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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    An equation to predict accuracy of multi-breed genomic prediction model with multiple random effects
    Raymond, Biaty ; Bouwman, A.C. ; Wientjes, Y.C.J. ; Schrooten, C. ; Houwing-Duistermaat, Jeanine J. ; Veerkamp, R.F. - \ 2018
    In: Book of Abstracts of the 69th Annual Meeting of the European Federation of Animal Science. - Wageningen : Wageningen Academic Publishers (Book of abstracts 24) - ISBN 9789086863235 - p. 121 - 121.
    Genomic prediction across populations, using pre-selected markers and differential weight models
    Raymond, Biaty ; Bouwman, A.C. ; Schrooten, Chris ; Houwing-Duistermaat, Jeanine J. ; Veerkamp, R.F. - \ 2018
    In: Proceedings of the World Congress on Genetics Applied to Livestock Production - 6 p.
    Genomic prediction (GP) in numerically small breeds is limited due to the requirement for a large reference set. Across breed prediction has not been very successful either. Our objective was to test alternative models for across breed and multi-breed GP in a small Jersey population, utilizing prior information on marker causality. We used data on 596 Jersey bulls from new Zealand and 5503 Holstein bulls from the Netherlands, all of which had deregressed proofs for stature. Two sets of genotype data were used, one containing 357 potential causal markers identified from a multi-breed meta-GWAS on stature (top markers), while the other contained 48,912 markers on the custom 50k chip, excluding the top markers. We used models in which only one GRM (either top markers, 50k, or top plus 50k markers combined) was fitted, and models in which two GRMs (both the top and 50k) were fitted simultaneously, however with different variance components to weight the GRMs differently. Moreover, we estimated the genetic correlation(s) between the breeds (for each GRM) using a multi-trait GP model, which implicitly weights the contribution of one breed’s information to another. Across breed, we observed low accuracies of GP when the 50k markers were fitted alone (0.06) or when the top markers were added to 50k (0.15). Higher accuracy was obtained when only the top markers were fitted (0.21), whereas the highest accuracy was obtained when fitting 50k and top markers simultaneously as two independent GRMs (0.25). Multi-breed prediction outperformed both within and across breed prediction with accuracies ranging from 0.34 to 0.45, with the same trend as in across breed prediction. Based on our results, the best approach for across and multi-breed GP is to fit models that are able to isolate and differentially weight the most important markers for the trait. Keywords: Across breed genomic prediction, marker pre-selection, multi-trait model, sequence data.
    Genomic prediction for numerically small breeds, using models with pre-selected and differentially weighted markers
    Raymond, Biaty ; Bouwman, Aniek C. ; Wientjes, Yvonne C.J. ; Schrooten, Chris ; Houwing-Duistermaat, Jeanine ; Veerkamp, Roel F. - \ 2018
    Genetics, Selection, Evolution 50 (2018)1. - ISSN 0999-193X

    Background: Genomic prediction (GP) accuracy in numerically small breeds is limited by the small size of the reference population. Our objective was to test a multi-breed multiple genomic relationship matrices (GRM) GP model (MBMG) that weighs pre-selected markers separately, uses the remaining markers to explain the remaining genetic variance that can be explained by markers, and weighs information of breeds in the reference population by their genetic correlation with the validation breed. Methods: Genotype and phenotype data were used on 595 Jersey bulls from New Zealand and 5503 Holstein bulls from the Netherlands, all with deregressed proofs for stature. Different sets of markers were used, containing either pre-selected markers from a meta-genome-wide association analysis on stature, remaining markers or both. We implemented a multi-breed bivariate GREML model in which we fitted either a single multi-breed GRM (MBSG), or two distinct multi-breed GRM (MBMG), one made with pre-selected markers and the other with remaining markers. Accuracies of predicting stature for Jersey individuals using the multi-breed models (Holstein and Jersey combined reference population) was compared to those obtained using either the Jersey (within-breed) or Holstein (across-breed) reference population. All the models were subsequently fitted in the analysis of simulated phenotypes, with a simulated genetic correlation between breeds of 1, 0.5, and 0.25. Results: The MBMG model always gave better prediction accuracies for stature compared to MBSG, within-, and across-breed GP models. For example, with MBSG, accuracies obtained by fitting 48,912 unselected markers (0.43), 357 pre-selected markers (0.38) or a combination of both (0.43), were lower than accuracies obtained by fitting pre-selected and unselected markers in separate GRM in MBMG (0.49). This improvement was further confirmed by results from a simulation study, with MBMG performing on average 23% better than MBSG with all markers fitted. Conclusions: With the MBMG model, it is possible to use information from numerically large breeds to improve prediction accuracy of numerically small breeds. The superiority of MBMG is mainly due to its ability to use information on pre-selected markers, explain the remaining genetic variance and weigh information from a different breed by the genetic correlation between breeds.

    Utility of whole-genome sequence data for across-breed genomic prediction
    Raymond, Biaty ; Bouwman, Aniek C. ; Schrooten, Chris ; Houwing-Duistermaat, Jeanine ; Veerkamp, Roel F. - \ 2018
    Genetics, Selection, Evolution 50 (2018). - ISSN 0999-193X

    Background: Genomic prediction (GP) across breeds has so far resulted in low accuracies of the predicted genomic breeding values. Our objective was to evaluate whether using whole-genome sequence (WGS) instead of low-density markers can improve GP across breeds, especially when markers are pre-selected from a genome-wide association study (GWAS), and to test our hypothesis that many non-causal markers in WGS data have a diluting effect on accuracy of across-breed prediction. Methods: Estimated breeding values for stature and bovine high-density (HD) genotypes were available for 595 Jersey bulls from New Zealand, 957 Holstein bulls from New Zealand and 5553 Holstein bulls from the Netherlands. BovineHD genotypes for all bulls were imputed to WGS using Beagle4 and Minimac2. Genomic prediction across the three populations was performed with ASReml4, with each population used as single reference and as single validation sets. In addition to the 50k, HD and WGS, markers that were significantly associated with stature in a large meta-GWAS analysis were selected and used for prediction, resulting in 10 prediction scenarios. Furthermore, we estimated the proportion of genetic variance captured by markers in each scenario. Results: Across breeds, 50k, HD and WGS markers resulted in very low accuracies of prediction ranging from - 0.04 to 0.13. Accuracies were higher in scenarios with pre-selected markers from a meta-GWAS. For example, using only the 133 most significant markers in 133 QTL regions from the meta-GWAS yielded accuracies ranging from 0.08 to 0.23, while 23,125 markers with a - log10(p) higher than 7 resulted in accuracies of up 0.35. Using WGS data did not significantly improve the proportion of genetic variance captured across breeds compared to scenarios with few but pre-selected markers. Conclusions: Our results demonstrated that the accuracy of across-breed GP can be improved by using markers that are pre-selected from WGS based on their potential causal effect. We also showed that simply increasing the number of markers up to the WGS level does not increase the accuracy of across-breed prediction, even when markers that are expected to have a causal effect are included.

    Utility of whole genome sequence data for across breed genomic prediction
    Raymond, Biaty ; Bouwman, Aniek ; Schrooten, C. ; Houwing-Duistermaat, Jeanine J. ; Veerkamp, R.F. - \ 2017
    - p. 143 - 143.
    Trends in genome-wide and region-specific diversity reflect Holstein Friesian breeding history
    Estimation of metabolite networks with regard to a specific covariable : applications to plant and human data
    Bartzis, Georgios ; Deelen, Joris ; Maia, Julio ; Ligterink, Wilco ; Hilhorst, Henk W.M. ; Houwing-Duistermaat, Jeanine J. ; Eeuwijk, Fred van; Uh, Hae Won - \ 2017
    Metabolomics 13 (2017)11. - ISSN 1573-3882 - 17 p.
