TY - JOUR

T1 - Whole genome resequencing data enables a targeted SNP panel for conservation and aquaculture of Oreochromis cichlid fishes

AU - Ciezarek, A.

AU - Ford, Antonia G.P.

AU - Etherington, Graham J.

AU - Kasozi, Nasser

AU - Malinsky, Milan

AU - Mehta, Tarang K.

AU - Penso-Dolfin, Luca

AU - Ngatunga, Benjamin P.

AU - Shechonge, Asilatu

AU - Tamatamah, Rashid

AU - Haerty, Wilfried

AU - Palma, Federica Di

AU - Genner, Martin J.

AU - Turner, George F.

N1 - © 2021 The Authors.

PY - 2022/2/15

Y1 - 2022/2/15

N2 - 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.

AB - 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.

KW - Tilapia

KW - Tanzania

KW - Fisheries

KW - Hybridization

U2 - https://doi.org/10.1016/j.aquaculture.2021.737637

DO - https://doi.org/10.1016/j.aquaculture.2021.737637

M3 - Article

C2 - 35177872

VL - 548

SP - 737637

JO - Aquaculture

JF - Aquaculture

SN - 0044-8486

IS - Part 2

M1 - 737637

ER -