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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    Genotypic and phenotypic characterization of Phytophthora infestans in South Korea during 2009–2016 reveals clonal reproduction and absence of EU_13_A2 genotype
    Choi, Jang Gyu ; Hong, Su Young ; Kessel, Geert J.T. ; Cooke, David E.L. ; Vossen, Jack H. ; Cho, Ji Hong ; Im, Ju Seong ; Park, Young Eun ; Cho, Kwang Soo - \ 2020
    Plant Pathology 69 (2020)5. - ISSN 0032-0862
    genotype - late blight - phenotype - potato - SSR

    In order to better understand the Phytophthora infestans population structure in South Korea, 172 isolates were collected between 2009 and 2016 from four major potato cultivation areas. Fungicide (metalaxyl and dimethomorph) response, mating type, and microsatellite (SSR) genetic fingerprints were analysed to characterize these isolates. Ten isolates collected in Gyeongnam Province, which specializes in protected winter cultivation in polytunnels, were A2 mating type. All other isolates were A1 mating type. Overall, 42% of the isolates were resistant to metalaxyl, and 43% were sensitive. All isolates were sensitive to dimethomorph. From the SSR fingerprints, 45 distinct genotypes were identified, which could be clustered into four clonal lineages: KR_1_A1, KR_2_A2, SIB-1, and US-11. KR_1_A1 was the predominant P. infestans genotype in South Korea. KR_2_A2 was only found in Gyeongnam Province; all isolates were A2 mating type and resistant to metalaxyl. SIB-1 was dominant until 2013 but its frequency has gradually decreased in more recent years. US-11 was first found in 2014, after which its frequency has increased to become codominant with KR_1_A1. The calculated standardized index of association (IA) suggests that the South Korean P. infestans population is undergoing clonal reproduction. When compared with populations of P. infestans from the Netherlands, it has less genetic diversity and the dominant Netherlands P. infestans genotype, EU_13_A2 (Blue_13), was not found in South Korea. Such monitoring of the pathogen population contributes to a more efficient integrated pest management-based control strategy for potato late blight control in South Korea.

    Stress response, peripheral serotonin and natural antibodies in feather pecking genotypes and phenotypes and their relation with coping style
    Eijk, Jerine A.J. van der; Lammers, Aart ; Kjaer, J.B. ; Rodenburg, T.B. - \ 2019
    Physiology and Behavior 199 (2019). - ISSN 0031-9384 - p. 1 - 10.
    Feather pecking - genotype - natural antibody - phenotype - serotonin - stress response

    Feather pecking (FP), a serious welfare and economic issue in the egg production industry, has been related to coping style. Proactive and reactive coping styles differ in, among others, the stress response, serotonergic activity and immune activity. Yet, it is unknown whether genetic lines divergently selected on FP (i.e. FP genotypes) or individuals differing in FP (i.e. FP phenotypes) can be categorized into coping styles. Therefore, we determined peripheral serotonin (5-HT) levels, natural antibody (NAb) titers, behavioral and corticosterone (CORT) responses to manual restraint (MR) in FP genotypes (high FP (HFP), low FP (LFP) and unselected control (CON) line) and FP phenotypes (feather pecker, feather pecker-victim, victim and neutral). We further examined the consistency of and relationships between behavioral and physiological measures. FP genotypes differed in behavioral responses to MR, 5-HT levels and NAb titers, but not in CORT levels after MR. HFP birds had less active responses at adolescent age, but more active responses at adult age compared to LFP and CON birds. The CON line had higher 5-HT levels at adolescent age, while the HFP line had lower 5-HT levels than the other lines at adult age. Overall, the HFP line had lower IgM NAb titers, while the LFP line had lower IgG NAb titers compared to the other lines. FP phenotypes differed in behavioral responses to MR and 5-HT levels, but not in CORT levels after MR or NAb titers. Within the HFP line, feather peckers tended to have less active responses compared to neutrals at adolescent age, while victims had more active responses compared to the other phenotypes at adult age. Feather peckers had higher 5-HT levels than neutrals at adult age. Behavioral and CORT responses to MR were not consistent over time, suggesting that responses to MR might not reflect coping style in this study. Furthermore, proactive behavioral responses were correlated with reactive physiological measures and vice versa. Thus, it was not possible to categorize FP genotypes or FP phenotypes into specific coping styles.

