Exploitation of Polymorphic Sequences in Chloroplast Genome for Identification of Commercial Tobacco Cultivars
Fingerprinting of Tobacco Cultivars with Cp DNA Marker
Keywords:
Tobacco, Varietal identification, Chloroplast markers, DNA fingerprintingAbstract
Tobacco is an important commercial commodity. Discrimination of tobacco cultivars at DNA level is extremely
important for selling of brand, free of mixing. Chloroplast markers have sufficient resolving power for differentiation
at intra-varietal level. In this study only chloroplast genome markers were used to amplify polymorphic regions
encoding genes involved in photosynthetic machinery of plants. This region encompassing 9000 to 9600bp harbors
SNPs, Indels and SSRs. Different bioinformatics and phylogenetic software were used to investigate relationship of
DNA sequences of 11 unknown plant samples with a reference sequence from NCBI. Multiple alignments exhibited
sequence conservation encompassing a substantial region. But it also revealed important variety specific SNPs. Sequence
similarity index was generated for grouping of unknown plants. The unidentified plants were differentiated into different clusters as revealed by phylogenetic analysis. Furthermore, a neighbor-net network analysis validated the results of Neighbor Joining tree. Our analysis indicates that there exist at least 5 varieties of tobacco. The V1 is the most distant cultivar. V5 is also separated from the rest of cultivars. But V2, V3 and reference sequence make further linage, and can be considered as separate clade. A bigger cluster including V7, S2 and V6 is differentiated into distinct group. The S1, V9, V10 and V8 are the 5th cluster that can be considered as a single variety. Hence there were 5 varieties in total that were mixed in 11 samples.
References
Davalieva, K., I. Maleva, K. Filiposki, O. Spiroski & G.D. Efremov. Genetic variability of Macedonian tobacco varieties determined by microsatellite marker analysis. Diversity 2: 439-449 (2010).
Denduangboripant, J., T. Piteekan & M. Nantharat. Genetic polymorphism between tobacco cultivargroups revealed by amplified fragment length polymorphism analysis. Journal of Agricultural Science 2: 41 (2010).
Caguiat, X.G.I., J.C. Yabes & D.A. Tabanao. Phylogenetic Similarity of Popular Rice Varieties from Different Sources. Journal of Phylogenetics & Evolutionary Biology: 1-4 (2016).
Giannoulia, K., F. Gazis, N. Nikoloudakis, D.Milioni & K. Haralampidis. Breeding, molecular markers and molecular biology of the olive tree. European Journal of Lipid Science and Technology 104: 574-586 (2002).
Yan, M., Y. Xiong, R. Liu, M. Deng & J. Song. The application and limitation of universal chloroplast markers in discriminating East Asian evergreen oaks. Frontiers in plant science 9 (2018).
Mariotti, R., N.G. Cultrera, C.M. Díez, L. Baldoni & A. Rubini. Identification of new polymorphic regions and differentiation of cultivated olives (Olea europaea L.) through plastome sequence comparison. BMC Plant Biology 10: 211 (2010).
Doyle, J.J. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19: 11-15 (1987).
Hall, T.A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41: [London]: Information Retrieval Ltd., c1979-c2000.: 95-98 (1999).
Thompson, J.D., D.G. Higgins & T.J. Gibson. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22: 4673-4680 (1994).
Tamura, K., G. Stecher, D. Peterson, A. Filipski & S. Kumar. MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution 30: 2725-2729 (2013).
Huson, D.H. & D. Bryant. Application of phylogenetic networks in evolutionary studies. Molecular biology and evolution 23: 254-267
(2006).
Noman, M., W. Ajmal, M.R. Khan, A. Shahzad & G.M. Ali. Exploitation of Concatenated Olive Plastome DNA Markers for Reliable Varietal
Identification for On-Farm Genetic Resource Conservation. American Journal of Plant Sciences 6: 3045 (2015).
Dizkirici, A., O. Yigit, M. Pinar & H. Eroglu. Molecular phylogeny of Muscari (Asparagaceae) inferred from cpDNA sequences. Biologia: 1-10(2018).
Liu, Y.-C., B.-Y. Lin, J.-Y. Lin, W.-L. Wu & C.-C. Chang. Evaluation of chloroplast DNA markers for intraspecific identification of Phalaenopsis equestris cultivars. Scientia Horticulturae 203: 86-94 (2016).
Chen, X., J. Zhou, Y. Cui, Y. Wang, B. Duan & H.Yao. Identification of Ligularia Herbs Using the Complete Chloroplast Genome as a Super-Barcode. Frontiers in Pharmacology 9: 695 (2018).
Osuna-Mascaró, C., R.R. de Casas & F. Perfectti. Comparative assessment shows the reliability of chloroplast genome assembly using RNA-seq. Scientific Reports 8: 17404 (2018).
Zhang, Y., B.J. Iaffaldano, X. Zhuang, J. Cardina & K. Cornish. Chloroplast genome resources and molecular markers differentiate rubber dandelion species from weedy relatives. BMC Plant Biology 17: 34 (2017).
Downloads
Published
How to Cite
Issue
Section
License
Creative Commons Attribution (CC BY). Allows users to: copy the article and distribute; abstracts, create extracts, and other revised versions, adaptations or derivative works of or from an article (such as a translation); include in a collective work (such as an anthology); and text or data mine the article. These uses are permitted even for commercial purposes, provided the user: includes a link to the license; indicates if changes were made; gives appropriate credit to the author(s) (with a link to the formal publication through the relevant DOI); and does not represent the author(s) as endorsing the adaptation of the article or modify the article in such a way as to damage the authors' honor or reputation.
