Whole genome resequencing data enables a targeted SNP panel for conservation and aquaculture of Oreochromis cichlid fishes

Cichlid fish of the genus Oreochromis form the basis of the global tilapia aquaculture and fisheries industry. Non-native farmed tilapia populations are known to be widely distributed across Africa and to hybridize with native Oreochromis species. However, many species are difficult to distinguish m...

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Bibliographic Details
Published inbioRxiv
Main Authors Ciezarek, Adam, d, Antonia, Etherington, Graham, Kasozi Nasser, Malinsky, Milan, Mehta, Tarang, Penso-Dolfin, Luca, Ngatunga, Benjamin, Shechonge, Asilatu, Rashid Tamatamah, Haerty, Wilfried, Federica Di Palma, Genner, Martin, Turner, George F
Format Paper
LanguageEnglish
Published Cold Spring Harbor Cold Spring Harbor Laboratory Press 24.03.2021
Subjects
Aquaculture
Biodiversity
Genomes
Genotyping
Hatcheries
Hybrids
Indigenous species
Introduced species
Oreochromis
Phenotypes
Single-nucleotide polymorphism
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Summary:Cichlid fish of the genus Oreochromis form the basis of the global tilapia aquaculture and fisheries industry. Non-native farmed tilapia populations are known to be widely distributed across Africa and to hybridize with native Oreochromis species. However, many species are difficult to distinguish morphologically, hampering attempts to maintain good quality farmed strains or to identify pure populations of native species. Here, we describe the development of a single nucleotide polymorphism (SNP) genotyping panel from whole-genome resequencing data that enables targeted species identification in Tanzania. We demonstrate that an optimized panel of 96 genome-wide SNPs based on FST outliers performs comparably to whole genome resequencing in distinguishing species and identifying hybrids. We also show this panel outperforms microsatellite-based and phenotype-based classification methods. Case studies indicate several locations where introduced aquaculture species have become established in the wild, threatening native Oreochromis species. The novel SNP markers identified here represent an important resource for assessing broodstock purity and helping to conserve unique endemic biodiversity, and in addition potentially for assessing broodstock purity in hatcheries. Competing Interest Statement The authors have declared no competing interest.
DOI:10.1101/2021.03.24.436760