    Data from: Unlocking the story in the swab: A new genotyping assay for the amphibian chytrid fungus Batrachochytrium dendrobatidis
    Byrne, Allison Q. ; Rothstein, Andrew P. ; Poorten, Thomas J. ; Erens, Jesse ; Settles, Matthew L. ; Rosenblum, Erica Bree - \ 2017
    University of California
    Fungi - swab - microfluidic multiplex PCR - Batrachochytrium dendrobatidis - Amphibians - Disease Biology - Ecological Genetics - genotype
    One of the most devastating emerging pathogens of wildlife is the chytrid fungus, Batrachochytrium dendrobatidis (Bd), which affects hundreds of amphibian species around the world. Genomic data from pure Bd cultures has advanced our understanding of Bd phylogenetics, genomic architecture, and mechanisms of virulence. However pure cultures are laborious to obtain and whole genome sequencing is comparatively expensive, so relatively few isolates have been genetically characterized. Thus we still know little about the genetic diversity of Bd in natural systems. The most common non-invasive method of sampling Bd from natural populations is to swab amphibian skin. Hundreds of thousands of swabs have been collected from amphibians around the world, but Bd DNA collected via swabs is often low in quality and/or quantity. In this study, we developed a custom Bd genotyping assay using the Fluidigm Access Array platform to amplify 192 carefully-selected regions of the Bd genome. We obtained robust sequence data for pure Bd cultures and field-collected skin swabs. This new assay has the power to accurately discriminate among the major Bd clades, recovering the basic tree topology previously revealed using whole genome data. Additionally, we established a critical value for initial Bd load for swab samples (150 Bd genomic equivalents) above which our assay performs well. By leveraging advances in microfluidic multiplex PCR technology and the globally distributed resource of amphibian swab samples, non-invasive skin swabs can now be used to address critical spatial and temporal questions about Bd and its effects on declining amphibian populations.
    Unlocking the story in the swab: A new genotyping assay for the amphibian chytrid fungus Batrachochytrium dendrobatidis
    Byrne, Allison Q. ; Rothstein, Andrew P. ; Poorten, Thomas J. ; Erens, Jesse ; Settles, Matthew L. ; Rosenblum, Erica Bree - \ 2017
    Molecular Ecology Resources 17 (2017)6. - ISSN 1755-098X - p. 1283 - 1292.
    Batrachochytrium dendrobatidis - genotype - microfluidic multiplex PCR - swab

    One of the most devastating emerging pathogens of wildlife is the chytrid fungus, Batrachochytrium dendrobatidis (Bd), which affects hundreds of amphibian species around the world. Genomic data from pure Bd cultures have advanced our understanding of Bd phylogenetics, genomic architecture and mechanisms of virulence. However, pure cultures are laborious to obtain and whole-genome sequencing is comparatively expensive, so relatively few isolates have been genetically characterized. Thus, we still know little about the genetic diversity of Bd in natural systems. The most common noninvasive method of sampling Bd from natural populations is to swab amphibian skin. Hundreds of thousands of swabs have been collected from amphibians around the world, but Bd DNA collected via swabs is often low in quality and/or quantity. In this study, we developed a custom Bd genotyping assay using the Fluidigm Access Array platform to amplify 192 carefully selected regions of the Bd genome. We obtained robust sequence data for pure Bd cultures and field-collected skin swabs. This new assay has the power to accurately discriminate among the major Bd clades, recovering the basic tree topology previously revealed using whole-genome data. Additionally, we established a critical value for initial Bd load for swab samples (150 Bd genomic equivalents) above which our assay performs well. By leveraging advances in microfluidic multiplex PCR technology and the globally distributed resource of amphibian swab samples, noninvasive skin swabs can now be used to address critical spatial and temporal questions about Bd and its effects on declining amphibian populations.

    Deriving estimates of individual variability in genetic potentials of performance traits for 3 dairy breeds, using a model of lifetime nutrient partitioning
    Phuong, H.N. ; Boer, I.J.M. de; Schmidely, P. ; Friggens, N.C. ; Martin, O. - \ 2015
    Journal of Dairy Science 98 (2015)1. - ISSN 0022-0302 - p. 618 - 632.
    repeated reproductive-cycles - milk-yield - lactating cow - holstein cows - body-size - cattle - parameters - efficiency - fertility - genotype
    This study explored the ability of an existing lifetime nutrient partitioning model for simulating individual variability in genetic potentials of dairy cows. Generally, the model assumes a universal trajectory of dynamic partitioning of priority between life functions and genetic scaling parameters are then incorporated to simulate individual difference in performance. Data of 102 cows including 180 lactations of 3 breeds: Danish Red, Danish Holstein, and Jersey, which were completely independent from those used previously for model development, were used. Individual cow performance records through sequential lactations were used to derive genetic scaling parameters for each animal by calibrating the model to achieve best fit, cow by cow. The model was able to fit individual curves of body weight, and milk fat, milk protein, and milk lactose concentrations with a high degree of accuracy. Daily milk yield and dry matter intake were satisfactorily predicted in early and mid lactation, but underpredictions were found in late lactation. Breeds and parities did not significantly affect the prediction accuracy. The means of genetic scaling parameters between Danish Red and Danish Holstein were similar but significantly different from those of Jersey. The extent of correlations between the genetic scaling parameters was consistent with that reported in the literature. In conclusion, this model is of value as a tool to derive estimates of genetic potentials of milk yield, milk composition, body reserve usage, and growth for different genotypes of cow. Moreover, it can be used to separate genetic variability in performance between individual cows from environmental noise.
