Volume 11, Issue 29 (3-2019)                   jcb 2019, 11(29): 29-39 | Back to browse issues page

XML Persian Abstract Print

Download citation:
BibTeX | RIS | EndNote | Medlars | ProCite | Reference Manager | RefWorks
Send citation to:

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. jcb. 2019; 11 (29) :29-39
URL: http://jcb.sanru.ac.ir/article-1-969-en.html
Research Department of Agronomy and Plant Breeding, Agricultural Research Institute, University of Zabol, Zabol, Iran
Abstract:   (562 Views)
Lettuce is belong to the Cichorium family with leaf consumption, Annual cold weather plants and rich in minerals, vitamins and nutrients. The aim of the present study was to evaluate the genetic diversity of 15 varieties and lettuce populations using the ITS area. Sequence quality was evaluated using Chromas 2.1.1 software, aligned by MegAlign 5 software and then similarity matrix and dendrogram of phylogenic relationships of Lettuce sequences were conducted using Mega 6 software. Also, a comparison was conducted among the lettuce were used in this research and other plants of the Asteraceae genus family (presented on NCBI site). The numerical value of the ratio (dN/dS) was 0.015, which indicates a pure selection in the examined gene and has not caused any key changes. Cluster analysis split the different genotypes of lettuce into 3 groups and could not differentiate by geographical location but it could separate the lettuce of this research and other plants from different species of the Asteraceae family related by NCBI. Therefore, it can be concluded that ITS can be a suitable tool for genetic evaluations among genus and among species. The inability of ITS marker to separate the intra-species of populations it could be because dN/dS was less than and a small number of deletion and insertion sites (376 out of 1551 positions) indicating low variation between different genotypes and populations. Considering that the Initial origin of the plants is belong to the centers that are most diverse and because varzaneh Lettuce populations of Isfahan have the most varieties, as a result, it is necessary to pay more attention to the Varzaneh region of Isfahan to collection of lettuce germplasms for breeding programs.
Full-Text [PDF 1128 kb]   (302 Downloads)    
Type of Study: Research | Subject: بيوتكنولوژي گياهي
Received: 2018/05/21 | Revised: 2019/05/14 | Accepted: 2018/08/25 | Published: 2019/05/8

