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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Data from: Distribution and functionality of copy number variation across European cattle populations
Upadhyay, M.R. ; Silva, Vinicius Da; Megens, H.J.W.C. ; Visker, M.H.P.W. ; Ajmone-Marsan, Paolo ; Bâlteanu, Valentin A. ; Dunner, Susana ; Garcia, Jose F. ; Ginja, Catarina ; Kantanen, Juha ; Groenen, M. ; Crooijmans, R.P.M.A. - \ 2017
copy number variations - European cattle - high density SNP array - population differentiation - purifying selection - drift - Kit gene
Copy number variation (CNV), which is characterized by large-scale losses or gains of DNA fragments, contributes significantly to genetic and phenotypic variation. Assessing CNV across different European cattle populations might reveal genetic changes responsible for phenotypic differences, which have accumulated throughout the domestication history of cattle as consequences of evolutionary forces that act upon them. To explore pattern of CNVs across European cattle, we genotyped 149 individuals, that represent different European regions, using the Illumina Bovine HD Genotyping array. A total of 9,944 autosomal CNVs were identified in 149 samples using a Hidden Markov Model (HMM) as employed in PennCNV. Animals originating from several breeds of British Isles, and Balkan and Italian regions, on average, displayed higher abundance of CNV counts than Dutch or Alpine animals. A total of 923 CNV regions (CNVRs) were identified by aggregating CNVs overlapping in at least two animals. The hierarchical clustering of CNVRs indicated low differentiation and sharing of high-frequency CNVRs between European cattle populations. Various CNVRs identified in the present study overlapped with olfactory receptor genes and genes related to immune system. In addition, we also detected a CNV overlapping the Kit gene in English longhorn cattle which has previously been associated with color-sidedness. To conclude, we provide a comprehensive overview of CNV distribution in genome of European cattle. Our results indicate an important role of purifying selection and genomic drift in shaping CNV diversity that exists between different European cattle populations.
Distribution and functionality of copy number variation across European cattle populations
Upadhyay, Maulik ; Silva, Vinicius Henrique Da; Megens, Hendrik Jan ; Visker, Marleen H.P.W. ; Ajmone-Marsan, Paolo ; Bâlteanu, Valentin A. ; Dunner, Susana ; Garcia, Jose F. ; Ginja, Catarina ; Kantanen, Juha ; Groenen, Martien A.M. ; Crooijmans, Richard P.M.A. - \ 2017
Frontiers in Genetics Livestock Genomics 8 (2017). - ISSN 1664-8021 - 12 p.
Copy number variations - Drift - European cattle - High density SNP array - Kit gene - Population differentiation - Purifying selection

Copy number variation (CNV), which is characterized by large-scale losses or gains of DNA fragments, contributes significantly to genetic and phenotypic variation. Assessing CNV across different European cattle populations might reveal genetic changes responsible for phenotypic differences, which have accumulated throughout the domestication history of cattle as consequences of evolutionary forces that act upon them. To explore pattern of CNVs across European cattle, we genotyped 149 individuals, that represent different European regions, using the Illumina Bovine HD Genotyping array. A total of 9,944 autosomal CNVs were identified in 149 samples using a Hidden Markov Model (HMM) as employed in PennCNV. Animals originating from several breeds of British Isles, and Balkan and Italian regions, on average, displayed higher abundance of CNV counts than Dutch or Alpine animals. A total of 923 CNV regions (CNVRs) were identified by aggregating CNVs overlapping in at least two animals. The hierarchical clustering of CNVRs indicated low differentiation and sharing of high-frequency CNVRs between European cattle populations. Various CNVRs identified in the present study overlapped with olfactory receptor genes and genes related to immune system. In addition, we also detected a CNV overlapping the Kit gene in English longhorn cattle which has previously been associated with color-sidedness. To conclude, we provide a comprehensive overview of CNV distribution in genome of European cattle. Our results indicate an important role of purifying selection and genomic drift in shaping CNV diversity that exists between different European cattle populations.

Microsatellite diversity of the Nordic type of goats in relation to breed conservation : How relevant is pure ancestry?
Lenstra, J.A. ; Tigchelaar, J. ; Biebach, I. ; Hallsson, J.H. ; Kantanen, J. ; Nielsen, V.H. ; Pompanon, F. ; Naderi, S. ; Rezaei, H.R. ; Sæther, N. ; Ertugrul, O. ; Grossen, C. ; Camenisch, G. ; Vos-Loohuis, M. ; Straten, M. van; Poel, E.A. de; Windig, J. ; Oldenbroek, K. - \ 2017
Journal of Animal Breeding and Genetics 134 (2017)1. - ISSN 0931-2668 - p. 78 - 84.
Conservation - Diversity - Goats - Microsatellite

In the last decades, several endangered breeds of livestock species have been re-established effectively. However, the successful revival of the Dutch and Danish Landrace goats involved crossing with exotic breeds and the ancestry of the current populations is therefore not clear. We have generated genotypes for 27 FAO-recommended microsatellites of these landraces and three phenotypically similar Nordic-type landraces and compared these breeds with central European, Mediterranean and south-west Asian goats. We found decreasing levels of genetic diversity with increasing distance from the south-west Asian domestication site with a south-east-to-north-west cline that is clearly steeper than the Mediterranean east-to-west cline. In terms of genetic diversity, the Dutch Landrace comes next to the isolated Icelandic breed, which has an extremely low diversity. The Norwegian coastal goat and the Finnish and Icelandic landraces are clearly related. It appears that by a combination of mixed origin and a population bottleneck, the Dutch and Danish Land-races are separated from the other breeds. However, the current Dutch and Danish populations with the multicoloured and long-horned appearance effectively substitute for the original breed, illustrating that for conservation of cultural heritage, the phenotype of a breed is more relevant than pure ancestry and the genetic diversity of the original breed. More in general, we propose that for conservation, the retention of genetic diversity of an original breed and of the visual phenotype by which the breed is recognized and defined needs to be considered separately.

