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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Genome wide association study of body weight and feed efficiency traits in a commercial broiler chicken population, a re-visitation
Mebratie, Wossenie ; Reyer, Henry ; Wimmers, Klaus ; Bovenhuis, Henk ; Jensen, Just - \ 2019
Scientific Reports 9 (2019)1. - ISSN 2045-2322

Genome wide association study was conducted using a mixed linear model (MLM) approach that accounted for family structure to identify single nucleotide polymorphisms (SNPs) and candidate genes associated with body weight (BW) and feed efficiency (FE) traits in a broiler chicken population. The results of the MLM approach were compared with the results of a general linear model approach that does not take family structure in to account. In total, 11 quantitative trait loci (QTL) and 21 SNPs, were identified to be significantly associated with BW traits and 5 QTL and 5 SNPs were found associated with FE traits using MLM approach. Besides some overlaps between the results of the two GWAS approaches, there are considerable differences in the detected QTL. Even though the genomic inflation factor (λ) values indicate that there is no strong family structure in this population, using models that account for the existing family structure may reduce bias and increase accuracy of the estimated SNP effects in the association analysis. The SNPs and candidate genes identified in this study provide information on the genetic background of BW and FE traits in broiler chickens and might be used as prior information for genomic selection.

Advances in research on the prenatal development of skeletal muscle in animals in relation to the quality of muscle-based food. I - Regulation of myogenesis and environmental impact
Rehfeldt, C. ; Pas, M.F.W. te; Wimmers, K. ; Brameld, J.M. ; Nissen, P.M. ; Berri, C. ; Valente, L.M.P. ; Power, D.M. ; Picard, B. ; Stickland, N.C. ; Oksbjerg, N. - \ 2011
Animal 5 (2011)5. - ISSN 1751-7311 - p. 703 - 717.
trout oncorhynchus-mykiss - receptor signal-transduction - seabream pagellus-bogaraveo - in-situ hybridization - gilthead sea bream - salmon salmo-salar - rainbow-trout - birth-weight - meat quality - igf-i
Skeletal muscle development in vertebrates – also termed myogenesis – is a highly integrated process. Evidence to date indicates that the processes are very similar across mammals, poultry and fish, although the timings of the various steps differ considerably. Myogenesis is regulated by the myogenic regulatory factors and consists of two to three distinct phases when different fibre populations appear. The critical times when myogenesis is prone to hormonal or environmental influences depend largely on the developmental stage. One of the main mechanisms for both genetic and environmental effects on muscle fibre development is via the direct action of the growth hormone–insulin-like growth factor (GH–IGF) axis. In mammals and poultry, postnatal growth and function of muscles relate mainly to the hypertrophy of the fibres formed during myogenesis and to their fibre-type composition in terms of metabolic and contractile properties, whereas in fish hyperplasia still plays a major role. Candidate genes that are important in skeletal muscle development, for instance, encode for IGFs and IGF-binding proteins, myosin heavy chain isoforms, troponin T, myosin light chain and others have been identified. In mammals, nutritional supply in utero affects myogenesis and the GH–IGF axis may have an indirect action through the partitioning of nutrients towards the gravid uterus. Impaired myogenesis resulting in low skeletal myofibre numbers is considered one of the main reasons for negative long-term consequences of intrauterine growth retardation. Severe undernutrition in utero due to natural variation in litter or twin-bearing species or insufficient maternal nutrient supply may impair myogenesis and adversely affect carcass quality later in terms of reduced lean and increased fat deposition in the progeny. On the other hand, increases in maternal feed intake above standard requirement seem to have no beneficial effects on the growth of the progeny with myogenesis not or only slightly affected. Initial studies on low and high maternal protein feeding are published. Although there are only a few studies, first results also reveal an influence of nutrition on skeletal muscle development in fish and poultry. Finally, environmental temperature has been identified as a critical factor for growth and development of skeletal muscle in both fish and poultry.
