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Chloroplast and Mitochondrial DNA Assay in Solving Issues Related to the Taxonomy of Beveragial Tea Clones

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Proceedings of the National Academy of Sciences, India Section B: Biological Sciences Aims and scope Submit manuscript

Abstract

Despite utilization of multidisciplinary approaches including nuclear DNA assay, the taxonomy of world beveragial tea clones is still contentious and elusive. They are considered to be constituted by 1–34 Camellia species. In the present study physical mapping of the chloroplast genome in combination with six restriction endonucleases, and restriction fragment length polymorphism of the six (nad5, nad3, atpA, rrn26, coxI and coxIII) mitochondrial genes in combination with six restriction endonucleases was analysed in 50 divergent beveragial tea clones. In chloroplast genomes, only six out of the 230 restriction sites identified by 186 enzyme-probe combinations exhibited variation among the tea clones. The six mutations were site mutations. The 36 enzyme-probe combinations in mitochondrial genome yielded 122 fragments that hybridized to the probe. Nine combinations generated monomorphic profiles across all the 50 clones while remaining 27 combinations produced 94 (77.0 %) polymorphic bands in 20 clones. To understand genetic relationships among the clones, Jaccard’s similarity coefficient and UPGMA clustering algorithm were applied to the cpDNA and mtDNA data. Strong correlation was observed between the two data. Both data grouped the clones into three clusters with very little or no heterogeneity within the clones forming two clusters. The present study makes it abundantly clear that the beveragial tea is not constituted by 34 species. In fact, the origin of the present day beveragial tea clones, cultivated in ~30 countries, lies in the origin of India hybrid tea as a result of extensive hybridization between closely related Assam (Camellia assamica ssp assamica) type and China (C. sinensis) type germplasm when the seeds of the latter were introduced in north east India.

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References

  1. Charles HB (1981) Seed to civilization: the story of food. Freeman, San Francisco

    Google Scholar 

  2. Ellis RT (1995) In: Smart J, Simmonds (eds) Tea-evolution of crop plants. Longman Scientific and Technical, Essex, pp 22–27

    Google Scholar 

  3. Chen L, Zhou Z, Yang Y (2007) Genetic improvement and breeding of tea plant (Camellia sinensis) in China: from individual selection to hybridization and molecular breeding. Euphytica 154:239–248

    Article  CAS  Google Scholar 

  4. Sealy JR (1958) A revision of the genus Camellia. Royal Horticultural Society, London

    Google Scholar 

  5. Chang HT (1981) A taxonomy of the genus Camellia. Acta Sci Nat Univ Sunyatseni Monogr Ser 1:1–180

    CAS  Google Scholar 

  6. Tan YJ (1989) New species and new varieties of tea trees. Int Camellia J 21:65–76

    Google Scholar 

  7. Wight W (1962) Tea classification revised. Curr Sci 31:298–299

    Google Scholar 

  8. Banerjee B (1992) Botanical classification of tea. In: Willson KC, Clifford MN (eds) Tea cultivation to consumption. Chapman and Hall, London, pp 25–52

    Google Scholar 

  9. Eden T (1968) Tea, 2nd edn. Longmans, Green and Co, London

    Google Scholar 

  10. Kingdon-Ward F (1950) Does wild tea exist? Nature 165:297–299

    Article  Google Scholar 

  11. Hung-ta Chang (1981) A taxonomy of the genus Camellia. Acta Sci Nat Univ Sunyatseni Monogr 1:1–180

    Google Scholar 

  12. Purseglove JW (1968) Tropical crops: dicotyledons, vol 2. Longmans green, London

    Google Scholar 

  13. Ikeda N, Kawada M, Takeda Y, (1991) Isozymic analysis of Camellia sinensis and its interspecific hybrids. International symposium of tea science, Shizouka, 26–28 Aug 1991

  14. Chengyin L, Weihua L, Mingjum L (1992) Relationship between evolutionary relatives and the variation of esterase isozymes in tea plant. J Tea Sci 12:15–20

    Google Scholar 

  15. Bezbaruah HP (1967) Tea chromosomes. Two Bud 14:96

    Google Scholar 

  16. Sharma S, Raina SN (2006) Chromosome constitution of some Indian tea clones. Int J Tea Sci 5:21–28

    CAS  Google Scholar 

  17. Wachira FN, Waugh R, Hackett CA, Powell W (1995) Detection of genetic diversity in tea (Camellia sinensis) using, RAPD markers. Genome 38:201–210

