Comparative Analysis of two DNA Extraction Protocols from Fresh and Dried wood of Cunninghamia Lanceolata (Taxodiaceae)

Abstract

DNA was isolated from the sapwood, transition wood and heartwood of fresh and dried Cunninghamia lanceolata wood using two DNA extraction protocols: the modified CTAB method and the modified Qiagen kit. Our major objective was to (i) determine an optimized method for retrieving good quality and sufficient quantity of DNA from wood, and to (ii) investigate the effect of different radial positions of fresh and dried wood for DNA extraction. In comparison with the modified CTAB method, a greater quantity of higher quality DNA – both chloroplast and nuclear ribosomal DNA – was retrieved using the Qiagen kit protocol. The chloroplast DNA regions retrieved from both fresh and dried wood were successfully amplified using both protocols, but the PCR amplification for the rDNA-ITS region from the heartwood failed using both protocols. The quantity and purity of the DNA from the sapwood and transition wood (derived from nuclei and plastids in the parenchyma cells) was greater than that from the heartwood (derived mainly from amyloplasts). Due to the influence of the drying treatment, the quantity of DNA decreased by more than 50%. The optimized radial position for DNA extraction in the stem was demonstrated based on anatomical observation.

Concentration and Distribution of Nuclei and Plastids in Xylem Cells in Cunninghamia lanceolata and Aquilaria sinensis

“…This indicates that the extraction quantity varies according to the content of nuclei and plastids. The quantity of DNA extracted from the same samples using the DNeasy Plant Mini Kit was 1.5 to 2 times more than what was extracted using CTAB (Jiao et al 2012). However, the kit did not succeed with the heartwood dried at a high-temperature (Jiao et al 2014).…”

“…A DNeasy Plant Mini Kit (QIAGEN, Germany) succeeded in extracting the DNA in fresh sapwood, fresh heartwood, and dried heartwood of A. sinensis, but failed with heartwood dried at a high-temperature (Jiao et al 2014). The same was true for both the Kit and CTAB when it came to DNA extraction from C. lanceolata (Jiao et al 2012). This indicates that the extraction quantity varies according to the content of nuclei and plastids.…”

“…Therefore, heartwood formation degraded the nuclei more than the storage time did (Table 3). Jiao (2012). Its treatment conditions and sample source of wood were same to this paper.…”

“…It was reported that hexadecyl trimethyl ammonium bromide (CTAB), the DNeasy Plant Mini Kit (Qiagen, Germany), and N-phenacylthiazolium bromide (PTB) had been successfully used in wood DNA extraction after modification (Asif and Cannon 2005;Jiao et al 2012;Jiao et al 2014). However, two or three extraction methods were used on the same wood sample in most of the existing research, because it is difficult to select the right wood DNA extraction procedure for wood that has unknown degrees of DNA degradation.…”

Extraction and amplification of DNA from aged and archaeological Populus euphratica wood for species identification

“…However, DNA extraction from dried wood stored for a long-term is more problematic (Finkeldey et al 2010;Abe et al 2011;Höltken et al 2011;Lowe and Cross 2011;Jiao et al 2012Jiao et al , 2014. After the death of an organism, hydrolytic and oxidative processes cause fragmentation and modification to its DNA (Pääbo et al 2004;Schlumbaum et al 2008).…”