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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    Waardekaarten van: Haisborough, Hammond & Winterton, North Norfolk Sandbanks & Saturn Reef
    Hintzen, N.T. - \ 2017
    IJmuiden : Wageningen Marine Research (Wageningen Marine Research rapport C009/17) - 18
    vissen - visserij - waarden - kaarten - natura 2000 - groot-brittannië - kustgebieden - fishes - fisheries - values - maps - natura 2000 - great britain - coastal areas
    Langs de Engelse kust staan een aantal gebieden op de UK Natura 2000 agenda voor sluiting voor de Nederlandse demersale vloot. Wageningen Marine Research bestudeerde in hoeverre de Nederlandse vloot actief was in dit gebied en hoe de voorgenomen te sluiten gebieden overlappen met voor de visserij interessante visgronden. Een grotere opbrengst (factor 3) wordt gehaald uit het North Norfolk Sandbanks & Saturn Reef gebied (dit is één gebied) ten opzichte van het Haisborough, Hammond and Winterton gebied (dit is ook één gebied). Vooral tong word in dit eerste gebied gevangen terwijl scholvangsten groter zijn in het tweede gebied. De voornaamste visgronden die interessant zijn voor de Nederlandse sector zijn niet opgenomen in de voorgenomen te sluiten gebieden, waarbij juist voor de visserij interessante delen van de totale zoekgebieden niet aangemerkt zijn als te sluiten gebied.
    Consumer interest in social sustainability issues of whitefish from capture fisheries in the north-east Atlantic
    Veldhuizen, Linda J.L. ; Lans, Ivo A. van der; Berentsen, Paul B.M. ; Boer, Imke J.M. de; Bokkers, Eddy - \ 2017
    Fish and Fisheries 18 (2017)3. - ISSN 1467-2960 - p. 527 - 542.
    Choice modelling - concern - consumer preferences - relevance - trust - values

    Capture fisheries in the north-east Atlantic account for approximately 10% of all fish consumed from capture fisheries globally. The literature shows that consumers show considerable interest in social sustainability of products in general and of fish specifically. This interest, however, has not yet been investigated for fish from the north-east Atlantic. The first objective of this study, therefore, was to investigate whether consumers are interested in social sustainability issues of whitefish from the north-east Atlantic by determining preferences for four social sustainability issues with distinct benefits in relation to a known reference point (i.e. approach to overfishing). The second objective of this study was to determine to what degree case-specific and general psychographic consumer characteristics explain preferences for these issues. Choice modelling results from an online survey among 457 Dutch consumers show that consumers have the strongest preference for the environmental sustainability issue approach to overfishing. In addition, results on the social sustainability issues showed that consumers prefer fish welfare over product quality, worker safety and local employment, indicating that in this case, consumers place animal benefits over personal, worker and community benefits. The case-specific psychographic characteristic concern contributed most to explaining preferences for the environmental sustainability issue, whereas the general psychographic characteristic personal relevance contributed most to explaining preferences for the social sustainability issues. This result is likely explained by the principal focus on MSC certification in markets for fish products, which caused consumers to form opinions (e.g. concern) on overfishing, but not on social sustainability.

    Fighting over water values : diverse framings of flower and food production with communal irrigation in the Ecuadorian Andes
    Mena-Vásconez, Patricio ; Vincent, Linden ; Vos, Jeroen ; Boelens, Rutgerd - \ 2017
    Water International 42 (2017)4. - ISSN 0250-8060 - p. 443 - 461.
    communal water resource management - Community irrigation - Ecuador - flowers - framing - values

    Water management studies often overlook community diversity, different stakeholders’ values, and frames to claim water rights. Using a political-ecology approach, this article examines an irrigation system in Ecuador’s highlands via Fraser’s principles of justice (recognition, representation, redistribution). Large flower companies and indigenous smallholders frame their arguments differently to legitimize water allocation claims. Framing is effective when it resonates with other stakeholders’ values. Some unexpected findings are explained: most of the water is still used by large companies since communities took control; rules regarding water use differ greatly among sectors in the system; and small flower producers have been appearing recently.

