Intraspecific SSR Marker Screening for Detection of Dendrobium crumenatum Mutants Generated from In Vitro Gamma Irradiation

Rindang Dwiyani(1*), I Putu Wahyu Sanjaya(2), Hestin Yuswanti(3), Ida Ayu Putri Darmawati(4), I Ketut Suada(5), Prila Kartika Manullang(6), Yuyun Fitriani(7)

(1) Faculty of Agriculture, Udayana University, Jl. PB Sudirman Denpasar, 80234, Indonesia
(2) Department of Biotechnology, Plant Production and Biotechnology Division, PT SMART Tbk. Jl. Raya Cijayanti, Babakan Madang, Bogor 16810, West Java, Indonesia
(3) Faculty of Agriculture, Udayana University, Jl. PB Sudirman Denpasar, 80234, Indonesia
(4) Faculty of Agriculture, Udayana University, Jl. PB Sudirman Denpasar, 80234, Indonesia
(5) Faculty of Agriculture, Udayana University, Jl. PB Sudirman Denpasar, 80234, Indonesia
(6) Faculty of Agriculture, Udayana University, Jl. PB Sudirman Denpasar, 80234, Indonesia
(7) Faculty of Agriculture, Udayana University, Jl. PB Sudirman Denpasar, 80234, Indonesia
(*) Corresponding Author


Determination of D. crumenatum mutant obtained from in vitro mutation breeding needs a long time due to its long-life cycle. SSR molecular markers can be used for early mutant detection. Specific SSR markers developed in D. crumenatum are not yet available. Alternative published SSR markers were developed from D. catenatum. The aims of this study are to screen the most informative SSR markers generated from D. catenatum tested in irradiated D. crumenatum population and to determine the gamma irradiation dose resulting the most mutants. Ten SSR markers were randomly selected and tested in 25 individuals of D. crumenatum plantlets irradiated with several doses (0, 5, 10, 15, and 20 Gy; 5 plantlets each dose). The result showed 7 of 10 primers were polymorphic and the other three were  monomorphic. All seven polymorphic primers can be used to identified intraspecific variation in the D. crumenatum mutant population. Markers dnsr28 and dnsr98 were the most informative, with the highest polymorphic information content (PIC) value of 0.5. Irradiation D. crumenatum protocorms using 10-15 gray doses were detected as the highest mutant percentage obtained up to 100% in the sample tested. This resulting marker information can be used to screen wider mutant population to decrease the non-mutant individuals in the population for maintenance and cost efficiency. The 10-15 Gy can be used as reference doses for gamma irradiation in 3 months old D. crumenatum protocorm materials.



Early detection; Mutation breeding; Orchid; Primer selection

Full Text:



Aisyah, S.I. et al., 2022a. The diversity of agromorphological characters of Portulaca grandiflora in the MV8 population deriving from recurrent irradiation. Biodiversitas, 23(9), pp.4432–4439. doi: 10.13057/biodiv/d230908.

Aisyah, S.I., Buchori, A. & Nurcholis, W., 2022b. Improving the morphology of Celosia argentea var . plumosa through induced mutation by gamma ray irradiation. Acta Horticulturae, pp.63–70. doi: 10.17660/ActaHortic.2022.1334.8.

Arrufitasari, P.N., Sutjahjo, S.H. & Wirnas, D., 2022. Performance of tomato M7 mutant lines and their similarities to the parents based on SSR markers. Biodiversitas, 23(3), pp.1239–1245. doi: 10.13057/biodiv/d230307.

Asadi et al., 2020. Evaluation of ssr and important agronomical characters of promising mutant lines of soybean. Biodiversitas, 21(1), pp.299–310. doi: 10.13057/biodiv/d210137.

Bhattarai, G., 2021. Genome-wide simple sequence repeats (SSR) markers discovered from whole-genome sequence comparisons of multiple spinach accessions. Scientific Reports, 11(1), 9999. doi: 10.1038/s41598-021-89473-0.

Cahyaningsih, A.P., Etikawati, N. & Yunus, A., 2022. Morphological characters variation of Indonesian accession Echinacea purpurea in response to gamma-ray irradiation. Biodiversitas, 23(10), pp.5351–5359. doi: 10.13057/biodiv/d231045.

Darmawati, I.A.P. et al., 2018. Short Communication : The diversity of wild Dendrobium ( Orchidaceae ) in Central Bali , Indonesia. Biodiversitas, 19(3), pp.1110–1116. doi: 10.13057/biodiv/d190345.

De, L.C. et al., 2015. Morphological Characterization In Dendrobium Species. Journal of Global Biosciences, 4(1), pp.1198–1215.

Fathin, T.S., Hartati, S. & Yunus, A., 2021. Diversity induction with gamma ray irradiation on Dendrobium odoardi orchid. IOP Conference Series: Earth and Environmental Science, 637(1). doi: 10.1088/1755-1315/637/1/012035.

