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 Footprints of Pig Domestication and Selection Revealed through Massive Parallel Sequencing of Pooled DNA
Amaral, A.J. ; Ferretti, L. ; Megens, H.J.W.C. ; Crooijmans, R.P.M.A. ; Nie, H. ; Ramos-Onsins, S.E. ; Perez-Enciso, M. ; Schook, L.B. ; Groenen, M.A.M. - \ 2011
PLoS ONE 6 (2011)4. - ISSN 1932-6203 - 12 p.
major histocompatibility complex - recent positive selection - class-i region - linkage disequilibrium - genetic diversity - breeds - generation - signatures - chimpanzee - mutation
Background Artificial selection has caused rapid evolution in domesticated species. The identification of selection footprints across domesticated genomes can contribute to uncover the genetic basis of phenotypic diversity. Methodology/Main Findings Genome wide footprints of pig domestication and selection were identified using massive parallel sequencing of pooled reduced representation libraries (RRL) representing ~2% of the genome from wild boar and four domestic pig breeds (Large White, Landrace, Duroc and Pietrain) which have been under strong selection for muscle development, growth, behavior and coat color. Using specifically developed statistical methods that account for DNA pooling, low mean sequencing depth, and sequencing errors, we provide genome-wide estimates of nucleotide diversity and genetic differentiation in pig. Widespread signals suggestive of positive and balancing selection were found and the strongest signals were observed in Pietrain, one of the breeds most intensively selected for muscle development. Most signals were population-specific but affected genomic regions which harbored genes for common biological categories including coat color, brain development, muscle development, growth, metabolism, olfaction and immunity. Genetic differentiation in regions harboring genes related to muscle development and growth was higher between breeds than between a given breed and the wild boar. Conclusions/Significance These results, suggest that although domesticated breeds have experienced similar selective pressures, selection has acted upon different genes. This might reflect the multiple domestication events of European breeds or could be the result of subsequent introgression of Asian alleles. Overall, it was estimated that approximately 7% of the porcine genome has been affected by selection events. This study illustrates that the massive parallel sequencing of genomic pools is a cost-effective approach to identify footprints of selection.
The Porcine HapMap Project: Genome-Wide Assessment Of Nucleotide Diversity, Haplotype Diversity And Footprints Of Selection In The Pig
Groenen, M.A.M. ; Amaral, A.J. ; Megens, H.J.W.C. ; Larson, B.A. ; Archibald, A.L. ; Muir, W.M. ; Malhi, Y. ; Crooijmans, R.P.M.A. ; Ferretti, L. ; Perez-Encizo, M. ; Schook, L.B. - \ 2010
In: Book of Abstracts of the Plant and Animal Genome XVIII Conference, San Diego, California, USA, 9-13 Januari 2010. - - p. w609 - w609.
The Porcine HapMap Consortium The pig has a complex and long history of domestication and breed formation and has been domesticated independently multiple times and has likely experienced introgression of local Wild boar after the spread of agriculture. Using the Illumina GA sequencing platform thousand s of SNPs were identified in the porcine genome and used these to develop the Illumin porcine 60K iSelect Beadchip. This chip has enabled whole-genome characterization of linkage disequilibrium and haplotype structure in commercial and local breeds and comparison with the Wild boar. The chip has also allowed an investigation into whole-genome patterns of variation, including signatures of selection associated with domestication and breed formation as well as elucidating demographic events such as population bottlenecks, and providing insights into the complex origin of domesticated populations by examining patterns of haplotype sharing. Signatures of selection were also identified using Illumina short read sequences generated from pooled reduced representation libraries of different breeds and covering approximately 2% of the genome. Signals of positive selection were identified and a GO term/KEGG pathway enrichment analysis provided evidence for specific gene families under selection in domesticated pigs and Wild boar. Currently approximately 2,000 pigs were been genotyped with the porcine 60K beadchip, including approximatley 50 pig breeds, and about 20 different Wild boar populations distributed throughout Eurasia. In addition, museum and archeological samples were included to provide a wider insight into domestication and geographic history. Inclusion of a range of other Suidae as outgroup species, supported an estimation of ancestral alleles and the origin and relative age of the porcine SNPs.
