Using Morphological and Phytochemical Traits and ITS (1, 4) and rbcl DNA Barcodes in the Assessment of Different Malva sylvestris L. Genotypes

Document Type : Research Paper

Authors

1 Department of Horticultural, Faculty of Agriculture, university of Zabol, Zabol, Iran

2 Department of Breeding and Biotechnology, Faculty of Agriculture, University of Zabol, Zabol, Iran

3 Research Department of Agronomy and Plant Breeding, Agricultural Research Institute, University of Zabol, Zabol, Iran

Abstract

Since rbcl gene and protein, as well as internal transcribed spacer (ITS1,4) regions, have not been used in the evaluation of Malva sylvestrisL., this study was aimed to assess different Iranian Malva sylvestris L. genotypes by evaluation of morphological and phytochemical traits, along with rbcl and ITS1,4 gene sequences. Furthermore, three-dimensional and functional structures of Malva sylvestris L. rbcl protein were examined, as well. Nine Malva sylvestris L.genotype samples were collected from different regions of Iran. After species identification, completely randomized design with three replicates was used to evaluate different genotypes, based on morphological and phytochemical traits. DNA extraction was carried out using the SDS method and then final PCR products were sent to Macrogen Company, South Korea for sequencing. Sequence quality was assessed using Chromas 2.1.1 software. Then, the sequences were aligned using the ClustalW method in MegAlign 5 software and the dendrogram of the phylogenetic relationships and similarity matrices were plotted, as well. SWISS-MODEL and QMEAN servers were used for modeling and validation of rbcl protein. Ramachandran plot analysis and Pro-SA servers were used to evaluate the structure and chemical quality of the protein.Comparison of the mean physio-morphological traits between different genotypes showed the highest stem diameter (9.58 mm), root length (61.22 cm), root fresh weight (18.86 g), root dry weight (4.84 g) as well as proline content (0.614mg/gDW) in Mashhad genotype. Based on stepwise regression results in the presented models, root fresh weight and plant dry weight had the most positive effect on root length, but stem diameter and plant fresh weight had the most negative effect. Moreover, while chlorophyll b had the most negative and direct effect on proline function, chlorophyll a, carotenoids, carbohydrates and total protein contents had the most positive effects, respectively. Assessment of protein-protein interaction networks revealed that most proteins encoded by matK, psb-tranH genes interact with rbcl protein. The results of cluster analysis, similarity matrix as well as dN/dS ratio showed high similarity and conservation of ITS and rbcl sequences among different Malva sylvestris L.genotypes. rbcl and ITS sequences were not suitable markers to evaluate phylogenetic relationships intraspecies (at subspecies level) but are useful to evaluate interspecies relationships. Furthermore, the Mashhad genotype is suitable for dry and water deficit conditions, withstanding such conditions. Therefore, it is recommended that this genotype can be used both as a parent and or directly to breed, develop and modify Malva sylvestris L. species.

