Genetic similarity among Dendrobium species from Indonesia using RAPD markers

##plugins.themes.bootstrap3.article.sidebar##

PDF
DOI https://doi.org/10.13057/biodiv/d240945
Issue
Vol. 24 No. 9 (2023)
Section
Articles
Creative Commons License

This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.

##plugins.themes.bootstrap3.article.main##

SRI HARTATI ♥
Department of Agrotechnology, Faculty of Agriculture, Universitas Sebelas Maret. Jl. Ir. Sutami 36A Surakarta 57 126, Central Java, Indonesia
SAMANHUDI
Department of Agrotechnology, Faculty of Agriculture, Universitas Sebelas Maret. Jl. Ir. Sutami 36A Surakarta 57 126, Central Java, Indonesia
ONGKO CAHYONO
Department of Soil Science, Faculty of Agriculture, Universitas Sebelas Maret. Jl. Ir. Sutami 36A Surakarta 57 126, Central Java, Indonesia

Abstract

Abstract. Hartati S, Samanhudi, Cahyono O. 2023. Genetic similarity among Dendrobium species from Indonesia using RAPD markers. Biodiversitas 24: 5015-5021. Dendrobium genus orchids are one of the most popular commodities in the world due to their diverse range of flower sizes, shapes, and colors. To enhance plant breeding programs and genetic resources, it is necessary to obtain information on genetic similarity between orchids of the Dendrobium genus through molecular analysis techniques. Therefore, this study aimed to assess the genetic similarity among five Dendrobium species using molecular markers, specifically RAPD. The plant material used was obtained from five species of the Dendrobium spp, namely (i) Dendrobium mirbelianum; (ii) Dendrobium lamellatum, (iii) Dendrobium secundum, (iv) Dendrobium bracteosum, and (v) Dendrobium purpureum. The analysis was carried out to determine the genetic diversity of the Dendrobium orchids using RAPD markers. A total of five RAPD primers were used for amplification, namely OPD 8, OPA 7, OPA 13, OPB 12, and OPB 18. The scoring data were analyzed using NTSYS-pc (Numerical Taxonomy and Multivariate Analysis System) version 2.02 which produced data in the form of cluster dendrograms. The dendrogram that was constructed by Unweighted Pair Group Method Using Arithmetic Average (UPGMA) classified the five Dendrobium species into two main clusters. The results showed that there were two clusters, namely Cluster A consisting of D. mirbelianum, D. lamellatum, and D. secundum while Cluster B consisted of D. bracteosum and D. purpureum. Furthermore, the polymorphism of the five RAPD primers was very high, ranging from 91.6 to 100%, measuring 250-1900 bp. The coefficient of genetic similarity analyzed using the five RAPD primers ranged from 0.24 to 0.77. The species D. mirbelianum and D. lamellatum had a high coefficient of genetic similarity. Which can be discovered through parental selection in breeding program.

