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Etude des polymorphismes altérant la régulation de l'expression des gènes chez le bovin

Abstract : An increasing number of genes and genomic loci have been associated with diseases or phenotypes of interest, by either linkage or association studies. Identifying causative genetic variants is crucial. The regulators with the strongest effect tend to be cis-acting regulatory polymorphisms, close to genes for which altered mRNA expression was detected. The overall objective of this PhD project is to develop a large-scale approach to identify regulatory polymorphisms that potentially alter the regulation of gene expression and impact phenotypes of interest, in cattle.We have developed an approach to ascertain causative SNPs (Single Nucleotide Polymorphisms) of gene expression regulation. To this end, we analysed genome and muscle transcriptome from 19 Limousine bull calves and genome and transcriptome of eight tissues (including ovary and uterus) transcriptome from 6 Holstein cows. For the Limousine breed, we identified 5,658 SNPs showing an allele-specific expression (ASE-SNPs) in 13% of genes with detectable expression in muscle; we linked some of them to SNPs in a regulatory region. Interestingly, we found genes involved in meat quality traits (AOX1, PALLD and CAST) with an allelic imbalance. For the Holstein breed, we identified 33, 527 ASE-SNPs across 8 tissues including 3,369 ASE-SNPs from muscle data, 5,771 from ovary data and 5,499 from uterus data. By analysing these two data records, we discovered genes impacted by ASE. This study is the first done for the Limousine breed and the second for thr Holstein breed.The results of these studies provide a best understanding of gene expression regulation in cattle, in particular by identifying candidate causal polymorphisms and by proposing new methods to detect them.
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Gabriel Guillocheau. Etude des polymorphismes altérant la régulation de l'expression des gènes chez le bovin. Biologie moléculaire. Université Paris-Saclay, 2018. Français. ⟨NNT : 2018SACLA045⟩. ⟨tel-02512598⟩

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