Imputation accuracy to whole genome sequence in Nellore beef cattle

Abstract

Advances in next-generation sequencing techniques associated to a drastically decreasing in sequencing costs is favoring the development of strategies to explore the complete DNA sequence in genetic evaluations due to the possibility of using causal mutations. Anyway, it is still cheaper genotyping a large number of animals than sequencing them. An alternative and cost-effective strategy would be to sequence key ancestors of the population, and impute sequence to the remaining reference population of animals genotyped with low density SNP panels. Our research group has a database with more than 10,000 animals, among bulls, dams, and young animals, from different breeding programs and genotyped with Illumina SNP panels with different densities. Using sequence data of influential Nellore bulls, we can carry out the imputation of this reference population to whole genome sequence, which will increase the amount of genomic information per animal. A previous investigation of the imputation accuracy is essential to determine the feasibility of this process. This issue will be investigated in the present research Project, in order to generate information on sequence imputation accuracy in Nellore cattle, in addition to develop a pipeline to impute sequence data to about 10,000 animals of an existing Nellore genotype database. (AU)