CNPQ 422863/2018-1. Genetic architecture of functional traits in Nelore cattle

Several cattle genetic improvement programs in Brazil have successfully promoted the genetic progress of herds. One of the major drivers of such programs was the establishment of the Special Certificate of Identification and Production (CEIP), granted by the Ministry of Agriculture, Livestock, and Supply (MAPA, 1995). In improvement programs authorized to issue CEIP, between 20% to 30% of the best animals from each crop become candidates to receive this certificate. After the genetic evaluation stage, the CEIP candidate animals undergo a final inspection, which covers different morphological and functional criteria. The identification of issues in any of these criteria may lead to the disqualification of a candidate, preventing it from receiving the CEIP. In some herds, a significant portion of the candidate animals do not receive this certificate due to the occurrence of these issues, which will be referred to in this project as 'disqualifying traits.' Depigmentation, testicular hypoplasia, pendulous prepuce or prolapse, and limb problems are among the main disqualifying traits. In addition to the economic losses resulting from the disqualification of CEIP candidate animals, the disqualifying traits imply functional problems that can negatively impact the performance of the affected animals, so reducing their incidence in herds could also contribute to increasing beef production efficiency. This project was designed to generate knowledge that could assist in defining selection and mating strategies to reduce the incidence of disqualifying traits in Nelore breed improvement programs by identifying markers and candidate genes associated with the expression of such traits. To achieve this, data from the Aliança Nelore database, which contains phenotypes of approximately one hundred thousand animals evaluated for disqualifying traits, as well as genotypic data of approximately fifteen thousand animals genotyped with medium to high-density marker panels, will be used. The animals' genotypes will be imputed to the sequence using around 250 Nelore bulls with sequenced genomes as the reference population for imputation. Genome-wide association studies will be conducted to identify regions and candidate genes associated with disqualifying traits. Animals presenting limb problems, depigmentation, pendulous prepuce, and testicular hypoplasia will have their genomes sequenced to help refine the search for causal mutations through comparative genomic studies of the 'case vs. control' type. The results of this project are expected to generate knowledge that will enhance selection and mating processes in the genetic improvement programs of the Nelore breed, positively impacting the efficiency and competitiveness of the beef production sector, which is an important source of food, employment, and income for Brazil.