    Incorporating relevant information - Metabolites - Network reconstruction - Study design

    Introduction: In systems biology, where a main goal is acquiring knowledge of biological systems, one of the challenges is inferring biochemical interactions from different molecular entities such as metabolites. In this area, the metabolome possesses a unique place for reflecting “true exposure” by being sensitive to variation coming from genetics, time, and environmental stimuli. While influenced by many different reactions, often the research interest needs to be focused on variation coming from a certain source, i.e. a certain covariable Xm. Objective: Here, we use network analysis methods to recover a set of metabolite relationships, by finding metabolites sharing a similar relation to Xm. Metabolite values are based on information coming from individuals’ Xm status which might interact with other covariables. Methods: Alternative to using the original metabolite values, the total information is decomposed by utilizing a linear regression model and the part relevant to Xm is further used. For two datasets, two different network estimation methods are considered. The first is weighted gene co-expression network analysis based on correlation coefficients. The second method is graphical LASSO based on partial correlations. Results: We observed that when using the parts related to the specific covariable of interest, resulting estimated networks display higher interconnectedness. Additionally, several groups of biologically associated metabolites (very large density lipoproteins, lipoproteins, etc.) were identified in the human data example. Conclusions: This work demonstrates how information on the study design can be incorporated to estimate metabolite networks. As a result, sets of interconnected metabolites can be clustered together with respect to their relation to a covariable of interest.

    Natural minus-strand RNAs of alfalfa mosaic virus as in vitro templates for viral RNA polymerase. 3'-Terminal non-coded guanosine and coat protein are insufficient factors for full-size plus-strand synthesis
    Houwing, C.J. ; Huis in 't Veld, M. ; Zuidema, D. ; Graaff, M. de; Jaspars, E.M.J. - \ 2001
    Archives of Virology 146 (2001). - ISSN 0304-8608 - p. 571 - 588.
    Replication complexes of alfalfa mosaic virus produce in vivo large quantities of plus-strand RNAs, but this production is fully dependent on the presence of coat protein. In order to study this process of RNA-dependent and coat protein-regulated RNA synthesis we have isolated the three natural minus-strand RNAs (containing any posttranscriptional modification that might have occurred) and have tested them for coat protein binding sites and template activity in an in vitro system with the viral RNA polymerase. The enzyme was prepared by an advanced isolation procedure. All three minus strands had a single non-coded G at their 3' terminus. They were not able to withdraw coat protein subunits from virions as free virion RNAs do. No sites protected by coat protein against ribonuclease T1 degradation were found. Two large T1 oligonucleotides from minus RNA 1 and one from minus RNA 3 were bound by coat protein to Millipore filters. Except for minus RNA 3 which caused a minute amount of full-size plus strand to be synthesized, the minus strands did not function as templates for full-size complementary strands. On the other hand, they gave rise to a number of well-defined shorter products, the synthesis of which was stimulated by the addition of coat protein. These products could not be elongated by a chase treatment and were probably the result of internal initiations. It is concluded that, although posttranscriptional modifications of the template and the presence of coat protein may be necessary factors for plus-strand RNA synthesis, they are certainly not sufficient. Our purified in vitro system needs further sophistication.
    Biological and abiotic factors influencing the settlement and survival of Salicornia dolichostachya in the intertidal pioneer zone
    Houwing, E.J. ; Duin, W.E. van; Smit-van der Waal, Y. ; Dijkema, K.S. ; Terwindt, J.H.J. - \ 1999
    Mangroves and salt marshes 3 (1999). - ISSN 1386-3509 - p. 197 - 206.
    Degradation of Toluene and Trichloroethylene by Burkholderia cepacia G4 in Growth-Limited Fed-Batch Culture.
    Mars, A. ; Houwing, J. ; Dolfing, J. ; Janssen, D.B. - \ 1996
    Applied and Environmental Microbiology 62 (1996). - ISSN 0099-2240 - p. 886 - 891.