1. Aćamović-Đoković, G., R. Pavlović, J. Mladenović and M. Đurić. 2011. Vitamin C content of different types of lettuce varieties. Acta Agriculturae Serbica, 16(32): 83-89.
2. Adams, M.D., J.M. Kelley, J.D. Gocayne, M. Dubnick, M.H. Polymeropoulos, H. Xiao, C.R. Merril, A. Wu, B. Olde and R.F. Moreno. 1991. Complementary DNA sequencing: expressed sequence tags and human genome project. Science, 252: 1651-1656. [DOI:10.1126/science.2047873]
3. Adlard, R.D., S.C. Barker, D. Blair and T.H. Cribb. 1993. Comparison of the second internal transcribed spacer (ribosomal DNA) from populations and species of Fasciolidae (Digenea). International journal for parasitology, 23(3): 423-425. [DOI:10.1016/0020-7519(93)90022-Q]
4. Azimzade, M., R. Amir, M.H. Osare, M.R. Bihamta and M. Frotan. 2014. Evaluation of genetic diversity of Iranian Cumin (Bunium persicum Boiss) of nuclear ribosomal DNA using ITS. The Journal of Genetic Research and plant breeding pasture and forest, 22(1): 1-10.
5. Bahari, Z., A. Shojaeiyan, S. Rashidi Monfared, A. Mirshekari, K. Nasiri and M. Amiriyan. 2015. Investigation of Genetic Diversity among Some Iranian Dill (Anethum graveolens L.) Landraces, Using ISSR Markers. Journal of Plant Genetic Research, 2(1): 11-22. [DOI:10.29252/pgr.2.1.11]
6. Balasaravanan, T., P. Chezhian, R. Kamalakannan, R. Yasodha, M. Varghese, K. Gurumurthi and M. Ghosh. 2006. Identification of species-diagnostic ISSR markers for six Eucalyptus species. Silvae Genetica, 55(3): 119-122. [DOI:10.1515/sg-2006-0017]
7. Bartha, C. 2012. Comparative Study of Physiological and Molecular Manifestations of Salt Stress Tolerance in Different Intraspecific Varieties of Lactuca Sativa L. Biology PH. D. School, Babes-Bolyai" University, Faculty of Biology and Geology, 100 Pages
8. Blaxter, M. 2003. Molecular systematics: counting angels with DNA. Nature, 421: 122-124. [DOI:10.1038/421122a]
9. Cubeta, M.A., R. Vilgalys and D. Gonzalez. 1996. Molecular analysis of ribosomal RNA genes in Rhizoctonia fungi, , Rhizoctonia Species: Taxonomy, Molecular Biology, Ecology, Pathology and Disease Control. Springer, 81-86. [DOI:10.1007/978-94-017-2901-7_7]
10. Cunnington, J.H., A.C. Lawrie and I.G. Pascoe. 2004. Unexpected ribosomal DNA internal transcribed spacer sequence variation within Erysiphe aquilegiae sensu lato. Fungal Diversity, 161-10.
11. De Vries, I. 1997. Origin and domestication of Lactuca sativa L. Genetic resources and crop evolution, 44(2): 165-174. [DOI:10.1023/A:1008611200727]
12. Dehdashtian, Z., M.R. Wahabi, M. Fazilati, K. Ghaedi and A. Salamian. 2011. Analysis of the Genetic Diversity of Astragalus Gossypinus Population in Isfahan. Genetics in the 3rd Millennium, 9(3): 2474-2467.
13. Dellaporta, S.L., J. Wood and J.B. Hicks. 1983. A plant DNA minipreparation: version II. Plant molecular biology reporter, 1(4): 19-21. DOI: 10.1007/BF02712670 [DOI:10.1007/BF02712670]
14. Druzhinina, I,S., A,G. Kopchinskiy, M. Komoń, J. Bissett, G. Szakacs and C.P. Kubicek. 2005. An oligonucleotide barcode for species identification in Trichoderma and Hypocrea. Fungal Genetics and Biology, 42(10): 813-828. [DOI:10.1016/j.fgb.2005.06.007]
15. Feliner, G.N., and J.A. Rosselló. 2007. Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants. Mol Phylogenet Evol, 44(2): 911-919. [DOI:10.1016/j.ympev.2007.01.013]
16. Forni, D., R. Cagliani, U. Pozzoli, M. Colleoni, S. Riva, M. Biasin, G. Filippi, L. De Gioia, F. Gnudi and G.P. Comi. 2013. A 175 million year history of T cell regulatory molecules reveals widespread selection, with adaptive evolution of disease alleles. Immunity, 38(6): 1129-1141. [DOI:10.1016/j.immuni.2013.04.008]
17. Fullerton, S.M., A. Bernardo Carvalho and A.G. Clark. 2001. Local rates of recombination are positively correlated with GC content in the human genome. Molecular biology and evolution, 18(6): 1139-1142. https://doi.org/10.1093/oxfordjournals.molbev.a003886 [DOI:10.1093/oxfordjournals.molbev, 003886]