Advances in research on the prenatal development of skeletal muscle in animals in relation to the quality of muscle-based food. II -Genetic factors related to animal performance and advances in methodology
Rehfeldt, C. ; Pas, M.F.W. te; Wimmers, K. ; Brameld, J.M. ; Nissen, P.M. ; Berri, C. ; Valente, L.M.P. ; Power, D.M. ; Picard, B. ; Stickland, N.C. ; Oksbjerg, N. - \ 2011
Animal 5 (2011)05. - ISSN 1751-7311 - p. 718 - 730.
trout oncorhynchus-mykiss - growth-factor-i - receptor signal-transduction - charr salvelinus-alpinus - breast meat quality - salmon salmo-salar - heavy-chain genes - igf-i - fiber types - rainbow-trout
Selective breeding is an effective tool to improve livestock. Several selection experiments have been conducted to study direct selection responses as well as correlated responses in traits of skeletal muscle growth and function. Moreover, comparisons of domestic with wild-type species and of extreme breeds provide information on the genetic background of the skeletal muscle phenotype. Structural muscular components that differed with increasing distance in lean growth or meat quality in mammals were found to be myofibre number, myofibre size, proportions of fibre types as well as the numbers and proportions of secondary and primary fibres. Furthermore, markers of satellite cell proliferation, metabolic enzyme activities, glycogen and fat contents, the expression of myosin heavy chain isoforms, of activated AMPKa and other proteins in skeletal muscle tissue and circulating IGF1 and IGF-binding proteins have been identified to be involved in selection responses observed in pigs, cattle and/or chicken. The use of molecular methods for selective breeding of fish has only recently been adopted in aquaculture and studies of the genetic basis of growth and flesh quality traits are scarce. Some of the molecular markers of muscle structure/metabolism in livestock have also been identified in fish, but so far no studies have linked them with selection response. Genome scans have been applied to identify genomic regions exhibiting quantitative trait loci that control traits of interest, for example, muscle structure and meat quality in pigs and growth rate in chicken. As another approach, polymorphisms in candidate genes reveal the relationship between genetic variation and target traits. Thus, in large-scale studies with pigs’ associations of polymorphisms in the HMGA2, CA3, EPOR, NME1 and TTN genes with traits of carcass and meat quality were detected. Other studies revealed the significance of mutations in the IGF2 and RYR1 genes for carcass lean and muscle fibre traits in pigs. Mutations in the myostatin (MSTN) gene in fish were also examined. Advances in research of the genetic and environmental control of traits related to meat quality and growth have been made by the application of holistic ‘omics’ techniques that studied the whole muscle-specific genome, transcriptome and proteome in relation to muscle and meat traits, the development of new methods for muscle fibre typing and the adaptation of biophysical measures to develop parameters of muscle fibre traits as well as the application of in vitro studies. Finally, future research priorities in the field are defined.
Assosiations of functional candidate genes derived from gene expression profiles of prenatal porcine muscle issue with meat quality and carcass traits
Wimmers, K. ; Murani, E. ; Pas, M.F.W. te; Chang, K.C. ; Davoli, R. ; Merks, J.W.M. ; Henne, H. ; Costa, N. da; Harlizius, B. ; Schellander, K. ; Braglia, S. ; Wit, A.A.C. de; Cagnazzo, M. ; Fontanesi, L. ; Prins, D. ; Ponsuksili, S. - \ 2007
Animal Genetics 38 (2007)5. - ISSN 0268-9146 - p. 474 - 484.