    Burkholderia (Pseudomonas) cepacia G4 was cultivated in a fed-batch bioreactor on either toluene or toluene plus trichloroethylene (TCE). The culture was allowed to reach a constant cell density under conditions in which the amount of toluene supplied equals the maintenance energy demand of the culture. Compared with toluene only, the presence of TCE at a toluene/TCE ratio of 2.3 caused a fourfold increase in the specific maintenance requirement for toluene from 22 to 94 nmol mg of cells (dry weight)(sup-1) h(sup-1). During a period of 3 weeks, approximately 65% of the incoming TCE was stably converted to unidentified products from which all three chlorine atoms were liberated. When toluene was subsequently omitted from the culture feed while TCE addition continued, mutants which were no longer able to grow on toluene or to degrade TCE appeared. These mutants were also unable to grow on phenol or m- or o-cresol but were still able to grow on catechol and benzoate. Plasmid analysis showed that the mutants had lost the plasmid involved in toluene monooxygenase formation (pTOM). Thus, although strain G4 is much less sensitive to TCE toxicity than methanotrophs, deleterious effects may still occur, namely, an increased maintenance energy demand in the presence of toluene and plasmid loss when no toluene is added.
    Salt marshes and sea level rise: boundary conditions for the growth of Salicornia dolichostachya
    Smit-van der Waaij, Y. ; Houwing, E.J. ; Duin, W.E. van; Dijkema, K.S. ; Smit, J.P.C. - \ 1995
    Unknown Publisher - 54 p.
    Salt marshes and sea level rise: plant dynamics in relation to accretion enhancement techniques
    Houwing, E.J. ; Waaij, Y. van der; Terwindt, J.H.J. ; Augustinus, P.G.E.F. ; Dijkema, K.S. ; Bossinade, J.H. - \ 1995
    Utrecht : IMAU - 146
    klimaatverandering - paleoklimatologie - wetlands - polders - zoutmoerassen - marien milieu - plantensuccessie - vegetatie - zeeniveau - waddenzee - climatic change - palaeoclimatology - salt marshes - marine environment - plant succession - vegetation - sea level - wadden sea
    The effect of chronic stress on respoductive hormones, cortisol and prolactin during the oestrous cycle of the pig.
    Janssens, C.J.J.G. ; Houwing, H. ; Helmond, F.A. ; Wiegant, V.M. - \ 1993
    In: Abstract 4th Int. Conf. Pig reproduction, Columbia, Mo, USA - p. 87 - 87.
    Influence of chronic stress on cortisol, prolactin and reproductive hormones during the oestrous cycle of the pig.
    Janssens, C.J.J.G. ; Houwing, H. ; Helmond, F.A. ; Wiegant, V.M. - \ 1993
    European Journal of Physiology 424 (1993). - p. R5 - R5.
    Onderzoek naar alternatieven voor dinoseb voor de loofdoding van aardappelenDevelopment of alternatives for dinoseb as a desiccant of potato foliage
    Loon, C.D. van; Houwing, J.F. - \ 1991
    In: Jaarboek 1987-1992 : verslagen van in 1987-1992 afgesloten onderzoekprojecten op Regionale Onderzoek Centra en het PAGV Lelystad : Proefstation voor de Akkerbouw en de Groenteteelt in de Vollegrond (Publikatie / Proefstation voor de Akkerbouw en de Groenteteelt in de Vollegrond, Regionale Onderzoekcentra no. 38-64) - p. 33 - 39.
    oogsten - loofvernietiging - nederland - prestatieniveau - aardappelen - kwaliteit - pootaardappelen - solanum tuberosum - aftoppen - harvesting - haulm destruction - netherlands - performance - potatoes - quality - seed potatoes - solanum tuberosum - topping
    Invloed van chemische en mechanische loofdoding op de kwaliteit van poot- en consumptieaardappelen
    Plasma concentrations of cortisol during the estrous cycle in pigs.
    Janssens, C.J.J.G. ; Houwing, H. ; Helmond, F.H. ; Oudenaarden, C. ; Wiegant, V.M. - \ 1990
    In: Proc. 31st Dutch Federation Meeting, Leiden - p. 135 - 135.
