Comparative assessment of quick and cost-efficient quality DNA extraction methods from rice leaves

Abstract

DNA extraction from rice leaves was developed earlier but a quick and cost-efficient DNA extraction method is still in search to conduct molecular research swiftly. Four DNA extraction methods i.e., extraction buffer (E1), K-acetate (E2) and two modified CTAB (E3 and E4) based protocols were tested for DNA concentration, purity of the extracted DNA, time and cost required per sample. Moreover, a Mixer mill (Mi; electrical method) and a Mortar and pestle (M; manual method) were used to test the performance of the four methods. DNA concentrations are insignificant among the methods MiE1 (266.61 ng/µL), MiE3 (260.58 ng/µL) and MiE4 (245.49 ng/µL) but these are all significantly different from the method MiE2 (137.13 ng/µL). ME2 required the maximum time (59 minutes), followed by ME1 (55 minutes), ME3 (40 minutes), and ME4 (21 minutes). In terms of cost, MiE3 and MiE4 required the highest (356.39 taka (4.19 dollars)/100 samples) amount of cost, whereas the lowest price (101.81 taka (1.20 dollars)/100 samples) was required in MiE2. For Purity-1 (260/280) (PU-1), no significant difference was found among the methods, but for Purity-2 (260/230) (PU-2), MiE2 significantly differed from the other methods. Through the mortar and pestle, the highest DNA concentration was found in ME1 (382.68 ng/µL) which significantly differed from ME2, ME3 and ME4. The highest times required in ME2 (59 min) followed by ME1 (55 min), ME3 (40 min) and ME4 (21 min) methods. The highest costs (356.39 taka (4.19 dollars)/100 samples) were required for ME3 and ME4 methods followed by ME2 (121.83 taka (1.43 dollars)/100 samples) and ME1 (101.81 taka (1.20 dollars)/100 samples). No significant difference was found among the methods for PU-1 but for PU-2, ME2 significantly differed from other methods. CTAB-based methods are the best and quick for DNA extraction but these methods are costly, whereas the other two methods are cheaper but they are time-consuming compared to CTAB.