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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    Estimates of genetic parameters for production, behaviour, and health traits in two Swiss honey bee populations
    Guichard, Matthieu ; Neuditschko, Markus ; Soland, Gabriele ; Fried, Padruot ; Grandjean, Mélanie ; Gerster, Sarah ; Dainat, Benjamin ; Bijma, Piter ; Brascamp, Evert W. - \ 2020
    Apidologie (2020). - ISSN 0044-8435
    Apis mellifera - genetic parameter - heritability - phenotypic correlation - Varroa destructor

    Successful honey bee breeding programmes require traits that can be genetically improved by selection. Heritabilities for production, behaviour, and health traits, as well as their phenotypic correlations, were estimated in two distinct Swiss Apis mellifera mellifera and Apis mellifera carnica populations based on 9 years of performance records and more than two decades of pedigree information. Breeding values were estimated by a best linear unbiased prediction (BLUP) approach, taking either queen or worker effects into account. In A. m. mellifera, the highest heritabilities were obtained for defensive behaviour, calmness during inspection, and hygienic behaviour, while in A. m. carnica, honey yield and hygienic behaviour were the most heritable traits. In contrast, estimates for infestation rates by Varroa destructor suggest that the phenotypic variation cannot be attributed to an additive genetic origin in either population. The highest phenotypic correlations were determined between defensive behaviour and calmness during inspection. The implications of these findings for testing methods and the management of the breeding programme are discussed.

    Genetic variation of biological control relevant traits in natural enemies: a systematic review, supporting data
    Pannebakker, Bart ; Ferguson, Kimberley - \ 2019
    Wageningen University & Research
    genome - biocontrol - biological control - parasitoid - predator - heritability - genetic variation
    This is supplementary material for a systematic review tentatively titled, "Genetic variation of biological control relevant traits in natural enemies: a systematic review" (2019). Three tables are available, and are referenced in the following manner in text: Table S1: Positive control group for search results, based on papers that fit the ideal search returns for the search term. Table S2: Combined search return hits, in unedited format received from CAB Abstracts. Table S3: Articles narrowed down to BCA, with duplicates and unavailable papers removed, prior to assessment for estimation method and traits.
    Identification of Climate and Genetic Factors That Control Fat Content and Fatty Acid Composition of Theobroma cacao L. Beans
    Mustiga, Guiliana M. ; Morrissey, Joe ; Stack, Joseph Conrad ; DuVal, Ashley ; Royaert, Stefan ; Jansen, Johannes ; Bizzotto, Carolina ; Villela-Dias, Cristiano ; Mei, Linkai ; Cahoon, Edgar B. ; Seguine, Ed ; Marelli, Jean Philippe ; Motamayor, Juan Carlos - \ 2019
    Frontiers in Plant Science 10 (2019). - ISSN 1664-462X
    cacao - fat content - fatty acid composition - heritability - linkage mapping - QTL - SNP - weather

    The main ingredients of chocolate are usually cocoa powder, cocoa butter, and sugar. Both the powder and the butter are extracted from the beans of the cacao tree (Theobroma cacao L.). The cocoa butter represents the fat in the beans and possesses a unique fatty acid profile that results in chocolate’s characteristic texture and mouthfeel. Here, we used a linkage mapping population and phenotypic data of 3,292 samples from 420 progeny which led to the identification of 27 quantitative trait loci (QTLs) for fatty acid composition and six QTLs for fat content. Progeny showed extensive variation in fat levels and composition, with the level of palmitic acid negatively correlated to the sum of stearic acid, oleic acid, and linoleic acid. A major QTL explaining 24% of the relative level of palmitic acid was mapped to the distal end of chromosome 4, and those higher levels of palmitic acid were associated with the presence of a haplotype from the “TSH 1188” parent in the progeny. Within this region of chromosome 4 is the Thecc1EG017405 gene, an orthologue and isoform of the stearoyl-acyl carrier protein (ACP) desaturase (SAD) gene in plants, which is involved in fatty acid biosynthesis. Besides allelic differences, we also show that climate factors can change the fatty acid composition in the beans, including a significant positive correlation between higher temperatures and the higher level of palmitic acid. Moreover, we found a significant pollen donor effect from the variety “SIAL 70” which was associated with decreased palmitic acid levels.