    Waardekaarten Markham’s Triangle & Hornsea 3
    Machiels, Marcel - \ 2016
    Wageningen : Wageningen Marine Research (Wageningen Marine Research rapport C085/16) - 15
    visserij - waarden - tabellen - gegevensanalyse - fisheries - values - tables - data analysis
    Diverging realities: how framing, values and water management are interwoven in the Albufera de Valencia wetland in Spain
    Hulshof, Mieke ; Vos, Jeroen - \ 2016
    Water International 41 (2016)1. - ISSN 0250-8060 - p. 107 - 124.
    Albufera de Valencia - framing - hydrosocial territory - Spain - values - water management - wetland
    The Albufera de Valencia is a coastal wetland in south-eastern Spain that has suffered from low water quality since the 1970s. This article explores two divergent framings or imaginaries of the Albufera as a hydrosocial territory. The first, the agro-economic waterscape framing, focuses on the economic and cultural importance of rice production. The second, the idyllic waterscape framing, emphasizes environmental values. The agro-economic waterscape frame is dominant in current water management. Stakeholders deploy highly diverging realities, and the political playing field is not level. Recognition and empowerment are the first steps towards more sustainable water management in the Albufera.
    De waarde van waarden
    Oosterhoff, W. ; Stokkers, G.J. ; Smit, A.B. - \ 2015
    V-focus 12 (2015)2. - ISSN 1574-1575 - p. 32 - 33.
    agrarische bedrijfsvoering - ondernemerschap - ondernemingen - persoonlijke ontwikkeling - bewustwording - waarden - economische samenwerking - farm management - entrepreneurship - enterprises - personal development - conscientization - values - economic cooperation
    Agrarische ondernemers schakelen voortdurend tussen de drie O’s: Ondernemer, Onderneming en Omgeving. De laatste jaren komt er steeds meer aandacht voor de relatie tussen onderneming en omgeving. We noemen dat omgevingsgericht ondernemen. Bij het Kenniscentrum Agrofood en Ondernemen in Dronten ligt de focus vooral op de ondernemer. Persoonlijke ontwikkeling van ondernemers in opleiding staat hoog in het vaandel. Onderdeel van die persoonlijke ontwikkeling is de bewustwording van de eigen waarden.
    Waardestellend onderzoek Renkumse landgoederen : themanummer over kennisco-creatie in wetenschapswinkelprojecten
    During, R. ; Jagt, P.D. van der; Kruit, J. - \ 2015
    Landschap : tijdschrift voor landschapsecologie en milieukunde 32 (2015)3. - ISSN 0169-6300 - p. 135 - 141.
    landgoederen - buitenplaatsen - participatie - waarden - conflict - kennisvalorisatie - samenwerking - estates - country estates - participation - values - conflict - knowledge exploitation - cooperation
    Een deel van de Nederlandse landschappen is ontworpen door landschapsarchitecten. Landschapsvorming is echter niet de enige functie van het ontwerp, betogen we in dit artikel. In een participatief ontwerpproces voor het Europaplein in Renkum bestudeerden we de verschillende functies van ontwerpen. Ondanks het feit dat die kunnen conflicteren, blijken ze op verschillende wijze een zeer productieve bijdrage te leveren aan het verloop van het proces.
    Waardekaarten Sylter Aussenriff
    Machiels, M.A.M. - \ 2015
    IJmuiden : IMARES (Rapport / IMARES Wageningen UR C129/15) - 11
    visserij - waarden - tabellen - boomkorvisserij - gegevensanalyse - fisheries - values - tables - beam trawling - data analysis
    Dit rapport is geschreven in opdracht van VisNed. IMARES is gevraagd om waardekaarten en tabellen te leveren van alle bodem beroerende Nederlandse visserijschepen binnen het gebied Sylter Außenriff.