    Article  CAS  PubMed  Google Scholar 

  18. Wachira FN, Powell W, Waugh R (1997) Assessment of genetic diversity among Camellia sinensis L. (cultivated tea) and its wild relatives based on randomly amplified polymorphic DNA and organelle specific STS. Heredity 78:603–611

    Article  CAS  Google Scholar 

  19. Wachira FN, Tanaka J, Takeda Y (2001) Genetic variation and differentiation in tea (Camellia sinensis) germplasm revealed by RAPD and AFLP variation. J Hortic Sci Biotechnol 76:557–563

    CAS  Google Scholar 

  20. Tanaka JI, Sawai Y, Yamaguchi S (1995) Genetic analysis of RAPD markers in tea. J Jpn Breed 45:198–199

    Google Scholar 

  21. Tanaka J, Yamaguchi N, Nakamura Y (2001) Pollen parent of tea cultivar Sayamakori with insect and cold resistance may not exist. Breed Res 3:43–48

    Article  Google Scholar 

  22. Mondal TK (2000) Studies on RAPD marker for detection of genetic diversity, in vitro regeneration and Agrobacterium mediated genetic transformation of tea (Camellia sinensis). Ph.D. thesis, Utkal University

  23. Mondal TK, Bhattacharya A, Sood A, Ahuja PS (2002) Factors effecting germination and conversion frequency of somatic embryos of tea. J Plant Physiol 159:317–1321

    Article  Google Scholar 

  24. Paul S, Wachira FN, Powell W, Waugh R (1997) Diversity and genetic differentiation among population of Indian and Kenyan tea (Camellia sinensis L. O. Kuntze) revealed by AFLP markers. Theor Appl Genet 94:255–263

    Article  CAS  Google Scholar 

  25. Balasarvanan T, Pius PK, Rajkumar R, Muraleedharan N, Shasany AK (2003) Genetic diversity among south Indian tea germplasm (Camellia sinensis, C. assamica and C. assamica ssp lasiocalyx) using AFLP markers. Plant Sci 165:35–372

    Google Scholar 

  26. Rajasekaran P (1997) Development of molecular markers using AFLP in tea. Molecular approaches to crop improvement. In: Varghese, JP (ed) Proceedings of national seminar on molecular approaches to crop improvement, Kottayam, 29–31 Dec 1997 pp 54–58

  27. Kaundun SS, Matasumoto S (2002) Heterologous nuclear and chloroplast microsatellite amplification and variation in tea, Camellia sinensis. Genome 45:1041–1048

    Article  CAS  PubMed  Google Scholar 

  28. Matsumoto S, Kiriiwa Y, Takeda Y (2002) Differentiation of Japanese green tea cultivars as revealed by RFLP analysis of phenylalanine ammonia-lysase DNA. Theor Appl Genet 104:998–1002

    Article  CAS  PubMed  Google Scholar 

  29. Kaundun SS, Matasumoto S (2003) Development of CAPS markers based on three key genes of the phenylpropanoid pathway in Tea, Camellia sinensis (L.) O. Kuntze, and differentiation between assamica and sinensis varieties. Theor Appl Genet 106:375–383

    CAS  PubMed  Google Scholar 

  30. Raina SN, Ahuja PS, Sharma RK, Das SC, Bhardwaj P, Negi R, Sharma V, Singh SS, Sud RK, Kalia RK, Pandey V, Banik J, Razdan V, Sehgal D, Dar TH, Kumar A, Bali S, Bhat V, Sharma S, Prasanna BM, Goel S, Negi MS, Vijayan P, Tripathi SB, Bera B, Hazarika M, Mandal AKA, Kumar RR, Vijayan D, Ramkumar S, Chowdhary BR, Mandi SS (2011) Genetic structure and diversity of India hybrid tea. Genet Resour Crop Evol 59:1527–1541

    Article  Google Scholar 

  31. Singh D, Ahuja PS (2006) 5S rDNA gene diversity in tea (Camellia sinensis (L.) O. Kuntze) and its use for variety identification. Genome 49:91–96

