Association between genomic inbreeding coefficients and reproductive traits in Nelore cattle

Abstract

Inbreeding has been suggested as a cause of reduced reproductive performance in cattle. This negative relationship is known as 'inbreeding depression', and evidence supporting this hypothesis comes from studies of association between reproductive measures and estimates of the inbreeding coefficient (F). Traditionally, the inbreeding coefficient is calculated based on expectations from pedigree data (FPED), which is often incomplete and susceptible to error. The emergence of high-throughtput DNA microarrays capable of determining the genotypic profile of hundreds of thousands of single site polymorphisms (SNP) genome-wide allowed for obtaining more robust estimates of inbreeding coefficients through the detection of runs of homozygosity (ROH) in the bovine genome. The present project aims at seeking associations between genomic inbreeding coefficients (FROH) and estimated breeding values (EBV) for Scrotal Circumference (SC), Age at First Calving (AFC) and Gestation Length (GL) in Nellore cattle, using data from over 2,000 Nellore samples genotyped for over 777,000 SNPs. Runs of homozygosity (ROH) will be identified for each individual using the software SNP & Variation Suite (Golden Helix) and levels of individual autozigosity shall be associated with phenotypes using linear mixed model weighted in order to identify regions of the genome that influence the manifestation of reproductive traits in cattle.Key Terms: Cattle, Nellore, Inbreeding, Genomics, SNP, Runs of homozigosity.