Local ancestry inference provides insight into Tilapia breeding programmes

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. g...

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Bibliographic Details
Published in:Scientific reports 2020-10, Vol.10 (1), p.18613-18613, Article 18613
Main Authors: Avallone, Alex, Bartie, Kerry L., Selly, Sarah-Louise C., Taslima, Khanam, Campos Mendoza, Antonio, Bekaert, Michaël
Format: Article
Language:English
Subjects:
631/114/2785
631/1647/48
631/181/457
631/181/757
631/208/1348
631/601/2722
Animals
Aquaculture
Aquaculture - methods
Breeding
Breeding - methods
Chromosomes - genetics
Cichlids - genetics
Genotype
Genotyping
Growth rate
Heredity
Humanities and Social Sciences
Hybrids
multidisciplinary
Offspring
Oreochromis niloticus
Polymorphism, Single Nucleotide - genetics
Ponds
Science
Science (multidisciplinary)
Selective breeding
Single-nucleotide polymorphism
Species
Tilapia - genetics
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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. 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.
ISSN:2045-2322
2045-2322
DOI:10.1038/s41598-020-75744-9