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 515733
Title The importance of endophenotypes to evaluate the relationship between genotype and external phenotype
Author(s) Pas, Marinus F.W. te; Madsen, Ole; Calus, Mario P.L.; Smits, Mari A.
Source International Journal of Molecular Sciences 18 (2017)2. - ISSN 1661-6596
DOI https://doi.org/10.3390/ijms18020472
Department(s) Animal Breeding & Genomics
WIAS
Animal Breeding and Genomics
Infection Biology
Publication type Refereed Article in a scientific journal
Publication year 2017
Keyword(s) Bioinformatics - Genomic variation and environment - Integration - Livestock science - Metabolome - Methylome - Phenome - Proteome - Systems biology - Transcriptome
Abstract

With the exception of a few Mendelian traits, almost all phenotypes (traits) in livestock science are quantitative or complex traits regulated by the expression of many genes. For most of the complex traits, differential expression of genes, rather than genomic variation in the gene coding sequences, is associated with the genotype of a trait. The expression profiles of the animal’s transcriptome, proteome and metabolome represent endophenotypes that influence/regulate the externally-observed phenotype. These expression profiles are generated by interactions between the animal’s genome and its environment that range from the cellular, up to the husbandry environment. Thus, understanding complex traits requires knowledge about not only genomic variation, but also environmental effects that affect genome expression. Gene products act together in physiological pathways and interaction networks (of pathways). Due to the lack of annotation of the functional genome and ontologies of genes, our knowledge about the various biological systems that contribute to the development of external phenotypes is sparse. Furthermore, interaction with the animals’ microbiome, especially in the gut, greatly influences the external phenotype. We conclude that a detailed understanding of complex traits requires not only understanding of variation in the genome, but also its expression at all functional levels.

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