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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Record number 562738
Title Accelerated discovery of functional variation in pigs
Author(s) Derks, M.F.L.; Megens, H.J.W.C.; Bosse, M.; Lopes, Marcos S.; Harlizius, Barbara; Groenen, M.
Source In: Wias Annual Conference 2020. - WIAS - p. 38 - 38.
Event WIAS Annual Conference 2020, Lunteren, 2020-02-13/2020-02-14
Department(s) Animal Breeding and Genomics
Aquaculture and Fisheries
WIAS
Publication type Abstract in scientific journal or proceedings
Publication year 2020
Abstract The genotype-phenotype link is a major research topic in the life sciences, but remains highly complex to disentangle. Part of the complexity arises from the polygenicity of phenotypes,in which many (interacting) genes contribute to the observed phenotype. Genome wide association studies have been instrumental to associate genomic markers to important phenotypes. However, despite the vast increase of molecular data (e.g. whole genome sequences), pinpointing the causal variant underlying a phenotype of interest is still a major challenge, especially due to high levels of linkage disequilibrium in livestock. In this study we present a method to prioritize genomic variation underlying traits of interest from genome wide association studies in pigs. First, we select all sequence variants associated with the trait. Subsequently, we prioritize variation by utilizing and integrating predicted variant impact scores, gene expression data, epigenetic marks for promotor and enhancer identification, and associated phenotypes in other (well-studied) mammalian species. The power of the approach heavily relies on variant impact scores, for which we used pCADD, a tool which can assign scores to any variant in the genome including those in non-coding regions. Using our methodology, we are able to either pinpoint the likely causal mutation or substantially narrow down the list of potentially causal candidates from any association result. We demonstrate the efficacy of the tool by reporting known and novel causal variants, of which many affect (non-coding) regulatory sequences associated with important phenotypes in pigs. This study provides an approach to pinpoint likely causal variation and genes underlying important phenotypes in pigs, accelerating the discovery of new causal variants that could be directly implemented to improve selection.
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