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Detection of Variation in Long-Term Micropropagated Mature Pistachio via DNA-Based Molecular Markers

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Abstract

Determination of genetic stability of in vitro-grown plantlets is needed for safe and large-scale production of mature trees. In this study, genetic variation of long-term micropropagated mature pistachio developed through direct shoot bud regeneration using apical buds (protocol A) and in vitro-derived leaves (protocol B) was assessed via DNA-based molecular markers. Randomly amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR), and amplified fragment length polymorphism (AFLP) were employed, and the obtained PIC values from RAPD (0.226), ISSR (0.220), and AFLP (0.241) showed that micropropagation of pistachio for different periods of time resulted in “reasonable polymorphism” among donor plant and its 18 clones. Mantel’s test showed a consistence polymorphism level between marker systems based on similarity matrices. In conclusion, this is the first study on occurrence of genetic variability in long-term micropropagated mature pistachio plantlets. The obtained results clearly indicated that different marker approaches used in this study are reliable for assessing tissue culture-induced variations in long-term cultured pistachio plantlets.

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Abbreviations

AFLP:

Amplified fragment length polymorphism

BA:

6-Benzyladenine

IAA:

Indole acetic acid

IBA:

Indole-3-butyric acid

EMR:

Effective multiplex ratio

Ib av :

Average band informativeness

ISSR:

Inter-simple sequence repeat

MI:

Marker index

PCA:

Principal component analysis

PC:

Principal coordinate

PIC:

Polymorphic information content

RAPD:

Randomly amplified polymorphic DNA

RFLP:

Restriction fragment length polymorphism

R p :

Resolving power

SSR:

Simple sequence repeat

TC:

Tissue culture

UPGMA:

Unweighted pair-group method with arithmetic

References

  1. Ozden-Tokatli, Y., Akdemir, H., Tilkat, E., & Onay, A. (2010). Current status and conservation of Pistacia germplasm. Biotechnology Advances, 28, 130–141.

    Article  CAS  Google Scholar 

  2. Tilkat, E., & Onay, A. (2009). Direct shoot organogenesis from in vitro derived mature leaf explants of pistachio. In Vitro Cellular & Developmental Biology. Plant, 45(1), 92–98.

    Article  CAS  Google Scholar 

  3. Yadav, K., Aggarwal, A., & Singh, N. (2013). Evaluation of genetic fidelity among micropropagated plants of Gloriosa superba L. using DNA-based markers—a potential medicinal plant. Fitoterapia, 89, 265–270.

    Article  CAS  Google Scholar 

  4. Barghchi, M., & Alderson, P. G. (1985). In vitro propagation of P. vera L. and commercial varieties of Ohadi and Kalleghochi. The Journal of Horticultural Science and Biotechnology, 60, 423–440.

    Article  Google Scholar 

  5. Parfitt, D. E., & Almehdi, A. (1994). Use of high CO2 atmospheric and medium modifications for the successful micropropagation of pistachio. Scientia Horticulturae, 56, 321–329.

    Article  CAS  Google Scholar 

  6. Onay, A. (2000). Micropropagation of pistachio from mature trees. Plant Cell, Tissue and Organ Culture, 60, 159–162.

    Article  Google Scholar 

  7. Tilkat, E. (2006). Micropropagation of male Pistacia vera L. via apical shoot tip culture. Ph.D. Thesis Institute of Science, University of Dicle, Turkey, 142 p. (in Turkish).

  8. Tilkat, E., Onay, A., Yıldırım, H., & Ozen, H. C. (2008). Micropropagation of mature male pistachio Pistacia vera L. The Journal of Horticultural Science and Biotechnology, 83(3), 328–333.

    Article  CAS  Google Scholar 

  9. Tilkat, E., Onay, A., Yıldırım, H., & Ayaz, E. (2009). Direct plant regeneration from mature leaf explants of pistachio, Pistacia vera L. Scientia Horticulturae, 121(3), 361–365.

    Article  CAS  Google Scholar 

  10. Orbovic, V., Calovic, M., Viloria, Z., Nielsen, B., Gmitter, F., Castle, W., & Grosser, J. (2008). Analysis of genetic variability in various tissue culture-derived lemon plant populations using RAPD and flow cytometry. Euphytica, 161, 329–335.

    Article  CAS  Google Scholar 

  11. Leva, A.R., Petruccelli, R. &, Rinaldi, L. M. R. (2012). Somaclonal variation in tissue culture: a case study with olive. Recent advances in plant in vitro culture, 10–17.

  12. Bhatia, R., Singh, K. P., Jhang, T., & Sharma, T. R. (2009). Assessment of clonal fidelity of micropropagated gerbera plants by ISSR markers. Scientia Horticulturae, 119, 208–211.

