High levels of endogamy in the population can increase the frequency of deleterious alleles combined in homozygotes and reduce the adaptive value of the animals. Traditional methods to calculate inbreeding use only estimates obtained with pedigree information. As most pedigrees are incomplete, methods that consider information from high density molecular markers have been used for this purpose. Genome regions in homozygous can be studied using, for example, runs of homozygosity (ROH), in order to identify the effects of inbreeding on productive traits. However, it is expected that ROH can be estimated more accurately using full-sequence data, because the use of SNP chips may overestimate or underestimate the number of ROHs. The objective of this project will be to calculate inbreeding coefficients using different methodologies and to perform functional annotation of the variants present in homozygous regions, classifying them as "deleterious" or "tolerant" in the Nellore breed, in order to generate information that will assist the programs of genetic improvement to direct the mating of these animals. For this, 50 animals with complete sequencing will be used to estimate the homozygosity based on ROH - FROH, genomic relation matrix (FGRM), homozygosity excess (FHOM) and correlation of uniting gamets (FUNI). The ROH islands will be identified by an autozygosity coefficient and the functional variants present in the islands will be studied using the VEP tool (predictor of the variant effect) of the ENSEMBL software. SIFT scores will also be used to classify mutations as "deleterious" or "tolerant".
News published in Agência FAPESP Newsletter about the scholarship: