BioProject

Tilapia are one of the most commercially important fish in aquaculture, with a worldwide production of Nile tilapia, Oreochromis niloticus, of over 5 million tonnes. More...

Tilapia are one of the most commercially important fish in aquaculture, with a worldwide production of Nile tilapia, Oreochromis niloticus, of over 5 million tonnes. It has become increasingly necessary to track the inheritance of selected traits under continuous improvement (e.g. growth rate, size at maturity or genetic gender), as selective breeding has also resulted in genes that can hitchhike as part of the process. Implementation of local ancestry inference in breeding programmes, such as for the Nile tilapia, allows to monitor the genetic makeup of individuals of interest, to track the movement of genes from parents to offspring, and to identify hybrids and their origin. We developed a workflow and implemented a suite of tools to resolve the local ancestry of each chromosomal locus based on reference panels of tilapia species of known origin. The focus of this study was the improvement of the pipeline accuracy, which was estimated based on its ability to recognise the genetic makeup of samples of known ancestry. We used tilapia species, wild populations as well as breeding programmes to validate our methods. We resolved the local ancestry of admixed individuals successfully at the chromosome level. These were applied to the samples sourced from the breeding programmes. We implemented a fast and accurate pipeline providing useful insights for breeding programmes, for both tilapia and other animals, whether these are aimed at maintaining specific broodstocks or producing new variants. Less...