Indian Journal of Plant Physiology

, Volume 23, Issue 4, pp 810–821 | Cite as

Molecular and physiological characterization of a natural interspecific coffee hybrid

  • Manoj Kumar MishraEmail author
  • Mallikarjuna Awati
  • Chandragupt Anand
  • Anil Kumar
Original Article


Natural hybridization is a common phenomenon in plants and considered to be a driving force of biodiversity and evolution. In coffee spontaneous hybridization between two different species is earlier documented. Here we investigated the morphological, molecular and physiological characteristics of a natural tetraploid interspecific coffee hybrid involving allopolyploid Coffea arabica and diploid C. excelsa species. The formation of the tetraploid hybrid was postulated on account of the production of unreduced female gametes in C. excelsa. In our findings, most morphological characters of the interspecific hybrid were found to be intermediate between the putative parental species, but the young leaf colour was found to be distinctively transgressive. Sequence-related amplified polymorphism marker analysis unequivocally supported the involvement of C. excelsa and C. arabica in hybrid formation. The gas exchange parameters, chlorophyll fluorescence parameters were compared between the hybrid and parents which revealed that the interspecific hybrid had the significantly higher substomatal CO2 concentration and non-photochemical quenching compared to parents. This tetraploid interspecific hybrid encompassing the genome of two divergent species could be of ascertainable importance in arabica coffee breeding program.


Coffee Natural hybridization Interspecific hybrid Molecular identification SRAP marker Chlorophyll fluorescence Gas exchange parameters 

Supplementary material

40502_2018_410_MOESM1_ESM.docx (15 kb)
Supplementary material 1 (DOCX 15 kb)
40502_2018_410_MOESM2_ESM.tif (45 kb)
Fig. S1: Scatter plot of the first and second principal coordinate analysis (PCoA) of parents and interspecific hybrid based on the SRAP marker analysis (TIFF 45 kb)


