Effect of DNA extraction in the Rosa canina L. identification under different processing temperature
Keywords:dog rose, DNA extraction, PCR effectivity
Rosa canina, L. is widely used for medicinal purposes as well as in food industry where it is a valuable source, bioactive compounds and natural colorants. Actually, no specific method is recommended as suitable one for DNA extraction from rose hips. The aim of the study was to compare three commercial and three non-commercial methods to extract total genomic DNA from rose hips hyphanthium. Four methods are based on the precipitation in principle and two methods are based on resin-binding. Extracted DNA was proved for the effectivity in following PCR. In total, six different DNA isolations was performed for differently heat processes rose hips - fresh hyphanthium, 2-weeks frozen hyphanthium, dried hyphanthium (50 °C) and boiled hyphanthium (100 °C). The amplification parameters of 500 bp chloroplast gene amplicon were evaluated. Obtained amounts of extracted DNA was very variable not only for every individual method used but for individual treatment of samples, too. In general, non-commercial method provided higher amount of extracted DNA, but the A260/280 ratio was lower. When regarding the processing treatment of the samples, high differences were found among the samples untreated by heat and those that were dried or boiled for three of the used extraction methods. All the samples were positive for amplification, but different amounts of amplified product were obtained. The comparison of data for concentrations of extracted DNA and concentrations of amplified product showed large differences when regarding the achieved purity of DNA in extraction.
Abu-Romnan, S. 2011. Comparison of methods for isolating high quality DNA from sage (Salvia officinalis). Journal of Medicinal Plants Research, vol. 5, no. 6, p. 938-941.
Bar, T., Kubista, M., Tichopad, A. 2012. Validation of kinetics similarity in qPCR. Nucleic Acids Research, vol. 40, p. 1395-1406. https://doi.org/10.1093/nar/gkr778 DOI: https://doi.org/10.1093/nar/gkr778
Balážová, Ž., Petrovičová, L., Gálová, Z., Vivodík, M. 2016. Molecular characterisation of rye cultivars. Potravinarstvo, vol. 10, no. 1, p. 54-58. https://doi.org/10.5219/522 DOI: https://doi.org/10.5219/522
Bokszczanin, K., Prazybyla, A. A. 2006. Copper (II) acetate improves the quality of pear (Pyrus) DNA during extraction. Plant Molecular Biology Reporter Journal, vol. 24, p. 249a-249d. https://doi.org/10.1007/BF02914065 DOI: https://doi.org/10.1007/BF02914065
Cankar, K., Stebih, D., Dreo, T., Zel, J., Gruden, K. 2006. Critical points of DNA quantification by real-time PCR -effects of DNA extraction method and sample matrix on quantification of genetically modified organisms. BMC Biotech, vol. 6, p. 37. https://doi.org/10.1186/1472-6750-6-37 DOI: https://doi.org/10.1186/1472-6750-6-37
Cota-Sánchez, H. J., Remarchuk, K., Ubayasena, K. 2006. Ready-to-Use DNA Extracted with a CTAB Method Adapted for Herbarium Specimens and Mucilaginous Plant Tissue. Plant Molecular Biology Reporter, vol. 24, no. 2, p.161-167. https://doi.org/10.1007/BF02914055 DOI: https://doi.org/10.1007/BF02914055
Dabo, S. M., Mitchell, E. D. Jr, Melcher, U. 1993. A method for the isolation of nuclear DNA from cotton (Gossypium) leaves. Analytical Biochemistry, vol. 210, no. 1, p. 34-38. https://doi.org/10.1006/abio.1993.1146 PMid:8098189 DOI: https://doi.org/10.1006/abio.1993.1146
Dellaporta, S. L., Wood, J., Hicks, J. B. 1983. A Plant DNA Minipreparation: Version II. Plant Molecular Biology Reporter, vol. 1, no. 4, p. 19-21. https://doi.org/10.1007/BF02712670 DOI: https://doi.org/10.1007/BF02712670
De Cock, K., Mijnsbrugge, K. V., Breyne, P., Van Bockstaele, E., Van Slycken, J. 2008. Morphological and AFLP-based differentiation within the taxonomical complex section Canine (subgenus Rosa). Annals of Botany, vol. 102, no. 5, p. 685-697. https://doi.org/10.1093/aob/mcn151 PMid:18723861 DOI: https://doi.org/10.1093/aob/mcn151
Doosty, B., Drikvand, R., Salahvarzi, E., Amiri, H., Hadian, J. 2012. Comparative Analysis and Optimization of Different DNA Extraction Protocols in Satureja khuzistanica. International Journal of Biology, vol. 4, no. 4, p. 112-116. https://doi.org/10.5539/ijb.v4n4p111 DOI: https://doi.org/10.5539/ijb.v4n4p111
Doyle, J. J., Doyle, J. L. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin, vol. 19, no. 1, p.11-15.
