Document Type : Original Article

Authors

Tea Research Center, Horticultural Sciences Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Lahijan, Iran

Abstract

Purpose: A significant number of genetic resources of Camellia sinensis and its allied genotypes have been collected and preserved in Iran TRC. Information about them is mostly based on morphological data. Research method: PCR-RFLP technique and morphological characters were used for the identification of organelle DNA (cpDNA) diversity in 25 tea genotypes. Twenty-one qualitative and quantitative characteristics were evaluated. Findings: A pair-wise similarity among the samples ranged from 0.14 to 0.66 based on morphological data. The dendrogram was designed, and samples were grouped into three main clusters at 0.38 similarity. Using three universal primer pairs which introduced for chloroplast amplified about 4070bp of cpDNA, following the digestion of fragments with three restriction endonucleases (HinfI, AluI and PstI) and the result of this method was introduced six haplotypes. The most significant and widespread haplotype was H2 (frequency ≈ 28%). All of the detected mutations were insertion-deletions and they ranged from 30 to 60 bp. The calculated total cpDNA diversity in populations (hT), a major portion of it was within populations were (hS) and genetic differentiation among populations (GST) were 0.43, 0.17 and 0.61, respectively. It should have been noted that the calculated GST was low and no structure could be identified. Limitations: Applying allied species and using more potent markers such as cpSSR and sequencing can lead to more accurate results. Originality/Value: The results of this study indicate that the PCR-RFLP method and morphological characters are applicable in the identification of tea genotypes and cultivars. In studying Camellia genus phylogeny, the polymorphism in cpDNA has to be considered carefully.

