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.

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Milk progesterone measures to improve genomic selection for fertility in dairy cows
Tenghe, Amabel Manyu Mefru - \ 2017
University. Promotor(en): Roel Veerkamp; B. Berglund, co-promotor(en): D. J. de Koning; Aniek 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 - 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.

Modeling genetic and nongenetic variation of feed efficiency and its partial relationships between component traits as a function of management and environmental factors
Lu, Y. ; Vandehaar, M.J. ; Spurlock, D.M. ; Weigel, K.A. ; Armentano, L.E. ; Staples, C.R. ; Connor, E.E. ; Wang, Z. ; Coffey, M. ; Veerkamp, R.F. ; Haas, Y. de; Tempelman, R.J. - \ 2017
Journal of Dairy Science 100 (2017)1. - ISSN 0022-0302 - p. 412 - 427.
dry matter intake - genetic correlation - heritability - hierarchical Bayesian modeling
Feed efficiency (FE), characterized as the fraction of feed nutrients converted into salable milk or meat, is of increasing economic importance in the dairy industry. We conjecture that FE is a complex trait whose variation and relationships or partial efficiencies (PE) involving the conversion of dry matter intake to milk energy and metabolic body weight may be highly heterogeneous across environments or management scenarios. In this study, a hierarchical Bayesian multivariate mixed model was proposed to jointly infer upon such heterogeneity at both genetic and nongenetic levels on PE and variance components (VC). The heterogeneity was modeled by embedding mixed effects specifications on PE and VC in addition to those directly specified on the component traits. We validated the model by simulation and applied it to a joint analysis of a dairy FE consortium data set with 5,088 Holstein cows from 13 research stations in Canada, the Netherlands, the United Kingdom, and the United States. Although no differences were detected among research stations for PE at the genetic level, some evidence was found of heterogeneity in residual PE. Furthermore, substantial heterogeneity in VC across stations, parities, and ration was observed with heritability estimates of FE ranging from 0.16 to 0.46 across stations.
Heritability of the backtest response in piglets and its genetic correlations with production traits
Iversen, M.W. ; Bolhuis, J.E. ; Camerlink, I. ; Ursinus, W.W. ; Reimert, I. ; Duijvesteijn, N. - \ 2017
Animal 11 (2017)4. - ISSN 1751-7311 - p. 556 - 563.
backtest - genetic correlations - heritability - pigs - production traits
The backtest response of a pig gives an indication of its coping style, that is, its preferred strategy to cope with stressful situations, which may in turn be related to production traits. The objective of this study was therefore to estimate the heritability of the backtest response and estimate genetic correlations with production traits (birth weight, growth, fat depth and loin depth). The backtest was performed by placing the piglet on its back for 60 s and the number of struggles (NrS) and vocalizations (NrV), and the latency to struggle and vocalize (LV) was recorded. In total, 992 piglets were subjected to the backtest. Heritability estimates for backtest traits were statistically moderate (although high for behavioral traits), with LV having the highest heritability estimate (0.56±0.10, P<0.001) and NrS having the lowest estimate (0.37±0.09, P<0.001). Backtest traits also had high genetic correlations with each other, with vocalization traits (NrV and LV) having the highest (−0.94±0.03, P<0.001), and NrS with NrV the lowest correlation (0.70±0.09, P<0.001). No significant correlations were found between backtest traits and production traits, but correlations between NrS and birth weight (−0.38±0.25), and NrV and loin depth (−0.28±0.19) approached significance (P=0.07). More research into genotype-by-environment interactions may be needed to assess possible connections between backtest traits and production traits, as this may depend on the circumstances (environment, experiences, etc.). In conclusion, heritability estimates of backtest traits are high and it would therefore be possible to select for them. The high genetic correlations between backtest traits indicate that it may be possible to only consider one or two traits for characterization and selection purposes. There were no significant genetic correlations found between backtest traits and production traits, although some of the correlations approached significance and hence warrant further research.
Heritabilities and genetic correlations for honey yield, gentleness, calmness and swarming behaviour in Austrian honey bees
Brascamp, Evert ; Willam, Alfons ; Boigenzahn, Christian ; Bijma, Piter ; Veerkamp, Roel F. - \ 2016
Apidologie 47 (2016)6. - ISSN 0044-8435 - p. 739 - 748.
estimated breeding value - genetic correlation - genetic parameter - heritability - honey bee

