1. Introduction
Aquaculture is the world’s fastest growing agricultural and food processing sector, and serves a critical role in developing economies through its value chain linkages in promoting food and nutrition security, rural development, and poverty alleviation [
1]. Tilapia is the world’s second most cultured fish species, after carp [
2,
3], and is currently cultured in more than 140 countries [
4]. China, the Philippines, Taiwan, Indonesia, Thailand, and Egypt are the leading suppliers of this agro-food product, with an estimated global production of 179 million metric tons [
5].
Nile tilapia is considered as the ideal fish species for aquaculture mainly due to its rapid growth, high fecundity, ability to resist poor water quality, and good performance under sub-optimal nutritional conditions [
6,
7,
8]. Additionally, the fish possesses adaptive life history characteristics especially fast growth, high fecundity, and large egg sizes that have few predators, as well as high dietary overlap across size class, habitat, and season [
9,
10]. Its omnivorous nature further prompts it to utilize the available resources, making it easy and affordable to grow even for small-scale farmers. Apart from being a model aquaculture species, the expansion of tilapia culture globally is also fueled by high genetic diversity in the available natural tilapia germplasm [
6] which makes it a good candidate for genetic manipulations for product improvement and thereafter the expansion of profit margins. Besides the economic returns from aquaculture, tilapiines have also been adopted for use as control agents for aquatic vegetation and elimination of unwanted aquatic fauna such as snails and mosquitoes [
8].
The Nile tilapia (
Oreochromis niloticus Linnaeus, 1758) is native to African freshwater systems and the Middle East, with its natural range encompassing the Nile River Basin, from the headwaters in East Africa to the Nile Delta in Egypt and lakes and streams connected to these drainages [
11]. In East Africa,
O. niloticus is native to Lakes; George, Edward, Albert, Kivu, Tanganyika, Turkana, and Baringo, and to River Nile [
11], and the species has been introduced to almost every tropical country in the world for aquaculture purposes [
12].
The fisheries sector in Uganda is the second largest exchange earner for the country after coffee and contributes 12% to the agricultural gross domestic product (GDP) and about 3.0% to the National GDP. The investment in the sector is estimated at
$200 million with employment of over 700,000 people [
13]. Uganda has more than 350 fish species; Nile perch and Tilapia remain the most important, making up to 46% and 38%, respectively, of the total fisheries production [
13]. Aquaculture production stands at around 111,000 tons, of which Largemouth African catfish and Nile tilapia contribute over 90% in the country [
14]. The sector has experienced a significant increase in production attributed to the commercialization of the fisheries sub-sector which has witnessed an increase in the number of people venturing into fish farming [
5].
Despite the aquaculture subsector being identified as an important pillar for food and nutritional security in the country, the rapid growth of the subsector is curtailed by inadequate quality seed with most hatcheries being plagued by inbreeding, hybridization of related stocks, and poor-quality broodstock [
15,
16]. In the context of farmed Nile tilapia, many studies on the domestication of this fish species have shown phenotypic variations in the subsequent generations with respect to the pure Tilapia strains of the brood stock [
8,
14,
16,
17]. This may be attributed to speciation due to change in the environment or formation of hybrids as a result of species interbreeding.
Consequently, there are questions on the possible deviations in the genetic and morphometric features of the organisms after several generations of recycling. Furthermore, without a clear known origin of the brood stock, the fish are most likely sourced from stocks suffering from genetic founder effects, as is common among farmed tilapia sources globally [
18], a practice that is difficult to avoid under farm conditions. Consequently, the fish suffer from high levels of inbreeding, which is frequently exacerbated by hybridization because tilapias are prolific breeders in culture conditions. Inbreeding leads to loss of genetic variability [
19] and inbreeding depression associated with lower growth rates, reduced fitness, low survival, and low fecundity [
19].
Morphometric and meristic methods remain the simplest and most direct way of species identification and can be used as a measure of delineating fish species into strains/types [
12]. Characterization of
O. niloticus based on morphometric and meristic traits have also been reported in several studies [
6,
8,
12,
17,
20,
21]. These studies report the existence of both genetic and morphometric differences in the cultured
O. niloticus fish species from similar indigenous fish species in the wild.
While the population characteristics (biology, abundance, condition factors, and the reproductive biology) of
O. niloticus in the three lakes have been fairly well studied by other researchers—L. Victoria [
14,
22,
23], L. Albert [
23,
24], and L. Kyoga [
22,
23]—research work on the morphometric characterization of farmed
O. niloticus sourced from the natural water bodies in Uganda is still understudied and this hinders development of selective breeding programs. Therefore, this study focused on comparing the possible morphometric variations between
O. niloticus populations from isolated pond systems with strains from three lake systems that had been isolated for two years and compared them with strains of
O. niloticus cultured by farmers in the region. The study hypothesized that the morphometric traits would show no significant differences among the populations investigated. This study is significant as it will generate and contribute baseline information for strain improvement of the
O. niloticus breed in East Africa. The study will further provide a broader diversity of knowledge on the phenotypic characteristics of the different
