• P-ISSN 0974-6846 E-ISSN 0974-5645

Indian Journal of Science and Technology

Article

Orobanche species identification through DNA barcoding in tomato crop in uplands of Balochistan, Pakistan
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Indian Journal of Science and Technology

DOI: 10.17485/IJST/v13i27.76

Year: 2020, Volume: 13, Issue: 27, Pages: 2747-2754

Original Article

Orobanche species identification through DNA barcoding in tomato crop in uplands of Balochistan, Pakistan

Nazir Ahmed1*, Muhammad Ali1, Hidayatullah2, Zahid Mustafa1, Tabeel Tariq Bashir1, Farooq Shehzad1

1Center for Advanced Studies in Vaccinology & Biotechnology (CASVAB), University of Balochistan, Pakistan
2Agriculture Research Institute (ARI), Quetta, Pakistan

Corresponding author
Email: [email protected]

Received Date:31 March 2020, Accepted Date:18 May 2020, Published Date:31 July 2020

Creative Commons License

This work is licensed under a Creative Commons Attribution 4.0 International License.

Abstract

Background/objectives: Orobanche is one of the important parasites of solanaceae crops and causes heavy yield losses. This study aimed to use DNA barcoding technique for identification of Orobanche species. Methods: Surveillance study was conducted in the year 2018 on tomato crops grown in four different districts in Balochistan. From these tomato fields, 15 Orobanche plant samples were collected and put in polyethylene bags containing silica gel for drying. The dried samples were processed for DNA extraction using CTAB method. The extracted DNA was confirmed through gel electrophoresis which were further amplified on PCR using rbcL, matK primers. Then, the PCR products were processed for DNA sequencing using Sanger method. Further, the DNA sequences were edited and aligned with BioEdit and MegaX software and the aligned sequences were matched on NCBI for BLAST. The FASTA results of both partial and/or complete genome were run on MegaX for phylogenetic analysis. Findings: The success rates for PCR amplification was 100% for rbcl primer, while it was 68% for matK primer. However, the resolution power of matK was higher than that obtained from rbcL as manifested in the rate of DNA acquisition sequence. The DNA barcode results of 15 samples revealed 99.16% rate of DNA acquisition sequence for identification of P. ramosa and 96.41 for P. purpurea. While, Rbcl rate of DNA sequencing show no results. Application/Improvement: from this study it was inferred that matK gene performed better than rbcL in Orobanche species identification and proved as a potential gene for other pseudogene plants species identification.