    Article  CAS  PubMed  Google Scholar 

  32. Karthigeyan S, Rajkumar S, Sharma RK, Gulati A, Sud RK, Ahuja PS (2008) High level of genetic diversity among selected accession of tea (Camellia sinensis) from abandoned tea gardens in western Himalayas. Biochem Genet 46:810–819

    Article  CAS  PubMed  Google Scholar 

  33. Chen L, Gao QK, Chen DM, Xu CJ (2005) 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 tea germplasm repository. Biodivers Conserv 14:1433–1444

    Article  Google Scholar 

  34. Chen L, Yamaguchi S (2005) RAPD markers for discriminating tea germplasms on the inter-specific level in China. Plant Breed 124:404–409

    Article  CAS  Google Scholar 

  35. Matasumoto S, Kiriiwa Y, Yamaguchi S (2004) The korean plant (Camellia sinensis): RFLP analysis of genetic diversity and relationship to Japanese tea. Breed Sci 54:231–237

    Article  Google Scholar 

  36. Ohsako T, Ohgushi T, Motosugi H, Oka K (2008) Microsatellite variability within and among local landrace populations of tea, Camellia sinensis (L.) O. Kuntze, in Kyoto, Japan. Genet Resour Crop Evol 55:1047–1053

    Article  Google Scholar 

  37. Yao MZ, Chen L, Liang YR (2008) Genetic diversity among tea cultivars from China, Japan and Kenya revealed by ISSR markers and its implication for parental selection in tea breeding progammes. Plant Breed 127:166–172

    Article  CAS  Google Scholar 

  38. Sharma RK, Negi MS, Sharma S, Bhardwaj P, Kumar R, Bhattchrya E, Tripathi SB, Vijayan D, Baruah AR, Das SC, Bera B, Rajkumar R, Thomas J, Sud RK, Muraleedharan N, Hazarika M, Lakshmikumaran M, Raina SN, Ahuja PS (2010) AFLP based genetic diversity assessment of commercially important tea germplasm in India. Biochem Genet 48:549–564

    Article  CAS  PubMed  Google Scholar 

  39. Barua PK (1965) Classification of tea plants: species hybrids. Two Bud 12:13–27

    Google Scholar 

  40. Roberts EAH, Wight W, Wood DJ (1958) Paper chromatography as an aid to the identification of Thea camellias. New Phytol 57:211–225

    Article  CAS  Google Scholar 

  41. Raina SN, Ogihara Y (1994) Chloroplast DNA diversity in Vicia faba and its close wild relatives. Implications of reassessment. Theor Appl Genet 88:261–266

    Article  CAS  PubMed  Google Scholar 

  42. Shiran B, Raina SN (2001) Evidence of rapid evolution and incipient speciation in Vicia sativa species complex based on nuclear and organellar RFLPs and PCR analysis. Genet Res Crop Evol 48:519–532

    Article  Google Scholar 

  43. Sasanuma T, Sehgal D, Sasakuma T, Raina SN (2008) Phylogenetic analysis of Carthamus species based on nucleotide sequence of nuclear—encoded SACPD gene and chloroplast trnL-F IGS region. Genome 51:721–727

    Article  CAS  PubMed  Google Scholar 

  44. Agrawal R, Agrawal N, Tandon R, Raina SN (2014) Chloroplast genes as genetic arkers for inferring patterns of change, maternal ancestry and phylogenetic relationships among Eleusine species. AOB Plants. doi:10.1093/aobpla/plt056

    PubMed Central  PubMed  Google Scholar 

  45. Tomaru N, Takahashi M, Tsumura Y, Ohba K (1998) Intraspecific variation and phylogeographic patterns of Fagus crenata (Fagaceae) mitochondrial DNA. Am J Bot 85:629–636

    Article  CAS  PubMed  Google Scholar 

  46. Mohanty A, Martin JP, Gonzalez LM, Agurinagalde I (2003) Association between chloroplast DNA and mitochondrial DNA haplotypes in Prunus spinosa L. (Rosaceae) populations across Europe. Ann Bot 92:749–755

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  47. Terachi T, Tsunewaki K (1986) The molecular basis of genetic diversity among cytoplasms of Triticum and Aegilops. 5. mitochondrial genome diversity among Aegilops species having identical chloroplast genomes. Theor Appl Genet 73:175–181

