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.

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Genome-Wide Assessment Of World-Wide Poultry Biodiversity
Muir, W.M. ; Wong, G.K. ; Zhang, Y. ; Wang, J. ; Groenen, M.A.M. ; Crooijmans, R.P.M.A. ; Megens, H.J.W.C. ; Rattink, A.P. - \ 2008
Genetic diversity is the key to all genetic progress, past and future. Over the last 10,000 years, poultry was domesticated first from the wild jungle fowl, then in the last 1,000 years into standard breeds. In the last century, those breeds have been further reduced into a few commercially produced types. These lines have since been strongly selected for both growth and egg production among other traits. During this process, genetic variability has been lost at each step. Important issues include: ¿How much variability has been lost¿ and ¿Is there adequate variability to meet future challenges, such as new diseases"? To achieve this goal, a panel of 2551 informative SNPs were genotyped on 2580 individuals including 1440 commercial birds. Allele loss was assessed by determining the relationship with inbreeding, and through the use of SNP ¿weights¿ that correct for ascertainment bias and avoid the need to extrapolate from the inbreeding coefficient. The methods presented are general and could be used to assess loss of biodiversity based on SNP panels. Results indicate that sampled broiler lines of multiple companies have lost between 55%-70% of allelic diversity while sampled layer lines of one commercial layer company have lost between 80%-90% of allelic diversity. However, Insillico crosses among lines show that many of the lost alleles can be found in other lines within the company resulting in true loss across the industry of approximately 50%. However, the alleles lost were primarily those that were rare; it is not known if rare vs. common alleles are more or less likely to be important for response to new challenges. These allele may still exist in standard breeds or wild birds, but the issue remains of how to assess the importance of those alleles to phenotype, and/or how to move them into commercial populations without introducing unwanted alleles.
Genetic variation at the tumor virus B locus in commercial and labratory chicken populations assessed by a medium-throughput or a high-throughput assay
Zhang, H.M. ; Bacon, L.D. ; Heidari, M. ; Muir, W.M. ; Groenen, M.A.M. ; Albers, G.A. ; Rattink, A.P. - \ 2007
Avian Pathology 36 (2007)4. - ISSN 0307-9457 - p. 283 - 291.
avian-leukosis virus - rous-sarcoma virus - mareks-disease vaccines - endogenous viral genes - subgroup-b - white leghorns - egg-production - immune-response - feathering dams - tvb locus
The tumour virus B (TVB) locus encodes cellular receptors mediating infection by three subgroups of avian leukosis virus (B, D, and E). Three major alleles, TVB*S1, TVB*S3, and TVB*R, have been described. TVB*S1 encodes a cellular receptor mediating infection of subgroups B, D, and E. TVB*S3 encodes the receptor for two subgroups, B and D, and TVB*R encodes a dysfunctional receptor that does not permit infection by any of the subgroups, B, D, or E. Genetic diversity at the TVB locus of chickens was investigated in both layer and broiler commercial pure lines and laboratory lines. Genotyping assays were developed for both medium-throughput and high-throughput analysis. Of the 36 broiler lines sampled, 14 were fixed for the susceptible allele TVB*S1. Across all broiler lines, 83% of chickens were typed as TVB*S1/*S1, 3% as TVB*R/*R, and 14% as TVB*S1/*R. In the egg-layer lines, five of the 16 tested were fixed for TVB*S1/*S1. About 44% of egg-layers were typed as TVB*S1/*S1, 15% as TVB*R/*R, with the rest segregating for two or three of the alleles. In the laboratory chickens, 60% were fixed for TVB*S1/*S1, 6% for TVB*S3/*S3, 14% for TVB*R/*R, and the rest were heterozygotes (TVB*S1/*S3 or TVB*S1/*R). All commercial pure lines examined in this study carry the TVB*S1 allele that sustains the susceptibility to avian leukosis viruses B, D, and E. More importantly, the TVB*R allele was identified in multiple populations, thus upholding the opportunities for genetic improvement through selection.
Genetic diversity in European pigs utilizing amplified fragment lenght polymorphism markers. AFLP markers
SanCristobal, M. ; Chevalet, C. ; Peleman, J. ; Heuven, H.C.M. ; Brugmans, B.W. ; Schriek, M. van; Joosten, R. ; Rattink, A.P. ; Harlizius, B. ; Groenen, M.A.M. ; Amigues, Y. ; Boscher, M.Y. ; Russell, G. ; Law, A. ; Davoli, R. ; Russo, V. ; Desautes, C. ; Alderson, L. ; Fimland, E. ; Bagga, M. ; Delgado, J.V. ; Vega-Pla, J.L. ; Marinez, A.M. ; Ramos, M. ; Glodek, P. ; Meyer, J.N. ; Gandini, G.C. - \ 2006
Animal Genetics 37 (2006)3. - ISSN 0268-9146 - p. 232 - 238.