18. Funk, V.A., R.J. Ba, R. Chan, L. Watson, B. Gemeinholzer, E. Schilling, J.L. Panero, B.G. Baldwin, N. Garcia-Jacas and A. Susanna. Year. Published. B555 343 Everywhere but Antarctica: Using a supertree to understand the diversity and distribution of the Compositae, p. 343. In, Plant Diversity and Complexity Patterns: Local, Regional and Global Dimensions: Proceedings of an International Symposium Held at the Royal Danish Academy of Sciences and Letters in Copenhagen, Denmark, May, 2003, 2005. Kgl. Danske Videnskabernes Selskab, 25-28 pp.
19. Gao, T., H. Yao, J. Song, C. Liu, Y. Zhu, X. Ma, X. Pang, H. Xu and S. Chen. 2010. Identification of medicinal plants in the family Fabaceae using a potential DNA barcode ITS2. J Ethnopharmacol, 130(1): 116-121. 10.1016/j.jep.2010.04.026 [DOI:10.1016/j.jep.2010.04.026]
20. Garcia, S., A. Kovařík, A.R. Leitch and T. Garnatje. 2017. Cytogenetic features of rRNA genes across land plants: analysis of the Plant rDNA database. The Plant Journal, 89(5): 1020-1030. [DOI:10.1111/tpj.13442]
21. Goka, K., J. Yokoyama, Y. Une, T. Kuroki, K. Suzuki, M. Nakahara, A. Kobayashi, S. Inaba, T. Mizutani and A. D. Hyatt. 2009. Amphibian chytridiomycosis in Japan: distribution, haplotypes and possible route of entry into Japan. Mol Ecol, 18(23): 4757-4774. [DOI:10.1111/j.1365-294X.2009.04384.x]
22. Gültepe, M., U. Uzuner, K. Coşkuncelebi, A.O. Beldüz and S. Terzioğlu. 2010. Internal transcribed spacer (ITS) polymorphism in the wild Primula (Primulaceae) taxa of Turkey. Turkish Journal of Botany, 34(3): 147-157.
23. Haidari, P., A.A. Mehrabi and A.A. Nasrollah Nejad Ghomi. 2014. Genetic Diversity of Balm (Melissa Officinalis L.) Landraces and Genetic Relationship Within and Between Them using ITS Markers. Journal of Crop Breeding, 6(13): 29-39.
24. Hall, T.A. Year. Published. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT, pp. 95-98. In, Nucleic acids symposium series, 1999. [London]: Information Retrieval Ltd., c1979-c2000.
25. Hebert, P.D., A. Cywinska and S.L. Ball. 2003. Biological identifications through DNA barcodes. Proceedings of the Royal Society of London B: Biological Sciences, 270: 313-321. [DOI:10.1098/rspb.2002.2218]
26. Hebert, P.D., S. Ratnasingham and J.R. de Waard. 2003. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society of London B: Biological Sciences, 270: S96-S99. [DOI:10.1098/rsbl.2003.0025]
27. Koopman, W.J., E. Guetta, C.C. vandeWiel, B. Vosman and R.G. van den Berg. 1998. Phylogenetic relationships among Lactuca (Asteraceae) species and related genera based on ITS-1 DNA sequences. American Journal of Botany, 85(11): 1517-1530. [DOI:10.2307/2446479]
28. Lindqvist, K. 1960. Cytogenetic studies in the serriola group of Lactuca. Hereditas. 46(1-2): 75-151. [DOI:10.1111/j.1601-5223.1960.tb03080.x]
29. Liu, F., Y. Hu, Q. Wang, H.M. Li, G.F. Gao, C.H. Liu and B. Zhu. 2014. Comparative genomic analysis of Mycobacterium tuberculosis clinical isolates. BMC Genomics, 15(1): 469. [DOI:10.1186/1471-2164-15-469]
30. Mehta, D. 2012. An Insight on Traditional System of Medicine in Pharmaceutical Industry, with Pharmacological Profile Reporting on Devadaru and Indian Rhubarb: Vital to Pharmaceutical Research Endeavor. Ethnopharmacology, 2012(4): 200-211.
31. Mikel, M.A. 2007. Genealogy of contemporary North American lettuce. HortScience, 42(3): 489-493. [DOI:10.21273/HORTSCI.42.3.489]
32. Mousavi, S., R. Choukan, N. Sepahvand and A. Ghanbari. 2014. Genetic Diversity of Iranian Lettuce Genotypes Based on RAPD Markers. Seed and Plant Improvment Journal, 30(1): 115-131.
33. Pang, X., L. Shi, J. Song, X. Chen and S. Chen. 2013. Use of the potential DNA barcode ITS2 to identify herbal materials. J Nat Med, 67(3): 571-575. [DOI:10.1007/s11418-012-0715-2]