    Increased plasma cortisol levels in tethered gilts.
    Janssens, C.J.J.G. ; Houwing, H. ; Helmond, F.H. ; Oudenaarden, C.P.J. ; Wiegant, V.M. - \ 1990
    In: Proc. Summermeeting Soc. Veterinary Ethology, Montecatini Terme, Italië (1990) Poster 72
    De invloed van de fysiologische leeftijd van pootgoed op de groei en opbrengst van aardappelen
    Loon, C.D. van; Houwing, J.F. - \ 1989
    In: Jaarboek 1987-1992 : verslagen van in 1987-1992 afgesloten onderzoekprojecten op Regionale Onderzoek Centra en het PAGV Lelystad : Proefstation voor de Akkerbouw en de Groenteteelt in de Vollegrond (Publikatie / Proefstation voor de Akkerbouw en de Groenteteelt in de Vollegrond, Regionale Onderzoekcentra no. 38-64) - p. 18 - 22.
    gewassen - groei - aardappelen - solanum tuberosum - oogsttoename - oogstverliezen - opbrengsten - crops - growth - potatoes - solanum tuberosum - yield increases - yield losses - yields
    Optimalisering van de stikstofvoeding van consumptie - aardappelen
    Loon, C.D. van; Houwing, J.F. - \ 1989
    Lelystad : PAGV (Publikatie / Proefstation voor de Akkerbouw en de Groenteteelt in de Vollegrond nr. 42) - 90
    stikstof - aardappelen - solanum tuberosum - nitrogen - potatoes - solanum tuberosum
    Op basis van literatuur lijkt het mogelijk om de stikstofbemesting te optimaliseren d.m.v. een middelmatige stikstofgift in het voorjaar, zo nodig gevolgd door een aanvullende bemesting bij een dreigend tekort bij het gewas. Vaststelling van een eventueel tekort lijkt goed mogelijk via bepaling van het nitraatgehalte in bladstelen gedurende de kritieke periode in het groeiseizoen. Om de bruikbaarheid van dit systeem onder Nederlandse omstandigheden vast te stellen is een onderzoek in 2 fasen uitgevoerd: 1e. het vaststellen gedurende het groeiseizoen van de minimale nitraatgehalten in de bladstelen nodig voor het behalen van een optimale knolopbrengst; 2e. toetsing van het op bladanalyse gebaseerde systeem van stikstofoptimalisatie in proeven met variabele stikstoftoediening. Tevens zijn stikstofdelingssystemen vergeleken en is de Merckoquant nitraatsneltest beproefd
    Invloed van de verkruimeling van de grond op verslemping en zuurstofgehalte in relatie tot de groei van aardappelen
    Ridder, J.K. ; Bus, C.B. ; Houwing, J.F. - \ 1988
    Lelystad : Proefstation voor de Akkerbouw en de Groenteteelt in de Vollegrond (Verslag / Proefstation voor de Akkerbouw en de Groenteteelt in de Vollegrond nr. 76) - 24
    gewassen, groeifasen - groeistadia - verbetering - nederland - aardappelen - zand - bodemverbeteraars - bodemdegradatie - bodemstructuur - solanum tuberosum - crop growth stage - growth stages - improvement - netherlands - potatoes - sand - soil conditioners - soil degradation - soil structure - solanum tuberosum
    De invloed van beregening op pootaardappelen bij hoge plantdichtheden
    Bus, C.B. ; Houwing, J.F. - \ 1987
    In: Jaarboek 1987-1992 : verslagen van in 1987-1992 afgesloten onderzoekprojecten op Regionale Onderzoek Centra en het PAGV Lelystad : Proefstation voor de Akkerbouw en de Groenteteelt in de Vollegrond (Publikatie / Proefstation voor de Akkerbouw en de Groenteteelt in de Vollegrond, Regionale Onderzoekcentra no. 38-64) - p. 13 - 16.
    plantdichtheid - rijenafstanden - pootaardappelen - beregening met sproeiers - plant density - row spacing - seed potatoes - sprinkler irrigation
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