    Impact of QTL properties on the accuracy of multi-breed genomic prediction
    Wientjes, Y.C.J. ; Calus, M.P.L. ; Goddard, M.E. ; Hayes, B.J. - \ 2015
    Genetics, Selection, Evolution 47 (2015). - ISSN 0999-193X
    dairy-cattle populations - residual feed-intake - complex traits - linkage disequilibrium - genotype imputation - data sets - selection - values - animals - reliability
    Background - Although simulation studies show that combining multiple breeds in one reference population increases accuracy of genomic prediction, this is not always confirmed in empirical studies. This discrepancy might be due to the assumptions on quantitative trait loci (QTL) properties applied in simulation studies, including number of QTL, spectrum of QTL allele frequencies across breeds, and distribution of allele substitution effects. We investigated the effects of QTL properties and of including a random across- and within-breed animal effect in a genomic best linear unbiased prediction (GBLUP) model on accuracy of multi-breed genomic prediction using genotypes of Holstein-Friesian and Jersey cows. Methods - Genotypes of three classes of variants obtained from whole-genome sequence data, with moderately low, very low or extremely low average minor allele frequencies (MAF), were imputed in 3000 Holstein-Friesian and 3000 Jersey cows that had real high-density genotypes. Phenotypes of traits controlled by QTL with different properties were simulated by sampling 100 or 1000 QTL from one class of variants and their allele substitution effects either randomly from a gamma distribution, or computed such that each QTL explained the same variance, i.e. rare alleles had a large effect. Genomic breeding values for 1000 selection candidates per breed were estimated using GBLUP modelsincluding a random across- and a within-breed animal effect. Results - For all three classes of QTL allele frequency spectra, accuracies of genomic prediction were not affected by the addition of 2000 individuals of the other breed to a reference population of the same breed as the selection candidates. Accuracies of both single- and multi-breed genomic prediction decreased as MAF of QTL decreased, especially when rare alleles had a large effect. Accuracies of genomic prediction were similar for the models with and without a random within-breed animal effect, probably because of insufficient power to separate across- and within-breed animal effects. Conclusions - Accuracy of both single- and multi-breed genomic prediction depends on the properties of the QTL that underlie the trait. As QTL MAF decreased, accuracy decreased, especially when rare alleles had a large effect. This demonstrates that QTL properties are key parameters that determine the accuracy of genomic prediction.
    Duurzaamheid van melkveebedrijven in Noord-Nederland : variatie in milieu-indicatoren tussen bedrijven in opdracht van Greenlincs
    Daatselaar, Co - \ 2015
    sustainable animal husbandry - dairy farming - north netherlands - sustainability indicators - sustainable development - values - performance traits - cattle husbandry
    Factoren die het foerageergedrag van honingbijen bepalen (deel I); Dracht in Nederland (cultuurgewassen en wilde planten) (deel II)
    Steen, J.J.M. van der; Cornelissen, B. - \ 2015
    Wageningen : Plant Research International, Wageningen UR (Rapport 606) - 94
    apis mellifera - honingbijen - diergedrag - bestuivers (dieren) - dansen (bijen) - door bijen verzameld stuifmeel - seizoenen - drachtplanten - veldgewassen - vruchtbomen - openbaar groen - wegbermplanten - wilde planten - waarden - apis mellifera - honey bees - animal behaviour - pollinators - dances - bee-collected pollen - seasons - pollen plants - field crops - fruit trees - public green areas - roadside plants - wild plants - values
    Om een inschatting te kunnen maken van het risico dat honingbijen blootgesteld worden aan gewasbeschermingsmiddelen, andere stoffen zoals atmosferische depositie van fijnstof en organismen zoals plantpathogene microorganismen, is in opdracht van het Ministerie van EZ/Landbouw een samenvatting gemaakt van de informatie, beschikbaar over de aantrekkelijkheid van Nederlandse gewassen voor honingbijen (Apis mellifera). De opdracht is vorm gegeven in twee delen. Deel I is een beschrijving van het bijenvolk met de focus op het foerageergedrag, gevolgd door een beschrijving van factoren die het foerageergedrag bepalen, hoe de bijen hun omgeving exploreren en exploiteren en een lijst met kengetallen over het foerageren van honingbijen. Deel II geeft een overzicht van cultuurgewassen en wilde planten met bijbehorende waarden van nectar en stuifmeel voor honingbijen met bloeitijden en verwijzingen naar goede drachtplantenboeken. Hieronder zijn puntsgewijs relevante zaken gegeven die in het rapport verder uitgewerkt