Heritabilities and genetic correlations were estimated for honey yield and behavioural traits in Austrian honey bees using data on nearly 15,000 colonies of the bee breeders association Biene Österreich collected between 1995 and 2014. The statistical models used distinguished between the genetic effect of workers and that of the queen of the colony. Heritability estimates for worker effect were larger than those for queen effect. Genetic correlations between both effects were negative. Heritability estimates for the sum of both effects (i.e. selection criterion) were 0.27, 0.37, 0.38 and 0.06 for honey yield, gentleness, calmness and swarming behaviour, respectively, indicating that meaningful genetic improvement is possible. Genetic correlations between these traits were generally small to medium, with large standard errors, with the exception of the high genetic correlation between gentleness and calmness. The models we present here can be used to estimate breeding values in honey bees.

Epigenetic inheritance in apomictic dandelions : stress-induced and heritable modifications in DNA methylation and small RNA
Preite, V. - \ 2016
University. Promotor(en): Wim van der Putten, co-promotor(en): K.J.F. Verhoeven. - Wageningen : Wageningen University - ISBN 9789462578715 - 152
taraxacum officinale - epigenetics - inheritance - apomixis - dna methylation - rna - heritability - stress - epigenetica - overerving - dna-methylering

Epigenetic variation, such as changes in DNA methylations, regulatory small RNAs (sRNAs) and chromatin modifications can be induced by environmental stress. There is increasing information that such induced epigenetic modifications can be transmitted to offspring, potentially mediating adaptive transgenerational responses to environmental changes. However, it is unclear if this phenomenon is common and relevant for adaptation under natural conditions. My thesis study aimed to examine epigenetic inheritance in common and widespread apomictic dandelions (Taraxacum officinale Wig.). Due to their asexual reproduction mode by producing clonal seeds offspring from seeds are genetically uniform and thus suitable to investigate epigenetic effects that are not confounded with genetic variation.

I exposed apomictic dandelion lineages to drought and salicylic acid (SA) stress, which induces plant defense responses following pathogen attack, and found effects on patterns of DNA methylation up to two stress-free offspring generations after exposure. However, a heritable stress signal was not present in all tests and was stress- and lineage-dependent. Drought stress triggered a weak and lineage-dependent signal that was lost again in the second offspring generation. SA treatment revealed a stress-related increased rate of DNA methylation changes in the two offspring generations, but no stress signal was found in the stressed generation itself. I also observed changes in small RNA production due the drought and SA stress experienced two generations ago. These transgenerational sRNA effects showed association with gene functions related to grandparental drought and SA stress, which suggests functional relevance of the transgenerational effects.

I used a reciprocal transplantation field experiment to investigate whether exposing dandelions to natural field stresses also triggers DNA methylation changes. The experiment revealed evidence of adaptive divergence between the populations, suggesting that non-native habitats are experienced as more stressful. However, under these field conditions no induction-based DNA methylation changes were found that persisted into offspring.

By using AFLP and MS-AFLP screening of natural apomictic dandelion populations across a north-south transect in Europe I examined if natural, heritable DNA methylation variation reflects underlying genetic variation, or if it shows patterns that are not predictable from underlying genetics. I found that a large part of heritable DNA methylation differentiation along the north-south transect was correlated with genetic differentiation. However, a fraction of differentiation in heritable DNA methylation was independent from genetic variation. This suggests a potential of epigenetics to play an evolutionary role independently, at least to some extent, from underlying genetics. Overall, I found indications of epigenetic inheritance in apomictic dandelions. Whether epigenetic variation would result in adaptive phenotypic variation in nature and whether it would persist long enough to play a relevant role in adaptation remains unclear and requires further study.