Guerrero, B.I., Guerra, M.E. & Rodrigo, J., 2022. Simple Sequence Repeat (SSR)-Based Genetic Diversity in Interspecific Plumcot-Type (Prunus salicina × Prunus armeniaca) Hybrids. Plants, 11(9), 1241. doi: 10.3390/plants11091241

Li, X. et al., 2021. SSR-sequencing reveals the inter-and intraspecific genetic variation and phylogenetic relationships among an extensive collection of radish (Raphanus) germplasm resources. Biology, 10(12). doi: 10.3390/biology10121250.

Lubis, U.Q.N., Sukma, D. & Sudarsono, 2020. Respon Plantlet In Vitro dan Induksi Ketahanan Bibit Phalaenopsis amabilis terhadap Dickeya dadantii Menggunakan Asam Salisilat. Jurnal Agronomi Indonesia (Indonesian Journal of Agronomy), 48(3), pp.331–338. doi: 10.24831/jai.v48i3.32014.

Mansyur et al., 2019. Genetic diversity of mutant napiergrass using expressed sequence tag simple sequence repeat (EST-SSR). Biodiversitas, 20(8), pp.2403–2409. doi: 10.13057/biodiv/d200839.

Mason, A.S., 2015. SSR Genotyping. Methods in molecular biology. Plant Genotyping, 1245, pp.77–89. doi: 10.1007/978-1-4939-1966-6.

Melinda, H, F., Harmida, H. & Aminasih, N., 2022. Orchid (Orchidaceae) Inventory in Isau-Isau Wildlife Conservation Resort Area IX Lawang Agung Village, South Sumatra. Jurnal Biodjati, 7(2), pp.331–342. doi: 10.15575/biodjati.v7i2.19271.

Pauldasan, A. et al., 2022. Characterization and Identification of Four Species of Casuarina and their Interspecific Hybrids using EST-SSR Markers. Research Journal of Biotechnology, 16(5), pp.126-132.

Putri, H.A., 2021. Morphological, molecular and resistance responses to soft-rot disease variability among plantlets of Phalaenopsis amabilis regenerated from irradiated protocorms. Biodiversitas, 22(3), pp.1077–1090. doi: 10.13057/biodiv/d220301.

Sanjaya, I P.W. et al., 2022. Molecular characterization of soft-rot disease pathogen from Phalaenopsis and differences in genotype response to its infection. Acta Horticulturae, 1334, pp.111–118. doi: 10.17660/ActaHortic.2022.1334.14.

Semiarti, E. et al., 2020. Innovation of Natural Orchid Cultivation Technology for Tourism Development in Banyunganti Hamlet, Jatimulyo Village, Girimulyo Sub-District, Kulon Progo District, Yogyakarta. Journal of Tropical Biodiversity and Biotechnology, 5(3), pp.178–182. doi: 10.22146/jtbb.46283.

Simanjuntak, N.A., Aisyah, S.I. & Nurcholis, W., 2020. Evaluasi Karakter Agro-morfologi Jengger Ayam (Celosia cristata L.) pada Genotipe Mutan M3. Jurnal Agronomi Indonesia (Indonesian Journal of Agronomy), 48(1), pp.68–74. doi: 10.24831/jai.v48i1.29939.

Tsai, C.C. et al., 2015. RNA-Seq SSRs of moth orchid and screening for molecular markers across genus Phalaenopsis (Orchidaceae). PLoS ONE, 10(11), pp.1–18. doi: 10.1371/journal.pone.0141761.

Udage, A.C., 2021. Introduction to plant mutation breeding: Different approaches and mutageniagents. Journal of Agricultural Sciences - Sri Lanka, 16(3), pp.466–483. doi: 10.4038/jas.v16i03.9472.

Vighneswaran, V. et al., 2022. SSR marker analysis and DNA fingerprinting of mutant rice variety VTL 10 (Lavanya). Oryza-An International Journal on Rice, 59(3), pp.292–300. doi: 10.35709/ory.2022.59.3.4.

Wang, L. et al., 2020. Morphological, cytological and molecular variations induced by gamma rays in Chrysanthemum morifolium “Donglinruixue.” Folia Horticulturae, 32(1), pp.87–96. doi: 10.2478/fhort-2020-0009.

Wang, Y.H., 2021. Traditional Uses and Pharmacologically Active Constituents of Dendrobium Plants for Dermatological Disorders: A Review. Natural Products and Bioprospecting, 11(5), pp.465–487. doi: 10.1007/s13659-021-00305-0.

Zhao, T.M. et al., 2019. Classification of interspecific and intraspecific species by genome-wide SSR markers on Dendrobium. South African Journal of Botany, 127, pp.136–146. doi: 10.1016/j.sajb.2019.08.051.


Article Metrics

Abstract views : 291 | views : 202


  • There are currently no refbacks.

Copyright (c) 2024 Journal of Tropical Biodiversity and Biotechnology

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

Editoral address:

Faculty of Biology, UGM

Jl. Teknika Selatan, Sekip Utara, Yogyakarta, 55281, Indonesia

ISSN: 2540-9581 (online)