    A multilevel analysis of fruit growth of two tomato cultivars in response to fruit temperature
    Okello, R.C. ; Visser, P.H.B. de; Heuvelink, E. ; Lammers, M. ; Maagd, R.A. de; Struik, P.C. ; Marcelis, L.F.M. - \ 2015
    Physiologia Plantarum 153 (2015)3. - ISSN 0031-9317 - p. 403 - 418.
    cell-division - size - endoreduplication - arabidopsis - expression - expansion - genotype - plants - genes - cycle
    Fruit phenotype is a resultant of inherent genetic potential in interaction with impact of environment experienced during crop and fruit growth. The aim of this study was to analyze the genetic and physiological basis for the difference in fruit size between a small (‘Brioso’) and intermediate (‘Cappricia’) sized tomato cultivar exposed to different fruit temperatures. It was hypothesized that fruit heating enhances expression of cell cycle and expansion genes, rates of carbon import, cell division and expansion, and shortens growth duration, whereas increase in cell number intensifies competition for assimilates among cells. Unlike previous studies in which whole-plant and fruit responses cannot be separated, we investigated the temperature response by varying fruit temperature using climate-controlled cuvettes, while keeping plant temperature the same. Fruit phenotype was assessed at different levels of aggregation (whole fruit, cell and gene) between anthesis and breaker stage. We showed that: (1) final fruit fresh weight was larger in ‘Cappricia’ owing to more and larger pericarp cells, (2) heated fruits were smaller because their mesocarp cells were smaller than those of control fruits and (3) no significant differences in pericarp carbohydrate concentration were detected between heated and control fruits nor between cultivars at breaker stage. At the gene level, expression of cell division promoters (CDKB2, CycA1 and E2Fe-like) was higher while that of the inhibitory fw2.2 was lower in ‘Cappricia’. Fruit heating increased expression of fw2.2 and three cell division promoters (CDKB1, CDKB2 and CycA1). Expression of cell expansion genes did not corroborate cell size observations.
    Genomic relationships computed from either next- generation sequence or array SNP data
    Perez Enciso, M. - \ 2014
    Journal of Animal Breeding and Genetics 131 (2014)2. - ISSN 0931-2668 - p. 85 - 96.
    genetic-variation - complex traits - selection - pig - predictions - genotype - samples - cattle
    The use of sequence data in genomic prediction models is a topic of high interest, given the decreasing prices of current next'-generation sequencing technologies (NGS) and the theoretical possibility of directly interrogating the genomes for all causal mutations. Here, we compare by simulation how well genetic relationships (G) could be estimated using either NGS or ascertained SNP arrays. DNA sequences were simulated using the coalescence according to two scenarios: a cattle' scenario that consisted of a bottleneck followed by a split in two breeds without migration, and a pig' model where Chinese introgression into international pig breeds was simulated. We found that introgression results in a large amount of variability across the genome and between individuals, both in differentiation and in diversity. In general, NGS data allowed the most accurate estimates of G, provided enough sequencing depth was available, because shallow NGS (4x) may result in highly distorted estimates of G elements, especially if not standardized by allele frequency. However, high-density genotyping can also result in accurate estimates of G. Given that genotyping is much less noisy than NGS data, it is suggested that specific high-density arrays (similar to 3M SNPs) that minimize the effects of ascertainment could be developed in the population of interest by sequencing the most influential animals and rely on those arrays for implementing genomic selection.