dierveredeling - varkens - varkensrassen - conservering - dna - allelen - genetische afstand - genetische diversiteit - genetische merkers - genotypen - heterozygotie - microsatellieten - wiskundige modellen - meishan - aflp - animal breeding - pigs - pig breeds - conservation - dna - alleles - genetic distance - genetic diversity - genetic markers - genotypes - heterozygosity - microsatellites - mathematical models - meishan - amplified fragment length polymorphism - population diversity - distance - trees - aflp
The use of DNA markers to evaluate genetic diversity is an important component of the management of animal genetic resources. The Food and Agriculture Organisation of the United Nations (FAO) has published a list of recommended microsatellite markers for such studies; however, other markers are potential alternatives. This paper describes results obtained with a set of amplified fragment length polymorphism (AFLP) markers as part of a genetic diversity study of European pig breeds that also utilized microsatellite markers. Data from 148 AFLP markers genotyped across samples from 58 European and one Chinese breed were analysed. The results were compared with previous analyses of data from 50 microsatellite markers genotyped on the same animals. The AFLP markers had an average within-breed heterozygosity of 0.124 but there was wide variation, with individual markers being monomorphic in 3¿98% of the populations. The biallelic and dominant nature of AFLP markers creates a challenge for their use in genetic diversity studies as each individual marker contains limited information and AFLPs only provide indirect estimates of the allelic frequencies that are needed to estimate genetic distances. Nonetheless, AFLP marker-based characterization of genetic distances was consistent with expectations based on breed and regional distributions and produced a similar pattern to that obtained with microsatellites. Thus, data from AFLP markers can be combined with microsatellite data for measuring genetic diversity.
Genetic diversity within and between European pig breeds using microsatellite markers
SanCristobal, M. ; Chevalet, C. ; Haley, C.S. ; Joosten, R. ; Rattink, A.P. ; Harlizius, B. ; Groenen, M.A.M. - \ 2006
Animal Genetics 37 (2006)3. - ISSN 0268-9146 - p. 189 - 198.
dierveredeling - varkens - wilde varkens - varkensrassen - conservering - rasverschillen - biodiversiteit - genetische afstand - genetische diversiteit - genetische merkers - heterozygotie - allelen - microsatellieten - populatiegenetica - statistische analyse - animal breeding - pigs - wild pigs - pig breeds - conservation - breed differences - biodiversity - genetic distance - genetic diversity - genetic markers - heterozygosity - alleles - microsatellites - population genetics - statistical analysis - populations - evolution - humans - loci - distance
An important prerequisite for a conservation programme is a comprehensive description of genetic diversity. The aim of this study was to use anonymous genetic markers to assess the between- and the within-population components of genetic diversity for European pig breeds at the scale of the whole continent using microsatellites. Fifty-eight European pig breeds and lines were analysed including local breeds, national varieties of international breeds and commercial lines. A sample of the Chinese Meishan breed was also included. Eleven additional breeds from a previous project were added for some analyses. Approximately 50 individuals per breed were genotyped for a maximum of 50 microsatellite loci. Substantial within-breed variability was observed, with the average expected heterozygosity and observed number of alleles per locus being 0.56 [range 0.43–0.68] and 4.5 respectively. Genotypic frequencies departed from Hardy–Weinberg expectations (P <0.01) in 15 European populations, with an excess of homozygotes in 12 of them. The European breeds were on average genetically very distinct, with a Wright FST index value of 0.21. The Neighbour-Joining tree drawn from the Reynolds distances among the breeds showed that the national varieties of major breeds and the commercial lines were mostly clustered around their breeds of reference (Duroc, Hampshire, Landrace, Large White and Piétrain). In contrast, local breeds, with the exception of the Iberian breeds, exhibited a star-like topology. The results are discussed in the light of various forces, which may have driven the recent evolution of European pig breeds. This study has consequences for the interpretation of biodiversity results and will be of importance for future conservation programmes.
An assessment of the European pig diversity using molecular markers: partitioning of diversity among breeds
Ollivier, L. ; Alderson, L. ; Gandini, G.C. ; Foulley, J.L. ; Haley, C.S. ; Joosten, R. ; Rattink, A.P. ; Harlizius, B. ; Groenen, M.A.M. - \ 2005
Conservation Genetics 6 (2005)5. - ISSN 1566-0621 - p. 729 - 741.
dierveredeling - varkens - varkensrassen - genetische diversiteit - genetische merkers - microsatellieten - moleculaire genetica - cryopreservering - kruising - conservering - uitsterven - rasverschillen - biodiversiteit - aflp - animal breeding - pigs - pig breeds - genetic diversity - genetic markers - microsatellites - molecular genetics - cryopreservation - crossbreds - conservation - extinction - breed differences - biodiversity - amplified fragment length polymorphism - subdivided populations - conservation genetics - livestock breeds - cattle breeds - management - distance - purposes - size
Genetic diversity within and between breeds (and lines) of pigs was investigated. The sample comprised 68 European domestic breeds (and lines), including 29 local breeds, 18 varieties of major international breeds, namely Duroc, Hampshire, Landrace, Large White and Piétrain, and 21 commercial lines either purebred or synthetic, to which the Chinese Meishan and a sample of European wild pig were added. On average 46 animals per breed were sampled (range 12–68). The genetic markers were microsatellites (50 loci) and AFLP (amplified fragment length polymorphism, 148 loci). The analysis of diversity showed that the local breeds accounted for 56% of the total European between-breed microsatellite diversity, and slightly less for AFLP, followed by commercial lines and international breeds. Conversely, the group of international breeds contributed most to within-breed diversity, followed by commercial lines and local breeds. Individual breed contributions to the overall European between- and within-breed diversity were estimated. The range in between-breed diversity contributions among the 68 breeds was 0.04–3.94% for microsatellites and 0.24–2.94% for AFLP. The within-breed diversity contributions varied very little for both types of markers, but microsatellite contributions were negatively correlated with the between-breed contributions, so care is needed in balancing the two types of contribution when making conservation decisions. By taking into account the risks of extinction of the 29 local breeds, a cryopreservation potential (priority) was estimated for each of them.
