Genetic Variability Analysis of Phaius spp Orchid based on RAPD Markers

Sri Hartati, - Samanhudi

Abstract


Phaius spp live in tropical forests with high humidity due to deforestation, which has resulted in the extinction of many endemic orchid species, especially orchids Phaius spp, so it needs to be conserved through a plant breeding program. There are not many research reports on the genetic diversity of orchids Phaius spp, even though the study of genetic diversity plays an important role in plant breeding programs and genetic conversation. This study aims to determine the genetic diversity of Phaius spp. This research was carried out using molecular markers RAPD (Random Amplified Polymorphic DNA). DNA from Phaius spp was extracted and then amplified by PCR using 6 RAPD primers. The results of this study found that four species of orchids of the genus Phaius spp (Phaius tankervillae (1); Phaius montanus (2); Phaius collasus (3); and Phaius amboinensis (4)) amplified using 6 RAPD primers to produce 37 DNA bands with a size of 250-1600 bp, and produce 100% polymorphic bands The genetic similarity coefficient of the 4 orchid species ranges from 0.19-0.53 and the genetic variability ranges from 47%-81%.

Keywords


Genetic diversity; orchid; Phaius spp; polymorphic; RAPD.

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References


D. M. Puspitaningtyas, "Orchid diversity in a logging concession in Tabalong District, South Kalimantan, Indonesia," Biodiversitas J. Biol. Divers., vol. 21, no. 11, pp. 5455–5464, Oct. 2020, doi: 10.13057/BIODIV/D211154.

C. G. Fajardo, F. de Almeida Vieira, L. P. Felix, and W. F. Molina, "Negligence in the Atlantic forest, northern Brazil: a case study of an endangered orchid," Biodivers. Conserv., vol. 26, no. 5, pp. 1047–1063, 2017, doi: 10.1007/s10531-016-1285-5.

R. Devadas, R. K. Pamarthi, A. L. Meitei, S. L. Pattanayak, and R. Sherpa, "Morphological description of novel phaius primary hybrid (Orchidaceae)," J. Exp. Biol. Agric. Sci., vol. 7, no. 2, pp. 138–147, Apr. 2019, doi: 10.18006/2019.7(2).138.147.

S. Hartini, "Orchids Diversity in the Sicikeh-Cikeh Forest, North Sumatra, Indonesia," Biodiversitas J. Biol. Divers., vol. 20, no. 4, pp. 1087–1096, Mar. 2019, doi: 10.13057/BIODIV/D200421.

M. Y. Chung, J. López-Pujol, S. Son, G. U. Suh, T. Yukawa, and M. G. Chung, "Patterns of Genetic Diversity in Rare and Common Orchids Focusing on the Korean Peninsula: Implications for Conservation," Bot. Rev., vol. 84, no. 1, pp. 1–25, Mar. 2018, doi: 10.1007/S12229-017-9190-5.

M. D. Baltazar and J. M. A. O. Fabella, "Assessment of the genetic diversity of Philippine Arabica coffee (Coffea Arabica L.) using SSR markers," Philipp. J. Sci., vol. 149, no. 3, pp. 993–1003, 2020.

G. Sandal Erzurumlu, N. Sultana, M. Vural, and S. Serçe, "Genetic and phenotypic variation among Turkish terrestrial orchid species as revealed by RAPD and morphological characteristics," Turkish J. Agric. For., vol. 42, no. 4, pp. 227–236, 2018, doi: 10.3906/tar-1711-37.

S. P. Khor, L. C. Yeow, R. Poobathy, R. Zakaria, B. L. Chew, and S. Subramaniam, "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, vol. 26, p. e00448, Jun. 2020, doi: 10.1016/J.BTRE.2020.E00448.

N. A. Ismail, M. Y. Rafii, T. M. M. Mahmud, M. M. Hanafi, and G. Miah, "Genetic Diversity of Torch Ginger (Etlingera elatior) Germplasm Revealed by ISSR and SSR Markers," Biomed Res. Int., vol. 2019, 2019, doi: 10.1155/2019/5904804.

W. L. Yuhanna, S. Hartati, Sugiyarto, and Marsusi, "Genetic variability of Phaius and Dendrobium orchids based on molecular markers," IOP Conf. Ser. Earth Environ. Sci., vol. 637, no. 1, 2021, doi: 10.1088/1755-1315/637/1/012036.