Keywords

References

1. Razavi M, Zarrini G, Molavi G, Ghasemi G. Bioactivity of Malva Sylvestris L., a Medicinal Plant from Iran. Iran. J Basic Med Sci. 2011;14:574-579.
2. Shoshtariyan S, Ghahramanlo A, Izadidarbandi E, Alirezaienoghondar M. Effect of cropping pattern (cultivar distance) on yield of bacon bacon. National Conference on Med Plants and Recognition of its Economic Potential and its Occupation, Islamic Azad University, Birjand Branch. 2010.
3. Riedl I. Flora Iranica: no. 120. Malvaceae. Graz: Akademische Druck 86p.-illus., keys.. Ge, La Icones. Geog. 1976; 2.
4. Pakravan M. New findings of the genus Malva L. in Iran. Iranian J of Botany. 2006;11:247-249.
5. Henry AG, Piperno DR. Using plant microfossils from dental calculus to recover human diet: a case study from Tell al-Raqā'i, Syria. J of Archaeological Sci. 2008;35:1943-1950.
6. Tabaraki R, Yousefi Z, Asadi-GHarneh H. Chemical composition and antioxidant properties of Malva sylvestris. J Agric Res. 2012;8:59-68.
7. Scherrer AM, Motti R, Weckerle CS. Traditional plant use in the areas of Monte Vesole and Ascea, Cilento National Park (Campania, Southern Italy). J Ethnopharmacology. 2005;97:129-143.
8. Kültür Ş. Medicinal plants used in Kırklareli province (Turkey). J of Ethnopharmacology. 2007;111:341-364.
9. Mustafa A, Ali M. New steroidal lactones and homomonoterpenic glucoside from fruits of Malva sylvestris L. L. Acta Pol Pharm. 2011;68:393-401.
10. Shale T, Stirk W, Van Staden J. Variation in antibacterial and anti-inflammatory activity of different growth forms of Malva parviflora and evidence for synergism of the anti-inflammatory compounds. J Ethnopharmacology. 2005;96:325-330.
11. Omidbeigi R. Production and processing of medicinal plants (Vol. 8). Mashahd: Beh nashr, Astan Ghods Razavi. 2015;348.
12. Ahmand Z, Fahmideh L, Fazeli-Nasab B. Genetic Evaluation of Cumin and Caraway Using Eryngium planum Microsatellite Markers. Sci J Manag Sys. 2017;8:59-71.
13. Ansari S, Solouki M, Fakheri B, Fazeli-Nasab B, Mahdinezhad N. Assessment of molecular diversity of Internal transcribed spacer region in some Lines and Landrace of Persian Clover (Trifolium resupinatum L). Potravinarstvo Slovak J Food Sci. 2018;12:657-666.
14. Davari A, Solouki M, Fazeli-Nasab B. Effects of jasmonic acid and titanium dioxide nanoparticles on process of changes of phytochemical and antioxidant in genotypes of Satureja hortensis L. Eco-Phytochemical J Med Plants. 2018;5:1-20. (In Persian).
15. Blaxter M. Molecular systematics: counting angels with DNA. Nature. 2003;421:122-124.
16. Hebert PD, Cywinska A, Ball SL. Biological identifications through DNA barcodes. Proceedings of the Royal Society of London B: Biological Sci. 2003;270:313-321.
17. Hebert PD, Ratnasingham S, de Waard JR. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society of London B: Biological Sci. 2003;270(Suppl 1):S96-S99.
18. Keshvari T, Najaphy A, Kahrizi D, Zebarjadi A. Callus induction and somatic embryogenesis in Stevia rebaudiana Bertoni as a Medicinal Plant. Cell Mol Biology. 2018;64:46-49.
19. Fazeli-Nasab B, Mehrabi AA, Eizadi-Drabandi A. Genetic diversity of different wheat genotypes using seed storage proteins and SSRs markers. Modern Gen J. 2010;5:83-91.
20. Ghahramanzadeh R, Esselink G, Kodde L, Duistermaat H, Van Valkenburg J, Marashi S, Smulders M, Van de Wiel C. Efficient distinction of invasive aquatic plant species from non-invasive related species using DNA barcoding. Mol Ecol Reso. 2013;13:21-31.
21. Fazeli-Nasab B, Naghavi MR, Mehrabi AA. Allelic Variation of Microsatellite Markers from Linkage Group A Genome in Wild Populations of Einkorn and Hexaploid Wheat. Agric Biotech. 2013;4:53-62.