PACE: An integrated pig genome database
Merks, W.M. ; Kampen, T.J.A. van; Wijk, H.J. van; Harlizius, B. ; Rattink, A.P. ; Albers, G. ; Groenen, M.A.M. - \ 2004
Poultry Science 83 (2004)Suppl. 1. - ISSN 0032-5791 - p. (905) - (905).
Knowledge of farm animal genomes has increased enormously over the last decade. A large part if this information is publicly available for a variety of species and through specific databases such as for pigs; PiGBASE for mapping data, Pig EST Database, TIGR SsGI for genes and data on their expression patterns and the INRA Comparative and Cytogenetic mapping home pages. Potentially these databases provide comprehensive public repositories for genome research. However, these data are difficult to combine from the different sources or with private data, but also with genome data of model organisms. This strongly hinders comparative mapping and positional fine-mapping. A new pig genome database - PACE was set up in the Netherlands to enable integration of data from the different sources. For this, the widespread database system of AceDB has been adapted and links with existing farm animal databases but also databases like LocusLink, Genbank, MGI, GeneCards are included to facilitate an efficient comparative mapping with human and mouse. In addition published information on porcine QTL has been included. This database with more than 5000 genetic markers and loci
PACE: An integrated pig genome database
Merks, W.M. ; Kampen, T.J.A. van; Wijk, H.J. van; Harlizius, B. ; Rattink, A.P. ; Albers, G. ; Groenen, M.A.M. - \ 2004
Journal of Dairy Science 87 (2004)Suppl. 1. - ISSN 0022-0302 - p. (905) - (905).
Knowledge of farm animal genomes has increased enormously over the last decade. A large part if this information is publicly available for a variety of species and through specific databases such as for pigs; PiGBASE for mapping data, Pig EST Database, TIGR SsGI for genes and data on their expression patterns and the INRA Comparative and Cytogenetic mapping home pages. Potentially these databases provide comprehensive public repositories for genome research. However, these data are difficult to combine from the different sources or with private data, but also with genome data of model organisms. This strongly hinders comparative mapping and positional fine-mapping. A new pig genome database - PACE was set up in the Netherlands to enable integration of data from the different sources. For this, the widespread database system of AceDB has been adapted and links with existing farm animal databases but also databases like LocusLink, Genbank, MGI, GeneCards are included to facilitate an efficient comparative mapping with human and mouse. In addition published information on porcine QTL has been included. This database with more than 5000 genetic markers and loci
PACE: An integrated pig genome database
Merks, W.M. ; Kampen, T.J.A. van; Wijk, H.J. van; Harlizius, B. ; Rattink, A.P. ; Albers, G. ; Groenen, M.A.M. - \ 2004
Journal of Animal Science 82 (2004)Suppl. 1. - ISSN 0021-8812 - p. (905) - (905).
Knowledge of farm animal genomes has increased enormously over the last decade. A large part if this information is publicly available for a variety of species and through specific databases such as for pigs; PiGBASE for mapping data, Pig EST Database, TIGR SsGI for genes and data on their expression patterns and the INRA Comparative and Cytogenetic mapping home pages. Potentially these databases provide comprehensive public repositories for genome research. However, these data are difficult to combine from the different sources or with private data, but also with genome data of model organisms. This strongly hinders comparative mapping and positional fine-mapping. A new pig genome database - PACE was set up in the Netherlands to enable integration of data from the different sources. For this, the widespread database system of AceDB has been adapted and links with existing farm animal databases but also databases like LocusLink, Genbank, MGI, GeneCards are included to facilitate an efficient comparative mapping with human and mouse. In addition published information on porcine QTL has been included. This database with more than 5000 genetic markers and loci and about 500 QTL¿s will be available publicly from July 2004
Pig Ace: an integrated pig genome database
Merks, J.W.M. ; Kampen, A.J.A. van; Wijk, H.J. van; Harlizius, B. ; Rattink, A.P. ; Albers, G.A. ; Groenen, M.A.M. - \ 2004
FABIB: Farm Animal Bioinformatics Platform
Wijk, H.J. van; Rattink, A.P. ; Mullaart, E. ; Lintel Hekkert, B. te; Harlizius, B. ; Groenen, M.A.M. ; Bink, M.C.A.M. ; Georges, M. ; Leunissen, J. ; Merks, J.W.M. ; Albers, G.A. ; Nap, J.P.H. - \ 2003
Development of a single nucleotide polymorphism map of porcine chromosome 2
Jungerius, B.J. ; Rattink, A.P. ; Crooijmans, R.P.M.A. ; Poel, J.J. van der; Oost, B.A. van; Pas, M.F.W. te; Groenen, M.A.M. - \ 2003
Animal Genetics 34 (2003)6. - ISSN 0268-9146 - p. 429 - 437.
