SNP marker detection and genotyping in tilapia

We have generated a unique resource consisting of nearly 175 000 short contig sequences and 3569 SNP markers from the widely cultured GIFT (Genetically Improved Farmed Tilapia) strain of Nile tilapia (Oreochromis niloticus). In total, 384 SNPs were selected to monitor the wider applicability of the...

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Bibliographic Details
Published in:Molecular ecology resources 2012-09, Vol.12 (5), p.932-941
Main Authors: Van BERS, N. E. M., CROOIJMANS, R. P. M. A., GROENEN, M. A. M., DIBBITS, B. W., KOMEN, J.
Format: Article
Language:English
Subjects:
Animals
Aquaculture
Brackish
Cichlids - classification
Cichlids - genetics
farmed tilapias
Fish
Genetic diversity
genetic-linkage map
Genotype
growth-performance
lake victoria
Molecular Typing - methods
next generation sequencing
NGS
nile tilapia
Oreochromis niloticus
oreochromis-niloticus l
Polymorphism, Single Nucleotide
Ponds
population genetics
population-structure
salmon oncorhynchus-nerka
single-nucleotide polymorphisms
SNP
sockeye-salmon
Tilapia
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Summary:We have generated a unique resource consisting of nearly 175 000 short contig sequences and 3569 SNP markers from the widely cultured GIFT (Genetically Improved Farmed Tilapia) strain of Nile tilapia (Oreochromis niloticus). In total, 384 SNPs were selected to monitor the wider applicability of the SNPs by genotyping tilapia individuals from different strains and different geographical locations. In all strains and species tested (O. niloticus, O. aureus and O. mossambicus), the genotyping assay was working for a similar number of SNPs (288–305 SNPs). The actual number of polymorphic SNPs was, as expected, highest for individuals from the GIFT population (255 SNPs). In the individuals from an Egyptian strain and in individuals caught in the wild in the basin of the river Volta, 197 and 163 SNPs were polymorphic, respectively. A pairwise calculation of Nei’s genetic distance allowed the discrimination of the individual strains and species based on the genotypes determined with the SNP set. We expect that this set will be widely applicable for use in tilapia aquaculture, e.g. for pedigree reconstruction. In addition, this set is currently used for assaying the genetic diversity of native Nile tilapia in areas where tilapia is, or will be, introduced in aquaculture projects. This allows the tracing of escapees from aquaculture and the monitoring of effects of introgression and hybridization.
ISSN:1755-098X
1755-0998
DOI:10.1111/j.1755-0998.2012.03144.x