    Genetic parameters for atypical reproductive patterns in dairy cows estimated from in-line milk progesterone profiles
    Binsbergen, R. van; Bouwman, A.C. ; Veerkamp, R.F. - \ 2019
    Journal of Dairy Science 102 (2019)12. - ISSN 0022-0302 - p. 11104 - 11115.
    endocrine - fertility - genetic correlation - heritability

    Our aim was to estimate genetic parameters of atypical reproductive patterns and estimate their genetic correlation with milk production and classical fertility traits for commercial dairy cows. In contrast with classical fertility traits, atypical reproductive patterns based on in-line milk progesterone profiles might have higher heritability and lower genetic correlation with milk production. We had in-line milk progesterone profiles available for 12,046 cycles in 4,170 lactations of 2,589 primiparous and multiparous cows (mainly Holstein Friesian) from 14 herds. Based on progesterone profiles, 5 types of atypical reproductive patterns in a lactation were defined: delayed ovulation types I and II, persistent corpus luteum types I and II, and late embryo mortality. These atypical patterns were detected in 14% (persistent corpus luteum type II) to 21% (persistent corpus luteum type I) of lactations. In 47% of lactations, at least 1 atypical pattern was detected. Threshold model heritabilities for atypical reproduction patterns ranged between 0.03 and 0.14 and for most traits were slightly higher compared with classical fertility traits. The genetic correlation between milk yield and calving interval was 0.56, whereas genetic correlations between milk yield and atypical reproductive patterns ranged between −0.02 and 0.33. Although most of these correlations between milk yield and atypical reproductive patterns are still unfavorable, they are lower compared with the correlations between classical fertility traits and milk yield. Therefore selection against atypical reproductive patterns may relax some constraints in current dairy breeding programs, to enhance genetic progress in both fertility and milk yield at a steady pace. However, as long as the target trait for fertility is calving interval, atypical reproductive patterns will not add additional value to the breeding goal in the near future due to the low number of available records.

    A genome-wide association study for susceptibility and infectivity of Holstein Friesian dairy cattle to digital dermatitis
    Biemans, F. ; Jong, M.C.M. de; Bijma, P. - \ 2019
    Journal of Dairy Science 102 (2019)7. - ISSN 0022-0302 - p. 6248 - 6262.
    claw health - generalized linear mixed model - genetic parameter - heritability - transmission

    Selection and breeding can be used to fight transmission of infectious diseases in livestock. The prevalence in a population depends on the susceptibility and infectivity of the animals. Knowledge on the genetic background of those traits would facilitate efficient selection for lower disease prevalence. We investigated the genetic background of host susceptibility and infectivity for digital dermatitis (DD), an endemic infectious claw disease in dairy cattle, with a genome-wide association study (GWAS), using either a simple linear mixed model or a generalized linear mixed model based on epidemiological theory. In total, 1,513 Holstein-Friesian cows of 12 Dutch dairy farms were scored for DD infection status and class (M0 to M4.1) every 2 wk for 11 times; 1,401 of these cows were genotyped with a 75k SNP chip. We performed a GWAS with a linear mixed model on 10 host disease status traits, and with a generalized linear mixed model with a complementary log-log link function (GLMM) on the probability that a cow would get infected between 2 scorings. With the GLMM, we fitted SNP effects for host susceptibility and host infectivity, while taking the variation in exposure of the susceptible cow to infectious herd mates into account. With the linear model we detected 4 suggestive SNP (false discovery rate < 0.20), 2 for the fraction of observations a cow had an active lesion on chromosomes 1 and 14, one for the fraction of observations a cow had an M2 lesion on at least one claw on chromosome 1 (the same SNP as for the fraction of observations with an active lesion), and one for the fraction of observations a cow had an M4.1 lesion on at least one claw on chromosome 10. Heritability estimates ranged from 0.09 to 0.37. With the GLMM we did not detect significant nor suggestive SNP. The SNP effects on disease status analyzed with the linear model had a correlation coefficient of only 0.70 with SNP effects on susceptibility of the GLMM, indicating that both models capture partly different effects. Because the GLMM better accounts for the epidemiological mechanisms determining individual disease status and for the distribution of the y-variable, results of the GLMM may be more reliable, despite the absence of suggestive associations. We expect that with an extended GLMM that better accounts for the full genetic variation in infectivity via the environment, the accuracy of SNP effects may increase.

    Hygienic behaviour in honeybees: a comparison of two recording methods and estimation of genetic parameters
    Facchini, Elena ; Bijma, Piter ; Pagnacco, Giulio ; Rizzi, Rita ; Brascamp, Evert Willem - \ 2019
    Apidologie 50 (2019)2. - ISSN 0044-8435 - p. 163 - 172.
    freeze-killed brood test - heritability - honeybee - hygienic behaviour - repeatability

    Hygienic behaviour (HB) in honeybees reflects social immunity against diseases and parasites. Young bees showing HB detect, uncap, and remove infested brood from a colony. We developed a new variant of freeze-killed brood (FKB*) test to optimise the duration of the HB test, the costs, and safety for the operator. In 2016, we performed a comparison between traditional FKB and FKB* on 25 unselected and unrelated colonies in the apiary of the University of Milano. To estimate repeatability and heritability, in 2017 and 2018, FKB* was used to phenotype, respectively, 56 and 95 colonies twice, in the context of a breeding programme. FKB* took less time and required a smaller amount of liquid nitrogen. The two methods showed a correlation between colony effects of 0.93, indicating that they measure the same trait. For single records, the phenotypic correlation between both methods was 0.64. Estimated heritability and repeatability for single records HB were 0.23 and 0.24, respectively, whilst heritability for the average HB value of two records was 0.37.

