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

Area of Science:

• Aquaculture genetics
• Molecular biology
• Population genetics

Background:

• Nile tilapia (Oreochromis niloticus) is a crucial aquaculture species, especially in Asia.
• Genetically improved strains are widely disseminated, but their accurate identification in hatcheries is challenging.
• Small-scale hatcheries in developing countries often lack robust strain verification methods.

Purpose of the Study:

• To develop and apply molecular genetic tools for identifying Nile tilapia strains in Bangladesh and the Philippines.
• To assess the accuracy of these tools in distinguishing between different and interrelated strains.
• To evaluate the concordance between hatchery-identified strains and genetically assigned strains.

Main Methods:

• Development of a low-density single-nucleotide polymorphism (SNP) panel.
• Application of genotyping-by-sequencing (GBS) for DNA analysis.
• Utilizing discriminant analysis of principal components (DAPC) for strain assignment.
• Analysis of 2,057 samples from 205 hatcheries across Bangladesh and the Philippines.

Main Results:

• The developed molecular tool achieved high agreement rates: 74.1% in Bangladesh and 80.6% in the Philippines.
• Genetically improved farmed tilapia (GIFT) was the dominant strain identified in Bangladesh.
• GET-Excel, a composite strain, was dominant in the Philippines, showing partial derivation from GIFT.

Conclusions:

• Molecular genetic tools, specifically SNP panels and DAPC, are effective for identifying and verifying Nile tilapia strains in aquaculture.
• These tools can accurately distinguish between genetically improved strains, aiding in quality control and dissemination.
• The findings support the use of genetic verification to ensure the integrity of improved tilapia strains in major aquaculture regions.