22. Balasaravanan T, Chezhian P, Kamalakannan R, Yasodha R, Varghese M, Gurumurthi K, Ghosh M. Identification of species-diagnostic ISSR markers for six Eucalyptus species. Silvae Gen. 2006;55:119-122.
23. Fazeli-Nasab B, Naghavi MR, Mardi M, Yazdi-Samadi B, Kazemi M. Genetic diversity and relationships of Iranian wheat cultivars using microsatellite markers. Iranian J of Agric Sci. 2006;37:93-99.
24. Group CPW, Hollingsworth PM, Forrest LL, Spouge JL, Hajibabaei M, Ratnasingham S, van der Bank M, Chase MW, Cowan RS, Erickson DL. A DNA barcode for land plants. Proceedings National Academy Sci. 2009;106:12794-12797.
25. Chang CC, Lin HC, Lin IP, Chow TY, Chen HH, Chen WH, Cheng CH, Lin CY, Liu SM, Chang CC. The chloroplast genome of Phalaenopsis aphrodite (Orchidaceae): comparative analysis of evolutionary rate with that of grasses and its phylogenetic implications. Mol Biol Evolution. 2005;23:279-291.
26. Gamache J, Sun G. Phylogenetic analysis of the genus Pseudoroegneria and the Triticeae tribe using the rbcL gene. Biochem Sys Ecol. 2015;62:73-81.
27. Liu L-X, Li R, Worth J R, Li X, Li P, Cameron K M, Fu C-X. The complete chloroplast genome of Chinese bayberry (Morella rubra, Myricaceae): implications for understanding the evolution of Fagales. Front Plant Sci. 2017;8:968.
28. Chen S, Yao H, Han J, Liu C, Song J, Shi L, Zhu Y, Ma X, Gao T, Pang X. Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species. PLoS One. 2010;5:e8613.
29. Park JH, Kim YH, Ham CS, Shin SE, Lee HJ, Ko KS, Choi J, Son GH, Park SH. Molecular identification of forensically important calliphoridae and sarcophagidae species using ITS2 nucleotide sequences. Forensic Sci Int. 2018;284:1-4. 10.1016/j.forsciint.2017.12.017
30. Paykarestan B, Seify M, Anajafi M, Chavoshi S. Effect of mint essence and ultraviolet on thyme and hock seed germination. New findings in agriculture J. 2012;6:215-220.
31. Arnon DI. Ferredoxin and photosynthesis. Sci. 1965;149:1460-1470.
32. Bates LS, Waldren RP, Teare I. Rapid determination of free proline for water-stress studies. Plant & Soil. 1973;39:205-207.
33. Keleş Y, Öncel I. Response of antioxidative defence system to temperature and water stress combinations in wheat seedlings. Plant Sci. 2002;163:783-790.
34. Bradford MM. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Analytical Biochemistry. 1976;72:248-254.
35. Dellaporta SL, Wood J, Hicks JB. A plant DNA minipreparation: version II. Plant Mol Biol Rep. 1983;1:19-21.
36. White TJ, Bruns T, Lee S, Taylor J. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. PCR protocols: a guide to methods and appli. 1990;18:315-322.
37. Levin RA, Wagner WL, Hoch PC, Nepokroeff M, Pires JC, Zimmer EA, Sytsma KJ. Family-level relationships of Onagraceae based on chloroplast rbcL and ndhF data. American J Botany. 2003;90:107-115.
38. Kress WJ, Erickson DL, Jones FA, Swenson NG, Perez R, Sanjur O, Bermingham E. Plant DNA barcodes and a community phylogeny of a tropical forest dynamics plot in Panama. [Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.]. Proceedings of the National Academy of Sci of the United States of America. 2009;106:18621-18626.
39. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden T L. BLAST+: Architecture and Appli. BMC Bioinformatics. 2009;10:421.
40. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol. Biol. Evol. 2013;30:2725-2729.
41. Schwede T, Kopp J, Guex N, Peitsch MC. SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res. 2003;31:3381-3385.
42. Brohee S, Van Helden J. Evaluation of clustering algorithms for protein-protein interaction networks. BMC Bioinformatics. 2006;7:488.