Estimating host genetic effects on susceptibility and infectivity to infectious diseases and their contribution to response to selection
Anche, M.T. - \ 2016
University. Promotor(en): Mart de Jong, co-promotor(en): Piter Bijma. - Wageningen : Wageningen University - ISBN 9789462577442 - 185 p.
livestock - hosts - genetic effects - susceptibility - infectivity - infectious diseases - breeding value - heritability - epidemics - vee - gastheren (dieren, mensen, planten) - genetische effecten - vatbaarheid - infectiviteit - infectieziekten - fokwaarde - epidemieën

Mahlet Teka Anche. (2016). Estimating host genetic effects on susceptibility and infectivity to infectious diseases and their contribution to response to selection. PhD thesis, Wageningen University, the Netherlands

Genetic approaches aiming to reduce the prevalence of an infection in a population usually focus on improving host susceptibility to an infection. The prevalence of an infection, however, is also affected by the infectivity of individuals. Studies reported that there exists among host (genetic/phenotypic) variation in susceptibility and infectivity to infectious diseases. The effect of host genetic variation in susceptibility and infectivity on the prevalence and risk of an infection is usually measured by the value of the basic reproduction ratio, R0. R0 is an important epidemiological parameter that determines the risk and prevalence of an infection. It has a threshold value of 1, where major disease outbreak can occur when R0 > 1 and the disease will die out when R0 < 1. Due to this threshold property, genetic improvements aiming to reduce the prevalence of an infection should focus on reducing R0 to a value below 1. The overall aim of this thesis was to develop methodologies that allow us to investigate the genetic effects of host susceptibility and infectivity on the prevalence of an infection, which is measured by the value of R0. Moreover, we also aim to investigating the effect of relatedness among groupmates on the utilization of among host genetic variation in susceptibility and infectivity so as to reduce the prevalence of infectious diseases. The theory of direct-indirect genetic effects and epidemiological concepts were combined to develop methodologies. In addition, a simulation study was performed to validate the methodologies developed and examine the effect of relatedness on the utilization of genetic variation in susceptibility and infectivity. It was shown that an individual’s genetic effect on its susceptibility and infectivity affect the prevalence of an infection and that an individual’s breeding value for R0 can be defined as a function of its own allele frequencies for susceptibility and infectivity and of population average susceptibility and infectivity. Moreover, simulation results show that, not only an individual’s infectivity but also an individual’s susceptibility represents an indirect genetic effect on the disease status of individuals and on the prevalence of an infection in a population. It was shown that having related groupmates allows breeders to utilize the genetic variation in susceptibility and infectivity, so as to reduce the prevalence of an infection.

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 - 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.
Genetic and phenotypic parameter estimates for growth traits of Hainan Black goat in southern China
Zhou, Han Lin ; Gu, Li Hong ; Sun, Yanyan ; Xu, Tie Shan ; Rong, Guang - \ 2015
Animal Production Science 55 (2015)4. - ISSN 1836-0939 - p. 447 - 453.
bodyweight - genetic correlation - growth rate - heritability

Genetic improvement of the growth of Hainan Black goats is a major concern as the breed is an important meat-type goat raised in southern China. To estimate genetic and phenotypic parameters for growth traits for this breed, a population of 1354 Hainan Black goats born and maintained at the Hainan Black Goat Breeding Farm from 2007 to 2011 was used. Heritabilities and phenotypic and genetic correlations for bodyweights (BWs) at birth and at 2, 4, 6, 8, 10 and 12 months of age (denoted as BW0, BW2, BW4, BW6, BW8, BW10 and BW12, respectively) and average daily weight gains (ADGs) from birth to 2 months, from 2 to 6 months, and from 6 to 12 months (denoted as ADG0-2, ADG2-6 and ADG6-12, respectively) were estimated using an animal model, with and without a permanent maternal environmental effect fitted as a random effect. Litter size, kidding year, birth season and sex, as well as their interactions, were investigated as fixed effects. Likelihood ratio testing indicated that the model with a permanent maternal environmental effect was better than that without a permanent maternal environmental effect for all traits. The direct additive heritability for BW and ADG ranged from 0.17 (ADG6-12) to 0.45 (BW0), indicating that growth traits of Hainan Black goats can be improved by phenotypic selection. Maternal permanent environmental variance was also estimated and varied from 0.08 (BW6) to 0.27 (BW10). The genetic and phenotypic correlations among ADG traits were positive and relatively low. However, the positive and relatively high genetic and phenotypic correlations among BW traits indicated that breeding programs are able to use selection at early ages to improve BW traits.

