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Local ancestry inference provides insight into Tilapia breeding programmes.
Alex Avallone1, Kerry L Bartie1, Sarah-Louise C Selly1
1Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, Scotland, UK.
Scientific Reports
|October 30, 2020
Summary
Researchers developed a new workflow to track genetic inheritance in tilapia, a vital aquaculture species. This method helps monitor breeding programs and understand gene movement across generations.
Area of Science:
- Aquaculture
- Genetics
- Animal Breeding
Background:
- Tilapia (Oreochromis niloticus) is a globally significant aquaculture species, with over 5 million tonnes produced annually.
- Selective breeding for traits like growth rate and size necessitates tracking genetic inheritance to manage hitchhiking genes.
Purpose of the Study:
- To develop a Local Ancestry Inference (LAI) workflow for tilapia.
- To leverage existing genotyping-by-sequencing data, including Double Digest RAD-seq derived Single-Nucleotide Polymorphism (SNP) markers.
Main Methods:
- Implemented a suite of tools to determine local ancestry at each chromosomal locus.
- Utilized reference panels from tilapia species with known origins for analysis.
- Validated the workflow using tilapia species, wild populations, and breeding programs.
Main Results:
- The LAI workflow accurately identified the genetic makeup of samples with known ancestry.
- The precision of the pipeline was confirmed through rigorous evaluation.
Conclusions:
- The developed LAI workflow provides an easy and inexpensive method for monitoring genetic profiles in tilapia breeding programs.
- Facilitates tracking gene flow from parents to offspring and identifying hybrids and their origins.
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