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Plant Science Today (PST)

Research Articles

Vol. 3 No. 2 (2016)

RAPD-based DNA fingerprinting in Lantana camara L. ecotypes and development of a digital database platform ‘LANRAD’

DOI
https://doi.org/10.14719/pst.2016.3.2.177
Submitted
8 December 2015
Published
01-04-2016

Abstract

This article has a correction. Please see:
RETRACTION - 24 June 2016

With objectives to assess molecular diversity and digitization of molecular data in relation to invasive potential of Lantana camara L., leaves of 12 ecotypes collected from five different eco-climatic zones of Eastern Indian state of West Bengal, were subjected to RAPD fingerprinting. Invasive potential (IP) was assessed by allelopathic effects of Lantana leaf extracts on seed germination of target crop (lentil), relative competition intensity (RCI) between weed and target crop and abundance (AB) of Lantana in quadrats. Genetic diversity was found between zones and between ecotypes within a zone. Polymorphism varied 25-70 % with highest magnitude was found in Indo-Gangetic Basin, followed by Western dry land, and parts of temperate and sub-Himalayan zones of Indian Himalayas. Moderate polymorphism with 50 % polymorphic markers was observed in coastal ecotypes. Strong positive correlation existed between polymorphism %, IP, RCI and AB, and 12 ecotypes were clearly distinguished in four categories of invasiveness. IP1 represented worst invasiveness in Gangetic basin and Western dry land while the lowest (IP4) was observed in parts of temperate and sub-Himalayan region. The ‘Darjeeling’ ecotype in temperate Himalayas (2000 m, msl) was identified as moderately-high invasive (IP2 category), possessing two unique RAPD markers. Phylogenetic tree revealed nine groups of 12 ecotypes exhibiting close similarity within coastal zones and within Western dry land ecotypes. The data are now being digitized using bio computation tools/software in a bio-digital platform ‘LANRAD’ (Lantana Random Amplified DNA), as the first eco-genomic on-line platform of an alien invasive plant in India.