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 - breeds - animal breeding - 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
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


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.

Heterogeneity in genetic variation and energy sink relationships for residual feed intake across research stations and countries
Tempelman, R. ; Spurlock, D.M. ; Coffey, M.P. ; Veerkamp, R.F. ; Armentano, L. ; Weigel, K. ; Haas, Y. de; Staples, C.R. ; Connor, E.E. ; Hanigan, M.D. ; Lu, Y.F. ; Haar, M.J. van de - \ 2015
Journal of Dairy Science 98 (2015)3. - ISSN 0022-0302 - p. 2013 - 2026.
random regression-models - dairy-cattle - lactation performance - efficiency - cows - selection - supplementation - heritability - components - variance
Our long-term objective is to develop breeding strategies for improving feed efficiency in dairy cattle. In this study, phenotypic data were pooled across multiple research stations to facilitate investigation of the genetic and nongenetic components of feed efficiency in Holstein cattle. Specifically, the heritability of residual feed intake (RFI) was estimated and heterogeneous relationships between RFI and traits relating to energy utilization were characterized across research stations. Milk, fat, protein, and lactose production converted to megacalories (milk energy; MilkE), dry matter intakes (DMI), and body weights (BW) were collected on 6,824 lactations from 4,893 Holstein cows from research stations in Scotland, the Netherlands, and the United States. Weekly DMI, recorded between 50 to 200 d in milk, was fitted as a linear function of MilkE, BW0.75, and change in BW (¿BW), along with parity, a fifth-order polynomial on days in milk (DIM), and the interaction between this polynomial and parity in a first-stage model. The residuals from this analysis were considered to be a phenotypic measure of RFI. Estimated partial regression coefficients of DMI on MilkE and on BW0.75 ranged from 0.29 to 0.47 kg/Mcal for MilkE across research stations, whereas estimated partial regression coefficients on BW0.75 ranged from 0.06 to 0.16 kg/kg0.75. Estimated partial regression coefficients on ¿BW ranged from 0.06 to 0.39 across stations. Heritabilities for country-specific RFI were based on fitting second-stage random regression models and ranged from 0.06 to 0.24 depending on DIM. The overall heritability estimate across all research stations and all DIM was 0.15±0.02, whereas an alternative analysis based on combining the first- and second-stage model as 1 model led to an overall heritability estimate of 0.18±0.02. Hence future genomic selection programs on feed efficiency appear to be promising; nevertheless, care should be taken to allow for potentially heterogeneous variance components and partial relationships between DMI and other energy sink traits across environments when determining RFI.
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


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.