    Article  CAS  Google Scholar 

  13. Sharma, M. M., Verma, R. N., Singh, A., & Batra, A. (2014). Assessment of clonal fidelity of Tylophora indica (Burm. f.) Merrill “in vitro” plantlets by ISSR molecular markers. Springer Plus, 3, 400.

    Article  Google Scholar 

  14. Rathore, M. S., Yadav, P., Mastan, S. G., Prakash, C. R., Singh, A., & Agarwal, P. K. (2014). Evaluation of genetic homogeneity in tissue culture regenerates of Jatropha curcas L. using flow cytometer and DNA-based molecular markers. Applied Biochemistry and Biotechnology, 172, 298–310.

    Article  CAS  Google Scholar 

  15. Bairu, M. W., Aremu, A. O., & Van Standen, J. (2011). Somaclonal variation in plants: causes and detection methods. Plant Growth Regulation, 63, 147–173.

    Article  CAS  Google Scholar 

  16. Polanco, C., & Ruiz, M. L. (2002). AFLP analysis of somaclonal variation in Arabidopsis thaliana regenerated plants. Plant Science, 162, 817–824.

    Article  CAS  Google Scholar 

  17. Prado, M., Rodriguez, E., Rey, L., Gonzalez, M., Santos, C., & Rey, M. (2010). Detection of somaclonal variants in somatic embryogenesis regenerated plants of Vitis vinifera by flow cytometry and microsatellite markers. Plant Cell, Tissue and Organ Culture, 103, 49–59.

    Article  Google Scholar 

  18. Reddy, M. P., Sarla, N., & Siddiq, E. A. (2002). Inter simple sequence repeat (ISSR) polymorphism and its application in plant breeding. Euphytica, 128, 9–17.

    Article  Google Scholar 

  19. Viehmannova, I., Bortlova, Z., Vitamvas, J., Cepkova, P. H., Eliasova, K., Svobodava, E., & Travnickova, M. (2014). Assessment of somaclonal variation in somatic embryo-derived plants of yacon [Smallanthus sonchifolius (Poepp. and Endl.) H. Robinson] using inter simple sequence repeat analysis and flow cytometry. Electronic Journal of Biotechnology, 17, 102–106.

    Article  Google Scholar 

  20. Henry, R. J. (1998). Molecular and biochemical characterization of somaclonal variation. In S. M. Jain, D. S. Brar, & B. S. Ahloowalia (Eds.), Somaclonal variation and induced mutations in crop improvement (pp. 485–499). Dordrecht: Kluwer Acad. Publ.

    Chapter  Google Scholar 

  21. Ozden-Tokatli, Y., Ozudogru, E. A., & Akcin, A. (2006). Optimization of an efficient micropropagation protocol and assessment of plant genetic fidelity by RAPD markers in pistachio (Pistacia vera). Scientia Horticulturae, 20(2), 162–169.

    Google Scholar 

  22. Murashige, T., & Skoog, M. (1962). A revised medium for rapid growth and bioassays with tobacco tissue culture. Physiologia Plantarum, 15, 473–497.

    Article  CAS  Google Scholar 

  23. Lodhi, M. A., Guang-Ning, Y., Weeden, N. F. N., & Reisch, B. I. (1994). A simple and efficient method for DNA extraction from grapevine cultivars and Vitis species. Molecular Biology Reports, 6–13.

  24. Kovach, W. L. (1999). MVSP—a multivariate statistical package for Windows, ver 3.1. Pentraeth: Kovach Computing Services.

    Google Scholar 

  25. Jaccard, P. (1908). Nouvelles recherches sur la distribution florale. Bulletin de la Societe Vaudoise des Sciences Naturelles, 44, 223–270.

    Google Scholar 

  26. Rohlf, F. J. (1993). NTSYS-pc: numerical taxonomy and multivariate analysis system. New York: Exeter Publishing Ltd.

    Google Scholar 

  27. Roldan-Ruiz, I., Calsyn, E., Gilliland, T. J., Coll, R., van Eijk, M. J. T., & De Loose, M. (2000). Estimating genetic conformity between related ryegrass (Lolium) varieties. 2. AFLP characterization. Molecular Breeding, 6, 593–602.

    Article  Google Scholar 

  28. Prevost, A., & Wilkinson, M. J. (1999). A new system of comparing PCR primers applied to ISSR fingerprinting of potato cultivars. Theoretical and Applied Genetics, 98, 107–112.