43. Feizi M, Fahmideh L. Evaluation of agronomic traits and Yield Potential Diversity Inbreed Wheat Inbred Lines Triticum aestivum L. Derived from Roshan×Falat Cultivar. [Research]. J Crop Breeding. 2017;8:30-24.
44. Goka K, Yokoyama J, Une Y, Kuroki T, Suzuki K, Nakahara M, Kobayashi A, Inaba S, Mizutani T, Hyatt AD. Amphibian chytridiomycosis in Japan: distribution, haplotypes and possible route of entry into Japan. Mol Ecol. 2009;18:4757-4774.
45. Druzhinina IS, Kopchinskiy AG, Komoń M, Bissett J, Szakacs G, Kubicek CP. An oligonucleotide barcode for species identification in Trichoderma and Hypocrea. Fungal Gen Biol 2005;42:813-828.
46. Parkin EJ, Butlin RK. Within-and between-individual sequence variation among ITS1 copies in the meadow grasshopper Chorthippus parallelus indicates frequent intrachromosomal gene conversion. Mol Biol Evol. 2004;21:1595-1601.
47. Jomeh Ghasem Abadi Z, Fakheri B, Fazeli-nasab B. Study of the Molecular Diversity of Internal Transcribed Spacer Region (ITS1.4) in Some Lettuce Genotypes. [Research]. J of Crop Breeding. 2019;11:29-39.
48. Varela ES, Lima JP, Galdino AS, Pinto LdS, Bezerra WM, Nunes EP, Alves MA, Grangeiro TB. Relationships in subtribe Diocleinae (Leguminosae; Papilionoideae) inferred from internal transcribed spacer sequences from nuclear ribosomal DNA. Phytochemistry. 2004;65:59-69.
49. Wu CT, Hsieh CC, Lin WC, Tang CY, Yang CH, Huang YC, Ko YJ. Internal transcribed spacer sequence-based identification and phylogenic relationship of I-Tiao-Gung originating from Flemingia and Glycine (Leguminosae) in Taiwan. J. Food. Drug. Anal. 2013;21:356-362.
50. Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, Simonovic M, Roth A, Santos A, Tsafou K P. STRING v10: protein–protein interaction networks, integrated over the tree of life. Nucleic. Acids. Res. 2014;43:D447-D452.
51. Omidbeigi R. Approaches to the production and processing of Medicinal plants (Vol. 1). Tehran: Fekreroz. 1996.
52. Shaykh F, Bazi H. Investigation on the variation of indigenous populations of squash in Golestan province. Paper presented at the National Symposium on Natural Products and Med Plants. 2013.
53. Abbaszadeh B, Rezaee M, Layegh haghighi M. Investigation Morphological Characteristics and Essential Oil Component of 2 Ecotypes of Watermint (Mentha aquatica L.). [Res]. J Med Plants. 2012;1:248-257.
54. Najarfiruzjaie M, Hemati K, Khorasaninejad S, khani AD g, fard AB. The effects of altitude on morphological characteristicsand biochemical plant leaf Urtica dioica L. In Mazandaran and Golestan. J Iranian Plant Ecophysiological Res. 2014;9:1-11.
55. Babaie k, Aminidehghi M, Modares sanavi A, M, Jabari R. Effect of drought stress on morphological traits, proline content and thymol percentage in Thyme. Iranian J Med Aromatic Plants Res. 2010;26:239-251.
56. Larkunthod P, Nounjan N, Siangliw JL, Toojinda T, Sanitchon J, Jongdee B, Theerakulpisut P. Physiological responses under drought stress of improved drought-tolerant rice lines and their parents. Notulae Botanicae Hortic Agrobotanici Cluj-Napoca. 2018;46:679-687.
57. Li J, Phan T-T, Li YR, Xing YX, Yang LT. Isolation, Transformation and Overexpression of Sugarcane SoP5CS Gene for Drought Tolerance Improvement. Sugar tech. 2018;20:464-473.
58. Lotfi M, Abbaszadeh B, Mirza M. The effect of drought stress on morphology, proline content and soluble carbohydrates of tarragon (Artemisia dracunculus L.). Iranian J Med Aromatic Plants Res. 2014;30:19-29.