Keywords

Main Subjects

Amane, M., Ouazzani, N., Lumaret, R., & Debain, C. (2000). Chloroplast-DNA variation in the wild and cultivated olives (Olea europaea L.) of Morocco. Euphytica116(1), 59-64. https://doi.org/10.1023/A:1004025431960
Andrew King, R., & Ferris, C. (1998). Chloroplast DNA phylogeography of Alnus glutinosa (L.) Gaertn. Molecular Ecology7(9), 1151-1161. https://doi.org/10.1046/j.1365-294x.1998.00432.x
Beris, F. S., Sandalli, C., Canakci, S., Demirbag, Z., & Belduz, A. O. (2005). Phylogenetic analysis of tea clones (Camellia sinensis) using RAPD markers. Biologia-Section Botany60, 457-461.
Chen, L., Gao, Q. K., Chen, D. M., & Xu, C. J. (2005a). The use of RAPD markers for detecting genetic diversity, relationship and molecular identification of Chinese elite tea genetic resources [Camellia sinensis (L.) O. Kuntze] preserved in a tea germplasm repository. Biodiversity and Conservation14(6), 1433-1444. https://doi.org/10.1007/s10531-004-9787-y
Chen, S. X., Qi, G. N., Li, H., Shan, H. L., & Zou, Y. (2012). Rapid establishment of polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) system for chloroplast DNA in tea [Camellia sinensis (L.) O. Kuntze]. African Journal of Biotechnology11(33), 8181-8188. http://dx.doi.org/10.5897/AJB11.4167
Chen, J., Wang, P., Xia, Y., Xu, M., & Pei, S. (2005b). Genetic diversity and differentiation of Camellia sinensis L. (cultivated tea) and its wild relatives in Yunnan province of China, revealed by morphology, biochemistry and allozyme studies. Genetic Resources and Crop Evolution52(1), 41-52. https://doi.org/10.1007/s10722-005-0285-1
Chen, L., & Yamaguchi, S. (2002). Genetic diversity and phylogeny of tea plant (Camellia sinensis) and its related species and varieties in the section Thea genus Camellia determined by randomly amplified polymorphic DNA analysis. The Journal of Horticultural Science and Biotechnology77(6), 729-732. https://doi.org/10.1080/14620316.2002.11511564
Cros, J., Combes, M. C., Trouslot, P., Anthony, F., Hamon, S., Charrier, A., & Lashermes, P. (1998). Phylogenetic analysis of chloroplast DNA variation in Coffea L.. Molecular Phylogenetics and Evolution9(1), 109-117. http://dx.doi.org/10.1006/mpev.1997.0453
Dellaporta, S. L., Wood, J., & Hicks, J. B. (1983). A plant DNA minipreparation: version II. Plant Molecular Biology Reporter1(4), 19-21. https://doi.org/10.1007/BF02712670
Demesure, B., Comps, B., & Petit, R. J. (1996). Chloroplast DNA phylogeography of the common beech (Fagus sylvatica L.) in Europe. Evolution50(6), 2515-2520. https://doi.org/10.1111/j.1558-5646.1996.tb03638.x
Demesure, B., Sodzi, N., & Petit, R. J. (1995). A set of universal primers for amplification of polymorphic non‐coding regions of mitochondrial and chloroplast DNA in plants. Molecular Ecology4(1), 129-134. https://doi.org/10.1111/j.1365-294x.1995.tb00201.x
Downie, S. R., & Palmer, J. D. (1992). Use of chloroplast DNA rearrangements in reconstructing plant phylogeny. In Molecular systematics of plants. Springer, Boston, MA. pp. 14-35. https://doi.org/10.1007/978-1-4615-3276-7_2
Dumolin‐Lapegue, S., Pemonge, M. H., & Petit, R. J. (1997). An enlarged set of consensus primers for the study of organelle DNA in plants. Molecular Ecology6(4), 393-397. https://doi.org/10.1046/j.1365-294x.1997.00193.x
El Mousadik, A., & Petit, R. J. (1996). Chloroplast DNA phylogeography of the argan tree of Morocco. Molecular Ecology5(4), 547-555. https://doi.org/10.1111/j.1365-294X.1996.tb00346.x
Falakro, K., & Jahangirzadeh Khiavi, S. (2020). Assessment of genetic diversity and relationships among tea genotypes in Iran based on RAPD and ISSR markers. Journal of Horticulture and Postharvest Research, 3(2), 209-220. https://doi.org/10.22077/jhpr.2019.2832.1094
Fang, W., Cheng, H., Duan, Y., Jiang, X., & Li, X. (2012). Genetic diversity and relationship of clonal tea (Camellia sinensis) cultivars in China as revealed by SSR markers. Plant Systematics and Evolution298(2), 469-483. https://doi.org/10.1007/s00606-011-0559-3
Fofana, B., Harvengt, L., Baudoin, J. P., & Du Jardin, P. (1997). New primers for the polymerase chain amplification of cpDNA intergenic spacers in Phaseolus phylogenyBelgian Journal of Botany, 129(2), 118-122.
Fulian, Y. (1986). Discussion on the originating place and the originating center of tea plant. Journal of Tea Science, 6(1): 1–8.
Golein, B., Bigonah, M., Azadvar, M., & Golmohammadi, M. (2012). Analysis of genetic relationship between ‘Bakraee’ (Citrus sp.) and some known Citrus genotypes through SSR and PCR-RFLP markers. Scientia Horticulturae148, 147-153. https://doi.org/10.1016/j.scienta.2012.10.012
Grivet, D., Heinze, B., Vendramin, G. G., & Petit, R. J. (2001). Genome walking with consensus primers: application to the large single copy region of chloroplast DNA. Molecular Ecology Notes1(4), 345-349. https://doi.org/10.1046/j.1471-8278.2001.00107.x
Hasimoto, M., & Simura, T. (1978). Morphological studies on the origin of the tea plant. Japanese Journal of Tropical Agriculture21(2), 93-101. https://doi.org/10.11248/jsta1957.24.1
Heinze, B. (1998). PCR-based chloroplast DNA assays for the identification of native Populus nigra and introduced poplar hybrids in Europe. Forest Genetics5(1), 31-38.
IPGRI (2000). Descriptors for tea. International Plant Genetic Resources Institute, Rome, Italy, Available at: http://www.cgiar.org/ipgri.
Ishikawa, S., Kato, S., Imakawa, S., Mikami, T., & Shimamoto, Y. (1992). Organelle DNA polymorphism in apple cultivars and rootstocks. Theoretical and Applied Genetics83(8), 963-967. https://doi.org/10.1007/BF00232957