Empirical and deterministic accuracies of across-population genomic prediction
Wientjes, Y.C.J. ; Veerkamp, R.F. ; Bijma, P. ; Bovenhuis, H. ; Schrooten, C. ; Calus, M.P.L. - \ 2015
Genetics, Selection, Evolution 47 (2015)5. - ISSN 0999-193X
dairy-cattle breeds - linkage disequilibrium - relationship matrix - complex traits - multi-breed - selection - values - markers - heritability - models
Background: Differences in linkage disequilibrium and in allele substitution effects of QTL (quantitative trait loci) may hinder genomic prediction across populations. Our objective was to develop a deterministic formula to estimate the accuracy of across-population genomic prediction, for which reference individuals and selection candidates are from different populations, and to investigate the impact of differences in allele substitution effects across populations and of the number of QTL underlying a trait on the accuracy. Methods: A deterministic formula to estimate the accuracy of across-population genomic prediction was derived based on selection index theory. Moreover, accuracies were deterministically predicted using a formula based on population parameters and empirically calculated using simulated phenotypes and a GBLUP (genomic best linear unbiased prediction) model. Phenotypes of 1033 Holstein-Friesian, 105 Groninger White Headed and 147 Meuse-Rhine-Yssel cows were simulated by sampling 3000, 300, 30 or 3 QTL from the available high-density SNP (single nucleotide polymorphism) information of three chromosomes, assuming a correlation of 1.0, 0.8, 0.6, 0.4, or 0.2 between allele substitution effects across breeds. The simulated heritability was set to 0.95 to resemble the heritability of deregressed proofs of bulls. Results: Accuracies estimated with the deterministic formula based on selection index theory were similar to empirical accuracies for all scenarios, while accuracies predicted with the formula based on population parameters overestimated empirical accuracies by ~25 to 30%. When the between-breed genetic correlation differed from 1, i.e. allele substitution effects differed across breeds, empirical and deterministic accuracies decreased in proportion to the genetic correlation. Using a multi-trait model, it was possible to accurately estimate the genetic correlation between the breeds based on phenotypes and high-density genotypes. The number of QTL underlying the simulated trait did not affect the accuracy. Conclusions: The deterministic formula based on selection index theory estimated the accuracy of across-population genomic predictions well. The deterministic formula using population parameters overestimated the across-population genomic accuracy, but may still be useful because of its simplicity. Both formulas could accommodate for genetic correlations between populations lower than 1. The number of QTL underlying a trait did not affect the accuracy of across-population genomic prediction using a GBLUP method
Cooperative and uniform fish? : social interactions and variability in live body weight in the GIFT strain (Nile tilapia, Oreochromic niloticus) in Malaysia
Khaw, H.L. - \ 2015
University. Promotor(en): Johan van Arendonk, co-promotor(en): Piter Bijma; R.W. Ponzoni. - Wageningen : Wageningen University - ISBN 9789462572157 - 161
oreochromis niloticus - sociaal gedrag - lichaamsgewicht - variatie - genetische effecten - inteelt - kenmerken - heritability - genotype-milieu interactie - genotypische variatie - genetische verbetering - veredelingsprogramma's - visteelt - maleisië - social behaviour - body weight - variation - genetic effects - inbreeding - traits - genotype environment interaction - genetic variance - genetic improvement - breeding programmes - fish culture - malaysia


Khaw, HL. (2014). Cooperative and uniform fish? Social interactions and variability in live body weight in the GIFT strain (Nile tilapia, Oreochromic niloticus) in Malaysia. PhD thesis, Wageningen University, the Netherlands.

Social interactions are present everywhere in the living world. Such social interactions may lead to indirect genetic effects (IGE), which are heritable effects of an individual on trait values of the other individuals its interacts with. IGEs may affect the direction and magnitude of response to selection in breeding programs. Moreover, social interactions may affect variability of traits. In aquaculture, competition for resources inflates size variation within populations. In this thesis, we used the Genetically Improved Farmed Tilapia (GIFT; Oreochromis niloticus) strain to investigate the genetic basis for social interactions and variability in harvest weight for tropical finfish. Social interaction experiments were established for quantifying the genetic and non-genetic indirect effects on harvest weight in the GIFT strain. We found evidence for IGEs on harvest weight, and a negative direct-indirect genetic correlation, which suggesting heritable competitive interactions for harvest weight in GIFT. Hence, breeding schemes may need to be adapted to avoid an increase in competition. A stochastic simulation study was conducted to examine the effect of BLUP selection on the rate of inbreeding for socially affected traits. The rates of inbreeding for scenarios with IGEs were greater than for scenarios without IGE. Therefore, with IGEs there is a greater need for a selection algorithm that restricts the increase of mean kinship. In aquaculture industry, there is a wide range of commercial production environments, which may leads to genotype by environment (GxE) interaction, for example due to differential social interactions. The GIFT fish were tested in ponds and cages to study the GxE interaction. The genetic correlations between environments (0.73 to 0.85, for harvest weight and body measurements) indicate little GxE-interaction. The data collected from the social interaction experiments were also used to investigate the presence of genetic variation in uniformity for harvest weight. The genetic coefficient of variation for standard deviation of harvest weight (0.17) shows that uniformity of harvest weight is heritable and can be increased by selective breeding. In the General Discussion of this thesis, the uniformity study was extended to incorporate IGE. The result indicates that more cooperative fish are not necessary more uniform for harvest weight. Overall, our results suggest that genetic improvement in fish breeding programs can be increased by accounting for social interactions.