    Article  CAS  Google Scholar 

  29. Belaj, A., Satovic, Z., Cipriani, G., Baldoni, L., Testolin, R., Rallo, L., & Trujillo, I. (2003). Comparative study of the discriminating capacity of RAPD, AFLP and SSR markers and of their effectiveness in establishing genetic relationships in olive. Theoretical and Applied Genetics, 107(4), 736–744.

    Article  CAS  Google Scholar 

  30. Campbell, B. C., LeMare, S., Piperidis, G., & Godwin, I. D. (2010). IRAP, a retrotransposon-based marker system for the detection of somaclonal variation in barley. Molecular Breeding, 27(2), 193–206.

    Article  Google Scholar 

  31. Legendre, P., & Legendre, L. (1998). Numerical ecology, 24.

  32. Jain, S. M. (1997). Micropropagation of selected somaclones of Begonia and Saintpaulia. Journal of Biosciences, 22(5), 585–592.

    Article  Google Scholar 

  33. Devarumath, R. M., Nandy, S., Rani, V., Marimuthu, S., & Muraleedharan, N. (2002). RAPD, ISSR and RFLP fingerprints 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 Reports, 21(2), 166–173.

    Article  CAS  Google Scholar 

  34. Mallon, R., Rodríguez-Oubiña, J., & González, M. L. (2010). In vitro propagation of the endangered plant Centaurea ultreiae: assessment of genetic stability by cytological studies, flow cytometry and RAPD analysis. Plant Cell, Tissue and Organ Culture, 101, 31–39.

    Article  Google Scholar 

  35. Rival, A., Bertrand, L., Beule, T., Combes, M. C., Trouslot, P., & Lashermes, P. (1998). Suitability of RAPD analysis for the detection of somaclonal variants in oil palm (Elaeis guineensis Jacq). Plant Breeding, 117, 73–76.

    Article  Google Scholar 

  36. Sahijram, L., Soneji, J. R., & Bollamma, K. T. (2003). Analyzing somaclonal variation in micropropagated bananas (Musa spp.). In Vitro Cellular & Developmental Biology. Plant, 39, 551–556.

    Article  Google Scholar 

  37. Martins, M., Sarmento, D., & Oleveira, M. M. (2004). Genetic stability of micropropagted almond plantlets as assessed by RAPD and ISSR markers. Plant Cell Reports, 23, 492–496.

    Article  CAS  Google Scholar 

  38. Venkatachalam, L., Sreedhar, R. V., & Bhagyalakshmi, N. (2007). Molecular analysis of genetic stability in long-term micropropagated shoots of banana using RAPD and ISSR markers. Electronic Journal of Biotechnology, 15, 106–113.

    Google Scholar 

  39. Huang, W. J., Ning, G. G., Liu, G. F., & Bao, M. Z. (2009). Determination of genetic stability of long-term micropropagated plantlets of Platanus acerifolia using ISSR markers. Biologia Plantarum, 53(1), 159–163.

    Article  Google Scholar 

  40. Rani, V., Parida, A., & Raina, S. N. (1995). Random amplified polymorphic DNA (RAPD) markers for genetic analysis in micropropagated plants of Populus deltoides Marsh. Plant Cell Reports, 14, 459–462.

    Article  CAS  Google Scholar 

  41. Rahman, M., & Rajora, O. (2001). Microsatellite DNA somaclonal variation in micropropagated trembling aspen (Populus tremuloides). Plant Cell Reports, 20(6), 531–536.

    Article  CAS  Google Scholar 

  42. Rani, V., Singh, K. P., Shiran, B., Goel, S. N. S., Devarumath, R. M., Sreenath, H. L., & Raina, S. N. (2000). Evidence for new nuclear and mitochondrial genome organizations among high-frequency somatic embryogenesis-derived plants of allotetraploid Coffea arabica L. (Rubiaceae). Plant Cell Reports, 19, 1013–1020.

    Article  CAS  Google Scholar 

  43. Rani, V., & Raina, S. N. (1998). Genetic analysis of enhanced-axillary-branching-derived Eucalyptus tereticornis Smith and E. camaldulensis Dehn. plants. Plant Cell Reports, 17, 236–242.

    Article  CAS  Google Scholar 

  44. Ngezahayo, F., Guo, W., Gong, L., Li, F., & Liu, B. (2006). Genomic variation in micropropagated Robinia ambigua ‘idahoensis’ revealed by RAPD markers. HortScience, 41(6), 1466–1468.

    CAS  Google Scholar 

  45. Guo, W. L., Gong, L., Ding, Z. F., Li, Y. D., Li, F. X., Zhao, S. P., & Liu, B. (2006). Genomic instability in phenotypically normal regenerants of medicinal plant Codonopsis lanceolata Benth. et Hook. F., as revealed by ISSR and RAPD markers. Plant Cell Reports, 25, 896–906.