    Consensus proposals for classification of the family Hepeviridae
    Smith, D.B. ; Simmonds, P. ; Jameel, S. ; Emerson, S.U. ; Harrison, T.J. ; Meng, X.J. ; Okamoto, H. ; Poel, W.H.M. van der; Purdy, M.A. - \ 2014
    Journal of General Virology 95 (2014). - ISSN 0022-1317 - p. 2223 - 2232.
    hepatitis-e virus - genetic-variability - phylogenetic analysis - molecular-cloning - wild rats - c virus - hev - genotype - china - recombination
    The family Hepeviridae consists of positive-stranded RNA viruses that infect a wide range of mammalian species, as well as chickens and trout. A subset of these viruses infects humans and can cause a self-limiting acute hepatitis that may become chronic in immunosuppressed individuals. Current published descriptions of the taxonomical divisions within the family Hepeviridae are contradictory in relation to the assignment of species and genotypes. Through analysis of existing sequence information, we propose a taxonomic scheme in which the family is divided into the genera Orthohepevirus (all mammalian and avian hepatitis E virus (HEV) isolates) and Piscihepevirus (cutthroat trout virus). Species within the genus Orthohepevirus are designated Orthohepevirus A (isolates from human, pig, wild boar, deer, mongoose, rabbit and camel), Orthohepevirus B (isolates from chicken), Orthohepevirus C (isolates from rat, greater bandicoot, Asian musk shrew, ferret and mink) and Orthohepevirus D (isolates from bat). Proposals are also made for the designation of genotypes within the human and rat HEVs. This hierarchical system is congruent with hepevirus phylogeny, and the three classification levels (genus, species and genotype) are consistent with, and reflect discontinuities in the ranges of pairwise distances between amino acid sequences. Adoption of this system would include the avoidance of host names in taxonomic identifiers and provide a logical framework for the assignment of novel variants.
    Estimating challenge load due to disease outbreaks and other challenges using reproduction records of sows
    Mathur, P.K. ; Herrero-Medrano, J. ; Alexandri, P. ; Knol, E.F. ; Napel, J. ten; Rashidi, H. ; Mulder, H.A. - \ 2014
    Journal of Animal Science 92 (2014)12. - ISSN 0021-8812 - p. 5374 - 5381.
    environment interaction - breeding programs - respiratory syndrome - genotype - pigs - cattle - models
    A method was developed and tested to estimate challenge load due to disease outbreaks and other challenges in sows using reproduction records. The method was based on reproduction records from a farm with known disease outbreaks. It was assumed that the reduction in weekly reproductive output within a farm is proportional to the magnitude of the challenge. As the challenge increases beyond certain threshold, it is manifested as an outbreak. The reproduction records were divided into 3 datasets. The first dataset called the Training dataset consisted of 57,135 reproduction records from 10,901 sows from 1 farm in Canada with several outbreaks of porcine reproductive and respiratory syndrome (PRRS). The known disease status of sows was regressed on the traits number born alive, number of losses as a combination of still birth and mummified piglets, and number of weaned piglets. The regression coefficients from this analysis were then used as weighting factors for derivation of an index measure called challenge load indicator. These weighting factors were derived with i) a two-step approach using residuals or year-week solutions estimated from a previous step, and ii) a single-step approach using the trait values directly. Two types of models were used for each approach: a logistic regression model and a general additive model. The estimates of challenge load indicator were then compared based on their ability to detect PRRS outbreaks in a Test dataset consisting of records from 65,826 sows from 15 farms in the Netherlands. These farms differed from the Canadian farm with respect to PRRS virus strains, severity and frequency of outbreaks. The single-step approach using a general additive model was best and detected 14 out of the 15 outbreaks. This approach was then further validated using the third dataset consisting of reproduction records of 831,855 sows in 431 farms located in different countries in Europe and America. A total of 41 out of 48 outbreaks detected using data analysis were confirmed based on diagnostic information received from the farms. Among these, 30 outbreaks were due to PRRS while 11 were due to other diseases and challenging conditions. The results suggest that proposed method could be useful for estimation of challenge load and detection of challenge phases such as disease outbreaks.
    Isoflavone supplement composition and equol producer status affect gene expression in adipose tissue: a double-blind, randomized, placebo-controlled crossover trial in postmenopausal women
    Velpen, V. van der; Geelen, A. ; Hollman, P.C.H. ; Schouten, E.G. ; Veer, P. van 't; Afman, L.A. - \ 2014
    American Journal of Clinical Nutrition 100 (2014)5. - ISSN 0002-9165 - p. 1269 - 1277.
