Efficient Genomic DNA Isolation and Quality Assessment in Prunus Rootstocks GF-677 and MaxMa-14 Using ISSR and SCoT Markers

The quality of genomic DNA is a critical factor for the reliability of molecular analyses in clonal plant materials. In Prunus species, DNA isolation is often challenging due to the high content of polysaccharides and phenolic compounds in leaf tissues, which can interfere with downstream enzymatic reactions. In this study, a CTAB-based DNA isolation protocol was evaluated for its efficiency in extracting high-quality genomic DNA from leaf tissues of GF 677 and MaxMa-14 Prunus rootstocks. The integrity of the isolated DNA was initially assessed by agarose gel electrophoresis, which revealed intact, high-molecular-weight genomic DNA with no evidence of degradation. Spectrophotometric analyses showed that DNA concentrations ranged from 200–285 ng/µl for GF 677 and 260–300 ng/µl for MaxMa-14. The A260/280 and A260/230 absorbance ratios fell within the accepted ranges, indicating minimal contamination by proteins, polysaccharides, and phenolic compounds. The quality of the extracted DNA was further confirmed by successful restriction enzyme digestion using BamHI and HindIII, demonstrating the effective removal of inhibitory substances. In addition, PCR amplification using ISSR and SCoT marker systems produced clear, bright, and reproducible banding patterns, confirming the suitability of the isolated DNA for PCR-based molecular analyses.Overall, the results demonstrate that the applied CTAB-based protocol provides a reliable, cost-effective, and practical approach for isolating high-quality genomic DNA from Prunus rootstocks. This method is suitable for routine laboratory use and supports downstream molecular applications such as marker-based genetic analyses and clonal identity verification.