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  • A. Ciezarek
    Earlham Institute, Norwich Research Park Innovation Centre
  • Antonia G.P. Ford
    University of Roehampton
  • Graham J. Etherington
    Earlham Institute, Norwich Research Park Innovation Centre
  • Nasser Kasozi
    National Agricultural Research Organisation, Abi Zonal Agricultural Research and Development Institute
  • Milan Malinsky
    University of Basel
  • Tarang K. Mehta
    Earlham Institute, Norwich Research Park Innovation Centre
  • Luca Penso-Dolfin
    Silence Therapeutics GmbH
  • Benjamin P. Ngatunga
    Tanzania Fisheries Research Institute (TAFIRI)
  • Asilatu Shechonge
    Tanzania Fisheries Research Institute (TAFIRI)
  • Rashid Tamatamah
    Tanzania Fisheries Research Institute (TAFIRI)
  • Wilfried Haerty
    Earlham Institute, Norwich Research Park Innovation Centre
  • Federica Di Palma
    University of East Anglia
  • Martin J. Genner
    University of Bristol
  • George F. Turner
Cichlid fish of the genus Oreochromis form the basis of the global tilapia aquaculture and fisheries industries. Broodstocks for aquaculture are often collected from wild populations, which in Africa may be from locations containing multiple Oreochromis species. However, many species are difficult to distinguish morphologically, hampering efforts to maintain good quality farmed strains. Additionally, non-native farmed tilapia populations are known to be widely distributed across Africa and to hybridize with native Oreochromis species, which themselves are important for capture fisheries. The morphological identification of these hybrids is particularly unreliable. 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 in hatcheries and helping to conserve unique endemic biodiversity.


  • Tilapia, Tanzania, Fisheries, Hybridization
Original languageEnglish
Article number737637
Pages (from-to)737637
Issue numberPart 2
Early online date26 Oct 2021
Publication statusPublished - 15 Feb 2022

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