    in-vivo - glucose-metabolism - lipid-metabolism - soy isoflavones - phytoestrogens - profiles - protein - macrophage - insights - genotype
    Background: Isoflavone supplements, consumed by women experiencing menopausal symptoms, are suggested to have positive effects on menopause-related adiposity and cardiovascular disease risk profile, but discussions about their safety are still ongoing. Objective: The objective was to study the effects of an 8-wk consumption of 2 different isoflavone supplements compared with placebo on whole-genome gene expression in the adipose tissue of postmenopausal women. Design: This double-blind, randomized, placebo-controlled crossover intervention consisted of 2 substudies, one with a low-genistein (LG) supplement (56% daidzein + daidzin, 16% genistein + genistin, and 28% glycitein + glycitin) and the other with a high-genistein (HG) supplement (49% daidzein + daidzin, 41% genistein + genistin, and 10% glycitein + glycitin). Both supplements provided ~100 mg isoflavones/d (aglycone equivalents). After the 8-wk isoflavone and placebo period, whole-genome arrays were performed in subcutaneous adipose tissue of postmenopausal women (n = 26 after LG, n = 31 after HG). Participants were randomized by equol-producing phenotype, and data analysis was performed per substudy for equol producers and nonproducers separately. Results: Gene set enrichment analysis showed downregulation of expression of energy metabolism–related genes after LG supplementation (n = 24) in both equol-producing phenotypes and oppositely regulated expression for equol producers (down) and nonproducers (up) after HG supplementation (n = 31). Expression of inflammation-related genes was upregulated in equol producers but downregulated in nonproducers, independent of supplement type. Only 4.4–7.0% of the genes with significantly changed expression were estrogen responsive. Body weight, adipocyte size, and plasma lipid profile were not affected by isoflavone supplementation. Conclusions: Effects of isoflavones on adipose tissue gene expression were influenced by supplement composition and equol-producing phenotype, whereas estrogen-responsive effects were lacking. LG isoflavone supplementation resulted in a caloric restriction–like gene expression profile for both producer phenotypes and pointed toward a potential beneficial effect, whereas both supplements induced anti-inflammatory gene expression in equol producers.
    Sire evaluation for total number born in pigs using a genomic reaction norms approach
    Silva, F.F. ; Mulder, H.A. ; Knol, E.F. ; Lopes, M.S. ; Guimaraes, S.E.F. ; Lopes, P.S. ; Mathur, P.K. ; Viana, J.M.S. ; Bastiaansen, J.W.M. - \ 2014
    Journal of Animal Science 92 (2014)9. - ISSN 0021-8812 - p. 3825 - 3834.
    environment interaction - dairy-cattle - genetic-parameters - production traits - genotype - models - pedigree - matrices - merit - milk
    In the era of genome-wide selection (GWS), genotype-by-environment (G×E) interactions can be studied using genomic information, thus enabling the estimation of SNP marker effects and the prediction of genomic estimated breeding values (GEBVs) for young candidates for selection in different environments. Although G×E studies in pigs are scarce, the use of artificial insemination has enabled the distribution of genetic material from sires across multiple environments. Given the relevance of reproductive traits such as the total number born (TNB) and the variation in environmental conditions encountered by commercial dams, understanding G×E interactions can be essential to choose the best sires for different environments. The present work proposes a two-step reaction norm approach for G×E analysis using genomic information. The first step provided estimates of environmental effects (herd-year-season - HYS), and the second step provided estimates of the intercept and slope for the TNB across different HYS levels, obtained from the first step, using a random regression model. In both steps, pedigree (A) and genomic (G) relationship matrices were considered. The genetic parameters (variance components, h2 and genetic correlations) were very similar when estimated using the A and G relationship matrices. The reaction norm graphs showed considerable differences in environmental sensitivity between sires, indicating a reranking of sires in terms of genetic merit across the HYS levels. Based on the G matrix analysis, SNP by environment interactions were observed. For some SNPs, the effects increased at increasing HYS levels, while for others, the effects decreased at increasing HYS levels or showed no changes between HYS levels. Cross-validation analysis demonstrated better performance of the genomic approach with respect to traditional pedigrees for both the G×E and standard models. The genomic reaction norm model resulted in an accuracy of GEBVs for “juvenile” boars varying from 0.14 to 0.44 across different HYS levels, while the accuracy of the standard genomic prediction model, without reaction norms, varied from 0.09 to 0.28. These results show that it is important and feasible to consider G×E interactions in evaluations of sires using genomic prediction models and that genomic information can increase the accuracy of selection across environments.
    Eidtorial : Control of scrapie by selective breeding: what are we getting for free?