Prevalence and co-occurrence of hip dysplasia and elbow dysplasia in Dutch pure-bred dogs
Lavrijsen, I.C.M. ; Heuven, H.C.M. ; Meij, B.P. ; Theyse, L.F.H. ; Nap, R.C. ; Leegwater, P.A.J. ; Hazewinkel, H.A.W. - \ 2014
Preventive Veterinary Medicine 114 (2014)2. - ISSN 0167-5877 - p. 114 - 122.
german-shepherd dogs - uk labrador retrievers - bernese mountain dog - canine hip - control program - cost-analysis - inheritance - osteochondrosis - heritability - breeds
Hip as well as elbow dysplasia (HD, ED) are developmental disorders leading to malformation of their respective joints. For a long time both disorders have been scored and targeted for improvement using selective breeding in several Dutch dog populations. In this paper all scores for both HD and ED, given to pure bred dogs in the Netherlands from 2002 to 2010, were analyzed. Heritabilities and correlations between HD and ED were calculated for the 4 most frequently scored breeds. Heritabilities ranged from 0.0 to 0.37 for HD related traits (FCI-score, osteoarthritis, congruity, shape and laxity (Norberg angle); FCI: Federation Cynologique Internationale) and from 0.0 to 0.39 for ED related traits (IEWG score, osteoarthritis, sclerosis and indentation; IEWG: International Elbow Working Group). HD related traits showed high genetic and residual correlations among each other but were only to a minor extent correlated with ED related traits, which also showed high correlations among each other. Genetic correlations were higher than residual correlations. Phenotypic and genetic trends since 2001 for the four most scored breeds were slightly positive but decreasing overtime, indicating that selection over the past decade has not been effective. (C) 2014 Published by Elsevier B.V.
Genetic variation of milk fatty acid composition between and within dairy cattle breeds
Maurice - Van Eijndhoven, M.H.T. - \ 2014
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 - milk fat - animal genetic resources - dairy farming


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.

Defining the role of common variation in the genomic and biological architecture of adult human height
Wood, A.R. ; Esko, T. ; Yang, J. ; Dhonukshe-Rutten, R.A.M. ; Groot, C.P.G.M. de - \ 2014
Nature Genetics 46 (2014). - ISSN 1061-4036 - p. 1173 - 1186.
genetic-variation - complex traits - heritability - mutations - snps
Using genome-wide data from 253,288 individuals, we identified 697 variants at genome-wide significance that together explained one-fifth of the heritability for adult height. By testing different numbers of variants in independent studies, we show that the most strongly associated ~2,000, ~3,700 and ~9,500 SNPs explained ~21%, ~24% and ~29% of phenotypic variance. Furthermore, all common variants together captured 60% of heritability. The 697 variants clustered in 423 loci were enriched for genes, pathways and tissue types known to be involved in growth and together implicated genes and pathways not highlighted in earlier efforts, such as signaling by fibroblast growth factors, WNT/ß-catenin and chondroitin sulfate–related genes. We identified several genes and pathways not previously connected with human skeletal growth, including mTOR, osteoglycin and binding of hyaluronic acid. Our results indicate a genetic architecture for human height that is characterized by a very large but finite number (thousands) of causal variants.
Missing heritability and soft inheritance of morphology and metabolism in Arabidopsis
Kooke, R. - \ 2014
University. Promotor(en): Harro Bouwmeester; Joost Keurentjes, co-promotor(en): Dick Vreugdenhil. - Wageningen University : Wageningen University - ISBN 9789462570412 - 283
arabidopsis - heritability - overerving - plantenmorfologie - metabolisme - plantenfysiologie - genetica - epigenetica - genetische variatie - inheritance - plant morphology - metabolism - plant physiology - genetics - epigenetics - genetic variation

The plant phenotype is shaped by complex interactions between its genotype and the environment. Although the genotype is stable and determined by the genomic sequence, plants are able to respond flexibly to changes in environmental conditions by orchestrated signal transduction pathways. The genomic sequence may change with each generation through chromosome rearrangements, meiotic recombination and spontaneous mutations. Through natural selection on these randomly induced changes, genotypes become adapted to their local environment. Because different genotypes adapt to different environments, natural variation within species expands in time and gives rise to a wide variety of genotypes and phenotypes. The genetic architecture that specifies the phenotype can be investigated by analyzing different genotypes in the same environment and associate the phenotypic variation with molecular markers that discriminate the genotypes. Recent advances in next-generation sequencing technology enabled the fast sequencing of entire genomes, and in Arabidopsisthalianaalone, more than 1000 different genotypes have been fully resequenced. The sequencing allows the association of phenotypic variation with large numbers of single nucleotide polymorphisms (SNPs) that greatly enhance resolution in genome-wide association studies (GWAS).