    Article  CAS  Google Scholar 

  46. Olmos, S. E., Lavia, G., Di Renzo, M., Mroginski, L., & Echenique, V. (2002). Genetic analysis of variation in micropropagated plants of Melia azedarach L. In Vitro Cellular and Development Biology - Plant, 38(6), 617–622.

    Article  CAS  Google Scholar 

  47. Rajpal, V. R., Sharma, S., Devarumath, R. M., Chaudhary, M., Kumar, A., Khare, N., & Raina, S. N. (2014). In K. G. Ramawat, J. M. Mérillon, & M. R. Ahuja (Eds.), Tree biotechnology (pp. 303–334). FL: CRC Press.

    Google Scholar 

  48. Palombi, M. A., & Damiano, C. (2002). Comparison between RAPD and SSR molecular markers in detecting genetic variation in kiwifruit (Actinidia deliciosa A. Chev). Plant Cell Reports, 20(11), 1061–1066.

    Article  CAS  Google Scholar 

  49. Agarwal, M., Shrivastava, N., & Padh, H. (2008). Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Reports, 27, 617–631.

    Article  CAS  Google Scholar 

  50. Botstein, D., White, R. L., Skolnick, M., & Davis, R. W. (1980). Construction of a genetic linkage map using restriction fragment length polymorphisms. American Journal of Human Genetics, 32, 314–331.

    CAS  Google Scholar 

  51. Duncan, R. R. (1997). Tissue culture-induced variation and crop improvement. Advances in Agronomy, 58, 201–240.

    Article  CAS  Google Scholar 

  52. Sharma, S., Bryan, G., Winfield, M., & Millam, S. (2007). Stability of potato (Solanum tuberosum L.) plants regenerated via somatic embryos, axillary bud proliferated shoots, microtubers and true potato seeds: a comparative phenotypic, cytogenetic and molecular assessment. Planta, 226, 1449–1458.

    Article  CAS  Google Scholar 

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Acknowledgments

The authors are grateful to MSc. Emrah Kirdok for helping to statistical analysis. This research was funded by a grant no. KBAG 209 T030 from The Scientific and Technological Research Council of Turkey (TUBITAK).

Author information

Authors and Affiliations

  1. Faculty of Basic Sciences, Department of Molecular Biology and Genetics, Gebze Technical University, 41400, Kocaeli, Turkey

    Hülya Akdemir & Yelda Ozden Çiftçi

  2. Vocational School of Health Services, Department of Medical Services and Techniques, Bingöl University, 12000, Bingöl, Turkey

    Veysel Suzerer

  3. Faculty of Science and Art, Department of Biology, Batman University, 72100, Batman, Turkey

    Engin Tilkat

  4. Faculty of Science, Department of Biology, Dicle University, 21280, Diyarbakır, Turkey

    Ahmet Onay

  5. Institute of Biotechnology, Gebze Technical University, 41400, Kocaeli, Turkey

    Yelda Ozden Çiftçi

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  1. Hülya Akdemir
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  2. Veysel Suzerer
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  3. Engin Tilkat
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  4. Ahmet Onay
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Correspondence to Yelda Ozden Çiftçi.

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Supply. Fig. 1

Diagram of plant regeneration protocol A and B for mature P. vera L. (JPG 105 kb)

Supply. Fig. 2

All PCR programmes used in this study. (DOCX 218 kb)

Supply. Fig. 3

Examples of RAPD patterns assessed with K-01 primer; lanes D: Donor plant, G: Greenhouse material, 1-10: 5-years micropropagated plants, 20-26: 7-years micropropagated plants, “M: marker (some polymorphic bands were shown with arrowheads)”. (DOCX 281 kb)

Supply. Fig. 4

Examples of ISSR patterns assessed with ISSR-12 primer; lanes D: Donor plant, G: Greenhouse material, 1-10: 5-year micropropagated plants, 20-26: 7-years micropropagated plants, “M: marker (some polymorphic bands were shown with arrowheads)”. (DOCX 374 kb)

Supply. Fig. 5

Examples of AFLP patterns assessed with E-AAC and M-CTA primer combinations; lanes D: Donor plant, G: Greenhouse material, 1-10: 5-year micropropagated plants, 20-26: 7-years micropropagated plants, “M: marker (some polymorphic bands were shown with arrowheads)”. (DOCX 460 kb)

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Akdemir, H., Suzerer, V., Tilkat, E. et al. Detection of Variation in Long-Term Micropropagated Mature Pistachio via DNA-Based Molecular Markers. Appl Biochem Biotechnol 180, 1301–1312 (2016). https://doi.org/10.1007/s12010-016-2168-7

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