Characterizing the genetic structure of introduced Nile tilapia (Oreochromis niloticus) strains in Tanzania using double digest RAD sequencing

Mbiru Moses, Matern Mtolera, Leonard J Chauk, Fernando A Lopes Pinto, Dirk-Jan De Koning, Ross Houston, Christos Palaiokostas

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

Tilapia hatcheries in Tanzania rely heavily on importing germplasm. Nevertheless, the genetic structure of the imported stocks is poorly understood. In the current study, the level of genetic diversity and differentiation of eight populations of Nile tilapia (Oreochromis niloticus) strains imported in Tanzania was investigated. Four of the studied strains originated from Thailand, three from Uganda, and one from the Netherlands. Double digest restriction-site associated DNA sequencing (ddRAD-seq) was applied to identify and genotype single nucleotide polymorphisms (SNPs). In total, 2,214 SNPs passed all the quality control steps and were utilized for downstream analysis. Mean heterozygosity estimates were higher for the Thailand strains (Ho: 0.23) compared to the strains from Uganda (Ho: 0.12). Low genetic distance was observed amongst populations from the same geographic origin (Fst: 0.01 – 0.04). However, genetic distance between populations from different geographic origins was substantial (Fst: 0.24 – 0.44). Bayesian model-based clustering (STRUCTURE) and discriminant analysis of principal components (DAPC) grouped the studied animals into three distinct clusters. A cross-validation approach (where 25% of animals from each population were considered of unknown origin) was conducted in order to test the efficiency of the SNP dataset for identifying the population of origin. The cross-validation procedure was repeated 10 times resulting in approximately 97 % of the tested animals being allocated to the correct geographic population of origin. The breeding history and hatchery practices used to manage these stocks prior and after import appear to be the main factors for the genetic diversity observed in this study. Our study, will help inform hatchery stock management and future breeding programme designs in Tanzania.
Original languageEnglish
JournalAquaculture International
Early online date4 Nov 2019
Publication statusE-pub ahead of print - 4 Nov 2019

Keywords / Materials (for Non-textual outputs)

  • Nile tilapia
  • ddRAD-seq
  • Genetic diversity


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