59. Ardekani MR, Abbaszadeh B, Sharifi-Ashourabadi E, Lebaschi MH, Paknejad F. The effect of water deficit on quantitative and qualitative characters of balm (Melissa officinalis L.). Iranian J Med Aromatic Plants. 2007;23:251-261.
60. Safikhani F. Investigation on physiological resistance aspects under drought stress of Dracocephalum moldavica L. (ph.D), Chamran University. 2006
61. Bettaieb I, Zakhama N, Wannes WA, Kchouk M, Marzouk B. Water deficit effects on Salvia officinalis fatty acids and essential oils composition. Sci Hortic. 2009;120:271-275.
62. Fatima S, Abad Farooqi A, Ansari S, Sharma S. Effect of water stress on growth and essential oil metabolism in Cymbopogon martinii (palmarosa) cultivars. J Essen Oil Res. 1999;11:491-496.
63. Sreevalli Y, Baskaran K, Chandrashekara R, Kulkarni R. Preliminary observations on the effect of irrigation frequency and genotypes on yield and alkaloid concentration in periwinkle. Preliminary observations on the effect of irrigation frequency and genotypes on yield and alkaloid concentration in periwinkle. 2000;22:356-358.
64. Heidari M, Karami V. Effects of different mycorrhiza species on grain yield, nutrient uptake and oil content of sunflower under water stress. J Saudi Aociety Agric Sci. 2014;13:9-13.
65. Good AG, Zaplachinski ST. The effects of drought stress on free amino acid accumulation and protein synthesis in Brassica napus. Physiol Plantarum. 1994;90:9-14.
66. Koopman WJ, Guetta E, van de Wiel CC, Vosman B, van den Berg RG. Phylogenetic relationships among Lactuca (Asteraceae) species and related genera based on ITS-1 DNA sequences. American J Botany. 1998;85:1517-1530.
67. Cunnington JH, Lawrie AC, Pascoe IG. Unexpected ribosomal DNA internal transcribed spacer sequence variation within Erysiphe aquilegiae sensu lato. Fungal Diversity, 2004; 16(16): 1-10.
68. Adlard RD, Barker SC, Blair D, Cribb TH. Comparison of the second internal transcribed spacer (ribosomal DNA) from populations and species of Fasciolidae (Digenea). Int J Parasitology. 1993;23:423-425.
69. Besendahl A, Qiu YL, Lee J, Palmer JD, Bhattacharya D. The cyanobacterial origin and vertical transmission of the plastid tRNA Leu group-I intron. Curr Genet. 2000;37:12-23.
70. Ledford H. Botanical identities. Nature Publishing Group. 2008;451.
71. Guldhe A, Renuka N, Singh P, Bux F. Effect of phytohormones from different classes on gene expression of Chlorella sorokiniana under nitrogen limitation for enhanced biomass and lipid production. Algal Res. 2019;40:101518.
72. Wolfe KH, Li WH, Sharp PM. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proceedings National Academy Sci. 1987;84:9054-9058.
73. Hapsari L, Trimanto T, Wahyudi D. Species diversity and phylogenetic analysis of Heliconia spp. collections of Purwodadi Botanic Garden (East Java, Indonesia) inferred by rbcL gene sequences. Biodiversitas J Biol Diversity. 2019;20:1266-1283.
74. Sarhan S, Hamed F, Al-Youssef W. The rbcL Gene Sequence Variations among and within Prunus Species. J of Agricultural Sci and Technol. 2016;18:1105-1115.
75. Nei M, Kumar S. Molecular evolution and phylogenetics: Oxford university press. 2000; 329 Pages, ISBN: 0-19-513584-9.
76. LI WH. Molecular evolution. Sinauer, Sunder-land, Massachusetts,  ISBN : 0878934634 , 487 Pages. 1997;
77. Newmaster S, Fazekas A, Steeves R, Janovec J. Testing candidate plant barcode regions in the Myristicaceae. Mol Ecol Resour. 2008;8:480-490. https://doi.org/10.1111/j.1471-8286.2007.02002.x
78. Steven GN, Subramanyam R. Testing plant barcoding in a sister species complex of pantropical Acacia (Mimosoideae, Fabaceae). Molecular Ecology Resources. 2009;9 Suppl s1:172-180. 10.1111/j.1755-0998.2009.02642.x