##plugins.themes.bootstrap3.article.details##

References
Cheng J, Dang PP, Zhao Z, Yuan LC, Zhou ZH, Wolf D, Luo YB. 2019. An assessment of the Chinese medicinal Dendrobium industry: Supply, demand and sustainability. J. Ethnopharmacology 229(2): 81–88. DOI: 10.1016/j.jep.2018.09.001.
Hartati S, Muliawati ES, Pardono, Cahyono O, Yuliyanto P. 2019. Morphological characterization of Coelogyne spp for germplasm conservation of orchids. Rev Ceres 66(4): 265–270. DOI: 10.1590/0034-737X201966040004
Lopes MS, El-Basyoni I, Baenziger PS, Singh S, Royo C, Ozbek K, Aktas H, Ozer E, Ozdemir F, Manickavelu A, Ban T, Vikram P. 2015. Exploiting genetic diversity from landraces in wheat breeding for adaptation to climate change. J. Experimental Botany 66(12): 3477–3486. DOI: 10.1093/jxb/erv122
Khor SP, Yeow LC, Poobathy R, Zakaria R, Chew BL, Subramaniam S. 2020. Droplet-vitrification of Aranda Broga Blue orchid: Role of ascorbic acid on the antioxidant system and genetic fidelity assessments via RAPD and SCoT markers. Biotechnol Reports 26: e00448. DOI: 10.1016/j.btre.2020.e00448.
Duangrath J, Sumontip B. 2020. The effects of vitrification method on the seed survival and genetic stability of Rhynchostylis gigantea (Lindl.) Ridl. Asia - Pacific Journal of Science and Technology 25(3): 1–9. DOI: 10.14456/apst.2020.25
Choopeng S, Te-chato S, Khawnium T. 2019. The use of RAPD marker for verification of Dendrobium hybrid, D. santana x D. friedericksianum orchid. Int J Agric Technol 15(3): 399–408.
Borah R, Atanu B, Satyawada RR, Vineet K, Pradeep S, Krishna U, Hiranjit C. 2021. Genetic diversity and population structure assessment using molecular markers and SPAR approach in Illicium griffithii, a medicinally important endangered species of Northeast India. J Genet Eng Biotechnol 19(1). DOI: 10.1186/s43141-021-00211-5.
Manners V, Kumaria S, Tandon P. 2013. SPAR methods revealed high genetic diversity within populations and high gene fl ow of Vanda coerulea Griff ex Lindl ( Blue Vanda ), an endangered orchid species. Gene 519(1): 91–97. DOI: 10.1016/j.gene.2013.01.037.
Permatasari F, Mercuriani IS, Yulianti E. 2018. Genetic similarity analysis of Rhynchostylis retusa (L.) Blume orchids using OPA 15 and OPA 03 RAPD marker. AIP Conf Proc. DOI: 10.1063/1.5062755.
Tikendra L, Koijam AS, Nongdam P. 2019. Molecular markers based genetic fidelity assessment of micropropagated Dendrobium chrysotoxum Lindl. Meta Gene 20: 100562. DOI: 10.1016/j.mgene.2019.100562.
Auvira FDP, Mercuriani IS, Aloysius S. 2021. Genetic Variability Analysis of Terrestrial Spathoglottis plicata Orchid Variants Based on RAPD Marker. Proc. 7th Int. Conf. Res. Implementation, Educ. Math. Sci. (ICRIEMS 2020): 528: 70–75. DOI: 10.2991/assehr.k.210305.011.
Hon YK, Yong CSY, Abdullah JO, Go R. 2021. Development of species-specific SCAR markers for identification and authentication of three rare Peninsular Malaysian endemic Coelogyne (Orchidaceae) orchids. F1000Research 9: 1–14. DOI: 10.12688/F1000RESEARCH.26170.2.
Mursyidin DH, Rubiansyah M, Badruzsaufari. 2022. Genetic Relationship Of Several Morphological And Molecular Characteristics Of Phalaenopsis amabilis (L.) Blume Orchids From The Meratus Mountains Of South Kalimantan, Indonesia. Indones J For Res 9(1): 63–72. DOI: 10.20886/ijfr.2022.9.1.63-72.
Poerba YS, Ahmad F. 2013. Genetic variation analyses of Musa balbisiana Colla based on RAPD and ISSR markers. Berita Biology 12: 259–267. DOI: 10.14203/beritabiologi.v12i2.540 [Indonesian]
The HV, Thi V, Duyen T, Phuc PL. 2020. Initial Application Of Rapd Molecular Markers To Evaluate The Genetic Diversity Of Jewel Orchid ( Anoectochilus spp .). Accessions 20 (3): 3–10.