    Hagenaars, T.H.J. - \ 2014
    Veterinary Record 174 (2014). - ISSN 0042-4900 - p. 528 - 529.
    active surveillance - genotype - sheep
    Role of the Goat K222-PrPC Polymorphic variant in Prion Infection Resistance
    Aguilar-Calvo, P. ; Espinosa, J.C. ; Pintado, B. ; Gutiérrez-Adán, A. ; Alamilo, E. ; Miranda, A. ; Prieto, I. ; Bossers, A. ; Andreoletti, O. ; Torres, J.M. - \ 2014
    Journal of Virology 88 (2014)5. - ISSN 0022-538X - p. 2670 - 2676.
    bovine spongiform encephalopathy - protein gene polymorphisms - caprine prp gene - natural scrapie - classical scrapie - transgenic mice - sheep - identification - association - genotype
    The prion protein-encoding gene (prnp) strongly influences the susceptibility of small ruminants to transmissible spongiform encephalopathies (TSEs). Hence, selective breeding programs have been implemented to increase sheep resistance to scrapie. For goats, epidemiological and experimental studies have provided some association between certain polymorphisms of the cellular prion protein (PrPC) and resistance to TSEs. Among them, the Q/K polymorphism at PrPC codon 222 (Q/K222) yielded the most promising results. In this work, we investigated the individual effects of the K222-PrPC variant on the resistance/susceptibility of goats to TSEs. For that purpose, we generated two transgenic mouse lines, expressing either the Q222 (wild type) or K222 variant of goat PrPC. Both mouse lines were challenged intracerebrally with a panel of TSE isolates. Transgenic mice expressing the wild-type (Q222) allele were fully susceptible to infection with all tested isolates, whereas transgenic mice expressing similar levels of the K222 allele were resistant to all goat scrapie and cattle BSE isolates but not to goat BSE isolates. Finally, heterozygous K/Q222 mice displayed a reduced susceptibility to the tested panel of scrapie isolates. These results demonstrate a highly protective effect of the K222 variant against a broad panel of different prion isolates and further reinforce the argument supporting the use of this variant in breeding programs to control TSEs in goat herds. IMPORTANCE The objective of this study was to determine the role of the K222 variant of the prion protein (PrP) in the susceptibility/resistance of goats to transmissible spongiform encephalopathies (TSEs). Results showed that transgenic mice expressing the goat K222-PrP polymorphic variant are resistant to scrapie and bovine spongiform encephalopathy (BSE) agents. This protective effect was also observed in heterozygous Q/K222 animals. Therefore, the single amino acid exchange from Q to K at codon 222 of the cellular prion protein provides resistance against TSEs. All the results presented here support the view that the K222 polymorphic variant is a good candidate for selective breeding programs to control and eradicate scrapie in goat herds.
    A heritable antiviral RNAi response limits Orsay virus infection in Caenorhabditis elegans N2
    Sterken, M.G. ; Snoek, L.B. ; Bosman, K.J. ; Daamen, J. ; Riksen, J.A.G. ; Bakker, J. ; Pijlman, G.P. ; Kammenga, J.E. - \ 2014
    PLoS ONE 9 (2014)2. - ISSN 1932-6203
    c. elegans - gene-expression - interference - requirements - inheritance - environment - diversity - pathways - genotype - immunity
    Orsay virus (OrV) is the first virus known to be able to complete a full infection cycle in the model nematode species Caenorhabditis elegans. OrV is transmitted horizontally and its infection is limited by antiviral RNA interference (RNAi). However, we have no insight into the kinetics of OrV replication in C. elegans. We developed an assay that infects worms in liquid, allowing precise monitoring of the infection. The assay revealed a dual role for the RNAi response in limiting Orsay virus infection in C. elegans. Firstly, it limits the progression of the initial infection at the step of recognition of dsRNA. Secondly, it provides an inherited protection against infection in the offspring. This establishes the heritable RNAi response as anti-viral mechanism during OrV infections in C. elegans. Our results further illustrate that the inheritance of the anti-viral response is important in controlling the infection in the canonical wild type Bristol N2. The OrV replication kinetics were established throughout the worm life-cycle, setting a standard for further quantitative assays with the OrV-C. elegans infection model.
    A rapid and massive gene expression shift marking adolescent transition in C. elegans
    Snoek, L.B. ; Sterken, M.G. ; Volkers, R.J.M. ; Klatter, M. ; Bosman, K.J. ; Bevers, R.P.J. ; Riksen, J.A.G. ; Smant, G. ; Cossins, A.R. ; Kammenga, J.E. - \ 2014
    Scientific Reports 4 (2014). - ISSN 2045-2322
    caenorhabditis-elegans - natural variation - genome - populations - robustness - diversity - profiles - genotype - project - age
    Organismal development is the most dynamic period of the life cycle, yet we have only a rough understanding of the dynamics of gene expression during adolescent transition. Here we show that adolescence in Caenorhabditis elegans is characterized by a spectacular expression shift of conserved and highly polymorphic genes. Using a high resolution time series we found that in adolescent worms over 10,000 genes changed their expression. These genes were clustered according to their expression patterns. One cluster involved in chromatin remodelling showed a brief up-regulation around 50 h post-hatch. At the same time a spectacular shift in expression was observed. Sequence comparisons for this cluster across many genotypes revealed diversifying selection. Strongly up-regulated genes showed signs of purifying selection in non-coding regions, indicating that adolescence-active genes are constrained on their regulatory properties. Our findings improve our understanding of adolescent transition and help to eliminate experimental artefacts due to incorrect developmental timing.