GWAS on human diseases suffer from missing heritability that is most likely caused by the genetic architecture of the disease traits. Many variants of small effect or rare variants most likely determine a large part of the genetic variation and these variants are difficult to identify in GWAS due to lack of statistical power. In plants, several GWAS have been performed and they have identified previously validated genes and genes involved in monogenic disease resistance, but elucidating quantitative traits such as many agronomic important traits might be problematic in plants as well. Chapter 2 describes a GWA study in which quantitative morphological traits, such as leaf area, flowering time and branching were examined in 350 accessions of Arabidopsis for association with about 200,000 SNPs. The morphological traits showed extensive variation and were highly heritable, but GWA mapping could not identify the genetic variants that explain the heritability. Therefore, missing heritability was addressed using genomic selection models and these models confirmed the quantitative complex architecture of the morphological traits. Based upon these results, the heritability was assumed to be hidden below the significance threshold, and indeed lowering the significance threshold enabled the identification of many candidate genes that have been implicated to play a role in the phenotype directly or indirectly, in previous studies. One candidate gene was studied in more detail; natural variants of ACS11, an ethylene biosynthesis gene, associated significantly with the petiole to leaf length ratio. ACS11is indeed expressed in petioles and ectopically supplied ethylene abolished the difference in the phenotype of natural variants at this locus, strongly suggesting that ACS11is involved in the regulation of petiole growth.

However, lowering the significance threshold also increases the number of false-positive associations, non-causal alleles that co-segregate with the trait values. Because regulation of the morphological traits occurs at multiple intermediate levels, increased certainty on the associations can be obtained by performing GWA mapping on the intermediate levels from genotype to phenotype such as gene expression, and protein and metabolite content. Chapter 3 describes a literature survey into the multi-dimensional regulation of metabolic networks that are regulated by inputs from the clock, the communication between cells and between source and sink tissues, and the environment. The metabolic status of the plant can be seen as the final product of the interaction with the environment, and as such, it can serve as a blueprint for growth and development. Chapter 4 describes the abundant variation in enzyme activities and metabolites involved in primary carbon and nitrogen metabolism. The metabolite and enzyme activity data were analyzed together with plant biomass data, and many pleiotropic regulators were identified with opposite effects on primary metabolism and biomass formation. Natural variants in two stress-responsive genes were oppositely associated with biomass and many enzymes and metabolites involved in primary metabolism, suggesting that higher enzyme activities and higher levels of sugars and proteins might be needed to support plant resistance to stress at the expense of growth.

Some studies indicated that epigenetic variation, independent of the genetic SNPs, may contribute to missing heritability. Epigenetic inheritance is defined as the inheritance of phenotypic variation to future generations without changes in DNA sequence. Epigenetic variation is caused by variation in chromatin marks such as DNA methylation, histone modifications and small RNAs. Recently, a recombinant inbred line (RIL) population was developed in Arabidopsis where the chromosomes are differentially methylated in lines with an otherwise isogenic background by crossing wild-type Col-0 with a hypomethylated ddm1-2mutant. Chapter 5 describes the epigenetic regulation of morphology and phenotypic plasticity by studying morphological variation in 99 epiRILs under control and saline conditions. The morphology and plasticity trait values were associated with differentially methylated regions (DMRs) that were used as molecular markers in QTL mapping. Many QTLs for various morphological traits and phenotypic plasticity parameters co-located, suggesting pleiotropic epigenetic regulation of growth, morphology and plasticity. Furthermore, methylation variation in the promoter of a salt-tolerance gene, HIGH-AFFINITY K+TRANSPORTER1 (HKT1)associated significantly with leaf area, especially under saline conditions.

