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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    Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals
    Bouwman, Aniek C. ; Daetwyler, Hans D. ; Chamberlain, Amanda J. ; Ponce, Carla Hurtado ; Sargolzaei, Mehdi ; Schenkel, Flavio S. ; Sahana, Goutam ; Govignon-Gion, Armelle ; Boitard, Simon ; Dolezal, Marlies ; Pausch, Hubert ; Brøndum, Rasmus F. ; Bowman, Phil J. ; Thomsen, Bo ; Guldbrandtsen, Bernt ; Lund, Mogens S. ; Servin, Bertrand ; Garrick, Dorian J. ; Reecy, James ; Vilkki, Johanna ; Bagnato, Alessandro ; Wang, Min ; Hoff, Jesse L. ; Schnabel, Robert D. ; Taylor, Jeremy F. ; Vinkhuyzen, Anna A.E. ; Panitz, Frank ; Bendixen, Christian ; Holm, Lars Erik ; Gredler, Birgit ; Hozé, Chris ; Boussaha, Mekki ; Sanchez, Marie Pierre ; Rocha, Dominique ; Capitan, Aurelien ; Tribout, Thierry ; Barbat, Anne ; Croiseau, Pascal ; Drögemüller, Cord ; Jagannathan, Vidhya ; Vander Jagt, Christy ; Crowley, John J. ; Bieber, Anna ; Purfield, Deirdre C. ; Berry, Donagh P. ; Emmerling, Reiner ; Götz, Kay Uwe ; Frischknecht, Mirjam ; Russ, Ingolf ; Sölkner, Johann ; Tassell, Curtis P. van; Fries, Ruedi ; Stothard, Paul ; Veerkamp, Roel F. ; Boichard, Didier ; Goddard, Mike E. ; Hayes, Ben J. - \ 2018
    Nature Genetics 50 (2018). - ISSN 1061-4036 - p. 362 - 367.
    Stature is affected by many polymorphisms of small effect in humans1. In contrast, variation in dogs, even within breeds, has been suggested to be largely due to variants in a small number of genes2,3. Here we use data from cattle to compare the genetic architecture of stature to those in humans and dogs. We conducted a meta-analysis for stature using 58,265 cattle from 17 populations with 25.4 million imputed whole-genome sequence variants. Results showed that the genetic architecture of stature in cattle is similar to that in humans, as the lead variants in 163 significantly associated genomic regions (P < 5 × 10−8) explained at most 13.8% of the phenotypic variance. Most of these variants were noncoding, including variants that were also expression quantitative trait loci (eQTLs) and in ChIP–seq peaks. There was significant overlap in loci for stature with humans and dogs, suggesting that a set of common genes regulates body size in mammals.
    Which individuals to choose to update the reference population? Minimizing the loss of genetic diversity in animal genomic selection programs
    Eynard, Sonia E. ; Croiseau, Pascal ; Laloë, Denis ; Fritz, Sebastien ; Calus, Mario P.L. ; Restoux, Gwendal - \ 2018
    G3 : Genes Genomes Genetics 8 (2018)1. - ISSN 2160-1836 - p. 113 - 121.
    Genetic diversity - Genomic selection - GenPred - Optimal contribution - Reference population - Shared data resources
    Genomic selection (GS) is commonly used in livestock and increasingly in plant breeding. Relying on phenotypes and genotypes of a reference population, GS allows performance prediction for young individuals having only genotypes. This is expected to achieve fast high genetic gain but with a potential loss of genetic diversity. Existing methods to conserve genetic diversity depend mostly on the choice of the breeding individuals. In this study, we propose a modification of the reference population composition to mitigate diversity loss. Since the high cost of phenotyping is the limiting factor for GS, our findings are of major economic interest. This study aims to answer the following questions: how would decisions on the reference population affect the breeding population, and how to best select individuals to update the reference population and balance maximizing genetic gain and minimizing loss of genetic diversity? We investigated three updating strategies for the reference population: random, truncation, and optimal contribution (OC) strategies. OC maximizes genetic merit for a fixed loss of genetic diversity. A French Montbéliarde dairy cattle population with 50K SNP chip genotypes and simulations over 10 generations were used to compare these different strategies using milk production as the trait of interest. Candidates were selected to update the reference population. Prediction bias and both genetic merit and diversity were measured. Changes in the reference population composition slightly affected the breeding population. Optimal contribution strategy appeared to be an acceptable compromise to maintain both genetic gain and diversity in the reference and the breeding populations.
    Updating reference population in genomic selection for genetic diversity conservation. What can we learn from real data and simulations?
    Eynard, S.E. ; Croiseau, P. ; Laloë, Denis ; Calus, M.P.L. ; Fritz, S. ; Restoux, G. - \ 2017
    Which individuals to phenotape? Optimal design of reference population for genomic selection while maintaining genetic diversity
    Eynard, S.E. ; Laloe, D. ; Croiseau, P. ; Calus, M.P.L. ; Fritz, S. ; Restoix, G. - \ 2016
    Bos taurus strain:dairy beef (cattle): 1000 Bull Genomes Run 2, Bovine Whole Genome Sequence
    Bouwman, A.C. ; Daetwyler, H.D. ; Chamberlain, Amanda J. ; Ponce, Carla Hurtado ; Sargolzaei, Mehdi ; Schenkel, Flavio S. ; Sahana, Goutam ; Govignon-Gion, Armelle ; Boitard, Simon ; Dolezal, Marlies ; Pausch, Hubert ; Brøndum, Rasmus F. ; Bowman, Phil J. ; Thomsen, Bo ; Guldbrandtsen, Bernt ; Lund, Mogens S. ; Servin, Bertrand ; Garrick, Dorian J. ; Reecy, James M. ; Vilkki, Johanna ; Bagnato, Alessandro ; Wang, Min ; Hoff, Jesse L. ; Schnabel, Robert D. ; Taylor, Jeremy F. ; Vinkhuyzen, Anna A.E. ; Panitz, Frank ; Bendixen, Christian ; Holm, Lars-Erik ; Gredler, Birgit ; Hozé, Chris ; Boussaha, Mekki ; Sanchez, Marie Pierre ; Rocha, Dominique ; Capitan, Aurelien ; Tribout, Thierry ; Barbat, Anne ; Croiseau, Pascal ; Drögemüller, Cord ; Jagannathan, Vidhya ; Vander Jagt, Christy ; Crowley, John J. ; Bieber, Anna ; Purfield, Deirdre C. ; Berry, Donagh P. ; Emmerling, Reiner ; Götz, Kay Uwe ; Frischknecht, Mirjam ; Russ, Ingolf ; Sölkner, Johann ; Tassell, Curtis P. van; Fries, Ruedi ; Stothard, Paul ; Veerkamp, R.F. ; Boichard, Didier ; Goddard, Mike E. ; Hayes, Ben J. - \ 2014
    Wageningen University & Research
    Bos taurus - PRJNA238491
    Whole genome sequence data (BAM format) of 234 bovine individuals aligned to UMD3.1. The aim of the study was to identify genetic variants (SNPs and indels) for downstream analysis such as imputation, GWAS, and detection of lethal recessives. Additional sequences for later 1000 bull genomes runs can be found at partners individual projects including PRJEB9343, PRJNA176557, PRJEB18113, PRNJA343262, PRJNA324822, PRJNA324270, PRJNA277147, PRJEB5462.
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