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

A Ciezarek,Antonia G.P Ford,Graham J Etherington,Nasser Kasozi,Milan Malinsky,Tarang K Mehta,Luca Penso-Dolfin,Benjamin P Ngatunga,Asilatu Shechonge,Rashid Tamatamah,Wilfried Haerty,Federica Di Palma,Martin J Genner,George F Turner

doi:10.1016/j.aquaculture.2021.737637

Abstract

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.

Highlights

Global tropical inland aquaculture production has increased rapidly in recent decades
We demonstrate that a reduced panel of 96 genome-wide single nucleotide polymorphism (SNP) performs comparatively well to full genome resequencing in dis tinguishing species and identifying hybrids of Oreochromis
We demonstrate that hybridization is persistent in the environment with multi-generation hybrids and backcrossing to parental species

Summary

Introduction

Global tropical inland aquaculture production has increased rapidly in recent decades. A group of cichlid fish dominated by the genus Oreochromis, native to Africa and the Middle East, have been a key part of this expansion. They accounted for 5.5 million tonnes of the global total of 47 million tonnes of inland finfish aquaculture production in 2018 (FAO, 2020). Farmed populations have frequently colonized water catchments where they are not native, due to both deliberate introductions and accidental escape from fish farms (She chonge et al, 2019a) This has threatened native species through ecological competition, habitat alteration and hybridization (Bbole et al, 2014; Canonico et al, 2005; Deines et al, 2014; Firmat et al, 2013; Macaranas et al, 1986; Ndiwa et al, 2014; Mwanja et al, 2012). Such safeguarding of the wild relatives of farmed species would protect unique genetic resources that could be used to enhance traits in cultured Oreochromis strains (Macaranas et al, 1986; Thodesen et al, 2013)

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Conclusion