quantitative trait loci - m.-longissimus-dorsi - skeletal-muscle - transcription factor - rapid communication - promoter region - myf5 gene - pig - polymorphisms - qtl
Ten genes (ANK1, bR10D1, CA3, EPOR, HMGA2, MYPN, NME1, PDGFRA, ERC1, TTN), whose candidacy for meat-quality and carcass traits arises from their differential expression in prenatal muscle development, were examined for association in 1700 performance-tested fattening pigs of commercial purebred and crossbred herds of Duroc, Pietrain, Pietrain × (Landrace × Large White), Duroc × (Landrace × Large White) as well as in an experimental F2 population based on a reciprocal cross of Duroc and Pietrain. Comparative sequencing revealed polymorphic sites segregating across commercial breeds. Genetic mapping results corresponded to pre-existing assignments to porcine chromosomes or current human¿porcine comparative maps. Nine of these genes showed association with meat-quality and carcass traits at a nominal P-value of ¿ 0.05; PDGFRA revealed no association reaching the P ¿ 0.05 threshold. In particular, HMGA2, CA3, EPOR, NME1 and TTN were associated with meat colour, pH and conductivity of loin 24 h postmortem; CA3 and MYPN exhibited association with ham weight and lean content (FOM) respectively at P-values of <0.003 that correspond to false discovery rates of <0.05. However, none of the genes showed significant associations for a particular trait across all populations. The study revealed statistical¿genetic evidence for association of the functional candidate genes with traits related to meat quality and muscle deposition. The polymorphisms detected are not likely causal, but markers were identified that are in linkage disequilibrium with causal genetic variation within particular populations.
Pordictor: Identification of genes controlling Pork Quality
Harlizius, B. ; Schellander, K. ; Pas, M.F.W. te; Chang, K.C. ; Davoli, R. ; Merks, J.W.M. ; Worner, R. ; Eping, H. ; Cagnazzo, M. ; Lama, B. ; Costa, N. da; Fontanesi, L. ; Henne, H. ; Murani, E. ; Ponsuksili, S. ; Priem, J. ; Wimmers, K. - \ 2004
Utilization of molecular information in selection of farm animals
Arendonk, J.A.M. van; Bovenhuis, H. ; Waaij, L. van der; Koning, D.J. de; Brascamp, E.W. - \ 2002
In: Genomics and Biotechnology in livestock breeding / Schellander, K., Li, N., Neeteson, A.M., Wimmers, K., - p. 19 - 32.
Physical mapping of the chicken genome
Groenen, M.A.M. ; dijkhof, R.M.J. ; Veenendaal, A. ; Visser, A. ; Jennen, D.G.J. ; Acar, R. ; Cornelissen, S.J.B. ; Buitenhuis, A.J. ; Poel, J.J. van der; Crooijmans, R.P.M.A. - \ 2002
In: Genomics and biotechnology in livestock breeding / Schellander, K., Li, N., Neeteson, A.M., Wimmers, K., - p. 97 - 104.
Empirical Evaluation of genetic clustering methods using multilocus genotypes from 20 chicken breeds
Rosenberg, N.A. ; Burke, T. ; Elo, K. ; Feldman, M.W. ; Friedlin, P.J. ; Groenen, M.A.M. ; Hillel, J. ; Maki-Tanila, A. ; Tixier-Boichard, M. ; Vignal, A. ; Wimmers, K. - \ 2001
Genetics 159 (2001). - ISSN 0016-6731 - p. 699 - 713.
We tested the utility of genetic cluster analysis in ascertaining population structure of a large data set for which population structure was previously known. Each of 600 individuals representing 20 distinct chicken breeds was genotyped for 27 microsatellite loci, and individual multilocus genotypes were used to infer genetic clusters. Individuals from each breed were inferred to belong mostly to the same cluster. The clustering success rate, measuring the fraction of individuals that were properly inferred to belong to their correct breeds, was consistently ∼98ÐWhen markers of highest expected heterozygosity were used, genotypes that included at least 8-10 highly variable markers from among the 27 markers genotyped also achieved >95␌lustering success. When 12-15 highly variable markers and only 15-20 of the 30 individuals per breed were used, clustering success was at least 90ÐWe suggest that in species for which population structure is of interest, databases of multilocus genotypes at highly variable markers should be compiled. These genotypes could then be used as training samples for genetic cluster analysis and to facilitate assignments of individuals of unknown origin to populations. The clustering algorithm has potential applications in defining the within-species genetic units that are useful in problems of conservation.
