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

Citation

Ciezarek, Adam et al. (2021), Whole genome resequencing data enables a targeted SNP panel for conservation and aquaculture of Oreochromis cichlid fishes, Dryad, Dataset, https://doi.org/10.5061/dryad.h44j0zpmg

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.

Methods

Set of 118 SNPs for the tested Oreochromis niloticusurolepisleucostictus and hybrids, as well as the reduced 96 SNP set.

Usage Notes

Datafiles:

all118.ped and .map are the full SNP panel dataset for all 168 individuals
top96.ped and .map are the most informative 96 SNPs (subset of the 118 SNPs) (according to PC loading scores) for all 168 individuals.

all118.ped - PLINK format ped file for all 118 SNP panel SNPs
all118.map - PLINK format map file for all118.ped
top96.ped - PLINK format ped file for all 118 SNP panel SNPs
top96.map - PLINK format map file for all118.ped

Citation:
Whole genome resequencing data enables a targeted SNP panel for conservation and aquaculture of Oreochromis cichlid fishes. 2022. Aquaculture. 548 part 2.

Contact:
adam.ciezarek@earlham.ac.uk