Inter Simple Sequence Repeat markers for analysis of molecular diversity and genetic structure of eighteen Dendrobium cultivars in Sri Lanka
DOI:
https://doi.org/10.31686/ijier.vol6.iss3.975Keywords:
Dendrobium, Genetic diversity, ISSR markers, PolymorphismAbstract
The genus Dendrobium is one of the largest genera in the family Orchidaceae having more than thousand species over the world with diverse morphological characters. Dendrobium is a popular ornamental plant with complex genetic background which emphasize on the species identification at molecular level. The present study was aimed to identify Inter-Simple Sequence Repeat (ISSR) markers capable of detecting genetic polymorphism to characterize 18 hybrid, commercially available Dendrobium cultivars. Genomic DNA of each cultivar was extracted using CTAB method. A total of 17 different ISSR primers were evaluated. Only the reproducible bands were scored and number of different alleles (Na), number of effective alleles (Ne), Shannon’s Information Index (I), Expected heterozygosity (He), Unbiased expected heterozygosity (UHe), polymorphic percentage and polymorphic information content (PIC) of each primer were calculated. The highest Shannon’s Information Index (0.537±0.08) was recorded by the primer UBC 826 while the highest polymorphic information content (PIC) was generated by primer UBC 807. The PIC values of the primers were ranged from 0.0068 to 0.451, indicating that primers are moderately informative. In total, 631 bands representing 120 loci were amplified showing 85.71% - 100% polymorphism. The genetic similarities between individuals were compiled in the Nei’s genetic identity matrix in order to construct the UPGMA dendrogram. Principle component analysis (PCA) and clustering analysis were done to divide different cultivars into groups. The analysis revealed the presence of four major clusters and two minor clusters among the cultivars. The study suggested that the ISSR markers originated from eight primers 12, 155, UBC 807, UBC 812, UBC 826, UBC 835, UBC 841 and UBC 842 can be used in the detection of molecular variation among cultivars in the genus Dendrobium.
References
Adams, P.B., Burke, J.M., Lawson, S.D., 2006. Systematic analysis of Dendrobium Swartz section Dendrocoryne in the Australian region. Plant Syst. Evol. 260 (1), 65-80. DOI: https://doi.org/10.1007/s00606-005-0406-5
Alikhani, L., Rahmani, M., Shabanian, N., Badakhshan, H., Khadivi-Khub, A., 2014. Genetic variability and structure of Quercus brantii assessed by ISSR, IRAP and SCoT markers. Gene, 552 (1), 176-83. DOI: https://doi.org/10.1016/j.gene.2014.09.034
Aryanegad, P., Farshadfar, E., Safari, H., Shirvani, H., 2013. Application of ISSR molecular markers in genetic diversity of three Trifolium species. Journal of Biodiversity and Environmental Sciences, 3 (12), 78-84.
Blair, M.W., Pedraza, F., Buendia, H., Gaitan-Solis, E., Beeb, S., Tohme, J., 2003. Development of a genome-wide anchored microsatellite map for common bean (Phaseolus vulgaris L.), Theoritical and Applied Genetics, 107, 1362-1374. DOI: https://doi.org/10.1007/s00122-003-1398-6
Bornet, B., Branched, M., 2001. Non-anchored Inter Simple Sequence Repeat (ISSR) markers: reproducible and specific tools for genomic finger printing. Plant Molecular Biology Reporter, 19, 109-215. DOI: https://doi.org/10.1007/BF02772892
Bosten, D., White, R.L., Skolnick, M., Davis, R.W., 1980. Construction of a genetic linkage map in man using restriction fragment length polymorphism. The American Journal of Human Genetics, 32, 314-331.
Burke J.M., Bayly M.J., Peter B., Adams P.B., Ladiges P.Y., 2008. Molecular phylogenetic analysis of Dendrobium (Orchidaceae), with emphasis on the Australian section Dendrocoryne, and implications for genetic classification. Aust. Syst. Bot., 21 (1), 1-4.Galvan, M.Z., Bornet, B., Balatti, P.A., Balachandra, M., 2003. Inter Simple Sequence Repeat (ISSR) markers as a tool for the assessment of both genetic diversity and gene pool origin in common bean (Phaseolus vulgaris L.) Euphytica 132: 297-301. DOI: https://doi.org/10.1071/SB07038
Jones, C.J., Edwards, K.J., Castaglione, S.,Winfield, M.O., Sale, F., Van de Wile, C., Bredemeijer, G., Buiatti, M., Maestri, E., Malcevshi, A., Marmiroli, N., Aert, R., Volckaert, G., Rueda,J., Karp, A., Kresovich, S., Bhat, K.V., Ayada, W.G. and Hodgkin, T., 1997. Molecular tools in plant genetic resources conservation: a guide to the technologies. IPGRI technical bulletin no 2. International Plant Genetic Resource Institute, Rome, Italy.
Kesari, V., Madurai, S.V., Parida, A., Rangan, L. 2010. Molecular marker-based characterization in candidate plus trees of Pongamia pinnata, a potential biodiesel legume. AoB Plants, 17 (3), 342-349. DOI: https://doi.org/10.1093/aobpla/plq017
Leitch, I.J., Kahandawala, I., Suda, J., Hanson, L., Ingrouille, M.J., Chase, M.W., and Fay, M.F., 2009. Genome size diversity in orchids: consequences and evolution. Annals of Botany, 104, 469-481. DOI: https://doi.org/10.1093/aob/mcp003
Lentner, M., Bishop, T., 1986. Experimental Design and Analysis. Valley Book Company, Blacksburg, VA.
Liu, J.J., Ekramoddoullah, A.K.M., Hunt, R., Zamani, A., 2006. Identification and characterization of RAPD markers linked to a major gene (Cr2) for resistance to Cronartium ribicola (Fish) in Pinus monticola (D.Don). Phytopathology, 96, 395-399. DOI: https://doi.org/10.1094/PHYTO-96-0395
Nei, M., 1972. Genetic distance between populations. American Naturalist, 106, 282-292. DOI: https://doi.org/10.1086/282771
Primrose, S., Woolfe, M., Rollinson, S., 2010. Food forensics: methods for determing the authenticity of foodstuffs. Trends Food Sci. Tech., 21,582-590. DOI: https://doi.org/10.1016/j.tifs.2010.09.006
Rajesh, P.N., Sant, V.J., Gupta, V.S., Muehlbauer, F.J., Ranjekar, P.K., 2002. Genetic relationships among annual and perennial wild species of Cicer using inter simple sequence repeat (ISSR) polymorphism. Euphytica 129, 15-23. DOI: https://doi.org/10.1023/A:1021567821141
Ramanatha Roa, V., Hodgkin, T., 2002. Genetic diversity and conservation and utilization of plant genetic resources. Plant Cell Tissue Org. 68, 1-19. DOI: https://doi.org/10.1023/A:1013359015812
Toth, G., Gaspari, Z., Jurka, J., 2000. Microsatellites in different eukaryotic genomes: survey and analysis. Genome Research, 10, 967-981. DOI: https://doi.org/10.1101/gr.10.7.967
Zietkiewicz, E., Rafallski, A., Labuda, D., 1994. Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification, Genomics 20, 176-183. DOI: https://doi.org/10.1006/geno.1994.1151
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