Species-Specific Marker Discovery in Tilapia

Abstract

Tilapias (family Cichlidae) are of importance in aquaculture and fisheries. Hybridisation and introgression are common within tilapia genera but are difficult to analyse due to limited numbers of species-specific genetic markers. We tested the potential of double digested restriction-site associated DNA (ddRAD) sequencing for discovering single nucleotide polymorphism (SNP) markers to distinguish between 10 tilapia species. Analysis of ddRAD data revealed 1,371 shared SNPs in the de novo-based analysis and 1,204 SNPs in the reference-based analysis. Phylogenetic trees based on these two analyses were very similar. A total of 57 species-specific SNP markers were found among the samples analysed of the 10 tilapia species. Another set of 62 species-specific SNP markers was identified from a subset of four species which have often been involved in hybridisation in aquaculture: 13 for Oreochromis niloticus, 23 for O. aureus, 12 for O. mossambicus and 14 for O. u. hornorum. A panel of 24 SNPs was selected to distinguish among these four species and validated using 91 individuals. Larger numbers of SNP markers were found that could distinguish between the pairs of species within this subset. This technique offers potential for the investigation of hybridisation and introgression among tilapia species in aquaculture and in wild populations.

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

“…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).…”

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

“…Both RAD and ddRAD-seq have been widely applied in aquaculture breeding and genetics studies (Robledo et al 2018). In particular, ddRAD-seq has been applied for genotyping large multiplexed datasets (e.g., Maroso et al 2018), construction of genetic linkage maps (e.g., Recknagel et al 2013;Oral et al 2017), analyzing life history traits (e.g., Pukk 2016), mapping sex determining loci (e.g., Palaiokostas et al 2015;Brown et al 2016), genomic predictions and genome-wide association studies (e.g., Barria et al 2018), assessing genetic diversity (e.g., Hosoya et al 2018;Tony et al 2015;Siccha-Ramirez et al 2018;Torati et al 2019), phylogeography (e.g., Stobie et al 2018, and species identification in tilapias (Syaifudin et al 2019).…”

Local ancestry inference provides insight into Tilapia breeding programmes

“… Species Location Origin Size Abbrev. Referenecs O. andersonii Zambia Reference species 6 AND Syaifudin et al 11 O. aureus Israel Reference species 10 AUR-I Syaifudin et al 11 Lake Manzala, Egypt Reference species 5 AUR-E Syaifudin et al 11 O. karongae Lake Malawi Reference species 4 KAR Syaifudin et al 11 O. macrochir Zambia Reference species 4 MAC Syaifudin et al 11 O. mossambicus South Africa Reference species 13 MOS-A Syaifudin et al 11 and This study Zimbabwe Reference species 9 MOS-Z Syaifudin et al 11 and This study O. n. cancellatus Ethiopia, Lake Hora Reference species 14 CAN-H Syaifudin et al 11 …”

“…Two libraries were constructed (Supplementary Table S1 online) following the ddRAD library preparation protocol with slight modifications 11 . Briefly, for each library, individual DNA samples (36 ng–4.5 μL) were simultaneously digested with two high fidelity restriction enzymes (New England Biolabs, NEB, UK): Sbf I (CCTGCA|GG recognition site), and Sph I (GCATG|C recognition site).…”

“…The goal of this project was to generate a LAI workflow that harnessed existing tilapia genotyping-by-sequencing studies 11 – 13 , such as Double Digest RAD-seq (ddRAD) derived Single-Nucleotide Polymorphism (SNP) markers 14 , 15 . This provided an insight into breeding programmes with a more in-depth look at the genetic makeup of admixed individuals, significantly contributing to the identification of hybrids, and the development of new variants for aquaculture.…”