zijn. Honingbijen zijn voor hun voedsel (nectar en stuifmeel) volledig afhankelijk van planten. Het foerageergedrag en de voorkeur voor gewassen hangt af van de behoefte in het volk en de aantrekkelijkheid van het gewas als nectar- en stuifmeelbron. Het foerageergedrag wordt voortdurend aangepast aan de beschikbare dracht en de behoeften van het bijenvolk. Honingbijen leven in volken die variëren in grootte van ~7000 individuen in het voorjaar (maart) tot 20 000 à 30 000 in de zomer en weer afnemend in oktober. In het actieve foerageer- en broedseizoen is een derde tot een vierde deel foerageerster (haalbij). In de loop van een seizoen halen de bijen ten behoeve van het volk 25 kg water, 20 - 30 kg stuifmeel, 125 kg nectar en kleine hoeveelheden hars (propolis). Voor het halen van deze voedselcomponenten vliegen bijen tot 2 km voor water, tot 6 km voor stuifmeel en tot 12 à 13 km voor nectar. Meestal zullen de vluchten echter beperkt zijn tot 600-800 meter. De foerageerafstanden zijn in de zomer (juli – augustus) langer dan in het voorjaar (maart – mei). Met andere woorden, in het voorjaar wordt het voedsel in een kleiner gebied verzameld dan in de zomer. Het risico dat bijen aan een bespuiting zullen worden blootgesteld zou daarom na half juni hoger kunnen zijn dan in het voorjaar. Maar aan de andere kant zijn dan de meeste bespuitingen met insecticiden achter de rug. Het risico van blootstelling aan een insecticide is hoger in een gewas met een goed nectar- (hoeveelheid en suikerconcentratie) en stuifmeelaanbod. Foerageersters vliegen per dag gemiddeld 10 keer uit om voedsel te verzamelen, elke trip kan van een paar minuten tot een uur duren. Door communicatie via de bijendans en trophallaxis (voedseluitwisseling) wordt de keuze voor het benutten van een bepaalde dracht sterk gestuurd. Dat betekent dat bijen zich niet homogeen verdelen over het drachtgebied maar focussen op de meest profijtelijke drachten. Als gevolg daarvan is ‘geen bezoek’ en ‘veel bezoek’ in de verdeling meer vertegenwoordigd dan ‘een beetje bezoek’. Bijenvolken van een bijenstand verdelen zich niet allemaal gelijk over het drachtgebied; verschillende volken bezoeken deels verschillende en deels overlappende drachten. Hoewel de triggers en veelal de drempels bekend zijn, evenals de manier van foerageren, is het nog niet mogelijk precies te voorspellen hoe een volk zich verdeelt over meerdere velden. Omgekeerd is ook niet te voorspellen welk aandeel van verschillende volken op verschillende locaties in een bepaald veld mag worden verwacht. De nectar die binnengebracht wordt, wordt binnen enkele uren verdeeld over het volk; foerageersters gebruiken het als brandstof voor nieuwe foerageervluchten, het komt in het larvenvoedsel terecht en het meeste wordt opgeslagen. Vaste deeltjes zoals fijnstof en microbiële plantpathogenen verdelen zich snel over de bijen in het volk door fysiek contact
    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
    Encouraging sustainability in the workplace: a survey on the pro-environmental behaviour of university employees
    Blok, V. ; Wesselink, R. ; Studynka, O. ; Kemp, R.G.M. - \ 2015
    Journal of Cleaner Production 106 (2015). - ISSN 0959-6526 - p. 55 - 67.
    planned behavior - proenvironmental behavior - life-styles - ecological behavior - situational factors - higher-education - values - attitudes - norms - determinants
    In order to enhance more sustainable behaviour in households, recent research focuses on the identification of factors that have an impact on sustainable or pro-environmental behaviour. The aim of this study is to identify factors that could predict pro-environmental behaviour in the workplace. While many studies focused on the behaviour of households, this study is one of the first that focuses exclusively on pro-environmental behaviour in the workplace. Based on a comprehensive literature review, two groups of factors were identified which could predict pro-environmental behaviour in the workplace: internal factors and external factors. Next, the model was tested among employees of a green university in the Netherlands. Based on the results of this study, it can be concluded that the theory of planned behaviour can explain pro-environmental behaviour in the workplace. At the same time, the results show that there are clear differences between factors influencing pro-environmental behaviour in households and in the workplace. Furthermore, also other factors like leadership support and exemplary pro-environmental behaviour by leaders are at stake in case of pro-environmental behaviour in the workplace, and have a significant positive impact on employee's intention to act pro-environmentally. The findings of this study have various managerial implications for green companies and organizations in general and green universities in particular.