Drábková, L., Kirschner, J., Vlček, E. 2002. Comparison of seven DNA extraction and amplification protocols in historical herbarium specimens of Juncaceae. Plant Molecular Biology Reporter, vol. 20, no. 2, 161-175. https://doi.org/10.1007/BF02799431 DOI: https://doi.org/10.1007/BF02799431
Gálová, Z., Vivodík, M., Balážová, Ž., Kuťka-Hlozáková, T. 2015. Identification and differentiation of Ricinus communis L. using SSR markers. Potravinarstvo, vol. 9, no. 1, p. 556-561. https://dx.doi.org/10.5219/516 DOI: https://doi.org/10.5219/516
Gryson, N. 2010. Effect of food processing on plant DNA degradation and PCR-based GMO analysis: a review. Analytical and Bioanalytical chemistry, vol. 396, no.6, p. 2003-20022. https://doi.org/10.1007/s00216-009-3343-2 DOI: https://doi.org/10.1007/s00216-009-3343-2
Halliwell, B. 2006 Polyphenols: antioxidant treats for healthy living or covert toxins? Journal Science Food Agriculture, vol. 86, no. 13, p. 1992-1995. https://doi.org/10.1002/jsfa.2612 DOI: https://doi.org/10.1002/jsfa.2612
Hedman, J., Rådström, P. 2013. Overcoming inhibition in real-time diagnostic PCR. Methods in Molecular Biology, vol. 943, p. 17-48. https://doi.org/10.1007/978-1-60327-353-4_2 DOI: https://doi.org/10.1007/978-1-60327-353-4_2
Hiesinger, M., Löffert, D., Ritt, CH., Oelműller, U. 2001. The effects of phenol on nucleic acid preparation and downstream applications. Qiagen News, vol. 5, p. 23-26.
Huaqiang, T., Haitao, H., Mamman, T., Jianyao, M., Huanxiu, L. 2013. Comparative Analysis of Six DNA Extraction Methods in Cowpea (Vigna unguiculata L.Walp). Journal of Agricultural Science, vol. 5, no. 7, p. 82-90. https://doi.org/10.5539/jas.v5n7p82 DOI: https://doi.org/10.5539/jas.v5n7p82
Hornero-Méndez, D., Mínguez-Mosquera, M. I. 2000. Carotenoid pigments in Rosa mosqueta hips, an alternative carotenoid source for foods. Journal of Agricultural Chemistry, vol. 48, no. 3, p. 825-828. https://doi.org/10.1021/jf991136n DOI: https://doi.org/10.1021/jf991136n
Jűrgens, A. H., Seitz, B., Kowarik, I. 2007. Genetic differentiation of Rosa canina (L.) at regional and continental scales. Plant Systematic and Evolution, vol. 269, no. 1, p.39-53. https://doi.org/10.1007/s00606-007-0569-3 DOI: https://doi.org/10.1007/s00606-007-0569-3
Kang, T. J., Yang, M. S. 2004. Rapid and reliable extraction of genomic DNA from various wild-type and transgenic plants. BMC Biotechnology, vol. 4, p. 20. https://doi.org/10.1186/1472-6750-4-20 DOI: https://doi.org/10.1186/1472-6750-4-20
Kaul, K., Dhyani, D., Sharma, R. K. 2009. Evaluation of DNA Extraction Methods for RAPD, SSR and AFLP Analyses of Wild Rose Species. Floriculture and Ornamental Biotechnology. vol. 3, no. 1, p. 25-30.
Kedong, X., Qinglin, L., Huifang, Y., Li, Z., Lili, D., Fengluan, L., Ling, Bi., Nan, M., Liangjun, Z. 2011. Isolation and molecular characterization of RcSERK1: A Rosa canina gene transcriptionally induced during initiation of protocorm-like bodies. African Journal of Biotechnology, vol. 10, p. 4011-4017.
Kharazmi, M., Bauer, T., Hammes, W. P., Hertel, C. 2003. Effect of food processing on the fate of DNA with regard to degradation and transformation capability in Bacillus subtilis. Systematic and Applied Microbiology, vol. 26, no 4, p. 495-501. https://doi.org/10.1078/072320203770865774 PMid:14666975 DOI: https://doi.org/10.1078/072320203770865774
Krizman, M., Jakse, J., Baricevic, D., Javornik, B., Prosek, M. 2006. Robust CTAB-activated charcoal protocol for plant DNA extraction. Acta Agriculturae Slovenica, vol. 87, no. 2, p. 427-433.