    Variation among sows in response to porcine reproductive and respiratory syndrome
    Rashidi, H. ; Mulder, H.A. ; Mathur, P.K. ; Knol, E.F. ; Arendonk, J.A.M. van - \ 2014
    Journal of Animal Science 92 (2014)1. - ISSN 0021-8812 - p. 95 - 105.
    syndrome virus - syndrome prrs - dairy-cattle - tolerance - resistance - performance - infection - selection - genotype - models
    Porcine reproductive and respiratory syndrome (PRRS) is a viral disease with negative impacts on reproduction of sows. Genetic selection to improve the response of sows to PRRS could be an approach to control the disease. Determining sow response to PRRS requires knowing pathogen burden and sow performance. In practice, though, records of pathogen burden are unavailable. We develop a statistical method to distinguish healthy and disease phases and to develop a method to quantify sows’ responses to PRRS without having individual pathogen burden. We analyzed 10,910 sows with 57,135 repeated records of reproduction performance. Disease phases were recognized as strong deviation of herd-year-week estimates for reproduction traits using two methods: Method 1 used raw weekly averages of the herd; Method 2 used a linear model with fixed effects for seasonality, parity, and year, and random effects for herd-year-week and sow. The variation of sows in response to PRRS was quantified using 2 models on the traits number of piglets born alive (NBA) and number of piglets born dead (LOSS): 1) bivariate model considering the trait in healthy and disease phases as different traits, and 2) reaction norm model modeling the response of sows as a linear regression of the trait on herd-year-week estimates of NBA. The linear model for NBA had the highest sensitivity (78%) for disease phases. Residual variances of both were more than doubled in the disease phase compared with the healthy phase. Trait correlations between healthy and disease phases deviated from unity (0.57 ± 0.13 – 0.87 ± 0.18). In the bivariate model, repeatabilities were lower in disease phase compared with healthy phase (0.07 ± 0.027 and 0.16 ± 0.005 for NBA; 0.07 ± 0.027 and 0.09 ± 0.004 for LOSS). The reaction norm model fitted the data better than the bivariate model based on Akaike’s information criterion, and had also higher predictive ability in disease phase based on cross validation. Our results show that the linear model is a practical method to distinguish between healthy and disease phases in farm data. We showed that there is variation among sows in response to PRRS, implying possibilities for selection, and the reaction norm model is a good model to study the response of animals toward diseases.
    WormQTL HD—a web database for linking human disease to natural variation data in C. elegans
    Velde, K.J. van der; Haan, M. de; Zych, K. ; Arends, D. ; Snoek, L.B. ; Kammenga, J.E. ; Jansen, R.C. ; Swertz, M.A. ; Li, Y. - \ 2014
    Nucleic acids research 42 (2014)D1. - ISSN 0305-1048 - p. D794 - D801.
    life-history traits - caenorhabditis-elegans - systems biology - stress-response - genotype - genome - qtl - environment - identification - polymorphism
    Interactions between proteins are highly conserved across species. As a result, the molecular basis of multiple diseases affecting humans can be studied in model organisms that offer many alternative experimental opportunities. One such organism— Caenorhabditis elegans—has been used to produce much molecular quantitative genetics and systems biology data over the past decade. We present WormQTLHD (Human Disease), a database that quantitatively and systematically links expression Quantitative Trait Loci (eQTL) findings in C. elegans to gene–disease associations in man. WormQTLHD, available online at, is a user-friendly set of tools to reveal functionally coherent, evolutionary conserved gene networks. These can be used to predict novel gene-to-gene associations and the functions of genes underlying the disease of interest. We created a new database that links C. elegans eQTL data sets to human diseases (34 337 gene–disease associations from OMIM, DGA, GWAS Central and NHGRI GWAS Catalogue) based on overlapping sets of orthologous genes associated to phenotypes in these two species. We utilized QTL results, high-throughput molecular phenotypes, classical phenotypes and genotype data covering different developmental stages and environments from WormQTL database. All software is available as open source, built on MOLGENIS and xQTL workbench.