To gain more insight into the epigenetic regulation of plant growth and morphology, chapter 6 describes the epigenetic regulation of secondary metabolite levels in leaves and flowers and studies the relationship with the morphological traits determined in chapter 5. Many of the QTLs that were found for growth and morphology overlapped with the QTLs for metabolic traits, and suggest pleiotropic regulation. Furthermore, subsets of the metabolites correlated well with the morphological traits and might thus be regulated by the same loci. The majority of metabolite QTLs was detected for glucosinolates and flavonoids in the flowers, and methylation variation was observed for some of the biosynthetic pathway genes of these compounds when comparing Col-0 and ddm1-2, which indicates a role for epigenetic regulation of these biosynthesis pathways.

Although stable, natural epialleles have been found in plant species and the environment can induce hypo- and hypermethylation of DNA, it remains elusive whether environmentally-induced epigenetic changes can be inherited to subsequent generations, independent of genetic variation. Chapter 7 describes the transgenerational inheritance of phenotypic variation in progeny derived from a common Arabidopsis founder line. The progeny of stressed parents and grandparents showed variation in morphological traits, metabolite accumulation and gene expression. For example, many salt-responsive genes were up-regulated in progeny of salt-stressed grandparents. The responses to biotic (methyljasmonate) and abiotic (salt) stress differed strongly and this suggests that different environments can cause different transgenerational responses. Because all lines are derived from a single ancestor, epigenetic variation and not DNA variation is most likely causal for the phenotypic variation. Further studies are, however, needed to provide conclusive evidence for transgenerational inheritance.

Chapter 8 provides a synthesis of the work and discusses the GWA studies in the light of missing heritability, genetic architecture and the verification of candidate genes. The work on epigenetic regulation of phenotypic plasticity, morphology and metabolism is discussed in relation to Lamarckian soft inheritance that gained new enthusiasm after some recent discoveries in the field of epigenetics. And finally, the metabolomics work is discussed in the light of the growth-defense hypothesis that states that investments in defense occur at the expense of growth.

The effect of genetic selection for Johne's disease resistance n dairy cattle: Results of a genetic-epidemiological model
Hulzen, K.J.E. van; Koets, A.P. ; Nielen, M. ; Heuven, H.C.M. ; Arendonk, J.A.M. van; Klinkenberg, D. - \ 2014
Journal of Dairy Science 97 (2014)3. - ISSN 0022-0302 - p. 1762 - 1773.
avium subspecies paratuberculosis - decision-analysis model - antibody-response - control program - fecal culture - holstein cows - mycobacterium - herd - infection - heritability
The objective of this study was to model genetic selection for Johne’s disease resistance and to study the effect of different selection strategies on the prevalence in the dairy cattle population. In the Netherlands, a certification-and-surveillance program is in use to reduce prevalence and presence of sources of infection in milk by culling ELISA-positive dairy cows in infected herds. To investigate the additional genetic effect of this program, a genetic-epidemiological model was developed to assess the effect of selection of cows that test negative for Johne’s disease (dam selection). The genetic effect of selection at the sire level was also considered (sire selection), assuming selection of 80% of sires producing the most resistant offspring based on their breeding values, as well as the combined effect. Parameters assumed to be affected by genetic selection were the length of the latent period, susceptibility (i.e., the number of infectious doses needed to become infected), or the length of susceptible period as a calf. The effect of selection was measured by the time in years required to eliminate infection. Sensitivity analysis was performed for heritability, accuracy of selection, and intensity of selection. For dam selection, responses to selection were small, requiring 379 to 702 yr for elimination. For sire selection, responses were much larger, although elimination still required 147 to 223 yr. The response to selection was largest if genetic selection affected the length of the susceptible period, followed by the susceptibility, and finally the length of the latent period. Genetic selection for Johne’s disease resistance by certification and surveillance is too slow for practical purpose, but that selection on the sire level is able to contribute to the control of Johne’s disease in the long run.
Quantitative genetic analysis of ascites in broilers
Closter, A.M. - \ 2014
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 - genetic parameters - 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.

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