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Identification of functional variants of the type SNP, indels and isoforms of alternative splicing associated with feed efficiency in Nelore cattle

Grant number: 19/01234-1
Support type:Scholarships in Brazil - Master
Effective date (Start): July 01, 2019
Effective date (End): February 29, 2020
Field of knowledge:Agronomical Sciences - Animal Husbandry
Cooperation agreement: Coordination of Improvement of Higher Education Personnel (CAPES)
Principal Investigator:Heidge Fukumasu
Grantee:Gabriela Ribeiro
Home Institution: Faculdade de Zootecnia e Engenharia de Alimentos (FZEA). Universidade de São Paulo (USP). Pirassununga , SP, Brazil
Associated research grant:14/02493-7 - Mammary tumors of dogs and the cancer stem cell theory: a comparative and translational approach, AP.JP

Abstract

Feed efficiency (FE) in animal protein production systems is a feature of great importance since the identification of more efficient animals reflects better productivity and sustainability indexes of the productive chain. However, the evaluation of this characteristic is complex, slow and costly, which has required more efficient approaches to identify animals with superior genetics for FE. A possible strategy is the identification of molecular markers that allow the selection of animals that present better FE. Approaches based on large association studies of the genome (GWAS) have generated a lot of information, but in the vast majority of cases the markers found are not responsible for the phenotypic (causal) effects, which makes the results analysis speculative using genes present in chromosomal windows. Another criticism of these studies is that the analysis of polymorphisms from the DNA of any cell fails to understand the functional and tissue-specific importance of the causal variants in a given phenotype. Therefore, the objective of this project is to identify functional variations of single nucleotide polymorphism (SNP) and Indels (insertions and deletions) and alternative splicing associated with FE from transcriptomic data (RNA-seq) of tissues representative for the efficiency phenotype as hypothalamus, pituitary, adrenal, liver and skeletal muscle of Nelore cattle. In order to achieve these goals, samples of the respective tissues of nine animals with high feed efficiency (HFE) and nine animals with low feed efficiency (LFE) from a population of 98 whole male Nelore animals evaluated for FE will be used. The multitecidual transcriptome analyzes were carried out in a PhD project (FAPESP) (2015 / 22276-3). In this project will be used the transcriptomic data to perform the identification of the functional variants with the use of bioinformatics programs. With the identification of functional variants related to FE, we will perform functional enrichment analyzes and analysis of the effect of these variants on the function of proteins. The most interesting variants will be validated in an independent population provided by the FZEA-USP Animal Breeding and Biotechnology Group. For the alternative splicing analysis, we will use bioinformatics programs to identify isoforms between the HFE and LFE groups, as well as evaluate the presence of polymorphisms in the Exonic Splicing Enhancer (ESE) and Exonic Splicing Silencer (ESS) regions. To integrate the data will be carried out the construction of biological networks from the functional variants significant for the FE. This last stage will be carried out in a research internship abroad by the CSIRO candidate under the tutelage of the Researcher Dr. Laercio Porto Neto.