Using acetone for rapid PCR-amplifiable DNA extraction from recalcitrant woody plant taxa

Abstract

Premise: Quick and effective DNA extraction from plants for subsequent PCR amplification is sometimes challenging when working across diverse plant taxa that may contain a variety of inhibitory compounds. Time-consuming methods may be needed to overcome these inhibitory effects as well as the effects of various preservation and collection methods to extract DNA from leaf samples. Our objective was to develop a rapid DNA extraction protocol that could be used with diverse plant taxa to produce high-quality DNA suitable for downstream PCR applications. Methods and Results: We tested the efficacy of acetone in extracting DNA from fresh, frozen, oven-dried, acetone-fixed, and herbarium leaf material of 22 species from 16 woody and herbaceous plant families. An improved simplified DNA extraction protocol was developed using acetone-fixed leaf material. The addition of 1% sodium dodecyl sulfate solution resulted in the optimal extraction from all tissue samples. The DNA resulting from the extraction protocol was readily amplified using real-time PCR assays. Conclusions: The protocol described here resulted in the extraction of DNA from recalcitrant plant species that was of sufficient quality and quantity for PCR amplification, as indicated by the low threshold cycle values from real-time assays. This method is simple, fast, and cost-effective, and is a reliable tool for extracting high-quality DNA from plant material containing PCR inhibitors.