Genome-wide detection of selective sweeps in domesticated animals

Abstract

Animal breeders traditionally aim to domesticated animals by judging a combination of the qualitative and quantitative properties of them. It is not only the genetic constitutions responsible for the traits of interests but also the changes in gene pool directly selected against during domestication process. With the next-generation sequencing, we aim to detect the recent selective sweep that has accelerated on the standing variation during domestication. We showed that the statistic based on FST and differences in sequence variability is likely the most powerful standard in detecting positive selection signatures against demographic history. In racing horses, the Thoroughbred is a recent breed, which has been artificially selected for structural and functional adaptation that contributes to athletic performance phenotypes. We conducted genomic-scan to detect highly divergent sites with reduced variability observed might contribute to the domestication of the racing horse lineage. We show three genetic pathways have been artificially selected in the racing horse

the high degree of specialized in synapse functions made them to be more exquisite to controlling muscle, their skeletal muscles prepares to prevent cells from the exercise-induced DNA damage, and tight cell-cell junction helps to enhance communication in synapse in skeletal muscle. Thus, selection signatures found in this study offer picture of link between cellular mechanism and breeding of racing-performance. A brief breeding history of Thoroughbred provides an opportunity to trace the tempo and mode of domestication. In pigs, maternal traits is an fundamental aspect of fitness is mammals. It is to note that reconstruction of domestication history can shed light on understanding the genetic basis for quantitative traits in pig. In this study, we aim to trace the operation of artificial selection for those maternal traits by detecting domesticated genes into two layers

a more primitive state of pig domestication when they introduced into human society and a more recent state of pig domestication progressed in breeding for quantitative traits such as more fertile and efficient characters. For selective sweep mapping takes advantage of the fact that strong positive selection is expected to leave a local footprint in form of reduced genetic diversity around selected locus when domesticated lineages were compared with their wild ancestor lineages. With the accurate estimation of single-nucleotide polymorphisms (SNP) probability for each site based on resequencing analysis, we found 420 potential domesticated genes underlying the maternal breeds through genome-wide analysis detecting selective sweeps that could be candidates of future genomic selection for breeding animals to enhance reproduction performance, and the network underlying maternal-traits could provide a starting point for integration of regulatory network with quantitative genetic studies for unveiling the epistatic effect of genes influencing complex life-history traits, such as age at reproduction, infant growth rate, and metabolic syndrome risk traits. The results provide a first glimpse into the genome-wide distribution of positive selection, identifying high-priority candidates for positive selection without the dependence on existing knowledge of presumed biology.