A Brief Review of Molecular Markers to Analyse Medically Important Plants

Öz

Suitable identification and characterisation of plants using in medicine are necessary for conservation plant resources, investigations of genes associated with desirable traits, and understanding of evolutionary relationships. Therefore, various molecular marker techniques such as RAPD, AFLP, SSR and ISSR, SNP, SCoT, ITS and SCAR have been improved to provide detail information about genomes, which were not previously possible with only phenotypic methods. This brief review represents usage of these markers for molecular diversity analyses of medically important plants.

Anahtar Kelimeler

• AFLP,ITS,SSR,SNP,SCoT

Kaynakça

1. 1. Global Industry Analyst, Inc., Herbal supplements and remedies market trends http://www.strategyr.com/MarketResearch/Herbal_Supplements_ and_Remedies_Market_Trends.asp, 2015.
2. 2. Baruah, J., et al., Genetic diversity study amongst Cymbopogon species from NE-India using RAPD and ISSR markers. Industrial Crops and Products, 2017. 95: p. 235-243.
3. 3. Hebert, P.D., A. Cywinska, S.L. Ball, JR, and deWaard., J.R., Biological identifications through DNA barcodes. Proceedings of the Royal Society of London B: Biological Sciences, 2003. 270: p. 313-321.
4. 4. Joshi, S.P., P.K., Ranjanekar, and V.S. Gupta, Molecular markers in plant genome analysis. Current Science, 1999. 77: p. 230-240.
5. 5. Hebert, P.D.N., and T.R., Gregory, The promise of DNA barcoding for taxonomy. Systematic Biology, 2005. 54: p. 852-859.
6. 6. Hajibabaei, M., G.A., Singer, P.D., Hebert, and D.A., Hickey, DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. Trends in Genetics, 2007. 23: p. 167-172.
7. 7. Valentini, A., F. Pompanon, and P. Taberlet, DNA barcoding for ecologists. Trends in Ecology & Evolution, 2009. 24: p. 110-117.
8. 8. Eurlings, M., F., Lens, C., Pakusza, T., Peelen, J.J. Wieringa, and B., Gravendeel, Forensic identification of Indian snakeroot (Rauvolfia serpentina Benth. ex Kurz) using DNA barcoding. Journal of Forensic Sciences, 2013. 58: p. 822-830.

