Assesment of molecular diversity of internal transcribed spacer region in some lines and landrace of Persian clover (Trifolium resupinatum L.)
DOI:
https://doi.org/10.5219/960Keywords:
Persian clover, haplotype, genetic diversity, Ribosomal DNA, dN/dSAbstract
Clover which is an herbaceous, annual, and self-pollinated plant belongs to fabaceae family (legumes) and has become naturalized in Iran, Asia Minor and the Mediterranean eastern suburban countries. The aim of the present study is ITS molecular evaluation of the nuclear ribosomal genes of lines and landraces of Persian Clover. The sequences were aligned using ClustalW method and by MegAlign software and the dendrogram of different phylogenetic and matrix relationships between the sequences were drawn. The results showed little genetic diversity between the lines and the landrace. The conserved sequence of the analyzed gene in the Persian clover is 561 base. Totally, 740 loci (69 and 671 loci, respectively, with and without removal and addition), 9 Singletons, and 5 haplotypes were identified. The highest rate of transfer was observed in pyrimidine (%16.3). The numerical value of the ratio (dN/dS) was 0.86, and since it was less than 1, the pure selection on the studied gene happened. The lines and landraces were not separated based on their geographic locations. In general, the results indicated that the highest rate of the regional diversity belonged to the clover plants in Lorestan region. Moreover, ITS markers did not seem suitable enough for evaluating the intra- species genetic variation, but it was quite well- suited for inter-species or intergeneric evaluation.
Downloads
References
Abbasi, M. R. 2008. Genetic diversity of Persian clover (Trifolium resupinatum) gene pools in National Plant Gene Bank of Iran. Iranian Journal of Rangelands and Forests Plant Breeding and Genetic Research, vol. 16, no. 1, p. 37-49.
Abbasi, M. R., Mirakhorli, A., Mahdipur, A., Hasanzadeh, A., Kanani, R., Alitabar, R. A., Mokhatarpur, H., Safaei, H., Fathi, A., Khakizad, G. R., Nadali, F., Nakhaei, A., Kamaledin Abbasi, M., Dadfar, S., Hajgholizadeh, G., Taheriun, G. R., Safari, S., Hamzenejad, A., Abaduz, G. R., Zamanian, M., Jahanbani, F., Samani, M., Darkhal, H. 2012. Seed collection and centers of diversity of Trifolium genetic resources in Iran. Electronic Journal of crop Production, vol. 5, no. 4, p. 191-204. Abdelmigid, H. M., El-Sayed, A. 2016. Molecular phylogenetic implications in Brassica napus based on internal transcribed spacer sequences. J. Genet., vol. 95, no. 2, p. 447-451. https://doi.org/10.1007/s12041-016-0631-4
Ainouche, A.-K., Bayer, R. J. 1999. Phylogenetic relationships in Lupinus (Fabaceae: Papilionoideae) based on internal transcribed spacer sequences (ITS) of nuclear ribosomal DNA. American Journal of Botany, vol. 86, no. 4, p. 590-607. https://doi.org/10.2307/2656820 PMid:10205079
Baghaee Ravari, S., Falahati Rastegar, M., Jafarpour, B., Shokoohifar, F. 2007. The study of probable variation in ITS- rDNA region of Fusarium solani in potato and its correlation with pathogenicity and geographical origin in Razavi and Northern Khorasan Provinces. Journsl of Agrictural Science and Natural Resource, vol. 14, no. 3, p. 1-9.
Bazdar, M., Sadeghi, H. 2018. Antioxidant activity of Trifolium resupinatum L. exposed to different extracts from leaves, flowers and shoots of Prangos ferulacea. Spanish Journal of Agricultural Research, vol. 15, no. 4, p. 0303.
