Identification of recombination events in Nellore cattle

• Grant number: 19/10123-9
• Support Opportunities: Scholarships abroad - Research Internship - Master's degree
• Effective date (Start): November 01, 2019
• Effective date (End): April 30, 2020
• Field of knowledge: Agronomical Sciences - Animal Husbandry - Genetics and Improvement of Domestic Animals
• Principal Investigator: Lucia Galvão de Albuquerque
• Grantee: Patrícia Iana Schmidt
• Supervisor: Li Ma
• Host Institution: Faculdade de Ciências Agrárias e Veterinárias (FCAV). Universidade Estadual Paulista (UNESP). Campus de Jaboticabal. Jaboticabal , SP, Brazil
• Research place: University of Maryland, College Park, United States
• Associated to the scholarship: 18/17812-1 - Identification of candidate lethal haplotypes in Nelore cattle, BP.MS

Abstract

Recombination is a fundamental biological process in which parental genetic materials are exchanged during the egg or sperm meiosis; in addition, failures in recombination may lead to a potentially deleterious outcome, as aneuploidy. The objectives of the present study are to identify recombination events in male and female Nellore cattle and, through functional analyzes, to identify deleterious candidate genes located in regions of low recombination. A total of 4,669 animals were genotyped with a high-density panel containing 777,962 SNP markers and 4,094 with a panel containing 70,000 markers, which will be imputed to the HD panel using findhap.f90 software. Recombination rates will be measured by an indirect method using pedigree. To construct recombination maps, the rate of recombination between consecutive SNPs as the mean number of crossovers by meiosis will be estimated by uniformly assigning a crossing event to all SNP intervals between two informative SNPs. Recombination data will be divided by sex to evaluate recombination map patterns in males and females, and the chi-square test will be applied to determine if the proportion of cross-events in a range of SNP by meiosis is different between the sexes. To identify the causal variants underlying the low recombination regions, we will use ENSEMBL software. SIFT scores will be used to classify mutations as deleterious or tolerant. Lethal genes during the development of all stages of life will be described and marked as candidate genes. The results of this work will provide information about the genetic mechanism and the evolution of recombination for Nellore breed.