Nucleotide variation and footprints of selection in the porcine and chicken genomes
Amaral, A.J. - \ 2010
Wageningen University. Promotor(en): Martien Groenen, co-promotor(en): Hendrik-Jan Megens; Henri Heuven. - [S.l. : S.n. - ISBN 9789085856559 - 160
varkens - kippen - genomen - nucleotiden - genetische diversiteit - kunstmatige selectie - selectief fokken - rassen (dieren) - genetica - pigs - fowls - genomes - nucleotides - genetic diversity - artificial selection - selective breeding - breeds - genetics
Finding selection footprints in the swine genome using massive parallel sequencing.
Amaral, A.J. ; Feretti, L. ; Megens, H.J.W.C. ; Crooijmans, R.P.M.A. ; Nie, H. ; Groenen, M.A.M. - \ 2009
We investigated whether selection footprints can be identified from GA (Genome analyzer) sequences generated from pooled Reduced Representation Libraries and covering approximately 2% of the genome of Large White, Landrace, Pietrain, Duroc and Wild Boar. Methods were developed to estimate Nucleotide Diversity (ND) considering that, GA sequences were obtained from pooled DNA, singletons were removed and the sequencing error rate. The average ND ranged from 0.0008 to 0.002 depending on chromosome and breed. Genomic locations that have been, putatively, under selection were identified. We found signals of positive selection on SSC8 in the region containing the KIT gene, for white breeds but not for Duroc and Wild Boar. Signals of balancing selection were found for regions on SSC7 containing genes from the MHC complex and from the olfactory receptors complex. Enrichment analysis of KEGG-pathways showed that for regions under positive selection, swine breeds showed higher enrichment of pathways related to growth whereas Wild Boar showed higher enrichment of pathways related to immunity and robustness. Balancing selection resulted in the significant enrichment of pathways related to the olfactory receptors activities in all swine breeds and Wild Boar. Our results raise the possibility of using GA sequencing of pools for identification of selection footprints and present the first global map of regions under selection in the swine genome
Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology
Ramos, A. ; Crooijmans, R.P.M.A. ; Affara, N.A. ; Amaral, A.J. ; Kerstens, H.H.D. ; Megens, H.J.W.C. ; Groenen, M.A.M. - \ 2009
PLoS ONE 4 (2009)8. - ISSN 1932-6203 - 13 p.
Background: The dissection of complex traits of economic importance to the pig industry requires the availability of a significant number of genetic markers, such as single nucleotide polymorphisms (SNPs). This study was conducted to discover several hundreds of thousands of porcine SNPs using next generation sequencing technologies and use these SNPs, as well as others from different public sources, to design a high-density SNP genotyping assay. Methodology/Principal Findings: A total of 19 reduced representation libraries derived from four swine breeds (Duroc, Landrace, Large White, Pietrain) and a Wild Boar population and three restriction enzymes (AluI, HaeIII and MspI) were sequenced using Illumina's Genome Analyzer (GA). The SNP discovery effort resulted in the de novo identification of over 372K SNPs. More than 549K SNPs were used to design the Illumina Porcine 60K+SNP iSelect Beadchip, now commercially available as the PorcineSNP60. A total of 64,232 SNPs were included on the Beadchip. Results from genotyping the 158 individuals used for sequencing showed a high overall SNP call rate (97.5%). Of the 62,621 loci that could be reliably scored, 58,994 were polymorphic yielding a SNP conversion success rate of 94%. The average minor allele frequency (MAF) for all scorable SNPs was 0.274. Conclusions/Significance: Overall, the results of this study indicate the utility of using next generation sequencing technologies to identify large numbers of reliable SNPs. In addition, the validation of the PorcineSNP60 Beadchip demonstrated that the assay is an excellent tool that will likely be used in a variety of future studies in pigs
Application of massive parallel sequencing to whole genome SNP discovery in the porcine genome