References

  1. Aarsen, L.W., and G. A. Epp. 1990. Neighbour manipulations in the natural vegetation: a review. Journal of Vegetation Science 1: 13-30. doi: 10.2307/3236049
  2. Ambika, S.R., S. Poornima, R. Palaniraj, S. C. Sati, and S. S. Narwal. 2003. Allelopathic plants. 10. Lantana camara L. Allelopathy J 12:147-162.
  3. Beest, M. te., J. J. Le Roux, D. M. Richardson, A. K. Brysting, J. Suda, M. Kubešova´, and P. Pyšek. 2012. The more the better? The role of polyploidy in facilitating plant invasions. Ann Bot 109: 19-45. doi: 10.1093/aob/mcr277
  4. Bhagwat, S. A., E. Breman, T. Thekaekara, T. F. Thornton, and K. J. Willis. 2012. A Battle lost? Report on two centuries of invasion and management of Lantana camara L. in Australia, India and South Africa. PLoS ONE 7:e32407. doi: 10.1371/journal.pone.0032407
  5. Biswas, S., M. Maity, G. Bhandari, R. Batabyal, J. Patra, A. Bhuiya, B. Ojha, N. Halder, and D. Talukdar. 2014a. Floral diversity and ecology in Kalyani area of Nadia district, West Bengal, India. Plant Sci Today 2(1): 38-42. doi:10.14719/pst.2015.2.1.88
  6. Biswas, S., M. Maity, S. Srimany, S. Chatterjee, T. Karmakar, R. Datta, J. Patra, M. Koley, and D. Talukdar. 2014b. Compositions, distributions and status of economic plants among invasive floras of Uttarpara, West Bengal, India. Int J Pharmacognosy 1: 800-809. doi: 10.13040/IJPSR.0975-8232.IJP.1(12).800-809
  7. Caspi, R., T. Altman, R. Billington, K. Dreher, H. Foerster, C. A. Fulcher, T. A. Holland et al. 2014. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res 42: D459-471. doi:10.1093/nar/gkm900
  8. Choyal, R., and S. K. Sharma. 2011. Allelopathic effects of Lantana camara (Linn) on regeneration in Funaria hygrometrica. Ind J Fund Appl Life Sc 1:177-182.
  9. Dar, P. A., Z. A. Reshi, and M. A. Shah. 2015. Roads act as corridors for the spread of alien plant species in the mountainous regions: A case study of Kashmir Valley, India. Trop Ecol 56: 183-190.
  10. Datta, S., S. R. Meena, P. Varma, and M. K. Saxena. 2013. Variety specific DNA markers for identification among population of six colored varieties of Lantana camara L. International Journal of Recent Scientific Research 4:1710-1713.
  11. Davuluri, R.V., H. Sun, S. K. Palaniswamy, N. Matthews, C. Molina, M. Kurtz, and E. Grotewold. 2003. AGRIS: Arabidopsis Gene Regulatory Information Server, an information resource of Arabidopsis cis regulatory elements and transcription factors. BMC Bioinformatics 4:25. doi: 10.1186/1471-2105-4-25
  12. Dobhal, P.K., R. K. Kohli, and D. R. Batish. 2011. Impact of Lantana camara L. invasion on riparian vegetation of Nayar region in Garhwal Himalayas (Uttarakhand, India). Journal of Ecology and the Natural Environment 3: 11-22.
  13. Gmerek, J., and B. Politycka. 2010. Generation of active oxygen species in roots of maize, pea and radish in response to exogenous ferulic and p-coumaric acid. Allelopathy J 25: 475-484.
  14. Goldberg, D.E., T. Rajaniemi, J. Gurevitch, and A. Stewart-Oaten. 1999. Empirical approaches to quantifying interaction intensity: competition and facilitation along productivity gradients. Ecology 80:1118-1131. doi: 10.1890/0012-9658(1999)080[1118:EATQII]2.0.CO;2
  15. Goswami-Giri, A.S., and R. Oza. 2014. Bioinformatics overview of lantana camara, an Environmental Weed. Research Journal of Pharmaceutical, Biological and Chemical Sciences 5:1712-1719.
  16. Hamada, K., K. Hongo, K. Suwabe, A. Shimizu, T. Nagayama, R. Abe, et al. 2011. OryzaExpress: an integrated database of gene expression networks and omics annotations in rice. Plant Cell Physiol 52: 220-229. doi: 10.1093/pcp/pcq195
  17. Hierro, J.L., and R. M. Callaway. 2003. Allelopathy and exotic plant invasion. Plant Soil 256: 29-39. doi: 10.1023/A:1026208327014
