From sequence to phenotype: the impact of deleterious variation in livestock

Research output: Thesisinternal PhD, WU

Abstract

The genome provides a blueprint of life containing the instruction, together with the environment, that determine the phenotype. In animal breeding, we try to understand this relationship between an animals genetic code (genome sequence) and its performance (phenotype) to select the best performing animals for the next generation. Recently, rapid improvements in genome sequencing have opened up new possibilities to explore and use the complete set of genetic variation seen in (livestock) animals that can be exploited by scientists to try and further close the genotype-phenotype link. However, despite the vast increase of molecular data, pinpointing the exact variants underlying a phenotype of interest is still challenging. In this thesis I provide an in-depth analysis of population genomics and transcriptomics data to identify deleterious and functional variation in livestock populations. More specifically, I report several variants that causes lethality in homozygous state within different stages of development. Moreover, I pinpoint the exact causal mutations and describe its functional consequences at the molecular, phenotypic, and population level. Subsequently, I focus on the identification of functional variation underlying important selection traits. I combine various sources of functional (epi)genomic data to predict the impact of variation in livestock. Together I provide a comprehensive overview of high-impact variation and molecular mechanisms affecting important phenotypes in various livestock breeds, and discuss that molecular genomics could benefit genomic prediction in livestock.

Original languageEnglish
QualificationDoctor of Philosophy
Awarding Institution
  • Wageningen University
Supervisors/Advisors
  • Groenen, M.A.M., Promotor
  • Megens, Hendrik-Jan, Co-promotor
Award date2 Sept 2020
Place of PublicationWageningen
Publisher
Print ISBNs9789463953207
DOIs
Publication statusPublished - 2 Sept 2020

Keywords

  • Cum laude

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