SNP marker detection and genotyping in tilapia

Area of Science:

• Aquaculture
• Genetics
• Molecular Biology

Background:

• The Genetically Improved Farmed Tilapia (GIFT) strain is widely cultured.
• Understanding genetic diversity is crucial for effective aquaculture management and conservation.

Purpose of the Study:

• To develop and validate a set of single nucleotide polymorphism (SNP) markers for Nile tilapia (Oreochromis niloticus).
• To assess the applicability of these markers across different tilapia strains and geographical locations.
• To provide a tool for genetic diversity assessment, pedigree reconstruction, and monitoring of aquaculture populations.

Main Methods:

• Generation of nearly 175,000 short contig sequences and 3569 SNP markers.
• Selection of 384 SNPs for wider applicability testing.
• Genotyping of tilapia individuals from various strains and geographical origins.
• Analysis of SNP polymorphism and calculation of Nei's genetic distance.

Main Results:

• A high number of SNPs (288-305) were functional across different tilapia species and strains.
• The highest number of polymorphic SNPs (255) was observed in the GIFT population.
• SNP data successfully discriminated between different strains and species.
• Genetic diversity varied among populations, with 197 SNPs polymorphic in an Egyptian strain and 163 in wild Volta River individuals.

Conclusions:

• The developed SNP set is broadly applicable for Nile tilapia aquaculture, including pedigree reconstruction.
• This resource is valuable for assessing genetic diversity in native populations and monitoring aquaculture impacts.
• The SNP markers facilitate tracing escaped fish and evaluating introgression and hybridization effects.