dna-sequence diversity - human genome - sus scrofa - pigs - identification - discovery - genes - loci
Single nucleotide polymorphism markers are developed on SSC2, predominantly on the p-arm. Several studies reported a quantitative trait loci (QTL) for backfat thickness in this region. Single nucleotide polymorphisms were identified by comparative re-sequencing of polymerase chain reaction (PCR) products from a panel of eight individuals. The panel consisted of five Large Whites (each from a different Dutch breeding company), a Meishan, a Pietrain and a Wild Boar. In total, 67 different PCR products were sequenced and 301 SNPs were identified in 32 429 bp of consensus sequence, an average of one SNP in every 108 bp. After correction for sample size, this polymorphism rate corresponds to a heterozygosity value of one SNP in every 357 bp. For 63% of the SNPs, there was variation among the five Large Whites, and these SNPs are relevant for linkage and association studies in commercial populations. Comparing the Whites with other breeds revealed higher variation rates with: (i) Meishan, 89%; (ii) Pietrain, 69%; (iii) Wild Boar, 70%. Because many of the experimental populations to identify QTL are based on crosses between these breeds, these SNPs are relevant for the fine mapping of the QTL identified within these crosses.
FABIP: A Farm Animal Bioinformatics Platform
Rattink, A.P. ; Wijk, H.J. van; Mullaart, E. ; Lintel Hekkert, B. te; Harlizius, B. ; Groenen, M.A.M. ; Bink, M.C.A.M. ; Georges, M. ; Leunissen, J.A.M. ; Merks, J. ; Albers, G.A. ; Nap, J.P.H. - \ 2003
In: Book of Abstracts 3rd European Poultry Genetics Symposium, Wageningen, the Netherlands, 17-19 September 2003 - p. 77 - 77.
The use of microsatellite genotyping for population studies in the pig with individual and pooled DNA samples
Groenen, M.A.M. ; Joosten, R. ; Bosher, M.Y. ; Amiges, Y. ; Rattink, A.P. ; Harlizius, B. ; Poel, J.J. van der; Crooijmans, R.P.M.A. - \ 2003
Archivos de Zootecnia 52 (2003). - ISSN 0004-0592 - p. 145 - 155.
Porcine BAC derived microsatellites linked to ADRBK1, CNTF and GAL on SSC2
Faivre, M. ; Rattink, A.P. ; Harlizius, B. ; Crooijmans, R.P.M.A. ; Groenen, M.A.M. - \ 2002
Animal Genetics 33 (2002). - ISSN 0268-9146 - p. 72 - 73.
Development and typing of Single Nucleotide Polymorphism (SNP) markers in a QTL-region for fatness traits on procine chromosome 2
Jungerius, B.J. ; Rattink, A.P. ; Harlizius, B. ; Oost, B.A. van; Pas, M.F.W. te; Groenen, M.A.M. - \ 2002
In: Plant, Animal and Microbe Genomes X Conference, January 12-16, San Diego, USA, Abstract nr. P241 - p. 137 - 137.
Development and typing of single nucleotide polymorphism markers in a QTL region for fatness on porcine chromosome 2
Jungerius, B.J. ; Rattink, A.P. ; Harlizius, B. ; Oost, B.A. van; Pas, M.F.W. te; Groenen, M.A.M. - \ 2002
In: XXVII International conference on Animal Genetics (ISAG), August 11-15, Göttingen, Germany, Section D161 - p. 148 - 148.
Molecular characterisation of QTLs controlling fatness in pigs
Rattink, A.P. - \ 2002
Wageningen University. Promotor(en): J.A.M. van Arendonk; M.A.M. Groenen. - S.l : S.n. - ISBN 9789058086129 - 125
varkens - kruising - loci - kwantitatieve kenmerken - chromosoomkaarten - genkartering - genetische gewasbescherming - genetische merkers - genomic imprinting - lichaamssamenstelling - rugspek - lichaamsvet - chromosomen - genen - moleculaire genetica - pigs - crossbreds - loci - quantitative traits - chromosome maps - gene mapping - genetic control - genetic markers - genomic imprinting - body composition - backfat - body fat - chromosomes - genes - molecular genetics

This thesis deals with the identification of genes controlling intramuscular fat and backfat thickness. Markers linked to quantitative trait loci (QTL) for these traits in the cross between Meishan x Large White breeds will lead to the identification of the underlying genetic causes. A whole-genome scan revealed significant evidence for five QTLs affecting body composition, of which four were imprinted. Additional markers were typed in this cross to further investigate the regions on pig chromosome (SSC) 2, SSC4 and SSC7. Imprinting analysis revealed a genome wise significant paternally expressed QTL on SSC2. A radiation hybrid (RH) map was constructed for SSC2. Comparison of the porcine RH map with homologous human chromosomes identified four conserved segments between SSC2 and HSA11, HSA19, and HSA5. To improve the existing comparative map for SSC2 and increase the gene density on this chromosome, a porcine BAC library was screened. Sequences from the BACs were compared with sequences in the nucleotide databases to identify homology with other mammalian sequences. For the investigation of the borders of the conserved segments between SSC2 and HSA11 genes located on HSA11 were mapped to SSC2. This resulted in refinement of the borders of the conserved segments and in the detection of a new rearrangement in the comparative map between HSA11 with the porcine genome. Through the use of radiation hybrid maps that include both Type I and II markers, homologous chromosomal locations for QTL of specific traits can be identified in other species. The conservation of genome organisation between pig, man and mouse makes it possible to take advantage of genetically well-characterised species for the selection of candidate genes for the imprinted QTL for backfat thickness on SSC2. Human obesity research can help to determine the direction and give clues for further porcine fat trait related genetic research, but emphasis should be on better understanding of the fat traits in pigs themselves and improvement of the genetic map of the pig.