  1. Arnold, M. L. (1997). Natural hybridization and evolution. New York: Oxford University Press.Google Scholar
  2. Baack, E. J., & Rieseberg, L. H. (2007). A genomic view of introgression and hybrid speciation. Current Opinion in Genetics & Development, 17(6), 513–518.CrossRefGoogle Scholar
  3. Bettencourt, A. (1973). Consideraçoes gerais sobre o ‘Hibrido de Timor’ (p. 31). Campinas: Instituto Agronomico de Campinas, Circular No.Google Scholar
  4. Bjorkman, W., & Demming, B. (1987). Photon yield of O2 evolution and chlorophyll fluorescence characteristics at 77 K among vascular plants of diverse origins. Planta, 170, 489–504.CrossRefGoogle Scholar
  5. Burke, J. J. (2007). Evaluation of source leaf responses to water-deficit stresses in cotton using a novel stress bioassay. Plant Physiology, 143, 108–121.CrossRefGoogle Scholar
  6. Caruso, C. M., Maherali, H., & Sherrard, M. (2006). Plasticity of physiology in Lobelia: testing for adaptation and constraint. Evolution, 60, 980–990.PubMedGoogle Scholar
  7. Cramer, P. J. S. (1957). In F. L. Wellman (Eds.), Review of literature of coffee research in Indonesia. SIC Editorial lnternational American Institute of Agricultural Sciences, Turrialba, Costa Rica.Google Scholar
  8. Das, G., Sengupta, T., Sahu, P. K., Mishra, A. K., Sen, S. K., & Saratchandra, B. (1999). Quantitative analysis of photosynthetic parameters in mulberry leaf. Indian Journal of Plant Physiology, 1(3), 171–174.Google Scholar
  9. Dudley, S. A. (1996). Differing selection on plant physiological traits in response to environmental water availability: A test of adaptive hypotheses. Evolution, 50, 92–102.CrossRefGoogle Scholar
  10. Ellstrand, N. C., Whitkus, R., & Rieseberg, L. H. (1996). Distribution of spontaneous plant hybrids. Proceedings of the National Academy of Sciences of the USA, 93, 5090–5093.CrossRefGoogle Scholar
  11. Geber, M. A., & Dawson, T. E. (1990). Genetic variation in and covariation between leaf gas exchange, morphology, and development in Polygonum arenastrum, an annual plant. Oecologia, 85, 153–158.CrossRefGoogle Scholar
  12. Genty, B., Briantais, J. M., & Baker, N. R. (1989). The relationship between the quantum yield of photosynthetic electron transport and quenching of chlorophyll fluorescence. Biochimica et Biophysica Acta, 990, 87–92.CrossRefGoogle Scholar
  13. Golluscio, R. A., & Oesterheld, M. (2007). Water use efficiency of twenty-five co-existing Patagonian species growing under different soil water availability. Oecologia, 154, 207–217.CrossRefGoogle Scholar
  14. Gomez, C., Batti, A., Le Pierres, D., Campa, C., Hamon, S., & de Kochko, A., et al. (2010). Favourable habitats for Coffea inter-specific hybridization in central New Caledonia: Combined genetic and spatial analyses. Journal of Applied Ecology, 47, 85–95.CrossRefGoogle Scholar
  15. Gomez, C., Despinoy, M., Hamon, S., Hamon, P., Salmon, D., & Akaffou, D. S., et al. (2016). Shift in precipitation regime promotes interspecific hybridization of introduced Coffea species. Ecology and Evolution, 6, 3240–3255. Scholar
  16. Grant, V. (1981). Plant speciation. New York: Columbia University Press.Google Scholar
  17. Hamerlynck, E. P., Huxman, T. E., Nowak, R. S., Redar, S., Loik, M. E., Jordan, D. N., et al. (2000). Photosynthetic responses of Larrea tridentata to a step-increase in atmospheric CO2 at the Nevada desert FACE facility. Journal of Arid Environments, 44, 425–436.CrossRefGoogle Scholar
  18. Harrison, R. G. (1993). Hybrid zones and the evolutionary process. New York: Oxford University Press.Google Scholar
  19. Hegarty, M. J., & Hiscock, S. J. (2004). Hybrid speciation in plants: New insights from molecular studies. New Phytologist, 165, 411–423.CrossRefGoogle Scholar
  20. Herrera, J. C., D’Hont, A., & Lashermes, P. (2007). Use of fluorescence in situ hybridization as a tool for introgression analysis and chromosome identification in coffee (Coffea arabica L.). Genome, 50, 619–626.CrossRefGoogle Scholar
