Comparison of six genomic DNA extraction methods for molecular downstream applications of apple tree (Malus X domestica)

Abstract

Background: The study of weed genomics is important for the effective management of weeds to enhance crop yield. A rapid, inexpensive and high quality DNA extraction is needed for genomic and other molecular studies. Here, we describe the protocols for DNA extraction from two different parts of the Echinochloa colona plant using modi ed cetyltrimethylammonium bromide (CTAB) and a commercial kit. Results: In the study, it was observed that the DNA extracted from plant leaf tissues and dry seeds with a modi ed CTAB protocol was of good quality, with no contaminations of polysaccharides and essential oils. Quality of DNA extracted from dry seeds was comparable with that of plant leaves under both protocols. The extracted DNA from both plant parts was successfully ampli ed by PCR using the EPSPS microsatellite marker. Compared to the protocol of DNA extracted from leaf tissue, dry seeds will save time and other valuable resources. Moreover, the same protocols can be implemented for the extraction of highquality DNA for molecular studies in other plant species where a large amount of polysaccharides, secondary metabolites and essential oils are present. Conclusions: Modi ed methods of DNA extraction from dry seeds are e cient and time-saving which can be used in genotypic and other molecular approaches. High-quality DNA can be isolated from plant leaf tissues using modi ed CTAB and commercial kits, however, DNA extracted from dry seeds will save time and other valuable resources.

Comparison of genomic DNA extraction methods to obtain high DNA quality from barnyard grass (Echinochloa colona)

“…Although commercially available kits are effective in extraction of DNA free from compounds, a signi cant amount of DNA was lost from the samples [5,20]. The genomic DNA extraction using CTAB protocol for suppressing the phenolic compounds was also carried out in E. colona in other studies [16,21].…”

Development of a minimal KASP marker panel for distinguishing genotypes in apple collections

“…DNA extraction was carried out as previously described [ 14 ]. Purification by Qiagen column was found to be a necessary step to reduce the levels of phenolic compounds [ 15 ] and so obtain accurate genotyping results. DNA was diluted with PCR-grade water to an average of 2.5 ng per reaction.…”

A RAPID AND EFFICIENT DNA EXTRACTION PROTOCOL FOR Ganoderma zonatum, A BASAL AND UPPER STEM ROT PATHOGEN OF OIL PALM IN MALAYSIA

“…In order for any sequencing project to proceed, such as PacBio sequencing, large amount of good purity DNA is required to meet this requirement. Usage of extraction kit is not suitable as it yields low amount of DNA and is not cost effective (Pipan et al, 2018;Psifidi et al, 2015;Umesha et al, 2016). Thus, the current study explored and recommend a time efficient and cost effective DNA extraction protocol of G. zonatum found in the oil palm plantations in Malaysia.…”

“…Firstly, we conducted experiments that showed PCR amplification of the extracted DNA from all the seven protocols (Figure 3). Despite disparity between the purity and concentrations of DNA, PCR amplification was successful from the seven protocols evaluated (Pipan et al, 2018). Apart from DNA quality and concentration, there are many factors to consider when assessment is based on PCR, such as suitability of primers, quality of reagents or even the thermal cycler used.…”