Development and typing of Single Nucleotide Polymorphism markers in a QTL region for fatness traits on porcine chromosome
Jungerius, B. ; Rattink, A. ; Harlizius, B. ; Oost, B. van; Pas, M. te; Groenen, M. - \ 2002
In: Abstracts of the 28th International conference on Animal Genetics, Göttingen, 11-15 August - p. 137 - 137.
Improving the comparative map of SSC2p-q13 by sample sequencing of BAC clones
Rattink, A.P. ; Jungerius, B.J. ; Faivre, M. ; Chardon, P. ; Harlizius, B. ; Groenen, M.A.M. - \ 2001
Animal Genetics 32 (2001)5. - ISSN 0268-9146 - p. 274 - 280.
muscle mass - igf2 locus - genome - pigs - mouse - scale - qtl
To improve the comparative map for pig chromosome 2 and increase the gene density on this chromosome, a porcine bacterial artificial chromosome (BAC) library was screened with 17 microsatellite markers and 18 genes previously assigned to pig chromosome 2. Fifty-one BAC clones located in the region of a maternally imprinted quantitative trait locus for backfat thickness (BFT) were identified. From these BACs 372 kb were sample sequenced. The average read length of a subclone was 442 basepair (bp). Contig assembly analysis showed that every bp was sequenced 1.28 times. Subsequently, sequences were compared with sequences in the nucleotide databases to identify homology with other mammalian sequences. Sequence identity was observed with sequences derived from 35 BACs. The average percentage identity with human sequences was 87.6%, with an average length of 143 bp. In total, sample sequencing of all BACs resulted in sequence identity with 29 human genes, 13 human expressed sequence tags (ESTs), 17 human genomic clones, one rat gene, one porcine gene and nine porcine ESTs. Eighteen genes located on human chromosome 11 and 19, and seven genes from other human locations, one rat gene and one porcine gene were assigned to pig chromosome 2 for the first time. The new genes were added to the radiation hybrid map at the same position as the locus from which the BAC that was sequenced was derived. In total 57 genes were placed on the radiation hybrid map of SSC2p-q13.
Disease suppressive soilless culture systems; characterisation of its microflora
Postma, J. ; Willemsen-de Klein, M.J.E.I.M. ; Rattink, H. ; Os, E.A. van - \ 2001
Acta Horticulturae 554 (2001). - ISSN 0567-7572 - p. 323 - 332.
The trend in glasshouse horticulture has always been to start culture systems as aseptic as possible. However, several root diseases still cause problems under these conditions. The present paper shows the importance of the microflora to suppress Pythium aphanidermatum, a fungal root pathogen which is a serious threat in cucumber. Introduced single antagonists as well as the indigenous microflora suppressed pythium root and crown rot. Pseudomonas fluorescens, Streptomyces griseoviridis, Pythium oligandrum, and 2 isolates of Trichoderma harzianum reduced the disease occurrence by 60 ␘r more in several, but not all, of the experiments. The indigenous microflora showed a very constant disease suppression of 50 to 100 &Eth;This was tested in experiments where P. aphanidermatum was added to sterilised and non-sterilised rockwool, and to sterilised rockwool that had been recolonised with the original microflora. Suppressiveness correlated with the number of filamentous actinomycetes present in the nutrient solution in the rockwool slabs. If a beneficial microflora is present in the cropping system, it should not be disturbed or eradicated by treatments such as disinfection of the recirculated nutrient solution. Therefore, the effects of different disinfection procedures on the composition of the microflora were compared. Numbers of filamentous actinomycetes in the nutrient solution in the tank after the disinfection treatment were highest without disinfection, intermediate after slow filtration, and lowest after UV treatment. Numbers of actinomycetes in the slabs, i.e. around the roots, were not distinctly different between the treatments. The implication of potential shifts in the microbial populations due to certain treatments for the disease development is not known. Increased knowledge on the beneficial microflora and the treatments that influence the composition of such a microflora, will stimulate the exploitation of microbially balanced and optimised soilless culture systems.
A whole genome scan for Quantitative Trait Loci (QTL) affecting teat number in pigs
Hirooka, H. ; Koning, D.J. de; Harlizius, B. ; Arendonk, J.A.M. van; Rattink, A.P. ; Groenen, M.A.M. ; Brascamp, E.W. ; Bovenhuis, H. - \ 2001
Journal of Animal Science 79 (2001). - ISSN 0021-8812 - p. 2320 - 2326.