Erratum: Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range
Henderson, Gemma ; Cox, Faith ; Ganesh, Siva ; Jonker, Arjan ; Young, Wayne ; Abecia, Leticia ; Angarita, Erika ; Aravena, Paula ; Nora Arenas, Graciela ; Ariza, Claudia ; Attwood, Graeme T. ; Mauricio Avila, Jose ; Avila-stagno, Jorge ; Bannink, André ; Barahona, Rolando ; Batistotti, Mariano ; Bertelsen, Mads F. ; Brown-Kav, Aya ; Carvajal, Andres M. ; Cersosimo, Laura ; Vieira Chaves, Alexandre ; Church, John ; Clipson, Nicholas ; Cobos-peralta, Mario A. ; Cookson, Adrian L. ; Cravero, Silvio ; Cristobal Carballo, Omar ; Crosley, Katie ; Cruz, Gustavo ; Cerón Cucchi, María ; Barra, Rodrigo de la; Menezes, Alexandre B. de; Detmann, Edenio ; Dieho, Kasper ; Dijkstra, Jan ; Reis, William L.S. Dos; Dugan, Mike E.R. ; Hadi Ebrahimi, Seyed ; Eythórsdóttir, Emma ; Nde Fon, Fabian ; Fraga, Martín ; Franco, Francisco ; Friedeman, Chris ; Fukuma, Naoki ; Gagić, Dragana ; Gangnat, Isabelle ; Javier Grilli, Diego ; Guan, Le Luo ; Heidarian Miri, Vahideh ; Hernandez-Sanabria, Emma ; Gomez, Alma Ximena Ibarra ; Isah, Olubukola A. ; Ishaq, Suzanne ; Jami, Elie ; Jelincic, Juan ; Kantanen, Juha ; Kelly, William J. ; Kim, Seon-Ho ; Klieve, Athol ; Kobayashi, Yasuo ; Koike, Satoshi ; Kopecny, Jan ; Nygaard Kristensen, Torsten ; Julie Krizsan, Sophie ; Lachance, Hannah ; Lachman, Medora ; Lamberson, William R. ; Lambie, Suzanne ; Lassen, Jan ; Leahy, Sinead C. ; Lee, Sang-Suk ; Leiber, Florian ; Lewis, Eva ; Lin, Bo ; Lira, Raúl ; Lund, Peter ; Macipe, Edgar ; Mamuad, Lovelia L. ; Cuquetto Mantovani, Hilário ; Marcoppido, Gisela Ariana ; Márquez, Cristian ; Martin, Cécile ; Martinez, Gonzalo ; Eugenia Martinez, Maria ; Lucía Mayorga, Olga ; McAllister, Tim A. ; McSweeney, Chris ; Mestre, Lorena ; Minnee, Elena ; Mitsumori, Makoto ; Mizrahi, Itzhak ; Molina, Isabel ; Muenger, Andreas ; Muñoz, Camila ; Murovec, Bostjan ; Newbold, John ; Nsereko, Victor ; O’donovan, Michael ; Okunade, Sunday ; O’neill, Brendan ; Ospina, Sonia ; Ouwerkerk, Diane ; Parra, Diana ; Pereira, Luiz Gustavo Ribeiro ; Pinares-patiño, Cesar ; Pope, Phil B. ; Poulsen, Morten ; Rodehutscord, Markus ; Rodriguez, Tatiana ; Saito, Kunihiko ; Sales, Francisco ; Sauer, Catherine ; Shingfield, Kevin ; Shoji, Noriaki ; Simunek, Jiri ; Stojanović-Radić, Zorica ; Stres, Blaz ; Sun, Xuezhao ; Swartz, Jeffery ; Liang Tan, Zhi ; Tapio, Ilma ; Taxis, Tasia M. ; Tomkins, Nigel ; Ungerfeld, Emilio ; Valizadeh, Reza ; Adrichem, Peter van; Hamme, Jonathan van; Hoven, Woulter van; Waghorn, Garry ; Wallace, John R. ; Wang, Min ; Waters, Sinéad M. ; Keogh, Kate ; Witzig, Maren ; Wright, Andre-Denis G. ; Yamano, Hidehisa ; Yan, Tianhai ; Yáñez-ruiz, David R. ; Yeoman, Carl J. ; Zambrano, Ricardo ; Zeitz, Johanna ; Zhou, Mi ; Wei Zhou, Hua ; Xia Zou, Cai ; Zunino, Pablo ; Janssen, Peter H. - \ 2016
Scientific Reports 6 (2016). - ISSN 2045-2322 - 2 p.
Domesticated Animal Biobanking : Land of Opportunity
Groeneveld, Linn F. ; Gregusson, Sigbjørn ; Guldbrandtsen, Bernt ; Hiemstra, Sipke J. ; Hveem, Kristian ; Kantanen, Juha ; Lohi, Hannes ; Stroemstedt, Lina ; Berg, Peer - \ 2016
PloS Biology 14 (2016)7. - ISSN 1545-7885

In the past decade, biobanking has fuelled great scientific advances in the human medical sector. Well-established domesticated animal biobanks and integrated networks likewise harbour immense potential for great scientific advances with broad societal impacts, which are currently not being fully realised. Political and scientific leaders as well as journals and ethics committees should help to ensure that we are well equipped to meet future demands in livestock production, animal models, and veterinary care of companion animals.

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