    Accuracy of genomic prediction when combining two related crossbred populations
    Vallee, A.A.A. ; Arendonk, J.A.M. van; Bovenhuis, H. - \ 2014
    Journal of Animal Science 92 (2014)10. - ISSN 0021-8812 - p. 4342 - 4348.
    dairy-cattle breeds - beef-cattle - selection - performance - animals - values - uterine - traits - impact - gene
    Charolais bulls are selected for their crossbreed performance when mated to Montbéliard or Holstein dams. To implement genomic prediction, one could build a reference population for each crossbred population independently. An alternative could be to combine both crossbred populations into a single reference population to increase size and accuracy of prediction. The objective of this study was to investigate the accuracy of genomic prediction by combining different crossbred populations. Three scenarios were considered: 1) using 1 crossbred population as reference to predict phenotype of animals from the same crossbred population, 2) combining the 2 crossbred populations into 1 reference to predict phenotype of animals from 1 crossbred population, and 3) using 1 crossbred population as reference to predict phenotype of animals from the other crossbred population. Traits studied were bone thinness, height, and muscular development. Phenotypes and 45,117 SNP genotypes were available for 1,764 Montbéliard × Charolais calves and 447 Holstein × Charolais calves. The population was randomly spilt into 10 subgroups, which were assigned to the validation one by one. To allow fair comparison between scenarios, size of the reference population was kept constant for all scenarios. Breeding values were estimated with BLUP and genomic BLUP. Accuracy of prediction was calculated as the correlation between the EBV and the phenotypic values of the calves in the validation divided by the square root of the heritability. Genomic BLUP showed higher accuracies (between 0.281 and 0.473) than BLUP (between 0.197 and 0.452). Accuracies tended to be highest when prediction was within 1 crossbred population, intermediate when populations were combined into the reference population, and lowest when prediction was across populations. Decrease in accuracy from a prediction within 1 population to a prediction across populations was more pronounced for bone thinness (–27%) and height (–29%) than for muscular development (–14%). Genetic correlation between the 2 crossbred populations was estimated using pedigree relationships. It was 0.70 for bone thinness, 0.80 for height, and 0.99 for muscular development. Genetic correlation indicates the expected gain in accuracy of prediction when combining different populations into 1 reference population. The larger the genetic correlation is, the larger the benefit is to combine populations for genomic prediction.
    Onderscheid in Vers : uitwerking discussie telers en groentespeciaalzaken n.a.v. het project PPP Paprika : een ketenaanpak voor duurzame vruchtgroenten met meer waarde
    Splinter, Gerben - \ 2014
    fruit vegetables - growers - retail marketing - shops - cooperation - supply chain management - discussion - consumer information - quality - values
    Genomic prediction based on data from three layer lines using non-linear regression models
    Huang, H. ; Windig, J.J. ; Vereijken, A. ; Calus, M.P.L. - \ 2014
    Genetics, Selection, Evolution 46 (2014). - ISSN 0999-193X - 11 p.
