Methylome and allele specific expression in Nellore with extreme fenotype for feed efficiency

• Grant number: 15/17802-8
• Support Opportunities: Scholarships in Brazil - Doctorate
• Start date: December 01, 2015
• End date: April 30, 2019
• Field of knowledge: Agronomical Sciences - Animal Husbandry - Genetics and Improvement of Domestic Animals
• Principal Investigator: Simone Cristina Méo Niciura
• Grantee: Marina Ibelli Pereira Rocha
• Host Institution: Centro de Ciências Biológicas e da Saúde (CCBS). Universidade Federal de São Carlos (UFSCAR). São Carlos , SP, Brazil
• Associated scholarship(s): 18/06785-3 - Genome-wide methylation profile and co-methylation analysis applied to feed efficiency in Nelore cattle, BE.EP.DR

Abstract

Due to the great importance of livestock to the Brazilian economy, there are many studies based on the improvement of meat and early selection of superior animals for traits of interest, such as the residual feed intake (RFI). With the development and improvement of molecular genetics, especially methods of new generation sequencing of DNA and RNA (RNA-seq), many information is generated and added to the understanding of regulation of gene expression and, consequently, to the biology of these characteristics. The study of the epigenome adds a lot of information to the relationship among genotype, environment and phenotype. Differences in methylation between alleles or allele-specific methylation (ASM) may result in allele-specific expression (ASE) and contribute to the studies of differential expression. In addition, wide epigenetic analysis associated with data from GWAS are necessary to integrate SNP and haplotype data with ASE and ASM. Thus, this project has as objective to analyze the ASE profile in transcriptome and to compare the profile between animals with extreme phenotypic values for RFI. Furthermore, it will characterize the methylation profile of the genome to identify differentially methylated regions (DMR) between the extreme phenotype animals. The results will be integrated to previous results of GWAS and of differentially expressed genes by bioinformatics analyses of RNA-seq data. The methylation analysis will be performed after enrichment of methylated DNA immunoprecipitation, treatment with sodium bisulfite and sequencing in HiSeq2500 (Illumina). Therefore, the development of this project will add new layers of information to the results allowing the enrichment of the information to be used in breeding and animal selection.