Received: 20 May 2020 | Revised: 16 July 2020 | Accepted: 20 July 2020 DOI: 10.1002/ece3.6664 ORIGINAL RESEARCH Assessing the genetic diversity of farmed and wild Rufiji tilapia (Oreochromis urolepis urolepis) populations using ddRAD sequencing Christer S. Nyinondi1,2 | Matern S. P. Mtolera2 | Aviti J. Mmochi2 | Fernando A. Lopes Pinto1 | Ross D. Houston3 | Dirk J. de Koning1 | Christos Palaiokostas1,3 1Department of Animal Breeding and Genetics, Swedish University of Agricultural Abstract Sciences, Uppsala, Sweden Rufiji tilapia (Oreochromis urolepis urolepis) is an endemic cichlid in Tanzania. In addi- 2 Institute of Marine Sciences, University of tion to its importance for biodiversity conservation, Rufiji tilapia is also attractive for Dar es Salaam, Zanzibar, Tanzania 3The Roslin Institute and Royal (Dick) farming due to its high growth rate, salinity tolerance, and the production of all-male School of Veterinary Studies, University of hybrids when crossed with Nile tilapia (Oreochromis niloticus). The aim of the cur- Edinburgh, Edinburgh, UK rent study was to assess the genetic diversity and population structure of both wild Correspondence and farmed Rufiji tilapia populations in order to inform conservation and aquacul- Christos Palaiokostas, Department of Animal Breeding and Genetics, Swedish University ture practices. Double-digest restriction-site-associated DNA (ddRAD) libraries were of Agricultural Sciences, Uppsala, Sweden. constructed from 195 animals originating from eight wild (Nyamisati, Utete, Mansi, Email:
[email protected] Mindu, Wami, Ruaha, Kibasira, and Kilola) and two farmed (Bwawani and Chemchem) Funding information populations. The identified single nucleotide polymorphisms (SNPs; n = 2,182) were Swedish International Development Agency; BBSRC Institute Strategic Program Grants, used to investigate the genetic variation within and among the studied populations.