    dairy-cattle breeds - dimensionality reduction - gaussian kernel - accuracy - traits - values - validation - selection - pedigree - plant
    Background - Most studies on genomic prediction with reference populations that include multiple lines or breeds have used linear models. Data heterogeneity due to using multiple populations may conflict with model assumptions used in linear regression methods. Methods - In an attempt to alleviate potential discrepancies between assumptions of linear models and multi-population data, two types of alternative models were used: (1) a multi-trait genomic best linear unbiased prediction (GBLUP) model that modelled trait by line combinations as separate but correlated traits and (2) non-linear models based on kernel learning. These models were compared to conventional linear models for genomic prediction for two lines of brown layer hens (B1 and B2) and one line of white hens (W1). The three lines each had 1004 to 1023 training and 238 to 240 validation animals. Prediction accuracy was evaluated by estimating the correlation between observed phenotypes and predicted breeding values. Results - When the training dataset included only data from the evaluated line, non-linear models yielded at best a similar accuracy as linear models. In some cases, when adding a distantly related line, the linear models showed a slight decrease in performance, while non-linear models generally showed no change in accuracy. When only information from a closely related line was used for training, linear models and non-linear radial basis function (RBF) kernel models performed similarly. The multi-trait GBLUP model took advantage of the estimated genetic correlations between the lines. Combining linear and non-linear models improved the accuracy of multi-line genomic prediction. Conclusions - Linear models and non-linear RBF models performed very similarly for genomic prediction, despite the expectation that non-linear models could deal better with the heterogeneous multi-population data. This heterogeneity of the data can be overcome by modelling trait by line combinations as separate but correlated traits, which avoids the occasional occurrence of large negative accuracies when the evaluated line was not included in the training dataset. Furthermore, when using a multi-line training dataset, non-linear models provided information on the genotype data that was complementary to the linear models, which indicates that the underlying data distributions of the three studied lines were indeed heterogeneous.
    Genomic prediction based on data from three layer lines: a comparison between linear methods
    Calus, M.P.L. ; Huang, H. ; Vereijken, J. ; Visscher, J. ; Napel, J. ten; Windig, J.J. - \ 2014
    Genetics, Selection, Evolution 46 (2014). - ISSN 0999-193X - 13 p.
    principal component approach - support vector regression - dairy-cattle breeds - linkage disequilibrium - prior-knowledge - discriminant-analysis - values - selection - accuracy - traits
    Background The prediction accuracy of several linear genomic prediction models, which have previously been used for within-line genomic prediction, was evaluated for multi-line genomic prediction. Methods Compared to a conventional BLUP (best linear unbiased prediction) model using pedigree data, we evaluated the following genomic prediction models: genome-enabled BLUP (GBLUP), ridge regression BLUP (RRBLUP), principal component analysis followed by ridge regression (RRPCA), BayesC and Bayesian stochastic search variable selection. Prediction accuracy was measured as the correlation between predicted breeding values and observed phenotypes divided by the square root of the heritability. The data used concerned laying hens with phenotypes for number of eggs in the first production period and known genotypes. The hens were from two closely-related brown layer lines (B1 and B2), and a third distantly-related white layer line (W1). Lines had 1004 to 1023 training animals and 238 to 240 validation animals. Training datasets consisted of animals of either single lines, or a combination of two or all three lines, and had 30 508 to 45 974 segregating single nucleotide polymorphisms. Results Genomic prediction models yielded 0.13 to 0.16 higher accuracies than pedigree-based BLUP. When excluding the line itself from the training dataset, genomic predictions were generally inaccurate. Use of multiple lines marginally improved prediction accuracy for B2 but did not affect or slightly decreased prediction accuracy for B1 and W1. Differences between models were generally small except for RRPCA which gave considerably higher accuracies for B2. Correlations between genomic predictions from different methods were higher than 0.96 for W1 and higher than 0.88 for B1 and B2. The greater differences between methods for B1 and B2 were probably due to the lower accuracy of predictions for B1 (~0.45) and B2 (~0.40) compared to W1 (~0.76). Conclusions Multi-line genomic prediction did not affect or slightly improved prediction accuracy for closely-related lines. For distantly-related lines, multi-line genomic prediction yielded similar or slightly lower accuracies than single-line genomic prediction. Bayesian variable selection and GBLUP generally gave similar accuracies. Overall, RRPCA yielded the greatest accuracies for two lines, suggesting that using PCA helps to alleviate the “n¿«¿p” problem in genomic prediction.