Manen, J. F., Sinitsyna, O., Aeschbach, L., Markov, A. V., Sinitsyn, A. 2005. A Fully Automatable Enzymatic Method for DNA Extraction from Plant Tissue. BMC Plant Biology, vol. 5, no. 23, p. 1-9. https://doi.org/10.1186/1471-2229-5-23 DOI: https://doi.org/10.1186/1471-2229-5-23
Murry, M. G., Thompson, W. F. 1980. Rapid isolation of high molecular weight plant DNA. Nucleic Acids Research, vol. 8, no. 19, 4321-4325. https://doi.org/10.1093/nar/8.19.4321 DOI: https://doi.org/10.1093/nar/8.19.4321
Padmalatha, K., Prasad, M. N. V. 2006. Optimization of DNA isolationand PCR protocol for RAPD analysis of selected medicinal and aromatic plants of conservation concern from Peninsular India. African Journal Biotechnology, vol. 5, no.3, p. 230-234.
Petrovičová, L., Gálová, Z., Balážová, Ž., Vivodík, M., Wójcik-Jagla, M., Rapacz, M. 2015. Assessment of RAPD polymorphism in rye (Secale cereale L.) genotypes. Journal of Microbiology, Biotechnology and Food Sciences, vol. 4, no. 2, p. 94-97. https://doi.org/10.15414/jmbfs.2015.4.special2.94-97 DOI: https://doi.org/10.15414/jmbfs.2015.4.special2.94-97
Ritz, Ch. M., Wissemann, V. 2011. Microsatellite analyses of artificial and spontaneous dogrose hybrids reveal the hybridogenic origin of Rosa micrantha by the contribution of unreduced gametes. Journal of Heredity, vol. 102, no. 2, p. 217-227. https://doi.org/10.1093/jhered/esq124 DOI: https://doi.org/10.1093/jhered/esq124
Sarwat, M., Negi, M. S., Lakshmikumaran, M., Tyagi, A. K., Das, S., Srivastava, P. S. 2006. A standardized protocol for the genomic DNA isolation from Terminalia arjuna for genetic diversity analysis. Electronic Journal of Biotechnology, vol. 9, no. 1, p. 86-91. https://doi.org/10.2225/vol9-issue1-fulltext-3 DOI: https://doi.org/10.2225/vol9-issue1-fulltext-3
Stănilă, A., Diaconeasa, Z., Roman, I., Sima, N., Măniuţiu, D., Roman, A., Sima, R. 2015. Extraction and Characterization of Phenolic Compounds from Rose Hip (Rosa canina L.) Using Liquid Chromatography Coupled with Electrospray Ionization - Mass Spectrometry. Notulae Botanicae Horti Agrobotanici Cluj-Napoca, vol. 43, no. 2, p. 349-354. DOI: https://doi.org/10.15835/nbha43210028
Rogers, S. O., Bendich, A. J. 1994. Extraction of total cellular DNA from plants, algae and fungi. In: Gelvin, S. B. et al. Plant Molecular Biology Manual D1. 2nd ed. Belgium : Kluwer Academic Publishers, pp. 1-8. ISBN 0-7923-2868-2. https://doi.org/10.1007/978-94-011-0511-8_12 DOI: https://doi.org/10.1007/978-94-011-0511-8_12
Tozzi, R., Mulinacci, N., Storlikken, K., Pasquali, I., Vincieri, F. F., Bettini, R. 2008. Supercritical extraction of carotenoids from Rosa canina L. hips and their formulation with beta-cyclodextrin. AAPS PharmSciTech, vol. 9, no. 2, p.693-700. https://doi.org/10.1208/s12249-008-9100-6 PMid:18528762 DOI: https://doi.org/10.1208/s12249-008-9100-6
Volk, H., Piskernik, S., Kurinčič, M., Klančnik, A., Toplak, N., Jeršek, B. 2014. Evaluation of different methods for DNA extraction from milk. Journal of Food and Nutrition Research, vol. 2, p. 1-10.
Winther, K., Vinther Hansen, A. S., Campbell-Tofte, J. 2016. Bioactive ingredients of rose hips (Rosa canina, L) with special reference to antioxidative and anti-inflamatory properties: in vitro studies. Botanics: Targets and Therapy, vol. 6, p. 11-23. https://doi.org/10.2147/BTAT.S91385 DOI: https://doi.org/10.2147/BTAT.S91385
Zhang, J., Stewart, J. M. 2000. Economic and rapid method for extracting cotton genomic DNA. Journal of Cotton Science, vol. 4, p. 193-201.
How to Cite
This license permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited, and is not altered, transformed, or built upon in any way.