Brown, G. K., Clowes, C., Murphy, D. J., Ladiges, P. Y. 2010. Phylogenetic analysis based on nuclear DNA and morphology defines a clade of eastern Australian species of Acacia s. s. (section Juliflorae): the 'Acacia longifolia group'. Australian Systematic Botany, vol. 23, no. 3, p. 162-172. https://doi.org/10.1071/SB09037
Dasmeh, P., Serohijos, A. W., Kepp, K. P., Shakhnovich, E. I. 2014. The influence of selection for protein stability on dN/dS estimations. Genome biology and evolution, vol. 6, no. 10, p. 2956-2967. https://doi.org/10.1093/gbe/evu223 PMid:25355808
De Luca, D., Cennamo, P., Del Guacchio, E., Di Novella, R., Caputo, P. 2018. Conservation and genetic characterisation of common bean landraces from Cilento region (southern Italy): high differentiation in spite of low genetic diversity. Genetica, p. 1-16. https://doi.org/10.1007/s10709-017-9994-6
Degtjareva, J. V., Kljuykov, E. V., Samigulli, T. H., Valiejo-Roman, C. M., Pimenov, M. G. 2009. Molecular Appraisal of Bunium and Some related arid and sub-arid geophilic Apiaceae-Apioideae taxa of ancient Mediterranean. Botanical Journal of the Linnean Society, vol. 160, p. 149-170. https://doi.org/10.1111/j.1095-8339.2009.00970.x
Dellaporta, S. L., Wood, J., Hicks, J. B. 1983. A plant DNA minipreparation: version II. Plant Molecular Biology Reporter, vol. 1, no. 4, p. 19-21. https://doi.org/10.1007/BF02712670
Fazeli-Nasab, B., Naghavi, M. R., Mehrabi, A. A. 2013. Allelic Variation of Microsatellite Markers from Linkage Group A Genome in Wild Populations of Einkorn and Hexaploid Wheat. Agricultural Biotechnology, vol. 4, no. 1, p. 53-62. http://doi.org/10.13140/RG.2.1.1434.4164
Haidari, P., Mehrabi, A. A., Nasrollah Nejad Ghomi, A. A. 2014. Genetic Diversity of Balm (Melissa Officinalis L.) Landraces and Genetic Relationship Within and Between Them using ITS Markers. Journal of Crop Breeding, vol. 6, no. 13, p. 29-39.
Hall, T. A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT, p. 95-98, [London]: Information Retrieval Ltd., c1979-c2000.
Hussain, S., Verry, I., Jahufer, M., Williams, W. 2017. Cytological and Morphological Evaluation of Interspecific Hybrids between Trifolium repens and T. uniflorum. Crop Science, vol. 57, no. 5, p. 2617-2625. https://doi.org/10.2135/cropsci2017.05.0314
Chapman, C. J., Oldham, M. J. 2018. Reversed Clover, Trifolium resupinatum L. (Fabaceae), Confirmed in Canada. The Canadian Field-Naturalist, vol. 131, no. 4, p. 328-330. https://doi.org/10.22621/cfn.v131i4.1866
Ji, L., Liu, C., Zhang, L., Liu, A., Yu, J. 2017. Variation of rDNA internal transcribed spacer sequences in Rhizoctonia cerealis. Curr. Microbiol., vol. 74, no. 7, p. 877-884. https://doi.org/10.1007/s00284-017-1258-2 PMid:28474105
Jordan, B., Culbreath, A., Brock, J., Dutta, B. 2018. First Report of Myrothecium Leaf Spot Caused by Myrothecium roridum on Pepper in the United States. Plant Disease, vol. 102, no. 1, p. 246. https://doi.org/10.1094/PDIS-06-17-0918-PDN
Lala, S., Amri, A., Maxted, N. 2018. Towards the conservation of crop wild relative diversity in North Africa: checklist, prioritisation and inventory. Genetic Resources and Crop Evolution, vol. 65, no. 1, p. 113-124. https://doi.org/10.1007/s10722-017-0513-5
Lalramnghaki, H. C. Morphological and molecular characterization of entomopathogenic nematode, Heterorhabditis baujardi (Rhabditida, Heterorhabditidae) from Mizoram, northeastern India. Journal of Parasitic Diseases, p. 1-9.