Zakiyah NM, Handoyo T, Kim KM. 2019. Genetic diversity analysis of indonesian aromatic rice varieties (Oryza sativa L.) using RAPD. J Crop Science and Biotechnology 22(1): 55–63. DOI: 10.1007/s12892-018-0271-0.
Kurniawati J, Sugiyarto L, Yulianti E, Nurcahyo H, Mercuriani IS. 2019. Molecular Identification of Several Orchid Species Based on OPA10 and OPA18 RAPD Marker. J Phys Conf Ser 1397(1). DOI: 10.1088/1742-6596/1397/1/012042.
Oliya BK, Chand K, Sen TL, Baniya MK, Sah AK, Pant B. 2021. Assessment of genetic stability of micropropagated plants of Rhynchostylis retusa (L.) using RAPD markers. Sci. Hortic. (Amsterdam) 281: 110008. DOI: 10.1016/j.scienta.2021.110008.
Al-Janabi ASA, Alhasnawi AN. 2021. Determination of genetic diversity based on rapd molecular marker and pararf3 gene expressions in some apricot genotypes in iraq. Basrah J Agric Sci 34(2): 60–74. DOI: 10.37077/25200860.2021.34.2.05.
Larekeng SH, Dermawan R, Iswoyo H, Mustari K. 2019. RAPD primer screening for amplification on Katokkon pepper from Toraja, South Sulawesi, Indonesia. IOP Conference Series: Earth and Environmental Science 270(1). DOI: 10.1088/1755- 1315/270/1/012023.
Tikendra L, Amom T, Nongdam P. 2019. Molecular genetic homogeneity assessment of micropropagated Dendrobium moschatum Sw. - A rare medicinal orchid, using RAPD and ISSR markers. Plant Gene 19: 100196. DOI: 10.1016/j.plgene.2019.100196.
Inglis PW, Marilia de Castro RP, Resende LV, Grattapaglia D. 2018. Fast and inexpensive protocols for consistent extraction of high quality DNA and RNA from challenging plant and fungal samples for high-throughput SNP genotyping and sequencing applications. PLoS ONE 13(10). DOI: 10.1371/journal.pone.0206085.
Aloysius S, Mercuriani IS, Ratnawati, Sudarsono. 2020. Molecular Characterization of Orchid Variants Spathoglottis plicata Blume Based on RAPD Analysis. Proc. 7th Int. Conf. Res. Implementation, Educ. Math. Sci. (ICRIEMS 2020) 528: 56–61. DOI: 10.2991/assehr.k.210305.009.
Al-Khayri JM,Mahdy EMB, Taha HSA, Eldomiaty AS, Abd-Elfattah MA, Latef AAHA, Rezk AA, Shehata WF, Almaghasla MI, Shalaby TA, Sattar MN, Ghazzawy HS, Awad MF, Alali KM, Jain SM, Hassanin AA. 2022. Genetic and Morphological Diversity Assessment of Five Kalanchoe Genotypes by SCoT, ISSR and RAPD-PCR Markers. Plants 11(13): 1722–1734. DOI: 10.3390/plants11131722
Hartati S, Samanhudi, Cahyono O. 2021. The appearance of DNA bands pattern based on the result of primary selection of RAPD orchid Phaius spp. IOP Conf. Ser. Earth Environ. Sci. 905(1): 6–11. DOI: 10.1088/1755-1315/905/1/012147.
Noflindawati, Anwar A, Sutanto A, Yusniwati. 2021. Optimization of annealing cycle and temperature SNAP T12 Primer distinguishing markers for male, female and hermaphrodite plants in papaya (Carica papaya L). IOP Conference Series: Earth and Environmental Science 715(1). DOI: 10.1088/1755-1315/715/1/012040.
Kurniawati J, Sugiyarto L, Yulianti E, Nurcahyo H, Mercuriani IS. 2019. Molecular Identification of Several Orchid Species Based on OPA10 and OPA18 RAPD Marker. J. Phys. Conf. Ser. 1397(1). DOI: 10.1088/1742-6596/1397/1/012042.
Nasution F, Theanhom AA, Sukartini, Bhuyar P, Chumpookam J. 2021. Genetic diversity evaluation in wild Muntingia calabura L. based on Random Amplified Polymorphic DNA (RAPD) markers. Gene Reports 25(4): 101335. DOI: 10.1016/j.genrep.2021.101335
Basavaraj B, Nagesha N, Jadeyegowda MY. 2020. Molecular Characterization of Dendrobium Orchid Species from Western Ghat Region of Karnataka using RAPD and SSR Markers. Int. J. Curr. Microbiol. Appl. Sci. 9(1): 2157–2169. DOI: 10.20546/ijcmas.2020.901.246.
Yuhanna WL, Hartati S, Sugiyarto, Marsusi. 2021. Genetic variability of Phaius and Dendrobium orchids based on molecular markers. IOP Conference Series: Earth and Environmental Science 637(1): 012036. DOI: 10.1088/1755-1315/637/1/012036.