  21. Heschel, M. S., & Riginos, C. (2005). Mechanisms of selection for drought stress tolerance and avoidance in Impatiens capensis (Balsaminaceae). American Journal of Botany, 92, 37–44.CrossRefGoogle Scholar
  22. Kumar, A., Ganesh, S., & Mishra, M. K. (2014). Confirmation of genome introgression in the interspecific hybrid progenies of Coffea species through SRAP marker technique. Scholars Academic Journal of Biosciences, 2(3), 224–235.Google Scholar
  23. Kumar, A., & Mishra, M. K. (2014). A new spontaneous interspecific hybrid in coffee (Coffea sp.). Scholars Academic Journal of Biosciences, 2(2), 168–171.Google Scholar
  24. Lanaud, C. (1979). Etude de problèmes génétiques posés chez le caféier par l’introgression de caractères d’une espèce sauvage C. kianjavatensis Mascarocoffea dans Iespece cultivee C. canephora Eucoffea. Café Cacao The, 23, 3–28.Google Scholar
  25. Li, G., & Quiros, C. F. (2001). Sequence-related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: Its application to mapping and gene tagging in Brassica. Theoretical and Appied Genetics, 103, 455–461.CrossRefGoogle Scholar
  26. Liu, L., Liu, G., Gong, Y., Dai, W., Wang, Y., Yu, F., et al. (2007). Evaluation of genetic purity of F1 hybrid seeds in cabbage with RAPD, ISSR, SRAP and SSR markers. HortScience, 42, 724–727.Google Scholar
  27. Mahé, L., Varzea, V. M. P., Le Pierrès, D., Combes, M. C., & Lashermes, P. (2007). A new source of resistance against coffee leaf rust from New-Caledonian natural interspecific hybrids between Coffea arabica and C. canephora. Plant Breeding, 126, 638–641.CrossRefGoogle Scholar
  28. McKay, J. K., Richards, J. H., & Mitchell-Olds, T. (2003). Genetics of drought adaptation in Arabidopsis thaliana: Pleiotropy contributes to genetic correlations among ecological traits. Molecular Ecology, 12, 1137–1151.CrossRefGoogle Scholar
  29. Mishra, M. K. (1997). Stomatal characteristics at different ploidy levels of Coffea L. Annals of Botany, 80, 689–692.CrossRefGoogle Scholar
  30. Mishra, M. K., Bhat, A. M., Suresh, N., Satheesh Kumar, S., Padmajyothi, D., Prakash, N. S., et al. (2011a). Molecular genetic analysis of arabica coffee hybrids using SRAP marker approach. Journal of Plantation Crops, 39(1), 41–47.Google Scholar
  31. Mishra, M. K., Nishani, S., & Jayarama, (2011b). Molecular identification and genetic relationships among coffee species (Coffea L.) inferred from ISSR and SRAP marker analyses. Archives of Biological Sciences, 63(3), 667–679.CrossRefGoogle Scholar
  32. Mishra, M. K., Ram, A. S., Jyothi, D. P., Prakash, N. S., & Srinivasan, C. S. (2003). Stomatal characteristics of different species of Coffea L. Journal of Plantation Crops, 31, 35–39.Google Scholar
  33. Mishra, M. K., & Slater, A. (2012). Recent advances in the genetic transformation of coffee. Biotechnology Research International. Scholar
  34. Mishra, M. K., Suresh, N., Bhat, A. M., Prakash, N. S., Satheesh Kumar, S., Kumar, A., et al. (2011c). Genetic molecular analysis of Coffea arabica (Rubiaceae) hybrids using SRAP markers. Revista Biologia Tropical, 59(2), 607–617.Google Scholar
  35. Müller, P., Li, X.-P., & Niyogi, K. K. (2001). Non-photochemical quenching. A response to excess light energy. Plant Physiology, 125, 1558–1566.CrossRefGoogle Scholar
  36. Oxborongh, K., & Baker, N. R. (1997). Resolving chlorophyll a fluorescence images of photosynthetic efficience into photochemical and non-photochemical components-calculation of qP and Fv-/Fm-without measuring Fo. Photosynthesis Research, 54, 135–142.CrossRefGoogle Scholar
  37. Petite, M. A., Moro, G. B., Murua, G. C., Lacuesta, M., & Rueda, M. A. (2000). Sequential effects of acidic precipitation and drought on photosynthesis and chlorophyll fluorescence parameters of Pinus radiata D. Don seedlings. Journal of Plant Physiology, 156, 84–92.CrossRefGoogle Scholar
  38. Quick, W. P., Chaves, M. M., Wendler, R., David, M., Rodrigues, M. L., Passaharinho, J. A., et al. (1992). The effect of water stress on photosynthetic carbon metabolism in four species grown under field conditions. Plant, Cell and Environment, 15, 25–35.CrossRefGoogle Scholar