    Article  CAS  PubMed  Google Scholar 

  48. Sehgal D, Rani V, Raina S, Sasanuma T, Sasakuma T (2008) Assaying polymorphism at DNA level for new and novel genetic diversity diagnostics of the safflower (Carthamus tintorius) world germplasm resources. Genetica 135:457–470

    Article  PubMed  Google Scholar 

  49. Sehgal D, Bhat V, Raina SN (2008) Advent of diverse DNA markers to decipher genome sequence polymorphism. In: Kirti PB (ed) Handbook of new technologies for genetic improvement of legumes. CRC Press, Boca Raton, pp 497–558

    Google Scholar 

  50. Sue PL, Grant B, Bernard R, Baum (1997) Modification of a CTAB DNA extraction protocol for palnts containing high polysacchride and polyphenol components. Plant Mol Biol Report 15:8–15

    Article  Google Scholar 

  51. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, New York

    Google Scholar 

  52. Reed KC, Mann DA (1985) Rapid transfer of DNA from agarose gels to nylon membranes. Nucleic Acid Res 3:7207–7221

    Article  Google Scholar 

  53. Perrier X, Flori A, Bonnot F (2003) Data analysis methods. In: Hamon P, Seguin M, Perrier X, Glaszmann JC (eds) Genetic diversity of cultivated tropical plants. Science Publisher, Enfield, pp 43–76

    Google Scholar 

  54. Sneath PHA, Sokal RR (1973) Numerical taxonomy. In: Freeman Co WH (ed) The principles and practice of numerical classification. California, San Francisco

    Google Scholar 

  55. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–426

    CAS  PubMed  Google Scholar 

  56. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791

    Article  Google Scholar 

  57. Jansen RK, Palmer JD (1988) Phylogenetic implications of chloroplast DNA restriction site variation in Mutisieae (Asteracae). Am J Bot 19:143–156

    Google Scholar 

  58. Van de Ven WTG, Duncan N, Ramsay G, Phillips M, Powell W, Waugh R (1993) Taxonomic relationships between V. faba and its relatives based on nuclear and Mitochondrial RFLPs and PCR analysis. Theor Appl Genet 86:71–80

    Article  PubMed  Google Scholar 

  59. Sharma VS (1974) Notes on the UPASI tea clones. UPASI Bull 31:57–65

    Google Scholar 

  60. Devarumath RM, Nandy S, Rani V, Marimuthu S, Muraleedharan N, Raina SN (2002) RAPD, ISSR and RFLP fingerprinting as useful markers to evaluate genetic integrity of micropropagated plants of three diploid and triploid elite tea clones representing Camellia sinensis (China type) and C. assamica ssp. assamica (Assam—India type). Plant Cell Rep 21:166–173

    Article  CAS  Google Scholar 

  61. Powell W, Morgante M, Andre C, Hanafey M, Vogel J, Tingey S, Rafalski A (1996) The comparision of RFLP, RAPD, AFLP and SSR markers for germplasm analysis. Mol Breed 2:225–238

    Article  CAS  Google Scholar 

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Acknowledgments

Grateful thanks are due to United Planters Association of South India (UPASI), Valparai, India for providing tea clones. The financial support from Council of Scientific Industrial Research Organisation (CSIR), Government of India (13061943) and National Academy of Sciences, India (NASI) (25091981) is gratefully acknowledged.

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Authors and Affiliations

  1. Department of Botany, Ramjas College, University of Delhi, Delhi, 110007, India

    Suman Sharma

  2. Amity Institute of Biotechnology, Amity University, Noida, 201303, U.P., India

    Manju Chaudhary & Soom Nath Raina

  3. Department of Botany, University of Delhi, Delhi, 110003, India

    Ved Pal Singh

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  1. Suman Sharma
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  2. Manju Chaudhary
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Correspondence to Soom Nath Raina.

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Sharma, S., Chaudhary, M., Singh, V.P. et al. Chloroplast and Mitochondrial DNA Assay in Solving Issues Related to the Taxonomy of Beveragial Tea Clones. Proc. Natl. Acad. Sci., India, Sect. B Biol. Sci. 85, 1039–1053 (2015). https://doi.org/10.1007/s40011-015-0512-2

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