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

## TL;DR

This study compares rapid DNA extraction methods for aquaculture genotyping, finding HotSHOT to be a cost-effective alternative to traditional methods.

## Contribution

The study identifies HotSHOT as a superior rapid DNA extraction method for scalable genotyping in aquaculture.

## Key findings

- HotSHOT DNA extraction achieved 82.3% SNP concordance compared to CTAB, with reliable microsatellite and gene sequencing results.
- CTAB produced the highest DNA quality but was outperformed by HotSHOT in cost-effectiveness and scalability.
- Chelex, Tween, and dipstick methods showed lower success due to poor DNA yield and purity.

## Abstract

Efficient DNA extraction is critical for high-throughput genotyping in aquaculture breeding programs, where cost, speed, and data quality must be balanced. This study compared five rapid extraction methods—HotSHOT, Chelex, Tween, wax-coated dipstick, and bare dipstick—against a conventional cetyltrimethylammonium bromide (CTAB) protocol for use in Lates calcarifer (barramundi) genotyping. DNA yield, purity, and integrity were measured by spectrophotometry, fluorometry, and Agilent TapeStation. Performance was tested in microsatellite genotyping, tyrosinase-related protein 1b (TYRP1b) gene sequencing, and single nucleotide polymorphism (SNP) genotyping on the Tecan Allegro Targeted Resequencing V2 platform. CTAB produced the highest-quality DNA (30.3 ± 17.4 ng/µL; A260/A280 = 1.91 ± 0.26; DIN = 8.78) with reliable results in all assays. Despite lower quality (1.07 ± 0.30 ng/µL; A260/A280 = 1.44 ± 0.18; DIN ≈ 1.6), HotSHOT performed similarly: SNP concordance with CTAB averaged 82.3%, microsatellite amplification reached 93.1% (vs. 99.3% for CTAB), and all HotSHOT samples yielded high-quality TYRP1b sequences. Chelex, Tween, and dipstick methods had lower success, likely due to inadequate yield and purity. HotSHOT was the most effective rapid alternative to CTAB, with significantly higher SNP concordance (82.3% vs. others; p < 0.005). These results show that method choice strongly influences target-capture genotyping success and support HotSHOT as a cost-effective, scalable option for aquaculture genomics.