A. Sabriu-Haxhijaha, G. Ilievska, V. Stojkovski, and K. Blagoevska, "A Modified SDS - Based Method Applied for Extraction of High-Quality DNA from Raw Corn and Roasted Soybean," Maced. Vet. Rev., vol. 43, no. 1, pp. 61–67, 2020, doi: 10.2478/macvetrev-2020-0017.

R. Shukla, D. C. Sharma, N. Pathak, and P. Bajpai, "Genomic DNA Isolation from High Polyphenolic Content Grewia asiatica L. Leaf Without Using Liquid Nitrogen," Iran. J. Sci. Technol. Trans. A Sci., vol. 42, no. 2, pp. 347–351, 2018, doi: 10.1007/s40995-016-0081-0.

C. M. L. Serrote, L. R. S. Reiniger, K. B. Silva, S. M. dos S. Rabaiolli, and C. M. Stefanel, "Determining the Polymorphism Information Content of a molecular marker," Gene, vol. 726, p. 144175, Feb. 2020, doi: 10.1016/J.GENE.2019.144175.

F. H. Pendi and H. Hussain, "Suitability of Various Buffers for Genomic DNA Extraction of Pineapple (Ananas comosus) VAR. MD2," J. Sustain. Sci. Manag., vol. 15, no. 8, pp. 90–101, 2020, doi: 10.46754/JSSM.2020.12.008.

Susilo and Meitiyani, "Genetic variation of three bruguiera species from Karimunjawa Islands detected by using RAPD molecular markers," Asian J. Plant Sci., vol. 17, no. 4, pp. 198–203, 2018, doi: 10.3923/AJPS.2018.198.203.

W. Suwankitti et al., "Population analysis of Epipactis flava Seidenf. in Thailand using SRAP and RAPD markers,†Songklanakarin J. Sci. Technol., vol. 42, no. 5, pp. 1065–1070, Oct. 2020, doi: 10.14456/SJST-PSU.2020.138.

J. R. Choi et al., "An integrated lateral flow assay for effective DNA amplification and detection at the point of care," Analyst, vol. 141, no. 10, pp. 2930–2939, May 2016, doi: 10.1039/C5AN02532J.

F. D. P. Auvira, I. S. Mercuriani, and S. Aloysius, "Genetic Variability Analysis of Terrestrial Spathoglottis plicata Orchid Variants Based on RAPD Marker," Proc. 7th Int. Conf. Res. Implementation, Educ. Math. Sci. (ICRIEMS 2020), vol. 528, pp. 70–75, Mar. 2021, doi: 10.2991/ASSEHR.K.210305.011.

G. K. Rao, C. Kapadia, N. B. Patel, K. D. Desai, and P. N. Narasimha Murthy, "Genetic diversity analysis of greater yam (Dioscorea alata L.) genotypes through RAPD and ISSR markers," Biocatal. Agric. Biotechnol., vol. 23, p. 101495, Jan. 2020, doi: 10.1016/J.BCAB.2020.101495.

S. H. Larekeng, M. Restu, A. Arif, Y. F. Cahyaningsih, and J. Mukti, "A genetic approach to study mating system on Jabon Merah (Anthocephalus macrophyllus Roxb.) from three different provenances in South Sulawesi," IOP Conf. Ser. Earth Environ. Sci., vol. 235, no. 1, 2019, doi: 10.1088/1755-1315/235/1/012049.

A. Yustiati, R. M. Hutagalung, Y. Andriani, W. Lili, and I. Bangkit, "Genetic Analysis of Tilapia (Oreochromis niloticus) Nirwana Strain Cultured in Aceh Besar and Wanayasa by Using Random Amplified Polymorphic DNA Method," Asian J. Biochem. Genet. Mol. Biol., pp. 1–9, Aug. 2020, doi: 10.9734/AJBGMB/2020/V4I430111.

G. Kiani and M. Siahchehreh, "Genetic Diversity in Tomato Varieties Assessed by ISSR Markers," Int. J. Veg. Sci., vol. 24, no. 4, pp. 353–360, 2018, doi: 10.1080/19315260.2017.1419397.

