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Doctoral thesis, 2022

Developing the basis of a breeding program for sustainable Rufiji tilapia aquaculture in Tanzania

Nyinondi, Christer Simon;


Tanzania has a rich natural fauna of tilapiine fish. However, a proper management of tilapia farming is lacking. Use of inappropriate technology to produce seed and inadequate extension efforts resulted in a poor production output from aquaculture. This aquaculture gap has led the society to rely on wild captures which are depleting and cannot be easily accessed by poor communities and hence increased the rate of child and infant malnutrition. Developing a breeding program for Rufiji tilapia will ensure the production of high-quality egg and larvae in culture systems and at the same time preserve the natural biodiversity of these species in Tanzania. This thesis aims to generate information that will be used for the development of a Rufiji tilapia strain that will be used as the base for a selective breeding program in Tanzania. This study was divided into two experiments. A pilot study survey was conducted beforehand on the status of fish farming in Tanzania. The survey provided key information that facilitated better understanding of the status and availability of infrastructure for effective dissemination of a structured breeding program. Poor infrastructure, poor fingerlings quality, and lack of health farming management practices were found. 
Thereafter, the genetic diversity and population structure of both wild and farmed Rufiji tilapia populations and their relation with exotic and local Nile tilapia (Oreochromis niloticus) were studied using high-throughput sequencing. Double-digest restriction-site-associated DNA (ddRAD) libraries were constructed from 195 animals originating from 8 wild and 2 farmed populations. Genetic distance estimates (FST) were low among populations from neighbouring locations, with the exception of Utete and Chemchem populations (FST = 0.34). Bayesian and multivariate statistical approaches indicated the existence of three distinct genetic clusters. The former analysis also revealed high admixture among Mindu and Wami populations and low admixture in Mansi and Utete populations. When compared to exotic and local Nile tilapia, Rufiji tilapia showed high genetic variation. High FST values (0.6 - 0.8) were observed between Rufiji strains and the local or exotic Nile tilapia strains. Interestingly, the aforementioned two highly admixed population from Rufiji tilapia were closely related to Nile tilapia but genetically distant to other Rufiji tilapia populations.  
The second part of this thesis was based on a common garden experiment where the existence of genotype by environment interaction was investigated by rearing Rufiji tilapia populations in two sites (Pangani and Kunduchi) of differing salinity and temperature levels. Nine populations were set-up for individual mating and 35 full-sib families were produced resulting in a pedigree that consisted of 1,392 animals. The best performing populations in terms of the recorded growth-related traits were Wami and Mindu that were reared in Pangani, while the lowest growth performance was recorded in the case of Ruaha population reared at Kunduchi. Moderate to high heritabilities (0.39 – 0.74) and genetic correlations (0.73 - 0.74) between these growth traits indicated the possibility of moderate reranking of the best performing animals. Overall, the mean family estimated breeding value (EBV) was higher in animals reared in Pangani compared to their full-sibs that were reared at Kunduchi. Furthermore, selecting a Rufiji tilapia as a base population for a selective breeding program needs to balance between best phenotypic performance and broad genetic variation. Notably, if rearing is to take place on sites of varying salinity and temperature levels selection should not only be based on using data from the breeding nucleus.


Aquaculture; ddRAD-seq; genetic diversity; common garden; selective breeding; genotype by environment interaction

Published in

Acta Universitatis Agriculturae Sueciae

2022, number: 2022:63
ISBN: 978-91-8046-002-6, eISBN: 978-91-8046-003-3
Publisher: Swedish University of Agricultural Sciences

Authors' information

Swedish University of Agricultural Sciences, Department of Animal Breeding and Genetics

UKÄ Subject classification

Fish and Aquacultural Science

URI (permanent link to this page)