Abstract
Tilapia is one of the most commercially valuable species in aquaculture with over 5 million tonnes of Nile tilapia, Oreochromis niloticus, produced worldwide every year. It has become increasingly important to keep track of the inheritance of the 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. The goal of this study was to generate a Local Ancestry Interence workflow that harnessed existing tilapia genotyping-by-sequencing studies, such as Double Digest RAD-seq derived Single-Nucleotide Polymorphism markers. 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. We used tilapia species, wild populations and breeding programmes to validate our methods. The precision of the pipeline was evaluated on the basis of its ability to identify the genetic makeup of samples of known ancestry. The easy and inexpensive application of local ancestry inference in breeding programmes will facilitate the monitoring of the genetic profile of individuals of interest, the tracking of the movement of genes from parents to offspring and the detection of hybrids and their origin.
Highlights
Tilapia is one of the most commercially valuable species in aquaculture with over 5 million tonnes of Nile tilapia, Oreochromis niloticus, produced worldwide every year
Local Ancestry Inference (LAI) applications are more frequent in studies of dog breeds, as in the case of Alaskan sled d ogs[1], in which tracing of ancestry in sprint and long-distance sled dogs contributed to the identification of the genomic regions that correlated with performance-enhancing traits
In humans, such tools have been more widely used to analyse how past migration events have impacted existing p opulations[2] and to improve identification of ancestry-specific genetic susceptibility to disease in genome-wide association s tudies[3]
Summary
Tilapia is one of the most commercially valuable species in aquaculture with over 5 million tonnes of Nile tilapia, Oreochromis niloticus, produced worldwide every year. The easy and inexpensive application of local ancestry inference in breeding programmes will facilitate the monitoring of the genetic profile of individuals of interest, the tracking of the movement of genes from parents to offspring and the detection of hybrids and their origin Despite their prominent role in aquaculture, the volume of research involving tilapia is relatively low when compared to other fish species, like salmonids. Local Ancestry Inference (LAI) applications are more frequent in studies of dog breeds, as in the case of Alaskan sled d ogs[1], in which tracing of ancestry in sprint and long-distance sled dogs contributed to the identification of the genomic regions that correlated with performance-enhancing traits In humans, such tools have been more widely used to analyse how past migration events have impacted existing p opulations[2] and to improve identification of ancestry-specific genetic susceptibility to disease in genome-wide association s tudies[3].
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