Assessment of genetic purity and diversity of farmed tilapia fish in Tanzania mainland
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Date
2021
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Publisher
Sokoine University of Agriculture
Abstract
Fish farming in Tanzania is done in ponds and cages by commercial and smallholder farmers, mostly using tilapia species. The productivity of fish farming is believed to be strongly influenced by the quality of the strain cultured. In Tanzania tilapia culture is mainly dominated by Oreochromis and Coptodon spp, and most authorities consider the
fast-growing Oreochromis niloticus to be the most appropriate species for aquaculture in various parts of the country. However, there other species that are farmed in some areas such as Oreochromis urolepis and Oreochromis leucostictus. These species are known to hybridise with Oreochromis niloticus. This study assessed the purity and genetic diversity
of tilapia fish in hatcheries and farms in Tanzania Mainland. The study focused on three
specific objectives which were; i) assessment of sources of tilapia broodstocks and
fingerlings in hatcheries and farms, ii) identification of farmed tilapia fish species and
hybrids using single nucleotide polymorphism (SNPs) and iii) assessment of within-and
between-population genetic diversity of Nile tilapia broodstock in hatcheries and farms.
Information on the sources of tilapia broodstock and fingerlings in hatcheries and farms in
Tanzania Mainland was collected through face-to-face interview using structured
questionnaires. A total of 248 and 16 respondents from fish farms and hatcheries,
respectively, were interviewed. Data on sources of tilapia broodstock and fingerlings were
analyzed using Statistical Package for Social Sciences (SPSS.Version, 21) to derive
descriptive and inferential statistics. Significant differences were judged at a probability
level of p ≤ 0.05. Tilapia species and hybrids cultured in hatcheries and farms were
determined through SNP analysis. Species identification was facilitated by inclusion of
reference samples of Oreochromis niloticus and O. leucostictus from Lake Albert in
Uganda and O. urolepis from the lower Wami River in Tanzania in the analysis. A total of
536 tilapia pectoral fin samples were collected from 10 fish hatcheries and 59 fish farms3
located in seven agro-ecological zones of Tanzania Mainland. Following euthanasia, clips
of the pectoral fin were cut and placed into labelled vials containing 95% ethanol. The
vials were put in a cool box packed with ice and transported to a laboratory where they
were stored at -20 o C, until DNA extraction. Overall, analysis was carried out on 190 fin
clips, which were selected from the initial collection of 536 tilapia specimens. DNA
extraction from fin clips was done using the BioArk extraction kit and SNP genotyping
was performed by LGC Genomics GmbH campany in Berlin. The SNP assay was
originally calibrated with three species of Oreochromis (O. niloticus, O. urolepis and O.
leucostictus), not with Coptodon. A pseudo-reference set for Coptodon was generated
using four specimens for which clear photographs of Coptodon were available. These
were then coded as reference samples and used to identify the genotypic profile of
Coptodons in the analysis, in an attempt to identify Coptodon specimens among the non-
photographed samples. Principal component analysis (PCA) was done using SNPRelate
package in R v4.01 software and used to preliminary identify the species and hybrids
present in the collected tilapia samples. Ancestry analysis was done using Admixture
v1.3.0 software to determine the proportion of ancestral admixture for assigning
appropriately the different types of species and their hybrid present in both fish hatcheries
and farms. A threshold of 80% cluster membership was used to classify samples as pure
species. Individuals with cluster membership of less than 80% were considered to be
potential hybrids. Based on cluster membership criterion, a total of 50 O. niloticus were
identified out of 190 genotyped samples, whereby 31 and 19 O. niloticus individuals were
from fish hatcheries and farms, respectively. These were then selected as samples for the
study of assessment of within and between population genetic diversity of Nile tilapia
broodstocks in hatcheries and farms. The population structure of the fish samples was
analyzed using Structure v.2.3.4 Software with K values ranging from 2 to 5. Markov4
Chain Monte Carlo (MCMC) of 100 000 iterations with a burn-in period of 10 000 was
carried out for each K value.
