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Analysis of functional polymorphisms associated with feed efficiency in Nelore cattle

Grant number: 16/11585-8
Support type:Scholarships in Brazil - Scientific Initiation
Effective date (Start): August 01, 2016
Effective date (End): November 17, 2017
Field of knowledge:Agronomical Sciences - Animal Husbandry
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:14/07566-2 - Genomics applied to ruminant production, AP.TEM

Abstract

Due to population growth and increased demand for beef, studies in the area of feed efficiency (FE) for beef cattle are justifiable, as this feature is related to increasing productivity. As a time-consuming and costly measure, the identification of molecular markers associated with FE is essential to easily select superior animals. This study aims to identify functional genomic variations associated with the FE by analyzing the sequence of transcripts expressed in the liver of beef cattle Nellore. We used liver samples from 8 high efficiency animal feed (EAF) and 8 animals low feed efficiency (LFE). The RNA from the samples were extracted and sequenced on Illumina HiSeq equipment 2500. In addition, the were aligned with the genome of bovine reference (UMD3.1) and passed through a quality control where PCR duplicates were excluded, secondary alignments and alignments with low quality. In order to identify functional polymorphisms associated with SAA, it will be used SAMtools software and the generated files will be used as input for the CLCbio software, in order to make the quality control that will keep only variations quality > 30 and sequencing depth > 4. Later the genotypes with the frequency difference between high and low and the groups will be identified. The variations found will be analyzed in the online tool VEP to identify their functional consequences. Polymorphisms that are important for the feature will be evaluated in animal population already phenotyped with genetic material kept in the sample bank Animal Breeding and Biotechnology Group FZEA-USP. After that, we expect to determine a set of molecular markers with potential functional implication in HE feature that after undergoing validation in a larger population of animals evaluated for this feature can be used to select more efficient animals.