Comparison of genomic DNA extraction methods for Colossoma macropomum fish fin clippings for single nucleotide polymorphism genotyping
Ideal DNA extraction techniques must be efficient in terms of time, labor, and costs, optimizing yield and quality of the DNA for the desired applications. We tested six DNA extraction methods: DNeasy® Blood & Tissue Kit, Cetyltrimethylammonium bromide (CTAB), Modified salting-out protocol (SA), Boiling Tissue, Proteinase K (PK) and Mini Kit Applied Biosystems, on fin clippings from tambaqui (Colossoma macropomum). DNA yield, purity, quality, and cost of each method were evaluated. The effectiveness of extraction was evaluated by PCR amplification and genotyping efficiency, repeatability and accuracy. DNA yield and purity were quantified using NanoDrop absorbance ratios. Cost was estimated in terms of time and material expenses. The results showed differences between the tested methods, with the PK method having the best performance, followed by SA and CTAB. PK was identified as the most economical and efficient technique in terms of time, cost, and scalability/potential automation, while also generating DNA of good quality for performing PCR amplification and SNP genotyping with tambaqui samples.