  18. Karp, P.D., S. Paley, and T. Altman. 2013. Data mining in the MetaCyc family of pathway databases. Methods Mol Biol 939: 183-200. doi: 10.1007/978-1-62703-107-3_12
  19. Kohli, R.K., D. R. Batish, H. P. Singh, and K. S. Dogra. 2006. Status, invasiveness and environmental threats of three tropical American invasive weeds (Parthenium hysterophorus L., Ageratum conyzoides L., Lantana camara L.) in India. Biological Invasions 8: 1501-1510. doi: 10.1007/s10530-005-5842-1
  20. Kosaka, Y., B. Saikia, T. Mingki, H. Tag, T. Riba, and K. Ando. 2010. Roadside distribution patterns of invasive alien plants along an altitudinal gradient in Arunachal Himalaya, India. Mountain Research and Development 30: 252-258. doi: http://dx.doi.org/10.1659/MRD-JOURNAL-D-10-00036.1
  21. Kudo, T., K. Akiyama, M. Kojima, N. Makita, T. Sakurai, H. Sakakibara. 2013. UniVIO: A multiple omics database with hormonome and transcriptome data from rice. Plant Cell Physiol 54: e9(1-12). doi: 10.1093/pcp/pct003
  22. Kumar, S., R. Sandhir, and S. Ojha. 2014. Evaluation of antioxidant activity and total phenol in different varieties of Lantana camara leaves. BMC Res Notes 7: 560. doi: 10.1186/1756-0500-7-560
  23. Lowe, S., S. Browne, S. M. Boudjela, and S. M. De poorter. 2000. 100 of the world’s worst invasive alien species. ‘Global Invasive Species Database’, The Invasive Species Specialist Group (ISSG), Species Survival Commission (SSC) of World Conservation Union IUCN, p.12.
  24. Maiti, P.P., R. K. Bhakat, and A. Bhattacharjee. 2008. Allelopathic effects of Lantana camara on physiobiochemical parameters of Mimosa pudica seeds. Allelopathy J 22: 59-68.
  25. Mamik, S., and A. Dev Sharma. 2014. Analysis of boiling stable antioxidant enzymes in invasive alien species of Lantana under abiotic stress-like conditions. Braz J Bot 37:129-141. doi: 10.1007/s40415-014-0060-7
  26. Martellos, S., and F. Attorre. 2012. New trends in biodiversity informatics. Plant Biosystems 146: 749-751. doi: 10.1080/11263504.2012.740092
  27. Mochida, K., T. Yoshida, T. Sakurai, K. Yamaguchi-Shinozaki, K. Shinozaki, L-S. Phan Tran. 2013. TreeTFDB: An integrative database of the transcription factors from six economically important tree crops for functional predictions and comparative and functional genomics. DNA Res 20:151-162. doi: 10.1093/dnares/dss040
  28. Nei, M., and W. H. Li. 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sc, USA 76: 5269-5273.
  29. Pavel, A.B., and C. L. Vasile. 2012. PyElph - a software tool for gel images analysis and phylogenetics. BMC Bioinformatics 13:9. doi: 10.1186/1471-2105-13-9
  30. Pavlíček, A., Š. Hrdá, and J. Flegr. 1999. FreeTree-Freeware program for construction of phylogenetic trees on the basis of distance data and bootstrap/jackknife analysis of the tree robustness. Application in the RAPD analysis of the genus Frenkelia. Folia Biol (Praha) 45: 97-99.
  31. Parker, I.M., D. Simberloff , W. M. Lonsdale, K. Goodell, M. Wonham, P. M. Kareiva, M. H. Williamson, B. Von Holle, P. B. Moyle, J. E. Byers, and L. Goldwasser. 1999. Impact: toward a framework for understanding the ecological effects of invaders. Biological Invasions 1: 3-19. doi: 10.1023/A:1010034312781
  32. Politycka, B., M. Kozłowska, and B. Mielcarz. 2004. Cell wall peroxidases in cucumber roots induced by phenolic allelochemicals. Allelopathy J 13:29-36.
  33. Priyanka, N., and P. K. Joshi. 2013. Effects of climate change on invasion potential distribution of Lantana camara. Journal of Earth Science & Climate Change 4:164.
  34. Ray, A., and R. Ray. 2014. Rapid divergence of ecotypes of an invasive plant. Ann Bot PLANTS 6: plu052. doi: 10.1093/aobpla/plu052
  35. Saini, H.S., 2008. Climate change and its future impact on the Indo-Gangetic Plain (IGP). e-Journal Earth Science India I: 138-147.