O. niloticus strains in aquatic systems that could be used when designing conservation measures.
2. Materials and Methods
2.1. The Study Area
The fish samples in this study were collected from different farms located in South Western Highland Agro-Ecological Zone (SWHAEZ) in the districts of Kanungu and Kabale (
Figure 1). SWHAEZ, formerly known as the Kigezi sub-region, consists of five districts; Kabale, Rubanda, Kisoro, Kanungu, Rukungiri, and Rukiga, located in southwestern Uganda. The zone lies between altitudes of 1262 and 3883 m above sea level. The zone experiences a bimodal rainfall pattern that ranges from 1000 to 1500 mm per annum. Kanungu and Rukungiri districts have analogous annual temperature in the range of 20.56 °C to 30.56 °C, while other districts in the region have an annual temperature range of 13.00 °C to 23.21 °C [
25]. Therefore, these districts (Kabale and Kanungu) were selected owing to varying climatic conditions and as representation of the other districts in the zone. Both private and government fish farms were incorporated in the study. The private farms included; Butare, Rwabirundo and Nyamabare in Kabale district; Masya and Kambuga in Kanungu district (
Figure 1). These farms were selected on account of their vast experience in fish farming and business for more than 10 years. Moreover, fish stocking data and farm history availed by the district fisheries officers and farmers in the respective districts indicated that stocking dates of the preferred farms were in a very close range; therefore, it was assumed that the fish sampled were in the same age bracket. At the time of sampling, all the fish in distinct localities had spent seven months under captive management.
Furthermore, Kyanamira aquaculture fish facility, located in the Kabale district, was also included in the study area. The facility is superintended by Kachwekano Zonal Agricultural Research and Development Institute of National Agricultural Research Organization. Most pertinently, the fish populations at Kyanamira facility were stocked and raised in independent pond systems with the native brood stock originating from three freshwater lakes in Uganda, namely, L. Victoria (Central Uganda), L. Kyoga (Central Uganda), and L. Kayumbu (South Western Uganda). The pond systems at the facility have a surface area of 800 m2 with a stocking rate of 4.0 fish/m−3. The water temperature in the ponds is maintained in a range of 21.13 °C to 23.03 °C while the dissolved oxygen (DO) level ranges between 4.24 and 5.76 mg/L. All the chosen fish farms were closely monitored where monthly sampling was performed to facilitate fish grading and sorting for invariable growth patterns.
2.2. Research Design
This study was conducted by taking nine different body measurements of
O. niloticus fish samples collected from three ponds systems between February and April, 2022. The fish samples were obtained from Kyanamira fish facility ponds holding the fish populations of three lakes, Kyoga, L. Victoria, and L. Kayumbu. Additionally, samples were obtained from five randomly selected farmers from Kabale and Kanungu districts in the region. The selected fish were those at maturity, swollen stomachs for the females and males with tapered shapes with well-developed external reproductive organs. A total of 258 specimens were obtained and morphometric measurements were taken onsite. The fish populations were analyzed as a whole and populations were compared without discriminating the sex. Any variations that would arise from sexual dimorphism in tilapia were catered for by applying the same data collection criteria for the fish across populations from the different lakes and farms. Morphometric traits were measured using a centimeter scale to the nearest 0.1 cm except for body weight (BW) which was measured to the nearest 0.1 g using a digital balance. The morphometric traits were: Total Length (TL), Standard Length (SL), Body Width (WID), Caudal fin Length (CL), Head Length (HL), Dorsal Length (DL), Pectoral fin Length (PEC), and Pelvic fin Length (PEL) (
Figure 2). Additionally, the body weight of the fish samples was also measured separately. These morphometric traits were chosen because they are easily measured longitudinal traits and normally present moderate to high heritability (10, 26). The body characters viz. TL, HL, DL, BD, CL, PEC, and PEL were expressed as percent to Standard Length of the fish to correct size dependent variation in morphometric characters [
26].
2.3. Data Analysis
All statistical analyses were performed using IBM SPSS Statistics for Windows, Version 23.0. IBM Corp (Armonk, NY, USA) developed by IBM for data management and Microsoft Excel. One-way Analysis of Variance (ANOVA) followed by Tukey post hoc test was used to test the significance of differences in the morphometric traits between populations (p < 0.05). Prior to the analyses, normal distributions were investigated using Kolmogorov–Smirnov test and homogeneity of variances was checked with Levene’s test. Morphological trait values were taken as dependent variables and populations as explanatory variables.
Morphometric variation among the eight populations of
O. niloticus was used to test for the presence of stock structuring using discriminant function analysis (DFA) [
27,
28]. Stepwise DFA on morphometric data was used to select all of the traits. A univariate analysis of seven measurements expressed as percentages of the standard length of fish was run to estimate the importance of the morphometric measurements for species identification.
The length–weight relationship of the fish was calculated using the equation by [
29] in the form of: W = aL^b to estimate the length–weight relationship of the fish in each population. The length–weight relationship of the collected fish samples was calculated based on the logarithmic transformation of the data. When analyzing the length–weight relationships between the fish samples, the data were logarithmically transformed to stabilize the variance that could result from size-dependent weight measurements [
30]. Fish body weight and standard length were used in this analysis.
W = body weight of fish in grams,
L = Standard length in centimeters,
“a” is the intercept,
“b” is the slope of the regression line,
The fish Condition Factor (K); Relative condition [
30] factor which is an expression of the degree of the wellbeing of fishes in their habitat was calculated as
K = W/W’ where:
W = Actual weight of Fish
W’ = Calculated weight of the fish.