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Unraveling important genetic associations and differential methylation profiles using reduced genome sequencing in chickens

Pértille, Fábio

Biblioteca Digital de Teses e Dissertações da USP; Universidade de São Paulo; Escola Superior de Agricultura Luiz de Queiroz 2016-11-01

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  • Título:
    Unraveling important genetic associations and differential methylation profiles using reduced genome sequencing in chickens
  • Autor: Pértille, Fábio
  • Orientador: Coutinho, Luiz Lehmann
  • Assuntos: Saúde E Bem-Estar Animal; Melhoramento Animal; Medips; Gwas; Galinha; Chicken; Animal Health And Welfare; Animal Breeding
  • Notas: Tese (Doutorado)
  • Descrição: Chickens are ideal model organism to improve understanding of several research areas as phylogenetic, embryology, biomedicine, livestock, and have recently been suggested as a promising model for epigenetic studies. In the livestock area, chickens are source of protein to humans and had been selected to achieve a high production standards based on genetic breeding by the traditional selection. We are now in the genomics and epigenomics era and it is time be concern about the use of new tools to improve selection not only thinking about production, but also in the health and welfare of animals. The use of molecular approaches, have been a fundamental tool to understand biological models and improve selection strategies based on genomic information in breeding programs. Molecular approaches have also contributed to understanding of the evolutionary history of these models and the genetics and epigenetics mechanisms involved in evolution process and genetic diversification of chickens. In this context, many technologies have emerged to produce high-throughput data using Next-generation sequencing (NGS) approaches. NGS provided a large amount of information for diverse purposes such as to detect single nucleotide polymorphisms (SNPs), and methylated DNA profiles in chickens. In addition, NGS has allowed the development of pre-designed SNP arrays for genome-wide association studies (GWAS) with specific phenotypes of interest. Moreover, although NGS has enough power to detect informative polymorphisms, its high cost makes it impractical to be used in GWAS and Methylated DNA immunoprecipitation sequencing (MeDIPseq) studies. The demand for an economical, efficient, simple-step and reliable genome-wide method of SNPs discovery, validation and characterization, was the reason for the development of this study. We applied reduced representation sequence by restriction enzyme (RE) cleavage of target chicken genome to be applied in GWAS. Thereafter, to combine the reduced representation of the genome with MeDIPseq method, we developed a novel approach to perform differential methylation studies using reduced libraries. These works allowed us to identify SNPs associated with performance traits and differential methylation windows related to different stress conditions in chickens.
  • DOI: 10.11606/T.11.2016.tde-29112016-121348
  • Editor: Biblioteca Digital de Teses e Dissertações da USP; Universidade de São Paulo; Escola Superior de Agricultura Luiz de Queiroz
  • Data de criação/publicação: 2016-11-01
  • Formato: Adobe PDF
  • Idioma: Inglês
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  • Realização: ABCD-USP USP   Logos de Redes Sociais: Freepik

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