Keywords: Orobanche; species; DNA barcode; rbcL; matK; tomato

References

  1. Plaza A, Martinez P, Perez R, Plaza J. A Quantitative and Comparative Analysis of Endmember Extraction Algorithms From Hyperspectral Data. IEEE Transactions on Geoscience and Remote Sensing. 2004;42(3):650–663. Available from: https://dx.doi.org/10.1109/tgrs.2003.820314
  2. Pusch J, Günther KF. Family Orobanchaceae s. str. summer plants. In: Wagenitz GW., ed. Illustrated Flora of Central Europe VI (1A). (Vol. 2, pp. 1-99) Weissdorn-Verlag. 2009.
  3. Lindpaintner K, Pfeffer MA, Kreutz R, Stampfer MJ, Grodstein F, LaMotte F, et al. A Prospective Evaluation of an Angiotensin-Converting–Enzyme Gene Polymorphism and the Risk of Ischemic Heart Disease. New England Journal of Medicine. 1995;332(11):706–712. Available from: https://dx.doi.org/10.1056/nejm199503163321103
  4. Uhlich H, Pusch J, Barthel KJ. European summer roots. 1995.
  5. Parker C, Riches CR. Parasitic weeds of the world: biology and control: CAB international. (pp. 332) Wallingford, UK.. 1993.
  6. Hashemi E, Kaviani A, Najafi M, Ebrahimi M, Hooshmand H, Montazeri AJ. Seroma formation after surgery for breast cancer. World Journal of Surgical Oncology. 2004;2(1):44. Available from: http://doi.org/ 10.1186/1477-7819-2-44
  7. Li MX, He XR, Tao R, Cao X. Phytochemistry and Pharmacology of the Genus Pedicularis Used in Traditional Chinese Medicine. The American Journal of Chinese Medicine. 2014;42:1071–1098.
  8. Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0. Molecular Biology and Evolution. 2007;24:1596–1599. Available from: https://dx.doi.org/10.1093/molbev/msm092
  9. Mauromicale G, Monaco AL, Longo AMG. Effect of Branched Broomrape (Orobanche ramosa) Infection on the Growth and Photosynthesis of Tomato. Weed Science. 2008;56(4):574–581. Available from: https://dx.doi.org/10.1614/ws-07-147.1
  10. Hebert PDN, Gregory TR. The Promise of DNA Barcoding for Taxonomy. Systematic Biology. 2005;54:852–859. Available from: https://dx.doi.org/10.1080/10635150500354886
  14. Savolainen V, Cowan RS, Vogler AP, Roderick GK, Lane R. Towards writing the encyclopaedia of life: an introduction to DNA barcoding. Philosophical Transactions of The Royal Society. 2005;360(1462):1805–1811. Available from: https://doi.org/10.1098/rstb.2005.1730
  15. Moritz C, Cicero C. DNA Barcoding: Promise and Pitfalls. PLoS Biology. 2004;2(10):e354. Available from: https://dx.doi.org/10.1371/journal.pbio.0020354
  16. Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM. Identification of Birds through DNA Barcodes. PLoS Biology. 2004;2(10):e312. Available from: https://dx.doi.org/10.1371/journal.pbio.0020312
  17. Kress WJ, Erickson DL. DNA barcodes: methods and protocols. Springer. 2012.
  18. Chase MW, Salamin N, Wilkinson M, Dunwell JM, Kesanakurthi RP, Haidar N, et al. Land plants and DNA barcodes: short-term and long-term goals. Philosophical Transactions of the Royal Sociey of London, Series B, Biological Sciences. 2016;371(1691):1889–1895. Available from: https://dxdoi.org/10.1098/rstb.2015.0063
  19. Lahaye R, Bank Mvd, Bogarin D, Warner J, Pupulin F, Gigot G, et al. DNA barcoding the floras of biodiversity hotspots. In: Proceedings of the National Academy of Sciences, 8. (Vol. 105, pp. 2923-2928) United States of America. National Academy of Sciences. 2008.
  20. Newmaster SG, Fazekas AJ, Ragupathy S. DNA barcoding in land plants: evaluation of rbcL in a multigene tiered approach. Canadian Journal of Botany. 2006;84(3):335–341. Available from: https://dx.doi.org/10.1139/b06-047
  21. , Li DZ, Gao LM, Li HT, Wang H, Ge XJ, et al. Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants. Proceedings of the National Academy of Sciences. 2011;108(49):19641–19646. Available from: https://dx.doi.org/10.1073/pnas.1104551108
  22. Group CPW, Hollingsworth PM, Forrest LL, Spouge JL, Hajibabaei M, Ratnasingham S. A DNA barcode for land plants. In: Proceedings of the National Academy of Sciences of the United States of America, 31. (Vol. 106, pp. 12794-12797) National Academy of Sciences of the United States of America. 2009.
  23. Li X, Yang Y, Henry RJ, Rossetto M, Wang Y, Chen SJ. Plant DNA barcoding: from gene to genome. Biological reviews of the Cambridge Philosophical Society. 2015;90(1):157–166. Available from: https://doi.org/10.1111/brv.12104
