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Lanigan, Simon, 2024. Estimating Variant Intolerance for Genes of Cattle. Second cycle, A2E. Uppsala: SLU, Dept. of Animal Breeding and Genetics

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Abstract

Cattle play a crucial role in providing nutrition and economic stability worldwide. Threats to their health, particularly infectious diseases, and genetic mutations, can have profound implications for both animal and human livelihoods. With advancements in high-throughput sequencing technologies, the wealth of genomic information available has enabled researchers to explore the relationships between genes, diseases, and phenotypic traits in cattle. Genes vary in their tolerance to mutation, influenced by factors such as functional importance, evolutionary conservation, redundancy, genomic location, presence of mutational hotspots, evolutionary history, regulatory elements, and their essentiality for fundamental biological processes. Using data from the 1000 Bull Genomes Project, encompassing over 1000 individual cattle, a comprehensive analysis of genic functional intolerance within the bovine population was conducted. The primary objective was to assess the tolerance levels of protein-coding bovine genes to functional variation, ranking them based on their level of tolerance using the RVIS method and by analysing the variants present within the dataset. Computational tools such as VEP, PLINK, PANTHER and GALLO were used to prioritize variants and determine their level of tolerance to mutation. The scoring and ranking of genes allowed for the identification of subsets of top and bottom genes, which were subject to further analysis. This contributed to the broader understanding of genomic variants and the impact in which they could potentially have in bovine animals, alongside the implications for selective breeding, disease resistance, and overall herd management, ultimately contributing to the sustainable and resilient future of cattle populations worldwide.

Main title:Estimating Variant Intolerance for Genes of Cattle
Authors:Lanigan, Simon
Supervisor:Johnsson, Martin and Derks, Martijn
Examiner:Johansson, Anna Maria
Series:UNSPECIFIED
Volume/Sequential designation:UNSPECIFIED
Year of Publication:2024
Level and depth descriptor:Second cycle, A2E
Student's programme affiliation:Other
Supervising department:(VH) > Dept. of Animal Breeding and Genetics
Keywords:Genes, Cattle
URN:NBN:urn:nbn:se:slu:epsilon-s-19744
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-s-19744
Language:English
Deposited On:05 Mar 2024 08:15
Metadata Last Modified:06 Mar 2024 02:01

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