    Quantitative genetic analysis of responses to larval food limitation in a polyphenic butterfly indicates environment- and trait-specific effects
    Saastamoinen, M. ; Brommer, J.E. ; Brakefield, P.M. ; Zwaan, B.J. - \ 2013
    Ecology and Evolution 3 (2013)10. - ISSN 2045-7758 - p. 3576 - 3589.
    bicyclus-anynana - phenotypic plasticity - life-history - adaptive responses - reaction norms - evolution - growth - genotype - evolvability - canalization
    Different components of heritability, including genetic variance (VG), are influenced by environmental conditions. Here, we assessed phenotypic responses of life-history traits to two different developmental conditions, temperature and food limitation. The former represents an environment that defines seasonal polyphenism in our study organism, the tropical butterfly Bicyclus anynana, whereas the latter represents a more unpredictable environment. We quantified heritabilities using restricted maximum likelihood (REML) procedures within an “Information Theoretical” framework in a full-sib design. Whereas development time, pupal mass, and resting metabolic rate showed no genotype-by-environment interaction for genetic variation, for thorax ratio and fat percentage the heritability increased under the cool temperature, dry season environment. Additionally, for fat percentage heritability estimates increased under food limitation. Hence, the traits most intimately related to polyphenism in B. anynana show the most environmental-specific heritabilities as well as some indication of cross-environmental genetic correlations. This may reflect a footprint of natural selection and our future research is aimed to uncover the genes and processes involved in this through studying season and condition-dependent gene expression
    Effect of predictor traits on accuracy of genomic breeding values for feed intake based on a limited cow reference population
    Pszczola, M.J. ; Veerkamp, R.F. ; Haas, Y. de; Wall, E. ; Strabel, T. ; Calus, M.P.L. - \ 2013
    Animal 7 (2013)11. - ISSN 1751-7311 - p. 1759 - 1768.
    dairy-cattle - selection - genotype - system - information - parameters - efficiency - fertility - holsteins - animals
    The genomic breeding value accuracy of scarcely recorded traits is low because of the limited number of phenotypic observations. One solution to increase the breeding value accuracy is to use predictor traits. This study investigated the impact of recording additional phenotypic observations for predictor traits on reference and evaluated animals on the genomic breeding value accuracy for a scarcely recorded trait. The scarcely recorded trait was dry matter intake (DMI, n = 869) and the predictor traits were fat-protein-corrected milk (FPCM, n = 1520) and live weight (LW, n = 1309). All phenotyped animals were genotyped and originated from research farms in Ireland, the United Kingdom and the Netherlands. Multi-trait REML was used to simultaneously estimate variance components and breeding values for DMI using available predictors. In addition, analyses using only pedigree relationships were performed. Breeding value accuracy was assessed through cross-validation (CV) and prediction error variance (PEV). CV groups (n = 7) were defined by splitting animals across genetic lines and management groups within country. With no additional traits recorded for the evaluated animals, both CV- and PEV-based accuracies for DMI were substantially higher for genomic than for pedigree analyses (CV: max. 0.26 for pedigree and 0.33 for genomic analyses; PEV: max. 0.45 and 0.52, respectively). With additional traits available, the differences between pedigree and genomic accuracies diminished. With additional recording for FPCM, pedigree accuracies increased from 0.26 to 0.47 for CV and from 0.45 to 0.48 for PEV. Genomic accuracies increased from 0.33 to 0.50 for CV and from 0.52 to 0.53 for PEV. With additional recording for LW instead of FPCM, pedigree accuracies increased to 0.54 for CV and to 0.61 for PEV. Genomic accuracies increased to 0.57 for CV and to 0.60 for PEV. With both FPCM and LW available for evaluated animals, accuracy was highest (0.62 for CV and 0.61 for PEV in pedigree, and 0.63 for CV and 0.61 for PEV in genomic analyses). Recording predictor traits for only the reference population did not increase DMI breeding value accuracy. Recording predictor traits for both reference and evaluated animals significantly increased DMI breeding value accuracy and removed the bias observed when only reference animals had records. The benefit of using genomic instead of pedigree relationships was reduced when more predictor traits were used. Using predictor traits may be an inexpensive way to significantly increase the accuracy and remove the bias of (genomic) breeding values of scarcely recorded traits such as feed intake.
    Letter: Search for possible additional reservoirs for human Q fever, the Netherlands
    Roest, H.I.J. ; Solt, C.B. van; Tilburg, J.J.H.C. ; Klaassen, C.H. ; Hovius, E.K. ; Roest, F.T.F. ; Vellema, P. ; Brom, R. van der; Zijderveld, F.G. van - \ 2013
    Emerging Infectious Diseases 19 (2013)5. - ISSN 1080-6040 - p. 834 - 835.
    coxiella-burnetii - epidemic - genotype - outbreak
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