79. Barker N, Howis S, Nordenstam B, Källersjö M, Eldenäs P, Griffioen C, Linder H. Nuclear and chloroplast DNA-based phylogenies of Chrysanthemoides Tourn. ex Medik.(Calenduleae; Asteraceae) reveal extensive incongruence and generic paraphyly, but support the recognition of infraspecific taxa in C. monilifera. South African J Botany. 2009;75:560-572.
80. Pfanzelt S, Albach DC, von Hagen KB. Extremely low levels of chloroplast genome sequence variability in Astelia pumila (Asteliaceae, Asparagales). PeerJ. 2019;7:e6244.
81. Azimzade M, Amir R, Osare MH, Bihamta MR, Frotan M. Evaluation of genetic diversity of Iranian Cumin (Bunium persicum Boiss) of nuclear ribosomal DNA using ITS. J Gen Res Plant Breeding Pasture Forest. 2014;22:1-10.
82. Bahari Z, Shojaeiyan A, Rashidi Monfared S, Mirshekari A, Nasiri K, Amiriyan M. Investigation of Genetic Diversity among Some Iranian Dill (Anethum graveolens L.) Landraces, Using ISSR Markers. Plant Gen Resour-C J. 2015;2:11-22.
83. Sindhu A, Tehlan SK, Chaudhury A. Analysis of genetic diversity among medicinal therapist Trigonella foenum-graecum L. genotypes through RAPD and SSR markers. Acta. Physiol. Plant. 2017;39:100. 10.1007/s11738-017-2395-8
84. Dehdashtian Z, Wahabi M r, Fazilati M, Ghaedi K, Salamian A. Analysis of the Genetic Diversity of Astragalus Gossypinus Population in Isfahan. [Research]. Gen in the 3rd Millennium. 2011;9:2474-2467.
85. Raman K. Construction and analysis of protein–protein interaction networks. Automated Experimentation. 2010;2:2.
86. Dietz KJ, Wesemann C, Wegener M, Seidel T. Toward an integrated understanding of retrograde control of photosynthesis. Antioxidants & Redox Signaling. 2019;30:1186-1205.
87. Nelson N, Ben-Shem A. The complex architecture of oxygenic photosynthesis. Nature Reviews Molecular Cell Biology, 2004; 5: 971.
88. Barthet MM. Expression and Function of the Chloroplast-encoded Gene matK. Virginia Tech. Retrieved from http://hdl.handle.net/10919/26287. 2006
89. Barthet MM, Hilu KW. Expression of matK: functional and evolutionary implications. American J Botany. 2007;94:1402-1412.
90. Barthet MM, Hilu KW. Evaluating evolutionary constraint on the rapidly evolving gene matK using protein composition. J Mol Evol. 2008;66:85-97.
91. Duan RY, Xiang GH, Lin YX, Luo YC, Peng RM. The complete chloroplast genome of the invasive plant Senecio vulgaris L.(Asteraceae). Mitochondrial DNA Part B. 2019;4:1794-1795.
92. Li Y, GAO LM, Poudel RC, Li DZ, Forrest A. High universality of matK primers for barcoding gymnosperms. J of Sys and Evolution, 2011; 49: 169-175.
93. Staff N. MatK Gene Is A "Barcode" DNA For Plants. 2008.
94. Williams BR, Mitchell TC, Wood JR, Harris DJ, Scotland RW, Carine MA. Integrating DNA barcode data in a monographic study of Convolvulus. Taxon. 2014;63:1287-1306.
95. Soltis DE, Soltis PS. Choosing an approach and an appropriate gene for phylogenetic analysis Molecular systematics of plants II (pp. 1-42): Springer. 1998.
96. Zhai W, Duan X, Zhang R, Guo C, Li L, Xu G, Shan H, Kong H, Ren Y. Chloroplast genomic data provide new and robust insights into the phylogeny and evolution of the Ranunculaceae. Mol Phylogenet Evol. 2019;135:12-21.
97. Federici S, Galimberti A, Bartolucci F, Bruni I, De Mattia F, Cortis P, Labra M. DNA barcoding to analyse taxonomically complex groups in plants: the case of Thymus (Lamiaceae). Botanical J Linnean Society. 2013;171:687-699.
98. Mahadani P, Ghosh S K. DNA Barcoding: A tool for species identification from herbal juices. DNA Barcodes. 2013;1:35-38.
Journal of Medicinal plants and By-product
Volume 10, Issue 1
April 2021
Pages 19-35

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