9. 9. Janjua, S., W.K. Fakhar-I-Abbas, I.U. Malik, and J. Mehr, DNA mini-barcoding for wildlife trade control: A case study on identification of highly processed animal materials. Mitochondrial DNA Part A, 2016. 28: p. 544-456.
10. 10. Di Pinto, A., et al., Packaged frozen fishery products: Species identification, mislabeling occurrence and legislative implications. Food Chemistry, 2016. 194: p. 279-283.
11. 11. Williams, J.G.K. et al., DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Research, 1990. 18: p. 6531-6535.
12. 12. Lal, N., and S.K., Awasthi, A comparative assessment of molecular marker assays (AFLP and RAPD) for Cymbopogon germplasm characterization. World Journal of Pharmaceutical Research, 2015. 4: p. 1019-1041.
13. 13. Bishoyi, A.K., A., Sharma, A., Kavane, and K.A., Geetha, Varietal discrimination andgenetic variability analysis of cymbopogon using RAPD and ISSR markers analysis. Applied Biochemistry and Biotechnology, 2016. 179: p. 659-670.
14. 14. Saikia, D., et al., RAPD and ISSR based intra-specific molecular genetic diversity analysis of Cymbopogon flexuosus L. Stapf with a distinct correlation of morpho-chemical observations. Research Journal of Biotechnology, 2015. 10: p. 105-113.
15. 15. Kumar, J., et al., Genetic diversity analysis in Cymbopogon species using DNA markers. PlantOmics Journal, 2009. 2: p. 20-29.
16. 16. Gantait, S., S., Kundu, L., Yeasmin, Md. N., Ali, Impact of differential levels of sodium alginate, calcium chloride and basal media on germination frequency of genetically true artificial seeds of Rauvolfia serpentina (L.) Benth. ex Kurz. Journal of Applied Research on Medicinal and Aromatic Plants, 2017. 4: p. 75-81.
17. 17. Klyushnichenko, V.E., et al., Determination of indole alkaloids from R. serpentina and R. vomitoria by high performance liquid chromatography and high-performance thin layer chromatography. Journal of Chromatography, 1995. 704: p. 357-362.
18. 18. Sharma, E., R., Sharma, and K.K., Singh, A boon for mountain populations: largecardamom farming in the Sikkim Himalaya. Mountain Research and Development, 2000. 20: p. 108-111.
19. 19. Purohit, S., S.K., Nandi, S., Paul, M., Traiq, and L.M., Palni, Micropropagation and genetic fidelity analysis in Amomum subulatum Roxb.: A commercially important Himalayan plant. Journal of Applied Research on Medicinal and Aromatic Plants, 2017. 4: p. 21-26.
20. 20. Vos, P., et al., AFLP: A new technique for DNA fingerprinting. Nucleic Acids Research, 1995. 23: p. 4407-4414.
21. 21. Moya-Hernández, A., et al., Analysis of genetic diversity of Cucurbita ficifolia Bouché from different regions of Mexico, using AFLP markers and study of its hypoglycemic effect in mice. South African Journal of Botany, 2018. 116: p. 110-115.
22. 22. Aversano, R., F., Di Dato, A., Di Matteo, L., Frusciante, and D., Carputo., AFLP analysis to assess genomic stability in solanum regenerants derived from wild and cultivated species. Plant Biotechnology Reports, 2011. 5: p. 265-271.
23. 23. Mehta, R., V., Sharma, A., Sood, M., Sharma and R.K. Sharma, Induction of somatic embryogenesis and analysis of genetic fidelity of in vitro-derived plantlets of Bambusa nutans wall., using AFLP markers. European Journal of Forest Research, 2011. 130: p. 729-736.
24. 24. Ebrahimi, M., A., Mokhtari, and R., Amirian, A highly efficient method for somatic embryogenesis of Kelussia odorotissima Mozaff., an endangered medicinal plant. Plant Cell, Tissue and Organ Culture, 2018. 132: p. 99-110.
25. 25. Ghosh, S., and S.S., Mandi, Altitudinal effect in active principle content in Murraya koenigii (L) correlated with DNA fingerprinting study. Journal of Medicinal Plants Studies, 2018. 6: p. 20-26.
26. 26. Bidichandani, S., T., Ashizawa, and P.I., Patel, The GAA triplet-repeat expansion in Friedreich ataxia interferes with transcription and may be associated with an unusual DNA structure. The American Journal of Human Genetics, 1998. 62: p. 111-121.
27. 27. Zhu, H.Y., et al., Genome wide characterization of simple sequence repeats in watermelon genome and their application in comparative mapping and genetic diversity analysis. BMC Genomics, 2016. 17: p. 557.
28. 28. Liu, S.R., et al., Construction of fingerprinting for tea plant (Camellia sinensis) accessions using new genomic SSR markers. Molecular Breeding, 2017. 37: p. 93.
29. 29. Kherwar, D., K., Usha, S.V.A., Mithra, and B., Singh, Microsatellite (SSR) marker assisted assessment of population structure and genetic diversity for morpho-physiological traits in guava (Psidium guajava L.), Journal of Plant Biochemistry and Biotechnology. 2018, 27: p. 284-292.
30. 30. Hernandez-Delgado, S., Padilla-Ramirez, J.S., Nava-Cedillo, A., Mayek-Perez, N., Morphological and genetic diversity of Mexican guava germplasm. Plant Genet Resources, 2007. 5: p. 131-141.
31. 31. Feria-Romero, I.A., et al., RAPD markers associated with quercetin accumulation in Psidium guajava. Biologia Plantarum. 2009, 53: p. 125-128.
32. 32. Bharti, R., S., Kumar, M.J., Parekh, Development of genomic simple sequence repeat (gSSR) markers in cumin and their application in diversity analyses and cross-transferability. Industrial Crops and Products, 111: p. 158-164.
33. 33. Liu, S., et al., Genome-wide identification of simple sequence repeats and development of polymorphic SSR markers for genetic studies in tea plant (Camellia sinensis). Molecular Breeding, 2018. 38: p. 59.
34. 34. Zhai, S.H., G.S., Yin, X.H., Yang, Population genetics of the endangered and wild edible plant Ottelia acuminata in southwestern china using novel SSR markers. Biochemical Genetics, 2018. 56: p. 235-254.