    Consequences of splitting whole-genome sequencing effort over multiple breeds on imputation accuracy
    Bouwman, A.C. ; Veerkamp, R.F. - \ 2014
    BMC Genetics 15 (2014). - ISSN 1471-2156 - 9 p.
    genotype imputation - cattle breeds - linkage disequilibrium - phase - populations - jersey - values
    The aim of this study was to determine the consequences of splitting sequencing effort over multiple breeds for imputation accuracy from a high-density SNP chip towards whole-genome sequence. Such information would assist for instance numerical smaller cattle breeds, but also pig and chicken breeders, who have to choose wisely how to spend their sequencing efforts over all the breeds or lines they evaluate. Sequence data from cattle breeds was used, because there are currently relatively many individuals from several breeds sequenced within the 1,000 Bull Genomes project. The advantage of whole-genome sequence data is that it carries the causal mutations, but the question is whether it is possible to impute the causal variants accurately. This study therefore focussed on imputation accuracy of variants with low minor allele frequency and breed specific variants. Results Imputation accuracy was assessed for chromosome 1 and 29 as the correlation between observed and imputed genotypes. For chromosome 1, the average imputation accuracy was 0.70 with a reference population of 20 Holstein, and increased to 0.83 when the reference population was increased by including 3 other dairy breeds with 20 animals each. When the same amount of animals from the Holstein breed were added the accuracy improved to 0.88, while adding the 3 other breeds to the reference population of 80 Holstein improved the average imputation accuracy marginally to 0.89. For chromosome 29, the average imputation accuracy was lower. Some variants benefitted from the inclusion of other breeds in the reference population, initially determined by the MAF of the variant in each breed, but even Holstein specific variants did gain imputation accuracy from the multi-breed reference population. Conclusions This study shows that splitting sequencing effort over multiple breeds and combining the reference populations is a good strategy for imputation from high-density SNP panels towards whole-genome sequence when reference populations are small and sequencing effort is limiting. When sequencing effort is limiting and interest lays in multiple breeds or lines this provides imputation of each breed.
    Heterogeneity in consumer perceptions of the animal friendliness of broiler production systems
    Jonge, J. de; Trijp, J.C.M. van - \ 2014
    Food Policy 49 (2014)Pt. 1. - ISSN 0306-9192 - p. 174 - 185.
    welfare - preferences - meat - standards - stakeholder - interests - attitudes - chickens - values - food
    Animal welfare-based product differentiation through private sector initiatives has led to the introduction of ‘compromise’ meat products, which are produced at beyond regulatory standards for animal welfare, but are cheaper than organic meat. A variety of production system characteristics serve as parameters to achieve higher animal welfare standards. Food policies will be more effective if they position compromise products on those production system characteristics that really matter to (segments of) consumers. The present study identifies that three market segments may be discerned; one that takes a more inclusive perspective on animal welfare, and two that take a more heuristic approach by viewing animal friendliness from a more uni-dimensional perspective (animal space vs. slaughter method). These segments do not only differ in their perception of animal welfare, but also regarding their background characteristics. An interesting finding of the research is that the different segments accord in their perceptions of overall animal welfare levels, but do so for different reasons. In terms of food policy implications this means that the further development of compromise products would benefit from communicating more specific information on animal space and slaughter method, in addition to the overall star-based animal welfare classification. Such communication would serve well to both 50% of the market that takes a more balanced and integrated view on animal welfare and the other half of the market that takes a more uni-dimensional perspective (space vs. slaughter method).
    Het belang van een stad vol groene daken en gevels : wat is het belang van groene daken en gevels op macroschaal?
    Hop, M.E.C.M. ; Hiemstra, J.A. - \ 2014
    Stad + groen : vakblad over openbaar groen en het vergroenen van de buitenruimte 2 (2014)4. - ISSN 2352-4634 - p. 44 - 47.
    groene gevels - groene daken - welzijn - stadsomgeving - effecten - meervoudig gebruik - kwaliteit van het leven - sociale indicatoren - waarden - green walls - green roofs - well-being - urban environment - effects - multiple use - quality of life - social indicators - values
    Het economisch effect van groen is de laatste jaren veelvuldig onderzocht, behalve dan op macroschaal. PPO heeft recent een onderzoek afgesloten waarbij met name op dat laatste effect is ingezoomd. Wat doen groene daken en gevels voor de stad als geheel?
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