Kafkas, S., Ercişli, S., Doğan, Y., Ertürk, Y., Haznedar, A., & Sekban, R. (2009). Polymorphism and genetic relationships among tea genotypes from Turkey revealed by amplified fragment length polymorphism markers. Journal of the American Society for Horticultural Science134(4), 428-434. https://doi.org/10.21273/JASHS.134.4.428
Kaundun, S. S., & Matsumoto, S. (2011). Molecular evidence for maternal inheritance of the chloroplast genome in tea, Camellia sinensis (L.) O. Kuntze. Journal of the Science of Food and Agriculture91(14), 2660-2663. https://doi.org/10.1002/jsfa.4508
Khadivi-Khub, A., Jahangirzadeh, S., Ahadi, E., & Aliyoun, S. (2014). Nuclear and chloroplast DNA variability and phylogeny of Iranian apples (Malus domestica). Plant Systematics and Evolution300(8), 1803-1817. https://doi.org/10.1007/s00606-014-1007-y
Khiavi, S. J., Azadi Gonbad, R., & Falakro, K. (2020). Identification of genetic diversity and relationships of some Iranian tea genotypes using SRAP markers. Journal of Horticulture and Postharvest Research3(1), 25-34. https://doi.org/10.22077/JHPR.2019.2582.1067
Khiavi, S. J., Zamani, Z., Mardi, M., & Moghdam, M. F. (2013). Evaluation of chloroplast relationship between some apple genotype from Azerbaijan of Iran and their comparison with other local genotypes, cultivars and rootstocks. African Journal of Agricultural Research8(1), 106-112. https://doi.org/10.5897/AJAR11.2348
Liston, A. (1992). Variation in the chloroplast genes rpoC1 and rpoC2 of the genus Astragalus (Fabaceae): evidence from restriction site mapping of a PCR‐amplified fragment. American Journal of Botany79(8), 953-961. https://doi.org/10.1002/j.1537-2197.1992.tb13679.x
Mantel, N. (1967). The detection of disease clustering and a generalized regression approach. Cancer Research27(2 Part 1), 209-220.
Mariac, C., Trouslot, P., Poteaux, C., Bezançon, G., & Renno, J. F. (2000). Chloroplast DNA extraction from herbaceous and woody plants for direct restriction fragment length polymorphism analysis. Biotechniques28(1), 110-113. https://doi.org/10.2144/00281st07
Palmer, J. D. (1985). Comparative organization of chloroplast genomes. Annual Review of Genetics19(1), 325-354. https://doi.org/10.1146/annurev.ge.19.120185.001545
Palmer, J. D., Jorgensen, R. A., & Thompson, W. F. (1985). Chloroplast DNA variation and evolution in Pisum: patterns of change and phylogenetic analysis. Genetics109(1), 195-213.
Palmer, J. D., & Zamir, D. (1982). Chloroplast DNA evolution and phylogenetic relationships in LycopersiconProceedings of the National Academy of Sciences79(16), 5006-5010.     https://doi.org/10.1073/pnas.79.16.5006
Panda, S., Martín, J. P., & Aguinagalde, I. (2003). Chloroplast DNA study in sweet cherry cultivars (Prunus avium L.) using PCR-RFLP method. Genetic Resources and Crop Evolution50(5), 489-495. https://doi.org/10.1023/A:1023986416037
Petit, R. J., Kremer, A., & Wagner, D. B. (1993). Geographic structure of chloroplast DNA polymorphisms in European oaks. Theoretical and Applied Genetics87(1-2), 122-128.       https://doi.org/10.1007/BF00223755
Rohlf, F. J. (1993). Numeric taxonomy and multivariate analysis systemNTSYS-pc.
Sugiura, M. (2005). History of chloroplast genomics. In Discoveries in Photosynthesis. Springer, Dordrecht. pp. 1057-1063. https://doi.org/10.1023/A:1024913304263
Sytsma, K. J., & Gottlieb, L. D. (1986). Chloroplast DNA evolution and phylogenetic relationships in Clarkia sect. Peripetasma (Onagraceae). Evolution40(6), 1248-1261. https://doi.org/10.2307/2408951
Taberlet, P., Gielly, L., Pautou, G., & Bouvet, J. (1991). Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Molecular Biology17(5), 1105-1109.       https://doi.org/10.1007/BF00037152
Takeda, Y. (2000). History and development in Japanese tea breeding. Tea Culture,Tea Food Industry and Tea Breeding in Korea, China and Japan. The Korea Tea Society, Korea, pp. 139-158.
Tanikawa, N., Onozaki, T., Nakayama, M., & Shibata, M. (2008). PCR-RFLP analysis of chloroplast DNA variations in the atpI-atpH spacer region of the genus Camellia. Journal of the Japanese Society for Horticultural Science, 77(4), 408-417. https://doi.org/10.2503/jjshs1.77.408
Turkec, A., Sayar, M., & Heinze, B. (2006). Identification of sweet cherry cultivars (Prunus avium L.) and analysis of their genetic relationships by chloroplast sequence-characterised amplified regions (cpSCAR). Genetic Resources and Crop Evolution, 53(8), 1635-1641. https://doi.org/10.1007/s10722-005-2285-6
Weir, B. S. (1996). Interspecific differentiation. In Molecular systematics. 2nd Edition. Hillis, D. M. et al. (Eds). Sinauer Associates, Sunderland. pp. 385-403.
Weising, K., & Gardner, R. C. (1999). A set of conserved PCR primers for the analysis of simple sequence repeat polymorphisms in chloroplast genomes of dicotyledonous angiosperms. Genome, 42(1), 9-19.
Whatley, J. M. (1982). Ultrastructure of plastid inheritance: green algae to angiosperms. Biological Reviews, 57(4), 527-569. https://doi.org/10.1111/j.1469-185X.1982.tb00373.x
Wolfe, K. H., Li, W. H., & Sharp, P. M. (1987). Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proceedings of the National Academy of Sciences, 84(24), 9054-9058. https://doi.org/10.1073/pnas.84.24.9054
Yang, H., Wei, C. L., Liu, H. W., Wu, J. L., Li, Z. G., Zhang, L., & Zhang, Z. Z. (2016). Genetic divergence between Camellia sinensis and its wild relatives revealed via genome-wide SNPs from RAD sequencing. PLoS One, 11(3). e0151424. https://doi.org/10.1371/journal.pone.0151424