Analysis of copy number variations in the genome of Nellore and its associations with the fatty acid profile of the meat

• Grant number: 13/11853-4
• Support Opportunities: Scholarships in Brazil - Doctorate
• Start date: September 01, 2013
• End date: May 31, 2017
• Field of knowledge: Agronomical Sciences - Animal Husbandry - Genetics and Improvement of Domestic Animals
• Principal Investigator: Fernando Sebastián Baldi Rey
• Grantee: Marcos Vinícius Antunes de Lemos
• Host Institution: Faculdade de Ciências Agrárias e Veterinárias (FCAV). Universidade Estadual Paulista (UNESP). Campus de Jaboticabal. Jaboticabal , SP, Brazil
• Associated research grant: 11/21241-0 - Study of the genetic variability of meat fatty acid profile in Nelore cattle finished in feedlot, AP.JP
• Associated scholarship(s): 15/08798-7 - Study of metabolic pathways of genes associated with fatty acid profile of Nellore cattle meat, BE.EP.DR

Abstract

In recent years, meat fatty acids can contribute harmful to human health and have received considerable attention. Several studies with taurine breeds have showed the existence of genetic variability and therefore the possibility of genetic improvement for fatty acid composition. However, there are still few works for Zebu breeds. For such traits the use of genomic information trough genomic selection, which is a type of marker assisted selection, is recommended. A newly recognized source of genomic variation called structural variation in the number of copies (CNV: Copy number variation), is gaining interest in genomic studies. The CNV is defined as a DNA segment which has 1 kb or more in length and is present at a variable copy number compared to the reference genome. The information obtained in the arrangements of SNPs allow CNVs are investigated in large-scale studies. The knowledge of the abundance and distribution of CNVs and their association with phenotypes are of great interest. However, up to now, relatively few studies have investigated CNVs in cattle. Due to the limited numbers of studies, and peeve??? the fatty acid profile of the meat palatability and on human health, it is essential to develop works that use genomic information to improve the fatty acid composition in Nellore cattle. The goal of this project is to identify and validate areas of the genome in Nellore cattle that have copy number variations (CNV: Copy Number Variation) and associate these CNV with meat fatty acid profile. The specific objectives are: 1. Identify areas of the genome that show variation in copy number from genomic information obtained with the BovineSNP BeadChip (High-Density Bovine BeadChip); 2. Quantify the frequency and distribution of the CNVs in Nellore cattle; 3 Use quantitative real-time PCR (qPCR) to validate 10 CNVs; 4. Study the genetic association between CNVs with the composition of fatty acids in meat. A total of 1000 Nelore males finished under feedlot conditions (minimum 90 days) and aged around two years old will be used. From the concentration of individual fatty acids, the proportion of saturated fatty acids, monounsaturated fatty acids, polyunsaturated fatty acids, the relationship between polyunsaturated fatty acids and saturated fatty acids, fatty acids of the series n-6 fatty acids from n-serie 3, and n-6/n-3 ratio. Moreover, the rates of desaturation (ID) (addition of a double bond) and elongation (EI) (conversion of the chains 16 to 18 carbon atoms) it will be calculated. The animals will be genotyped with a panel with more than 777,000 SNP BovineSNP BeadChip. The process of identification of CNVs will be accomplished through data generated by genotyping of animals through GenomeStidio 1.0 software, which analyzes each SNP in particular. The algorithm used for detection of CNV will be PennCNV. The real time quantitative PCR (qPCR) will be use to validate 10 CNVs detected. The association analyzes will be carried out considering the phenotypic records and breeding values for fatty acids. The genome wide association analysis with the phenotypic records will be performed with a general linear model. The model will include the fixed effect of contemporary group, the fixed effect of CNV state and the age of the animal at slaughter as a covariable (linear and quadratic effect). For association analysis with breeding values, the model to be used include the fixed effect of CNV state of. The results of this project will establish new elements to differentiate, develop and promote the attributes of Brazilian beef meat on the basis of a solid scientific and technical support.

Scientific publications

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

DE LEMOS, MARCOS VINICIUS ANTUNES; PERIPOLLI, ELISA; BERTON, MARIANA PIATTO; BRAGA FEITOSA, FABIELE LOISE; OLIVIERI, BIANCA FERREIRA; STAFUZZA, NEDENIA BONVINO; TONUSSI, RAFAEL LARA; KLUSKA, SABRINA; JUSTINO CHIAIA, HERMENEGILDO LUCAS; MUELLER, LENISE; et al. Association study between copy number variation and beef fatty acid profile of Nellore cattle. JOURNAL OF APPLIED GENETICS, v. 59, n. 2, p. 203-223, MAY 2018. (09/16118-5, 13/11853-4)

Academic Publications

(References retrieved automatically from State of São Paulo Research Institutions)

LEMOS, Marcos Vinícius Antunes de. Copy number variations and single-nucleotide polymorphisms associated with beef fatty acid profile in nellore cattle. 2017. Doctoral Thesis - Universidade Estadual Paulista (Unesp). Faculdade de Ciências Agrárias e Veterinárias. Jaboticabal Jaboticabal.