to create a high vs. low contrast for IGEg in the offspring (n= 480). The contrast was 14 g average daily gain (ADG). Offspring were studied in a 2×2 arrangement with IGEg (high vs. low) and housing conditions (conventional vs. enriched with straw bedding) to examine genotype × environment (GxE) interactions. Selection did not alter production traits, including ADG. Behaviour showed consistent changes, whereby high IGEg pigs showed less biting behaviour towards group mates and objects. High and low IGEg pigs did not differ in aggression or body lesions during 24-h regrouping with unfamiliar pigs. They did, however, differ in aggression towards their own group members when they were reunited after the temporary regrouping test. In combination with other tests and observations, this might indicate that high IGEg pigs are less fearful or less stress sensitive than low IGEg pigs. There were no G×E interactions, but enrichment had a positive effect on behaviour which was additive to that of selection. Despite the lack of response in ADG, genetic selection for IGEg and enriched housing conditions improved the behaviour and welfare of pigs.

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 - 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.
Kaf van het koren scheiden
Calus, Mario - \ 2014
dairy farming - ai bulls - dairy bulls - animal breeding - breeding value - selective breeding - genome analysis - genomes
Optimizing genomic selection for scarcely recorded traits
Pszczola, M.J. - \ 2013
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.

Snow shoes and sandals? : genetic aspects of heat stress sensitivity and sow reproduction
Bloemhof, S. - \ 2013
University. Promotor(en): Johan van Arendonk; I. Misztal, co-promotor(en): E.F. Knol; Liesbeth van der Waaij. - S.l. : s.n. - ISBN 9789461735881 - 173
zeugen - warmtestress - diergenetica - gevoeligheid - geslachtelijke voortplanting - voortplantingsvermogen - kritische temperatuur - hittetolerantie - selectief fokken - genetische correlatie - veredelingsprogramma's - varkensfokkerij - sows - heat stress - animal genetics - sensitivity - sexual reproduction - reproductive performance - critical temperature - heat tolerance - selective breeding - genetic correlation - breeding programmes - pig breeding

Globally the average size of pig herds are increasing and amount of labour spent per sow / finisher pig is decreasing. These changes require sows which need less management interventions. In addition to easier manageable sows modern genotypes will also need to be more adaptable considering that global temperatures are expected to increase and pork production is partially moving to warmer climates. The end result is that commercial pigs nowadays will potentially face more heat stress challenges during their productive lives.

In this thesis, a model was developed which was used to estimate upper critical temperatures for sows’ reproductive performance. Additionally the possibility to breed for reduced heat tolerance of sows was investigated. Therefore heritability for the random regression slope of farrowing rate against increasing temperature at day of insemination (= heat tolerance) and the genetic correlation between farrowing rate and heat tolerance was estimated.Commercial production pigs are crossbreds farmed all over the world. In contrast, selection is practiced mainly in temperate climates, in nucleus herds using purebred pigs. The success of genetic selection depends on how much genetic progress is realized in crossbred pigs. Within this thesis these genetic correlations for farrowing rate between purebreds and crossbreds were estimated.

Sow productivity depends on a number of related traits, such as ovulation rate, the number of litters per sow per year, the number of weaned piglets per sow per year, and the length of productive live. Traditionally pig breeding programs have improved sow productivity by increasing number weaned piglets per sow per year. To improve herd-level litters per sow per year a new trait was proposed called problem free sow production by parity, which incorporates the traits interval weaning first insemination, non-return rate, farrowing rate, and selection for next parity. Heritability of problem free sow production and genetic correlations with other sow production traits were estimated.

The main conclusion of this thesis was that it is possible to select for improved heat resistance in addition to improved commercial production levels in commercial pigs. However, genetic correlation between production in temperate and hot climates is high. This high correlation implies that, within-line, pigs with the best performance in a hot climate will be the best in temperate climate too. Most important for the success of a pig breeding program is to define appropriate breeding goals which are based on the environment(s) that market pigs are expected to perform in. The overall data collection for the genetic evaluation needs to be done in those specific environments and this will favour pigs which are able to produce over more than one specific environment.

Optimisation of selective breeding program for Nile tilapia (Oreochromis niloticus)
Trong, T.Q. - \ 2013
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 - selective breeding - breeding programmes - genetic parameters - reproductive traits - spawning - fecundity - fertility - 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.

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?
One size fits all? : optimization of rainbow trout breeding program under diverse preferences and genotype-by-environment interaction
Sae-Lim, P. - \ 2013
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.

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.
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