Population Structure and Genetic Diversity of Nile Tilapia (Oreochromis niloticus) Strains Cultured in Tanzania

Abstract

Understanding population structure and genetic diversity within and between local Nile tilapia lines cultured in Tanzania is important for sustainable aquaculture production. This study investigated the genetic structure and diversity among seven Nile tilapia populations in Tanzania (Karanga, Igunga, Ruhila, Fisheries Education and Training Agency, Tanzania Fisheries Research Institute, Kunduchi, and Lake Victoria). Double-digest restriction site-associated DNA (ddRAD) libraries were prepared from 140 individual fish (20 per population) and sequenced using an Illumina HiSeq 4000 resulting in the identification of 2,180 informative single nucleotide polymorphisms (SNPs). Pairwise F st values revealed strong genetic differentiation between the closely related populations; FETA, Lake Victoria, and Igunga and those from TAFIRI and Karanga with values ranging between 0.45 and 0.55. Population structure was further evaluated using Bayesian model-based clustering (STRUCTURE) and discriminant analysis of principal components (DAPC). Admixture was detected among Karanga, Kunduchi, and Ruhila populations. A cross-validation approach (25% of individual fish from each population was considered of unknown origin) was conducted in order to test the efficiency of the SNP markers to correctly assign individual fish to the population of origin. The cross-validation procedure was repeated 10 times resulting in 77% of the tested individual fish being allocated to the correct population. Overall our results provide a new database of informative SNP markers for both conservation management and aquaculture activities of Nile tilapia strains in Tanzania.

Assessing the genetic diversity of farmed and wild Rufiji tilapia (Oreochromis urolepis urolepis) populations using ddRAD sequencing

“…Compared to previous population genetics studies on aquatic organisms using RAD‐family genotyping protocols (Drinan et al., 2018; Lemopoulos et al., 2019; Sherman et al., 2020; Vendramin et al, 2016), the obtained genetic diversity metrics for several of the populations in our study lie on the lower range of the reported values (Table 2). Nevertheless, in comparison to our previous studies on farmed Nile tilapia populations in Tanzania (Kajungiro, Palaiokostas, et al, 2019; Moses et al., 2019) where the same ddRAD library preparation protocol was used, the obtained genetic diversity metrics were in general higher in the current study. Additionally, it is worth to point out that low levels of heterozygosity were obtained for several tilapia populations in an extensive study across West Africa (Lind et al., 2019).…”

“…Moreover, a similar approach was followed in our prior studies on Nile tilapia strains (mainly of farmed origin) where the SNP information allowed for correctly classifying between 77% and 97% of the tested dataset to the respective population of origin (Kajungiro, Palaiokostas, et al, 2019; Moses et al., 2019). However, in the aforementioned studies we used mainly farmed populations of more pronounced genetic distance as opposed to the Rufiji populations of the current study which facilitated their discrimination in the followed cross‐validation schemes.…”

“…ddRAD‐seq is one of the most commonly utilized member of the reduced‐representation family combining simplicity and cost efficiency during library construction (Peterson et al., 2012). Over the last years, ddRAD‐seq has been successfully utilized in a plethora of tilapia focussed studies investigating the underlying genetic structure of traits of economic value (Jiang et al., 2019; Li, Zhu, Gu, Lin, & Xia, 2019; Li et al., 2017; Palaiokostas et al., 2015; Taslima et al., 2020), for species‐specific SNPs (Syaifudin et al., 2019) and for deciphering the genetic diversity–population structure of wild and farmed populations (Kajungiro, Palaiokostas, et al, 2019; Moses et al., 2019).…”

Monitoring of genetic variation in mono-sex tilapia stocks using randomly amplified polymorphic DNA markers in some private hatcheries of Bangladesh

“…One of the possible reasons for the significant higher F ST values in the brac hatchery was that the individuals of brac population were highly isolated one originated from improved strains of unique genetic characteristics. A similar possibility has been reported by Mireku et al (2017) and Kajungiro et al (2019) in the assessments of genetic structure of different tilapia strains who found that improved tilapia strain had significantly higher genetic differentiation than others. In contrast, low with insignificant genetic differentiations among matshay-kanon, khan, nancy and city hatcheries (Table 6) indicated that those were genetically relevant to each other with some common genetic characters which might be the result of inter-mixing of genetic materials among the populations.…”

Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr (Salvelinus alpinus)

“…Double digest RAD (ddRAD) relying on the simultaneous usage of two enzymes is one of the most popular reduced-representation sequencing platforms. The combination of a relatively easy library construction workflow and cost-efficiency [ 6 ] makes ddRAD particularly useful for studying the genetic diversity of populations [ 17 , 18 , 19 , 20 ], constructing genetic maps [ 21 , 22 , 23 , 24 ] and quantitative trait loci mapping [ 25 , 26 , 27 , 28 , 29 ].…”