Amaral, A.J. ; Kerstens, H.H.D. ; Megens, H.J.W.C. ; Heuven, H.C.M. ; Dibbits, B.W. ; Dungen, J. den; Crooijmans, R.P.M.A. ; Groenen, M.A.M. - \ 2009
BMC Genomics 10 (2009). - ISSN 1471-2164
single-nucleotide polymorphisms - reduced representation - linkage disequilibrium - pig genome - technologies - populations - diversity - selection - sites - swine
Background - Although the Illumina 1 G Genome Analyzer generates billions of base pairs of sequence data, challenges arise in sequence selection due to the varying sequence quality. Therefore, in the framework of the International Porcine SNP Chip Consortium, this pilot study aimed to evaluate the impact of the quality level of the sequenced bases on mapping quality and identification of true SNPs on a large scale. Results - DNA pooled from five animals from a commercial boar line was digested with DraI; 150–250-bp fragments were isolated and end-sequenced using the Illumina 1 G Genome Analyzer, yielding 70,348,064 sequences 36-bp long. Rules were developed to select sequences, which were then aligned to unique positions in a reference genome. Sequences were selected based on quality, and three thresholds of sequence quality (SQ) were compared. The highest threshold of SQ allowed identification of a larger number of SNPs (17,489), distributed widely across the pig genome. In total, 3,142 SNPs were validated with a success rate of 96%. The correlation between estimated minor allele frequency (MAF) and genotyped MAF was moderate, and SNPs were highly polymorphic in other pig breeds. Lowering the SQ threshold and maintaining the same criteria for SNP identification resulted in the discovery of fewer SNPs (16,768), of which 259 were not identified using higher SQ levels. Validation of SNPs found exclusively in the lower SQ threshold had a success rate of 94% and a low correlation between estimated MAF and genotyped MAF. Base change analysis suggested that the rate of transitions in the pig genome is likely to be similar to that observed in humans. Chromosome X showed reduced nucleotide diversity relative to autosomes, as observed for other species. Conclusion - Large numbers of SNPs can be identified reliably by creating strict rules for sequence selection, which simultaneously decreases sequence ambiguity. Selection of sequences using a higher SQ threshold leads to more reliable identification of SNPs. Lower SQ thresholds can be used to guarantee sufficient sequence coverage, resulting in high success rate but less reliable MAF estimation. Nucleotide diversity varies between porcine chromosomes, with the X chromosome showing less variation as observed in other species
Detection of hybridization and species identification in domesticated and wild quails using genetic markers
Amaral, A.J. ; Silva, A.B. ; Grosso, A.R. ; Chikhi, L. ; Bastos-Silveira, C. ; Dias, D. - \ 2007
Folia Zoologica 56 (2007)3. - ISSN 0139-7893 - p. 285 - 300.
coturnix-c.-japonica - multilocus genotype data - population-structure - mitochondrial genome - dna - primers - number - individuals - vertebrates - simulation
Hybridization is particularly widespread in birds and can affect species status and recovery. The common quail Coturnix coturnix is a protected game species that has undergone significant population decrease due to habitat changes. The release of Japanese quail C. japonica and or hybrids for restocking has been occurring since the 1970¿s. Both species have not developed reproductive isolating mechanisms and hybridization is occurring. Species distinction based on morphology and male callings is difficult. In this work cytochrome b gene and five microsatellite loci were used with the aim of establishing an identification test for quails sampled in Portugal. Cytochrome b gene revealed to be of promising use to identify the quail maternal lineage. Success in species assignment with the studied microsatellite loci was moderate to identify samples with suspicion of being hybrids with common quail maternal lineage.
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