Li, X., Xie, R., Lu, Z., Zhou, Z. 2010. The origin of cultivated citrus as inferred from internal transcribed spacer and chloroplast DNA sequence and amplified fragment length polymorphism fingerprints. Journal of the American Society for Horticultural Science, vol. 135, no. 4, p. 341-350.
McKain, M. R., Johnson, M. G., Uribe‐Convers, S., Eaton, D., Yang, Y. 2018. Practical considerations for plant phylogenomics. Appl. Plant Sci., vol. 6, no. 3, p. e1038. https://doi.org/10.1002/aps3.1038 PMid:29732268
Mirzaei, K., Mirzaghaderi, G. 2017. Genetic diversity analysis of Iranian Nigella sativa L. landraces using SCoT markers and evaluation of adjusted polymorphism information content. Plant Genetic Resources, vol. 15, no. 1, p. 64-71. https://doi.org/10.1017/S1479262115000386
Murphy, D. J., Miller, J. T., Bayer, R. J., Ladiges, P. Y. 2003. Molecular phylogeny of Acacia subgenus Phyllodineae (Mimosoideae: Leguminosae) based on DNA sequences of the internal transcribed spacer region. Australian Systematic Botany, vol. 16, no. 1, p. 19-26. https://doi.org/10.1071/SB01042
Ndjiondjop, M. N., Semagn, K., Sow, M., Manneh, B., Gouda, A. C., Kpeki, S. B., Pegalepo, E., Wambugu, P., Sié, M., Warburton, M. L. 2018. Assessment of Genetic Variation and Population Structure of Diverse Rice Genotypes Adapted to Lowland and Upland Ecologies in Africa Using SNPs. Front. Plant Sci., vol. 9, no., p. 1-13.
Ninou, E. G., Mylonas, I. G., Tsivelikas, A. L., Ralli, P. E. 2017. Phenotypic diversity of Greek dill (Anethum graveolens L.) landraces. Acta Agriculturae Scandinavica, Section B-Soil & Plant Science, vol. 67, no. 4, p. 318-325.
Petrova, G., Petrov, S., Delcheva, M., Bancheva, S. 2017. Genetic diversity and conservation of Bulgarian endemic Verbascum tzar-borisii (Scrophulariaceae), BioOne, p. 307-316,
Rauf, M. A., Meetani, M. A., Khaleel, A., Ahmed, A. 2010. Photocatalytic degradation of methylene blue using a mixed catalyst and product analysis by LC/MS. Chemical Engineering Journal, vol. 157, no. 2-3, p. 373-378. https://doi.org/10.1016/j.cej.2009.11.017
Robinson, J., Harris, S., Juniper, B. 2001. Taxonomy of the genus Malus Mill.(Rosaceae) with emphasis on the cultivated apple, Malus domestica Borkh. Plant Systematics and Evolution, vol. 226, no. 1-2, p. 35-58. https://doi.org/10.1007/s006060170072
Roma-Marzio, F., D'Antraccoli, M., Astuti, G., Maccioni, S., Amadei, L., Peruzzi, L. 2018. Typification of the names in Trifolium described by Gaetano Savi. Taxon, vol. 67, no. 2, p. 411-421. https://doi.org/10.12705/672.10
Sani, S. G. A. S., Chang, P. L., Zubair, A., Carrasquilla-Garcia, N., Cordeiro, M., Penmetsa, R. V., Munis, M. F. H., Nuzhdin, S. V., Cook, D. R., von Wettberg, E. J. 2018. Genetic Diversity, Population Structure, and Genetic Correlation with Climatic Variation in Chickpea (Cicer arietinum) Landraces from Pakistan. The Plant Genome, vol. 11, no. 1, p. 1-11. https://doi.org/10.3835/plantgenome2017.08.0067 PMid:29505627
Shahverdi, M. 2014. Evaluation of final forage yield lines of Persian clover. Lorestan Natural resources and Agriculture Research Center, (Final report of the research project; 059-03-87089 Code), p. 1-36.
