Swift SNPs: Evaluating Rapid DNA Extraction Methods for Scalable Genotyping in Aquaculture.

Area of Science:

• Aquaculture genomics
• Molecular biology
• Biotechnology

Background:

• Efficient DNA extraction is crucial for high-throughput genotyping in aquaculture breeding programs.
• Balancing cost, speed, and data quality is essential for these applications.
• Conventional methods like CTAB can be time-consuming and resource-intensive.

Purpose of the Study:

• To compare the efficacy of five rapid DNA extraction methods against the conventional CTAB protocol.
• To evaluate DNA yield, purity, and integrity for genotyping applications in Lates calcarifer (barramundi).
• To identify the most suitable rapid method for cost-effective and scalable aquaculture genomics.

Main Methods:

• Five rapid DNA extraction methods (HotSHOT, Chelex, Tween, wax-coated dipstick, bare dipstick) were tested.
• Conventional CTAB protocol served as the benchmark.
• DNA quality was assessed using spectrophotometry, fluorometry, and Agilent TapeStation; performance evaluated via microsatellite genotyping, TYRP1b gene sequencing, and SNP genotyping.

Main Results:

• CTAB yielded the highest quality DNA, but HotSHOT demonstrated comparable performance in genotyping assays.
• HotSHOT achieved 82.3% SNP concordance with CTAB, 93.1% microsatellite amplification, and high-quality gene sequencing.
• Chelex, Tween, and dipstick methods showed lower success rates due to inadequate DNA yield and purity.

Conclusions:

• HotSHOT is the most effective rapid DNA extraction method, offering a significant improvement in SNP concordance compared to other rapid methods.
• The choice of DNA extraction method critically impacts the success of target-capture genotyping.
• HotSHOT is a viable, cost-effective, and scalable option for routine aquaculture genomics.