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

Abstract

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, 2214 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 with 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 program designs 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).…”

Distinguishing Between Nile Tilapia Strains Using a Low-Density Single-Nucleotide Polymorphism Panel

“…For example, among Nile tilapia populations, GIFT/GIFT-derived and non-GIFT populations were readily distinguished, with the notable exception of Chitralada. The close SNP genetic affinity of Chitralada with GIFT and GIFT-derived strains—BEST, ExCEL, GIFT-WF, and GIFTFF—seems incongruous, given their putative ancestry ( Figure 1 ), but has been observed in other studies involving similar populations (Moses et al, 2020 ).…”

“…Numerous tools relying on a small number of genetic markers to identify genetically homogenous inbred crop lines and clonal horticultural varieties have been developed, and the extent of seed misidentification in crops is increasingly recognized in agriculture through the application of these methods (Rabbi et al, 2015 ; Chen et al, 2016 ; Floro et al, 2018 ; Kosmowski et al, 2019 ; Wineman et al, 2020 ). However, the development of comparable tools to distinguish between strains of outcrossing aquaculture species is challenging, and information on the extent of misidentification of tilapia strains is currently limited (Baggio et al, 2016 ; Oponda et al, 2017 ; Ordoñez et al, 2017 ; Moses et al, 2020 ).…”