Singh, N. K., Patel, D. B., Chaudhari, S. R., Morad, B. G., Rabari, S. M., Chattopadhyay, A., Tetarwal, M. L. 2018. Morphometric and internally transcribed spacer gene sequence-based characterization of Alternaria burnsii. Curr. Sci., vol. 114, no. 9, p. 1927-1933.
Tamura, K., Nei, M. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution, vol. 10, no. 3, p. 512-526. PMid:8336541
Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., Kumar, S. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, vol. 28, no. 10, p. 2731-2739. https://doi.org/10.1093/molbev/msr121 PMid:21546353
Thormann, I., Reeves, P., Thumm, S., Reilley, A., Engels, J. M., Biradar, C. M., Lohwasser, U., Börner, A., Pillen, K., Richards, C. 2017. Genotypic and phenotypic changes in wild barley (Hordeum vulgare subsp. spontaneum) during a period of climate change in Jordan. Genetic Resources and Crop Evolution, vol. 64, no. 6, p. 1295-1312. https://doi.org/10.1007/s10722-016-0437-5
Úrbez-Torres, J., Castro-Medina, F., Mohali, S., Gubler, W. 2016. Botryosphaeriaceae species associated with cankers and dieback symptoms of Acacia mangium and Pinus caribaea var. hondurensis in Venezuela. Plant Disease, vol. 100, no. 12, p. 2455-2464. https://doi.org/10.1094/PDIS-05-16-0612-RE
Varela, E., Lima, J., Galdino, A., Pinto, L. d. S., Bezerra, W., Nunes, E., Alves, M., Grangeiro, T. 2004. Relationships in subtribe Diocleinae (Leguminosae; Papilionoideae) inferred from transcribed spacer sequences from nuclear ribosomal DNA. Phytochemistry, vol. 65, no. 1, p. 59-69. https://doi.org/10.1016/j.phytochem.2003.08.005 PMid:14697271
Varela, R. O., Albornoz, P. L. 2013. Morpho-anatomy, imbibition, viability and germination of the seed of Anadenanthera colubrina var. cebil (Fabaceae). Rev. Biol. Trop., vol. 61, no. 3, p. 1109-1118. https://doi.org/10.15517/rbt.v61i3.11907 PMid:24027911
Vivodík, M., Saadaoui, E., Balážová, Ž., Gálová, Z., Petrovičová, L. 2018. Genetic diversity and population structure in tunisian castor genotypes (Ricinus communis L.) Detected using scot markers. Potravinarstvo Slovak Journal of Food Sciences, vol. 12, no. 1, p. 143-149. https://doi.org/10.5219/873
Wu, C.-T., Hsieh, C.-C., Lin, W.-C., Tang, C.-Y., Yang, C.-H., Huang, Y.-C., Ko, Y.-J. 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, vol. 21, no. 4, p. 356-362. https://doi.org/10.1016/j.jfda.2013.08.002
Yadav, P., Koul, K., Srivastava, N., Mendki, M., Bhagyawant, S. 2017. ITS-PCR sequencing approach deciphers molecular phylogeny in chickpea. Plant Biosystems-An International Journal Dealing with all Aspects of Plant Biology, vol. 151, no. 3, p. 429-435. https://doi.org/10.1080/11263504.2016.1179694
Yousef, E. A., Mueller, T., Börner, A., Schmid, K. J. 2018. Comparative analysis of genetic diversity and differentiation of cauliflower (Brassica oleracea var. botrytis) accessions from two ex situ genebanks. PLoS One, vol. 13, no. 2, p. e0192062. https://doi.org/10.1371/journal.pone.0192062 PMid:29420661
Yousefi, S., Saeidi, H., Assadi, M. 2018. Genetic Diversity Analysis of Red Clover (Trifolium pratense L.) in Iran Using Sequence Related Amplified Polymorphism (SRAP) Markers. Journal of Agricultural Science and Technology, vol. 20, no. 2, p. 373-386.
Downloads
Published
How to Cite
Issue
Section
License
Authors who publish with this journal agree to the following terms:- Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.
- Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.
- Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).