A whole-genome scan was conducted using 132 microsatellite markers to identify chromosomal regions that have an effect on teat number. For this purpose, an experimental cross between Chinese Meishan pigs and five commercial Dutch pig lines was used. Linkage analyses were performed using interval mapping by regression under line cross models including a test for imprinting effects. The whole-genome scan revealed highly significant evidence for three quantitative trait loci (QTL) affecting teat number, of which two were imprinted. Paternally expressed (i.e., maternally imprinted) QTL were found on chromosomes 2 and 12. A Mendelian expressed QTL was found on chromosome 10. The estimated additive effects showed that, for the QTL on chromosomes 10 and 12, the Meishan allele had a positive effect on teat number, but, for the QTL on chromosome 2, the Meishan allele had a negative effect on teat number. This study shows that imprinting may play an important role in the expression of teat number.
Detection and characterization of quantitative trait loci for growth and reproduction traits in pigs
Koning, D.J. de; Rattink, A.P. ; Harlizius, B. ; Groenen, M.A.M. ; Brascamp, E.W. ; Arendonk, J.A.M. van - \ 2001
Livestock Production Science 72 (2001). - ISSN 0301-6226 - p. 185 - 198.
Detection and characterization of quantitative trait loci for meat quality traits in pigs
Koning, D.J. de; Harlizius, B. ; Rattink, A.P. ; Groenen, M.A.M. ; Brascamp, E.W. ; Arendonk, J.A.M. van - \ 2001
Journal of Animal Science 79 (2001). - ISSN 0021-8812 - p. 2812 - 2819.
In an experimental cross between Meishan and Dutch Large White and Landrace lines, 785 F2 animals with carcass information and their parents were typed for molecular markers covering the entire porcine genome. Linkage was studied between these markers and eight meat quality traits. Quantitative trait locus analyses were performed using interval mapping by regression under two genetic models: 1) the line-cross approach, where the founder lines were assumed to be fixed for different QTL alleles and 2) a half-sib model where a unique allele substitution effect was fitted within each of the 38 half-sib families. The line-cross approach included tests for genomic imprinting and sex-specific QTL effects. In total, three genome-wide significant and 26 suggestive QTL were detected. The significant QTL on chromosomes 3, 4, and 13, affecting meat color, were only detected under the half-sib model. Failure of the line-cross approach to detect the meat color QTL suggests that the founder lines have similar allele frequencies for these QTL. This study provides information on new QTL affecting meat quality traits. It also shows the benefit of analyzing experimental data under different genetic and statistical models.
A high-resolution comparative RH map of porcine chromosome (SSC) 2.
Rattink, A.P. ; Faivre, M. ; Jungerius, B.J. ; Groenen, M.A.M. ; Harlizius, B. - \ 2001
Mammalian Genome 12 (2001)5. - ISSN 0938-8990 - p. 366 - 370.
A high-resolution comparative map was constructed for porcine Chromosome (SSC) 2, where a QTL for back fat thickness (BFT) is located. A radiation hybrid (RH) map containing 33 genes and 25 microsatellite markers was constructed for this chromosome with a 3000-rad porcine RH panel. In total, 16 genes from human Chromosome (HSA) 11p, HSA19p, and HSA5q were newly assigned to SSC2. One linkage group was observed at LOD 3.0, and five linkage groups at LOD 4.0. Comparison of the porcine RH map with homologous human gene orders identified four conserved segments between SSC2 and HSA11, HSA19, and HSA5. Concerning HSA11, a rearrangement of gene order is observed. The segment HSA11p15.4-q13 is inverted on SSC2 when compared with the distal tip of SSC2p, which is homologous to HSA11p15.5. The boundaries of the conserved segments between human and pig were defined more precisely. This high-resolution comparative map will be a valuable tool for further fine mapping of the QTL area.
Fine mapping and imprinting analysis for fatness trait QTL's in pigs
Rattink, A.P. ; Koning, D.J. de; Faivre, M. ; Harlizius, B. ; Arendonk, J.A.M. van; Groenen, M.A.M. - \ 2000
Mammalian Genome 11 (2000). - ISSN 0938-8990 - p. 656 - 661.
Comparative mapping of a region on pig chromosome 2 containing a QTL for backfat thickness
Rattink, A.P. ; Harlizius, B. ; Chardon, P. ; Faivre, M. ; Groenen, M.A.M. - \ 2000
In: Book of Abstracts : NWO retraite genetica, Rolduc - p. 7 - 7.
Comparison mapping of a region on pig chromosome 2 containing a QTL for backfat thickness
Rattink, A.P. ; Harlizius, B. ; Chardon, P. ; Faivre, M. ; Groenen, M.A.M. - \ 2000
In: Proceedings of the : XXVI International Conference on Animal Genetics (ISAG) - p. 46 - 46.
Major genes affecting backfat pigs : fine mapping of a paternally expressed QTL on chromosome 2
Rattink, A.P. ; Harlizius, B. ; Koning, D.J. de; Faivre, M. ; Joosten, R.G. ; Arendonk, J.A.M. van; Groenen, M.A.M. - \ 2000
In: Proceedngs : Plant and Animal Genome VIII Conference, San Diego - p. 149 - 149.