35. 35. Fadaei Heidari, E., M., Rahimmalek, S., Mohammadi, M.H., Ehtemam, Genetic structure and diversity of ajowan (Trachyspermum ammi) populations based on molecular morphological markers, and volatile oil content. Industrial Crops and Products, 2016. 92: p. 186-196.
36. 36. Demisew, S., A description of some essential oil bearing plants in Ethiopia and their indigenous uses. Journal of Essential Oil Research, 1993, 5: p. 465-79.
37. 37. Chombe, D., and E., Bekele, Genetic diversity analysis of cultivated Korarima [Aframomum corrorima (Braun) P.C.M. Jansen] populations from southwestern Ethiopia using inter simple sequence repeats (ISSR) marker. Journal of Biological Research-Thessaloniki, 2018. 25: 1.
38. 38. Hashemifar, Z., and M., Rahimmalek, Genetic structure and variation in Perovskia abrotanoides Karel and P. atriplicifolia as revealed by molecular and morphological markers. Scientia Horticulturae, 2018. 230: p. 169-177.
39. 39. Abraham, E.M., et al., Genetic diversity of Thymus sibthorpii Bentham in mountainous natural grasslands of Northern Greece as related to local factors and plant community structure. Industrial Crops and Products, 2018. 111: p. 651-659.
40. 40. Kuhn, D., Design of an Illumina Infinium 6k SNPchip for genotyping two large avocado mapping populations, in Proceedings of the 20th Conference on Plant andAnimal Genome. 2012: SanDiego, Calif, USA.
41. 41. Lee, O.R., M.K., Kim, and D.C., Yang, Authentication of medicinal plants by SNP-based multiplex PCR, in: Plant DNA fingerprinting and barcoding: methods and protocols. 2012, New York: Humana Press, p. 135-147.
42. 42. Manivannan, A., et al., Next-generation sequencing approaches in genome-wide discovery of single nucleotide polymorphism markers associated with pungency and disease resistance in pepper. BioMed Research International, 2018. https://doi.org/10.1155/2018/5646213.
43. 43. Collard, B.C.Y., and D.J., Mackill, Start codon targeted (SCoT) polymorphism: a simple, novel DNA marker technique for generating gene-targeted markers in plants. Plant Molecular Biology Reporter, 2009. 27: p. 86-93.
44. 44. Bhattacharyya, P., S., Kumaria, S., Kumar, and P., Tandon, Start codon targeted (SCoT) marker reveals genetic diversity of Dendrobium nobile Lindl., an endangered medicinal orchid species. Gene, 2013. 529: p. 21-26.
45. 45. Singh, N., et al., Genetic stability in micropropagated Cleome gynandra revealed by SCoT analysis. Acta Physiologiae Plantarum, 2014. 36: p. 555-559.
46. 46. Tiwari, G., et al., Study of arbitrarily amplified (RAPD and ISSR) and gene targeted (SCoT and CBDP) markers for genetic diversity and population structure in Kalmegh [Andrographis paniculata, (Burm. f.) Nees]. Industrial Crops and Products, 2016. 86: p. 1-11.
47. 47. Mao, R., P., Xia, J., Liu, X., Li, R., Han, F., Liu, H., Zhao, and Z., Liang, Genetic diversity and population structure assessment of Chinese Senna obtusifolia L. by molecular markers and morphological traits of seed. Acta Physiologiae Plantarum, 2018. 40: 12.
48. 48. Xiang, X.G., et al., Molecular systematics of Dendrobium (Orchidaceae, Dendrobieae) from mainland Asia based on plastid and nuclear sequences. Molecular Phylogenetics and Evolution, 2013. 69: 950-960.
49. 49. Jiang, C., Y., Luo, Y., Yuan, X., Dong, Y., Zhao, and L., Huang, Conventional octaplex PCR for the simultaneous identification of eight mainstream closely related Dendrobium species. Industrial Crops and Products, 2018. 112: p. 569-576.
50. 50. Kshirsagar, P., S., Umdale, J., Chavan, and N., Gaikwad, Molecular authentication of medicinal plant, Swertia chirayita and its adulterant species, Proceedings of the National Academy of Sciences, India Section B: Biological Sciences, 2017. 87(1): p. 101-107.
51. 51. Lee, S-C., C-H., Wang, C-E., Yen, and C., Chang, DNA barcode and identification of the varieties and provenances of Taiwan's domestic and imported made teas using ribosomal internal transcribed spacer 2 sequences, Journal of Food and Drug Analysis, 2017, 25: p. 260-274.
52. 52. Hollingsworth, P.M., S.W., Graham, and D.P. Little, Choosing and Using a Plant DNA Barcode. PLoS ONE, 2011. 6: e19254.
53. 53. Ali, M.A., G., Gyulai, and F. Al-Hermaid, Plant DNA Barcoding and Phyogenetics, LAP LAMBERT Academic Publishing, 2015, Saarbrücken, Germany.
54. 54. Sucher, N.J., and M.C., Carles, Genome-based Approaches to the authentication of medicinal plants. Planta Medica, 2008. 74: p. 603-623.
55. 55. Bhagyawant, S.S., RAPD-SCAR markers: an ınterface tool for authentication of Traits. Journal of Biosciences and Medicines, 2016. 4: p. 1-9.
56. 56. Daniell, H., C.S., Lin, M., Yu, and W.J. Chang, Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Biology, 2016. 17: 134.
57. 57. Fu, J., L., Yang, M.A., Khan, Z., Mei, Genetic characterization and authentication of Lonicera japonica Thunb. by using improved RAPD analysis. Molecular Biology Reports, 2013. 40: p. 5993-5999.
58. 58. Moon, B.C., et al., Differentiating Authentic adenophorae radix from ıts adulterants in commercially-processed samples using multiplexed ITS sequence-based SCAR markers. Applied Sciences, 2017. 7: 660.
59. 59. Fu, S., et al., Development of diagnostic SCAR markers for genomic DNA amplifications in breast carcinoma by DNA cloning of high-GC RAMP-PCR fragments. Oncotarget, 2017. 8: p. 43866-43877.
60. 60. Rafalski, J.A., and S.V. Tingey, Genetic diagnostics in plant breeding: RAPDs, microsatellites and machines. Trends in Genetics, 1993. 9: p. 275-280.
61. 61. Rafalski, J.A., Novel genetic mapping tools in plants: SNPs and LD-based approaches. Plant Science, 2002. 162: p. 329-333.