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.
Highlights
The tilapias are a group of African and Middle Eastern cichlid fish, with more than 70 species[1,2]
The objective of the research described here was to test the potential of double digest restriction-site associated DNA25 for discovering single-nucleotide polymorphism (SNP) markers to distinguish between 10 tilapia species and analyse the distribution of such markers in the genome
O. aureus and some O. niloticus were in a group with S. galilaeus, while S. melanotheron was in a separate group from S. galilaeus
Summary
The tilapias are a group of African and Middle Eastern cichlid fish, with more than 70 species[1,2]. Distinguishing tilapia species, hybrids and introgressed populations is of importance for both farmed and wild populations. While mitochondrial DNA (mtDNA) analysis has been used to distinguish tilapia species[23,24], it is of limited use in analysing hybridisation and introgression. The nuclear DNA markers used to date have limitations, the most important being the small number of markers available that distinguish between tilapia species (e.g. species-specific alleles have been found using allozymes, but only for a few loci[12]). The objective of the research described here was to test the potential of double digest restriction-site associated DNA25 (ddRADseq) for discovering SNP markers to distinguish between 10 tilapia species (including two sub-species of O. niloticus) and analyse the distribution of such markers in the genome. Based on the ddRADseq results, a panel of 24 candidate species-specific SNP markers for four tilapia species was selected and validated against a wider selection of fish using Kompetitive Allele Specific PCR (KASP) assays
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