  39. Ren, X., Huang, J., Liao, B., Zhang, X. H., & Jiang, H. (2010). Genomic affinities of Arachis genus and inter-specific hybrids were revealed by SRAP markers. Genetic Resources and Crop Evolution, 57, 903–913.CrossRefGoogle Scholar
  40. Rieseberg, L. H., & Carney, S. E. (1998). Plant hybridization (Tansley review no. 102). New Phytologist, 140, 599–624.CrossRefGoogle Scholar
  41. Rohácek, K., & Barták, M. (1999). Technique of the modulated chlorophyll fluorescence: Basic concepts, useful parameters, and some applications. Photosynthetica, 37(3), 339–363.CrossRefGoogle Scholar
  42. Rohlf, F. J. (2000). NTSYS pc: Numerical taxonomy and multivariate analysis system version 2.10. Setauket, NY: Exeterior Software.Google Scholar
  43. Ruban, A. V., Berera, R., Ilioaia, C., van Stokkum, I. H., Kennis, J. T., Pascal, A. A., et al. (2007). Identification of a mechanism of photoprotective energy dissipation in higher plants. Nature, 450(7169), 575–578.CrossRefGoogle Scholar
  44. Schreiber, U., Schliwa, U., & Bilger, W. (1986). Continuous recording of photochemical and non-photochemical chlorophyll fluorescence quenching with a new type of modulation fluorometer. Photosynthesis Research, 10, 51–61.CrossRefGoogle Scholar
  45. Seiler, G. J., Qi, L. L., & Marek, L. (2017). Utilization of sunflower crop wild relatives for cultivated sunflower improvement. Crop Science, 57, 1–19.CrossRefGoogle Scholar
  46. Setotaw, T. A., Pena, G. F., Zambolin, E. M., Pereira, A. A., & Sakiyama, N. S. (2010). Breeding potential and genetic diversity of “Híbrido do Timor” coffee evaluated by molecular markers. Crop Breeding and Applied Biotechnology, 10, 298–304.CrossRefGoogle Scholar
  47. Shasany, A. K., Darokar, M. P., Dhawan, S., Gupta, A. K., Gupta, S., Shukla, A. K., et al. (2005). Use of RAPD and AFLP markers to identify inter- and intraspecific hybrids of Mentha. Journal of Heredity, 96(5), 542–549.CrossRefGoogle Scholar
  48. Sheng, X., Wen, G., Guo, Y., Yan, H., Zhao, H., & Liu, F. (2012). A semi-fertile interspecific hybrid of Brassica rapa and B. nigra and the cytogenetic analysis of its progeny. Genetic Resources and Crop Evolution, 59,(1), 73–81. Scholar
  49. Sneath, P. H., & Sokal, R. R. (1973). Numerical taxonomy: The principal and practice of numerical classification. San Francisco: W. H. Freeman and Company.Google Scholar
  50. Sreenivasan, M. S., & Govindappa, D. A. (1984). Cytology of polyploids in robusta arabica hybrids of coffee. Journal of Coffee Research, 14, 75–84.Google Scholar
  51. Sreenivasan, M. S., Prakash, N. S., & Mishra, M. K. (1992). Evaluation of some indirect ploidy indicators in Coffea L. Café Cacao The, 36, 199–205.Google Scholar
  52. Venkataramanan, D. (1985). Physiological studies in coffee. Ph.D. thesis, University of Mysore, India.Google Scholar
  53. Wolf, J. B., Brodie, E. D., Cheverud, J. M., Moore, A. J., & Wade, M. J. (1998). Evolutionary consequences of indirect genetic effects. Trends in Ecology & Evolution, 13, 64–69.CrossRefGoogle Scholar
  54. Xuan, C., Hailin, G., Dandan, X., & Jianxiu, L. (2008). Identification of Zyosia hybrids by SRAP analysis. Molecular Plant Breeding, 6, 1233–1238.Google Scholar
  55. Zhu, X. F., Li, Y., Wu, G. L., Fang, Z. D., Li, Q. J., & Liu, J. Q. (2009). Molecular and morphological evidence for natural hybridization between primula secundiflora franchet and p. poissonii franchet (primulaceae). Acta Biologica Cracoviensia Series Botanica, 51(2), 29–36.Google Scholar

Copyright information

© Indian Society for Plant Physiology 2018

Authors and Affiliations

  1. 1.Plant Biotechnology DivisionUnit of Central Coffee Research Institute, Coffee BoardManasagangothri, MysoreIndia
  2. 2.Central Coffee Research Institute, Coffee Research StationDistrict ChikmagalurIndia
  3. 3.Regional Coffee Research Station, Coffee BoardNarsipatnam, Visakhapatnam DistrictIndia

Personalised recommendations