34. Park, J.H., Y.H. Kim, C.S. Ham, S.E. Shin, H.J. Lee, K.S. Ko, J. Choi, G.H. Son and S.H. Park. 2018. Molecular identification of forensically important calliphoridae and sarcophagidae species using ITS2 nucleotide sequences. Forensic Sci Int, 10: 28-41.1016/j.forsciint.2017.12.017
35. Parkin, E.J. and R.K. Butlin. 2004. Within-and between-individual sequence variation among ITS1 copies in the meadow grasshopper Chorthippus parallelus indicates frequent intrachromosomal gene conversion. Molecular biology and evolution, 21(8): 1595-1601. [DOI:10.1093/molbev/msh163]
36. Patras, A., C.E. Luchian, M. Niculaua and V. Stoleru. 2013. Effects of some Abiotic Factors on Brassica Oleracea Var. Capitata Sprouts. Bulletin of the University of Agricultural Sciences & Veterinary Medicine Cluj-Napoca. Horticulture, 70(1): 172-179.
37. Perrier, X. and J.P. Jacquemoud-Collet. 2006. DARwin software http://darwin.cirad.fr/darwin computer program, version By Perrier, X. and J. P. Jacquemoud-Collet,
38. Rodriguez-Lanetty, M. 2003. Evolving lineages of Symbiodinium-like dinoflagellates based on ITS1 rDNA. Mol Phylogenet Evol, 28(1): 152-168. https://doi.org/10.1016/S1055-7903(03)00033-2 [DOI:10.1016/S1055-7903(03)00033-2.]
39. Schultz, J. and M. Wolf. 2009. ITS2 sequence-structure analysis in phylogenetics: a how-to manual for molecular systematics. Mol Phylogenet Evol, 52(2): 520-523. [DOI:10.1016/j.ympev.2009.01.008]
40. Silva, S.R., R. Gibson, L. Adamec, Y. Domínguez and V.F. Miranda. 2018. Molecular phylogeny of bladderworts: A wide approach of Utricularia (Lentibulariaceae) species relationships based on six plastidial and nuclear DNA sequences. Mol Phylogenet Evol, 118: 244-264. [DOI:10.1016/j.ympev.2017.10.010]
41. Sindhu, A., S.K. Tehlan and A. Chaudhury. 2017. Analysis of genetic diversity among medicinal therapist Trigonella foenum-graecum L. genotypes through RAPD and SSR markers. Acta Physiologiae Plantarum, 39(4): 100. 10.1007/s11738-017-2395-8. [DOI:10.1007/s11738-017-2395-8]
42. Sun, Z. and S. Chen. 2013. Identification of cortex herbs using the DNA barcode nrITS2. J Nat Med, 67(2): 296-302. [DOI:10.1007/s11418-012-0681-8]
43. Tamura, K., G. Stecher, D. Peterson, A. Filipski and S. Kumar. 2013. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Molecular biology and evolution, 30: 2725-2729. [DOI:10.1093/molbev/mst197]
44. Uwai, S., N. Yotsukura, Y. Serisawa, D. Muraoka, M. Hiraoka and K. Kogame. 2006. Intraspecific genetic diversity of Undaria pinnatifida in Japan, based on the mitochondrial cox3 gene and the ITS1 of nrDNA. Hydrobiologia, 553(1): 345-356. [DOI:10.1007/s10750-005-0883-0]
45. Varela, E., J. Lima, A. Galdino, L.D.S. Pinto, W. Bezerra, E. Nunes, M. Alves and T. Grangeiro. 2004. Relationships in subtribe Diocleinae (Leguminosae; Papilionoideae) inferred from transcribed spacer sequences from nuclear ribosomal DNA. Phytochemistry, 65(1): 59-69. doi: 10.1016/j.phytochem.2003.08.005. [DOI:10.1016/j.phytochem.2003.08.005]
46. White, T.J., T. Bruns, S. Lee and J. Taylor. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. PCR protocols: a guide to methods and applications, 18(1): 315-322. [DOI:10.1016/B978-0-12-372180-8.50042-1]
47. Wu, C.T., C.C. Hsieh, W.C. Lin, C.Y. Tang, C.H. Yang, Y.C. Huang and Y.J. Ko. 2013. Internal transcribed spacer sequence-based identification and phylogenic relationship of I-Tiao-Gung originating from Flemingia and Glycine (Leguminosae) in Taiwan. Journal of food and drug analysis, 21(4): 356-362. doi: 10.1016/j.jfda.2013.08.002. [DOI:10.1016/j.jfda.2013.08.002]
48. Zarea, M., B. Fakheri and S. Farokhzadeh. 2016. Effect of Salinity on Morphological Characteristics of Lettuce Genotypes (Lactuca Sativa L.) Journal of Horticultural Science, 30(3): 457-468 (In Farsi with Abstract English).

Add your comments about this article : Your username or Email:

Send email to the article author

© 2020 All Rights Reserved | Journal of Crop Breeding

Designed & Developed by : Yektaweb