E. V. Tambarussi, E. A. Veasey, L. Menezes, B. Ibañes, K. C. Lombardi, and R. Vencovsky, "Genetic diversity between native and improved Cattleya walkeriana Gardner famous clones ," Acta Sci. - Agron., vol. 39, no. 3, pp. 315–320, 2017, doi: 10.4025/ACTASCIAGRON.V39I3.32520.

D. O. Igwe, C. A. Afiukwa, B. E. Ubi, K. I. Ogbu, O. B. Ojuederie, and G. N. Ude, "Assessment of genetic diversity in Vigna unguiculata L. (Walp) accessions using inter-simple sequence repeat (ISSR) and start codon targeted (SCoT) polymorphic markers," BMC Genet., vol. 18, no. 1, pp. 1–13, 2017, doi: 10.1186/s12863-017-0567-6.

A. N. Bhanu, "Assessment of Genetic Diversity in Crop Plants - An Overview," Adv. Plants Agric. Res., vol. 7, no. 3, pp. 279–286, 2017, doi: 10.15406/apar.2017.07.00255.

G. M, V. M, and S. M, "Importance of genetic diversity assessment in crop plants and its recent advances: an overview of its analytical perspectives," Genet. Res. Int., vol. 2015, 2015, doi: 10.1155/2015/431487.

S. Kumar, M. Kumar, H. K. Yadav, S. Sharma, and S. Kumar, "Genetic diversity and population structure analysis of Chrysanthemum (Dendranthema grandiflora Tzvelev) germplasm based on RAPD markers," J. Environ. Biol., vol. 38, no. 3, pp. 457–464, May 2017, doi: 10.22438/JEB/38/3/MS-201.

S. Hartati, Samanhudi, I. R. Manurung, and O. Cahyono, "Morphological characteristics of Phaius spp. orchids from Indonesia," Biodiversitas, vol. 22, no. 4, pp. 1991–1995, Apr. 2021, doi: 10.13057/biodiv/d220447.

J. Jiemjuejun, S. Damrianant, T. Thanananta, and N. Thanananta, "Genetic Relationship Assessment and Identification of Orchids in the Genus Eria Using HAT-RAPD Markers," Sci. Technol. Asia, vol. 22, no. 4, pp. 19–26, Dec. 2017.

B. Abbas, M. Dailami, F. H. Listyorini, and Munarti, "Genetic Variations and Relationships of Papua's Endemic Orchids Based on RAPD Markers," Nat. Sci., vol. 9, no. 11, pp. 377–385, Nov. 2017, doi: 10.4236/NS.2017.911035.

T. Meesangiem, S. Damrianant, T. Thanananta, and N. Thanananta, "Genetic Relationship among Paphiopedilum Subgenus Brachypetalum Section Brachypetalum Using HAT-RAPD Markers," Thai J. Sci. Technol., vol. 7, no. 1, pp. 99–105, 2018, doi: 10.14456/TJST.2018.2.

P. Bhattacharyya and J. van Staden, "Molecular insights into genetic diversity and population dynamics of five medicinal Eulophia species: a threatened orchid taxa of Africa," Physiol. Mol. Biol. Plants, vol. 24, no. 4, p. 631, Jul. 2018, doi: 10.1007/S12298-018-0523-6.

S. Hoban et al., "Genetic diversity targets and indicators in the CBD post-2020 Global Biodiversity Framework must be improved," Biol. Conserv., vol. 248, p. 108654, Aug. 2020, doi: 10.1016/J.BIOCON.2020.108654.

J. C. Teixeira and C. D. Huber, "The inflated significance of neutral genetic diversity in conservation genetics," Proc. Natl. Acad. Sci., vol. 118, no. 10, Mar. 2021, doi: 10.1073/PNAS.2015096118.

H. P. Doekes, R. F. Veerkamp, P. Bijma, G. De Jong, S. J. Hiemstra, and J. J. Windig, “Inbreeding depression due to recent and ancient inbreeding in Dutch Holstein-Friesian dairy cattle,†Genet. Sel. Evol., vol. 51, no. 1, pp. 1–16, 2019, doi: 10.1186/s12711-019-0497-z.




DOI: http://dx.doi.org/10.18517/ijaseit.12.4.16250

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