Combining high-density SNP genotypes and next generation sequence data to map disadvantageous genetic variants in Nellore cattle

Abstract

All animal species carry a genetic load of disadvantageous allelic variants. Those that are lethal occur only in the heterozygous state while those non-lethal can reduce the fitness of homozygous individuals for the variant. The long-term destiny of these mutations in outbred species is to decrease in frequency, due to negative selection, and disappear. However, in livestock populations they could be kept or even increase in frequency, when occurring in linkage with favourable alleles or carried by important sires. This proposal aims to detect these disadvantageous variants in Nellore cattle, the most important beef breed in Brazil. Inbreeding or fertility problems are not commonly reported in the Nellore population although there are real chances to have them increased in the future, due to artificial selction. The general objective of this research proposal is to build knowledge and anticipate possible problems caused by disadvantageous variants by implementing actions to avoid their spreading. High- density SNP genotyping data will be use to identify loss-of-homozygosity haplotypes. The characterization of them will be conducted using public information (i.e. previous research results, gene function information, associations with genetic diseases) and putative causative variants database of potential disadvantageous sequence variants (coding and noncoding conserved sequences) and structural variants, which will be created using the complete sequence data from twenty four key Nellore bulls. (AU)