The -323Ins10 polymorphism for factor VII is not associated with coronary atherosclerosis in symptomatic men
Lievers, K.J.A. ; Mennen, L.I. ; Rattink, A.P. ; Zwinderman, A.H. ; Jukema, J.W. ; Schouten, E.G. ; Maat, M.P.M. de - \ 2000
Thrombosis Research 97 (2000). - ISSN 0049-3848 - p. 275 - 280.
Fine mapping of a paternally expressed QTL for backfat thickness on porcine chromosome 2
Harlizius, B. ; Rattink, A.P. ; Faivre, M. ; Jungerius, B. ; Keijzer, L. ; Joosten, R.G. ; Koning, D.J. de; Arendonk, J.A.M. van; Groenen, M.A.M. - \ 2000
In: book of abstracts : 51th meeting of the European Association of animal Production, The Hague, Wageningen : Wageningen Pers - p. 90 - 90.
The X chromosome harbors quantitative trait loci for backfat thickness and intramuscular fat content in pigs
Harlizius, B. ; Rattink, A.P. ; Koning, D.J. de; Faivre, M. ; Joosten, R.G. ; Arendonk, J.A.M. van; Groenen, M.A.M. - \ 2000
Mammalian Genome 11 (2000). - ISSN 0938-8990 - p. 800 - 802.
Genome-wide scan for body composition in pigs reveals important role of imprinting
Koning, D.J. de; Rattink, A.P. ; Harlizius, B. ; Arendonk, J.A.M. van; Brascamp, E.W. ; Groenen, M.A.M. - \ 2000
Proceedings of the National Academy of Sciences of the United States of America 97 (2000)14. - ISSN 0027-8424 - p. 7947 - 7950.
The role of imprinting in body composition was investigated in an experimental cross between Chinese Meishan pigs and commercial Dutch pigs. A whole-genome scan revealed significant evidence for five quantitative trait loci (QTL) affecting body composition, of which four were imprinted. Imprinting was tested with a statistical model that separated the expression of paternally and maternally inherited alleles. For back fat thickness, a paternally expressed QTL was found on Sus scrofa chromosome 2 (SSC2), and a Mendelian-expressed QTL was found on SSC7. In the same region of SSC7, a maternally expressed QTL affecting muscle depth was found. Chromosome 6 harbored a maternally expressed QTL on the short arm and a paternally expressed QTL on the long arm, both affecting intramuscular fat content. The individual QTL explained from 2 p to 10 f the phenotypic variance. The known homologies to human and mouse did not reveal positional candidate genes. This study demonstrates that testing for imprinting should become a standard procedure to unravel the genetic control of multifactorial traits.
Detection of QTL's controlling intramuscular and backfat in pigs
Rattink, A.P. ; Koning, D.J. de; Janss, L.L.G. ; Oers, P.A.M. van; Vries, B.J. de; Groenen, M.A.M. ; Poel, J.J. van der; Groot, P.N. de; Brascamp, E.W. ; Arendonk, J.A.M. van - \ 1999
In: Book of Abstracts of the XXVI International conference on Animal Genetics (ISAG). - [S.l.] : [s.n.], 1999. - (abstractnr. E043) - p. 106 - 106.
Detection of QTL's controlling intramuscular and backfat in pigs
Rattink, A.P. ; Koning, D.J. de; Janss, L.L.G. ; Oers, P.A.M. van; Vries, B.J. de; Groenen, M.A.M. ; Poel, J.J. van der; Groot, P.N. de; Brascamp, E.W. ; Arendonk, J.A.M. van - \ 1999
Animal Genetics (1999)supplement. - ISSN 0268-9146 - p. 69 - 69.
Deep-vein thrombosis is not associated with the P/S186 polymorphism of histidine-rich glycoprotein
Rattink, A.P. ; Hennis, B.C. ; Lievers, C.J.A. ; Maat, M.P.M. de; Bertina, R. ; Mennen, M.I. ; Rosendaal, F.R. - \ 1999
Fibrinolysis and Proteolysis 13 (1999)1. - p. 35 - 38.
A second maternally imprinted QTL affecting backfat thickness on chromosome 2 in pigs
Rattink, A.P. ; Harlizius, B. ; Koning, D.J. de; Faivre, M. ; Arendonk, J.A.M. van; Groenen, M.A.M. - \ 1999
In: Book of Abstracts NWO-MW Genetics retraite Rolduc, Kerkrade. - [S.l.] : [s.n.], 1999 - p. 1 - 1.
A second maternally imprinted QTL affecting backfat thickness on chromosome 2 in pigs
Rattink, A.P. ; Harlizius, B. ; Koning, D.J. de; Faivre, M. ; Arendonk, J.A.M. van; Groenen, M.A.M. - \ 1999
In: Abstract International Genomic Imprinting meeting, University college Dublin. - [S.l.] : [s.n.], 1999 - p. 37 - 37.
Detection of Quantitative Trait Loci for Backfat Thichness and Intramuscular Fat content in Pigs (Sus scrofa)
Koning, D.J. de; Janss, L.L.G. ; Rattink, A.P. ; Oers, P.A.M. van; Vries, B.J. de; Groenen, M.A.M. ; Poel, J.J. van der; Groot, P.N. de; Brascamp, E.W. ; Arendonk, J.A.M. van - \ 1999
Genetics 152 (1999). - ISSN 0016-6731 - p. 1679 - 1690.