  24. Fazekas AJ, Maria LK, Steven GN, Peter MH. DNA Barcoding Methods for Land Plants. In: Kress WJ, Erickson LD., eds. DNA Barcodes: Methods and Protocols, Methods in Molecular Biology. Springer Science+Business Media, LLC. 2012.
  25. Doyle JJ, Doyle JL. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin. 1987;19:11–15.
  26. Li JL, Wang S, Jing Y, Wang L, Zhou S. A modified CTAB protocol for plant DNA extraction. Chinese Bulletin of Botany. 2013;48:72–78. Available from: http://doi.org/10.3724/SP.J.1259.2013.00072
  27. Kress WJ, Erickson DL. Methods in Molecular Biology. In: DNA barcodes: methods and protocols. (Vol. 858, pp. 3-8) 2012.
  28. Liu J, Yan HF, Newmaster SG, Pei N, Ragupathy S, Ge XJ. The use of DNA barcoding as a tool for the conservation biogeography of subtropical forests in China. Diversity and Distributions. 2015;21:188–199. Available from: https://dx.doi.org/10.1111/ddi.12276
  29. Burgess KS, Fazekas AJ, Kesanakurti PR, Graham SW, Husband BC, Newmaster SG, et al. Discriminating plant species in a local temperate flora using the rbcL+matK DNA barcode. Methods in Ecology and Evolution. 2011;2(4):333–340. Available from: https://dx.doi.org/10.1111/j.2041-210x.2011.00092.x
  30. Wattoo JI, Saleem MZ, Shahzad MS, Arif A, Hameed A, Saleem MA. DNA Barcoding: Amplification and sequence analysis of rbcL and matK genome regions in three divergent plant species. Advancement in Life Sciences. 2016;4(1):3–07. Available from: http://www.als-journal.com/for-authors/
  31. Khanuja SP, Shasany AK, Darokar MP, Kumar S. Rapid isolation of DNA from dry and fresh samples of plants producing large amounts of secondary metabolites and essential oils. Plant Molecular Biology Reporter. 1999;17(1).
  32. Awad M, Fahmy RM, Mosa KA, Helmy M, El-Feky FA. Identification of effective DNA barcodes for Triticum plants through chloroplast genome-wide analysis. Computational Biology and Chemistry. 2017;71:20–31. Available from: https://dx.doi.org/10.1016/j.compbiolchem.2017.09.003
  33. Román B, Rubiales D, Torres AM, Cubero JI, Satovic Z. Genetic diversity in Orobanche crenata populations from southern Spain. Theoretical and Applied Genetics. 2001;103:1108–1114. Available from: https://dx.doi.org/10.1007/s001220100644
  34. Saitou N, Nei M. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution. 1987;4:406–425.
  35. Tamura K, Nei M, Kumar S. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proceedings of the National Academy of Sciences. 2004;101(30):11030–11035. Available from: https://dx.doi.org/10.1073/pnas.0404206101
  36. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Molecular Biology and Evolution. 2018;35(6):1547–1549. Available from: https://dx.doi.org/10.1093/molbev/msy096
  37. Notredame C, Higgins DG, Heringa J. T-coffee: a novel method for fast and accurate multiple sequence alignment 1 1Edited by J. Thornton. Journal of Molecular Biology. 2000;302(1):205–217. Available from: https://dx.doi.org/10.1006/jmbi.2000.4042
  38. Savolainen V, Chase MW, Hoot SB, Morton CM, Soltis DE, Bayer C, et al. Phylogenetics of Flowering Plants Based on Combined Analysis of Plastid atpB and rbcL Gene Sequences. Systematic Biology. 2000;49(2):306–362. Available from: https://dx.doi.org/10.1093/sysbio/49.2.306
  40. Mattia FD, Bruni I, Galimberti A, Cattaneo F, Casiraghi M, Labra M, et al. A comparative study of different DNA barcoding markers for the identification of some members of Lamiacaea. Food Research International. 2011;44(3):693–702. Available from: https://dx.doi.org/10.1016/j.foodres.2010.12.032
  41. Rolland M, Dupuy A, Pelleray A, Delavault P. Molecular identification of Broomrape species from a single seed by high resolution melting analysis. Frontiers in Plant Science. 2016. Available from: https://doi.org/10.3389/fpls.2016.01838
  42. Ghorbani A, Saeedi Y, De Boer HJ. Unidentifiable by morphology: DNA barcoding of plant material in local markets in Iran. PLOS ONE. 2012;12(4).

Copyright

© 2020 Ahmed, Ali, Mustafa, Bashir, Shehzad. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Published By Indian Society for Education and Environment (iSee).

  • 02 August 2020

Year: 2020, Volume: 13, Issue: 27

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