  36. Saitou, N., and M. Nei. 1987. The Neighbor-joining method: a new method for reconstruction of phylogenetics trees. Mol Biol Evol 4: 406-425.
  37. Scott, L.J., G. C. Graham, M. Hannan-Jones, and D. K. Yeates. 1997. DNA profiling resolves the limited importance of flower color in defining varieties of Lantana camara. Electrophoresis 18: 1560-1563.
  38. Sharma, P., P. Singh, and A. K. Tiwari. 2009. Effects of Lantana camara invasion on plant biodiversity and soil erosion in a forest watershed in lower Himalayas, India. Indian Journal of Forestry 32: 369-374.
  39. Singh, S.P., V. Singh, and M. Skutsch. 2010. Rapid warming in the Himalayas: Ecosystem responses and development options. Climate and Development 2: 221-232. doi: 10.3763/cdev.2010.0048
  40. Stirton, H.S. 1999. The naturalized Lantana camara L. (Lantaneae Verbenaceae) complex in KwaZulu Natal, South Africa: A dilemma for the culton concept. In: Taxonomy of Cultivated Plants. S. Andrews, SC Leslie, G. Alexander, Eds. Royal Botanical Gardens, Kew, UK. p. 311-324.
  41. Talukdar, D. 2013a. Allelopathic effects of Lantana camara L. on Lathyrus sativus L.: Oxidative imbalance and cytogenetic consequences. Allelopathy J 31: 71-90.
  42. Talukdar, D. 2013b. Species richness and floral diversity around ‘Teesta Barrage Project’ in Jalpaiguri district of West Bengal, India with emphasis on invasive plants and indigenous uses. Biol Med 5: 01-14.
  43. Talukdar, D. 2013c. Floristic compositions and diversity of weed taxa in lentil (Lens culinaris Medik.) fields. Bull Environ, Pharmacol Life Sc 2: 33-39.
  44. Talukdar, D. 2014. Increasing nuclear ploidy enhances the capability of antioxidant defense and reduces chromotoxicity in Lathyrus sativus roots under cadmium stress. Turk J Bot 38: 696-712. doi: 10.3906/bot-1310-9
  45. Talukdar, D., and T. Talukdar. 2012. Floral diversity and its indigenous use in old basin (Khari) of river Atreyee at Balurghat block of Dakshin Dinajpur district, West Bengal. NeBIO 3: 26-32.
  46. Taylor, S., L. Kumar, N. Reid, and D.J. Kriticos. 2012. Climate change and the potential distribution of an invasive shrub, Lantana camara L.. PLoS ONE 7: e35565. doi: 10.1371/journal.pone.0035565
  47. Tũrker, M., P. Battal, G. Agar, M. Gulluce, F. Sahin, M. E. Erez, and N. Yildirim. 2008. Allelopathic effects of plants extracts on physiological and cytological processes during maize seed germination. Allelopathy J 21: 273-286.
  48. Umesh Adiga, P.S., A. Bhomra, M. G. Turri, A. Nicod, S. R. Datta, P. Jeavons, R. Mott, J. Flint. 2001. Automatic analysis of agarose gel images. Bioinformatics 17:1084-1089.
  49. Uribe-Carvajal, S., S. Guerrero-Castillo, B. King-Díaz, and H. B. Lotina. 2008. Allelochemicals targeting the phospholipid bilayer and the proteins of biological membranes. Allelopathy J 21: 1-24.
  50. Vilà, R., M. Williamson, and M. Lonsdale. 2004. Competition experiments on alien weeds with crops: lessons for measuring plant invasion impact? Biological Invasions 6: 59-69. doi: 10.1023/B:BINV.0000010122.77024.8a
  51. Wangspaa, R., R. W. Cutlerb, S. Sitthiproma, R. Chundeta, N. Dumampaic, and S. Anuntalabhochai. 2005. DNA fingerprint database of some economically important Thai plants: Litchi chinensis Sonn, Dimocarpus longan Lour, and Peuraria spp. ScienceAsia 31: 145-149.
  52. Xu, C.Y., M. H. Julien, M. Fatemi, C. Girod, D. V. R. Klinken, C. L. Gross, and S. J. Novak. 2010. Phenotypic divergence during the invasion of Phyla canescence in Australia and France: Evidence for selection-driven evolution. Ecol Lett 13:32-44. doi: 10.1111/j.1461-0248.2009.01395.x
  53. Zhao, W., Y. Q. Chen, G. Casella, J. M. Cheverud & R. Wu. 2005. A non-stationary model for functional mapping of complex traits. Bioinformatics 21:2469-2477.

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