In an experimental cross between Meishan and Dutch Large White and Landrace lines, 619 F(2) animals and their parents were typed for molecular markers covering the entire porcine genome. Associations were studied between these markers and two fatness traits: intramuscular fat content and backfat thickness. Association analyses were performed using interval mapping by regression under two genetic models: (1) an outbred line-cross model where the founder lines were assumed to be fixed for different QTL alleles; and (2) a half-sib model where a unique allele substitution effect was fitted within each of the 19 half-sib families. Both approaches revealed for backfat thickness a highly significant QTL on chromosome 7 and suggestive evidence for a QTL at chromosome 2. Furthermore, suggestive QTL affecting backfat thickness were detected on chromosomes 1 and 6 under the line-cross model. For intramuscular fat content the line-cross approach showed suggestive evidence for QTL on chromosomes 2, 4, and 6, whereas the half-sib analysis showed suggestive linkage for chromosomes 4 and 7. The nature of the QTL effects and assumptions underlying both models could explain discrepancies between the findings under the two models. It is concluded that both approaches can complement each other in the analysis of data from outbred line crosses.
Detection of quantitative trait loci for fatness traits in Dutch Meishan-crossbreds
Koning, D.J. de; Janss, L.L.G. ; Rattink, A.P. ; Groenen, M.A.M. ; Groot, P.N. de; Brascamp, E.W. ; Arendonk, J.A.M. van - \ 1999
In: 50th Annual Meeting EAAP, Zürich, Paper GPH1.6(1999) - p. 3 - 3.
Minder Pythium in komkommer
Postma, J. ; Rattink, H. - \ 1998
Groenten en Fruit. Vakdeel glasgroenten (1998)13 februari. - ISSN 1380-3573 - p. 4 - 5.
Biologische buffering van steenwol ten aanzien van Pythium aphanidermatum in de komkommerteelt
Postma, J. ; Rattink, H. - \ 1997
Gewasbescherming 28 (1997)1/2. - ISSN 0166-6495 - p. 15 - 15.
Biologische buffering van gesloten teeltsystemen t.a.v. Pythium aphanidermatum bij komkommer
Rattink, H. - \ 1997
Biological control of fusarium wilt in carnations on a recirculation system by a nonpathogenic Fusarium oxysporum isolate
Rattink, H. ; Postma, J. - \ 1996
Mededelingen - Universiteit Gent, Faculteit Landbouwkundige en Toegepaste Biologische Wetenschappen 61 (1996)2b. - ISSN 1373-7503 - p. 491 - 498.
snijbloemen - hydrocultuur - plantenziekteverwekkende schimmels - fusarium oxysporum - dianthus caryophyllus - glastuinbouw - cut flowers - hydroponics - plant pathogenic fungi - greenhouse horticulture
Besmet uitgangsmateriaal veroorzaakt problemen Phytophthora in eb/vloed-systemen bij saintpaulia.
Rattink, H. ; Kerssies, A. ; Jong-Lanser, C. de; Vicedo López, Y. - \ 1996
Vakblad voor de Bloemisterij 51 (1996)44. - ISSN 0042-2223 - p. 74 - 75.
plantenziekteverwekkende schimmels - potplanten - saintpaulia - binnen kweken (van planten) - glastuinbouw - plant pathogenic fungi - pot plants - indoor culture - greenhouse horticulture
Geen schimmmelverspreiding in eb/vloed-systemen
Rattink, H. ; Kerssies, A. ; Jong-Lanser, C. de - \ 1996
Vakblad voor de Bloemisterij 51 (1996)24. - ISSN 0042-2223 - p. 44 - 44.
Opmerkelijke bestrijding tegen Pythium
Rattink, H. - \ 1996
Groenten en fruit 6 (1996)9. - ISSN 0017-4491 - p. 19 - 19.
Root pathogens in modern cultural systems. Assessment of risks and suggestions for integrated control
Rattink, H. - \ 1996
IOBC/WPRS Bulletin 19 (1996)6. - ISSN 0253-1100 - p. 1 - 11.
Het nedersaksische groeiplaatsclassificatiesysteem en zijn toepasbaarheid in Nederland.
Fanta, J. ; Kuiper, B. ; Bianchi, F.J.J.A. ; Rattink, M. - \ 1996
Nederlands Bosbouwtijdschrift 68 (1996). - ISSN 0028-2057 - p. 168 - 170.
bosbouw - houtteelt - bosbouwkundige handelingen - groei - milieufactoren - vegetatietypen - bossen - classificatie - duitsland - forestry - silviculture - forestry practices - growth - environmental factors - vegetation types - forests - classification - germany
Biological control of soil-borne fungi in glasshouse crops on closed systems
Rattink, H. ; Postma, J. - \ 1995
In: Environmental biotic factors in integrated plant disease control / Manka, M., Poznan : The Polish Phytopathological Society - p. 455 - 459.
Rootpathogens in modern cultural systems. Assessment of risks and suggestions for integrated control
Rattink, H. - \ 1995
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