Observed (Ho) and expected (He) heterozygosity parameters were used to assess the
within population genetic diversity for the hatchery populations. Similarly average
individual inbreeding coefficient (F IS ) for O. niloticus identified in fish hatcheries were
estimated using stacks v2 software. The R package StAMPP was used to perform
Analysis of Molecular Variance (AMOVA) using 1 000 permutations. Also, the principal
component analysis (PCA) was carried out using the R package Adegenet version 2.1.1.
The results on sources of tilapia fingerlings and broodstock indicate that, the main sources
of tilapia broodstocks in fish hatcheries were other hatcheries within the country (45.5%).
However, some fish hatchery managers (12.3%) were importing broodstock from Uganda
and Thailand. The results revealed that fish hatcheries and natural water bodies were used
as sources of fingerlings in all agro-ecological zones, but the extent of utilization differed
significantly among the agro-ecological zones. Fingerlings from the wild were more
utilized in the Northern, Western and Lake Zones while the use of fingerlings from
hatcheries predominated in the Eastern zone. The results on tilapia fish species and hybrid
identification in fish farms and hatcheries, indicate that 91.52% of the fish farms and 70%
of the hatcheries were not culturing pure O. niloticus, but hybrids or tilapia of other
species. The pure O. niloticus (percentage of pure individuals in brackets) were observed
at Ruvu fish farm (12.90%), Safina bigfish (12.90%) and 821KJ-Bulamba (51.61%).
Likewise the results for within and between population genetic diversity of Nile tilapia
broodstocks in hatcheries and farms indicated that pairwise F ST values varied from 0.072
to 0.359 in some of fish hatcheries. The lowest F ST values were found between 821KJ-
Bulamba and populations from Mwamapuli, Ruvu fish farm, and Safina bigfish. The
highest F ST values were observed between 821KJ-Bulamba and Faiza fish farm.
Admixture was detected at Mwamapuli, Faiza fish farm, Ruvu fish farm and Safina5
bigfish, but was not detected at 821KJ-Bulamba. In fish farms admixture was detected at
SUA-Morogoro and Babati populations. Result on Analysis of molecular variance
(AMOVA) show that 17.71% of genetic variation was found among populations, -7.69%
among individuals within populations and 89.98% of variation was within individuals.
Principal component analysis indicated one genetic group of O. niloticus clustering to O.
niloticus reference with no any individual clustering with either O. urolepsi reference or
O. leucostictus reference. This study concluded that, the main sources of tilapia
broodstock for fingerlings production in hatcheries are other hatcheries within and outside
Tanzania as well as wild sources. The main sources of tilapia fingerlings for stocking fish
farms in Tanzania mainland are hatcheries within Tanzania, wild sources and recruits
from other fish farms. A large number of sampled fish farms (91.52%) and hatcheries
(70%) do not culture pure Oreochromis niloticus, instead they culture hybrids and a
mixture of either Oreochromis niloticus with other species of tilapia or unknown tilapia
species. There is high number of hybrid individuals both in fish farms and hatcheries than
any pure single species. The high level of genetic impurity in farmed tilapia fish in both
hatcheries and farms is contributed by existence of O. leucostictus, O. jipe, and O.
urolepsi and Coptodon species. There is high genetic diversity within populations than
among Nile tilapia populations. Based on the findings of this study it is recommended to
establish certified hatcheries in each agro-ecological zone to increase accessibility of
quality seeds. Also it is recommended to establish a practical tilapia breeding program for
maintaining the purity of different tilapia strains as well as conducting regular training to
fish farmers and hatchery managers on how to handle and manage tilapia broodstock.
Description
Dissertation
Keywords
Genetic purity, Tilapia Fish Farming, Aquaculture, Tanzania mainland, Agro - ecological zone, Fish farmers, Quality broodstock, Wild source