Assessment of biodiversity in a wide range of chicken breeds by genotyping DNA pools for microsatellite loci
Weigend, S. ; Hillel, J. ; Groenen, M.A.M. ; Tixier-Boichard, M. ; Korol, A. ; Kirzner, V. ; Freidlin, P. ; Crooijmans, R.P.M.A. ; Vignal, A. ; Wimmers, K. ; Ponsuksili, S. ; Thomson, P.A. ; Burke, T. ; Maki-Tanila, A. ; Elo, K. ; Barredirie, A. ; Zhivotovsky, L.A. ; Fledman, M.W. - \ 2000
In: book of Abstracts : 27th International Conference on Animal Genetics, 22-26 July, Minneapolis, Minnesota, USA - p. 83 - 83.
Estimation of SNP frequencies in European chicken populations
Vignal, A. ; Monbrun, C. ; Thompson, P. ; Barre-Dirie, A. ; Burke, T. ; Groenen, M.A.M. ; Hillel, M. ; Mäki-Tanila, A. ; Tixier-Boichard, M. ; Wimmers, K. ; Weigend, S. - \ 2000
In: Book of Abstracts : 27th International conference on Animal Genetics, 22-26 July, Minneapolis, Minnesota, USA - p. 71 - 71.
First report on chicken genes and chromosomes 2000
Schmid, M. ; Nanda, I. ; Guttenbach, M. ; Steinlein, C. ; Hoehn, H. ; Schartl, M. ; Haaf, T. ; Weigend, S. ; Fries, R. ; Buerstedde, J.M. ; Wimmers, K. ; Burt, D.W. ; Smith, J. ; A'hara, S. ; Law, A. ; Griffin, D.K. ; Bumstead, N. ; Kaufman, J. ; Thomson, P.A. ; Burke, T. ; Groenen, M.A.M. ; Crooijmans, R.P.M.A. ; Vignal, A. ; Fillon, V. ; Morisson, M. ; Pitel, F. ; Tixier-Boichard, M. ; Ladjali-Mohammedi, K. ; Hillel, J. ; Maki-Tanila, A. - \ 2000
Cytogenetics and cell genetics 90 (2000). - ISSN 0301-0171 - p. 169 - 218.
Het culturele erfgoed van een natuurgebied. Honderden eeuwen menselijke activiteit in het natuurlandschap van de Bussumer- en Westerheide.
Wimmers, W.H. ; Groenman-van Waateringe, W. ; Spek, Th. - \ 1993
Historisch Geografisch Tijdschrift 11 (1993)2. - ISSN 0167-9775 - p. 53 - 74.
bodemkarteringen - kaarten - landbouwgrond - landschap - vestigingspatronen - nederzetting - geografie - geschiedenis - cultuurlandschap - noord-holland - het gooi - soil surveys - maps - agricultural land - landscape - settlement patterns - settlement - geography - history - cultural landscape
Archeologische en historisch - geografische elementen in een natuurgebied : antropogene achtergronden van de Gooise natuurgebieden
Wimmers, W.H. ; Zweden, R.R. van - \ 1992
Wageningen : DLO-Staring Centrum (Rapport / DLO-Staring Centrum 143) - 203
geografie - geschiedenis - nederzetting - vestigingspatronen - noord-holland - prehistorie - overblijfselen - het gooi - geography - history - settlement - settlement patterns - prehistory - remains
Gebiedsbeschrijving van het Gooi
Een archeologisch onderzoek in de akker van de Aardjesberg, Westerheide, gem. Hilversum : de staat van het monument en de aard van de vindplaats
Wimmers, W.H. - \ 1991
Wageningen : Staring Centrum (Rapport / Staring Centrum 122) - 59
nederland - noord-holland - prehistorie - overblijfselen - het gooi - netherlands - prehistory - remains
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