Data from: Genetic diversity of Nile tilapia (Oreochromis niloticus) throughout West Africa
Lind, Curtis et al. (2019), Data from: Genetic diversity of Nile tilapia (Oreochromis niloticus) throughout West Africa, Dryad, Dataset, https://doi.org/10.5061/dryad.bk3j9kd6m
Nile tilapia (Oreochromis niloticus) is a globally significant aquaculture species rapidly gaining status as a farmed commodity. In West Africa, wild Nile tilapia genetic resources are abundant yet knowledge of fine-scale population structure and patterns of natural genetic variation are limited. Coinciding with this is a burgeoning growth in tilapia aquaculture in Ghana and other countries within the region underpinned by locally available genetic resources. Using 192 single nucleotide polymorphism (SNP) markers this study conducted a genetic survey of Nile tilapia throughout West Africa, sampling 23 wild populations across eight countries (Benin, Burkina Faso, Côte d’Ivoire, Ghana, Togo, Mali, Gambia and Senegal), representing the major catchments of the Volta, Niger, Senegal and Gambia River basins. A pattern of isolation-by-distance and significant spatial genetic structure was identified throughout West Africa (Global FST = 0.144), which largely corresponds to major river basins and, to a lesser extent, sub-basins. Two populations from the Gambia River (Kudang and Walekounda), one from the western Niger River (Lake Sélingué) and one from the upper Red Volta River (Kongoussi) showed markedly lower levels of diversity and high genetic differentiation compared to all other populations, suggesting genetically isolated populations occurring across the region. Genetic structure within the Volta Basin did not always follow the pattern expected for sub-river basins. This study identifies clear genetic structuring and differentiation amongst West African Nile tilapia populations, which concur with broad patterns found in previous studies. In addition, we provide new evidence for fine-scale genetic structuring within the Volta Basin and previously unidentified genetic differences of populations in Gambia. The 192 SNP marker suite used in this study is a useful tool for differentiating tilapia populations and we recommend incorporating this marker suite into future population screening of O. niloticus. Our results form the basis of a solid platform for future research on wild tilapia genetic resources in West Africa, and the identification of potentially valuable germplasm for use in ongoing breeding programs for aquaculture.
Dataset of 192 SNP genotypes of wild Nile tilapia, Oreochromis niloticus. Detailed methodology outlined in:
Lind C.E. et al. Genetic diversity of Nile tilapia (Oreochromis niloticus) throughout West Africa (2019). Scientific Reports doi: 10.1038/s41598-019-53295-y
Alleles for each SNP are provided separate columns, with the suffix "##.1" and "##.2" indicating alleles 1 and 2 for each SNP.
Full names of each SNP are given in a separate file. Originally described in: Van BERS, N. E., CROOIJMANS, R. P., GROENEN, M. A., DIBBITS, B. W. and KOMEN, J. (2012), SNP marker detection and genotyping in tilapia. Molecular Ecology Resources, 12: 932-941. doi:10.1111/j.1755-0998.2012.03144.x