    Effect of dietary fat intake and genetics on fat taste sensitivity : A co-twin randomized controlled trial
    Costanzo, Andrew ; Nowson, Caryl ; Orellana, Liliana ; Bolhuis, Dieuwerke ; Duesing, Konsta ; Keast, Russell - \ 2018
    American Journal of Clinical Nutrition 107 (2018)5. - ISSN 0002-9165 - p. 683 - 694.
    co-Twin - fat intake - fat taste - heritability - randomized controlled trial - weight - zygosity

    Background Individuals with impaired fat taste (FT) sensitivity have reduced satiety responses after consuming fatty foods, leading to increased dietary fat intake. Habitual consumption of dietary fat may modulate sensitivity to FT, with high consumption decreasing sensitivity [increasing fatty acid taste threshold (FATT)] and low consumption increasing sensitivity (decreasing FATT). However, some individuals may be less susceptible to diet-mediated changes in FATT due to variations in gene expression. Objective The objective of this study was to determine the effect of an 8-wk low-fat or high-fat diet on FATT while maintaining baseline weight (<2.0 kg variation) to assess heritability and to explore the effect of genetics on diet-mediated changes in FATT. Design A co-Twin randomized controlled trial including 44 pairs (mean ± SD age: 43.7 ± 15.4 y; 34 monozygotic, 10 dizygotic; 33 women, 10 men, 1 gender-discordant) was conducted. Twins within a pair were randomly allocated to an 8-wk low-fat (<20% of energy from fat) or high-fat (>35% of energy from fat) diet. FATT was assessed by a 3-Alternate forced choice methodology and transformed to an ordinal scale (FT rank) at baseline and at 4 and 8 wk. Linear mixed models were fit to assess diet effect on FT rank and diet effect modification due to zygosity. A variance components model was fit to calculate baseline heritability. Results There was a significant time × diet interaction for FT rank after the 8-wk trial (P < 0.001), with the same conclusions for the subset of participants maintaining baseline weight (low-fat; n = 32; high-fat: n = 35). There was no evidence of zygosity effect modification (interaction of time × diet × zygosity: P = 0.892). Heritability of baseline FT rank was 8%. Conclusions There appears to be little to no genetic contribution on heritability of FATT or diet-mediated changes to FATT. Rather, environment, specifically dietary fat intake, is the main influencer of FT sensitivity, regardless of body weight. This trial was registered with the Australian New Zealand Clinical Trials Registry at http://www.anzctr.org.au/ as ACTRN12613000466741.

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

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

    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
    Wageningen 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 - taraxacum officinale - epigenetica - overerving - apomixis - dna-methylering - rna - heritability - stress

    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
    Wageningen University. Promotor(en): Mart de Jong, co-promotor(en): Piter Bijma. - Wageningen : Wageningen University - ISBN 9789462577442 - 185
    livestock - hosts - genetic effects - susceptibility - infectivity - infectious diseases - breeding value - heritability - epidemics - vee - gastheren (dieren, mensen, planten) - genetische effecten - vatbaarheid - infectiviteit - infectieziekten - fokwaarde - heritability - 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 - heritability - inbreeding - kinship - groningen horse
    In drie voorgaande artikelen in deze serie zijn achtereenvolgens het fokdoel, de registratie van gegevens en de basisprincipes van de erfelijkheid besproken. In dit laatste artikel wordt het belang van genetische variatie en de selectie van ouderdieren besproken. Twee belangrijke elementen in het fokprogramma van een zeldzaam ras.
    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 - heritability - breeds - animal breeding - dna - properties - spermatozoa - ova - fertilization - genes - alleles - homozygotes - heterozygotes - mutations - genetic markers
    Eigenschappen van dieren zijn in meer of mindere mate erfelijk. Ze gaan over van ouders op nakomelingen. Maar ervaren fokkers weten dat in de fokkerij 1+1 geen 2 is. Welke wetmatigheden en welke toevalligheden spelen een rol in de erfelijkheid? Wat heeft het DNA-onderzoek ons daar recentelijk over geleerd en wat kunnen we daarmee?
    Genetic background of claw health in dairy cattle
    Spek, D. van der - \ 2015
    Wageningen University. Promotor(en): Johan van Arendonk, co-promotor(en): Henk Bovenhuis. - Wageningen : Wageningen University - ISBN 9789462573475 - 158
    melkvee - klauwen - diergezondheid - voetziekten - genetische parameters - heritability - genomica - selectief fokken - dierveredeling - dairy cattle - claws - animal health - foot diseases - genetic parameters - heritability - genomics - selective breeding - animal breeding

    Abstract

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

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

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

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

    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
    Wageningen 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 - heritability - 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.

    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). - 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
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