Genetic Diversity and Relationship of Native Phalaenopsis Orchids: A Case Study of Indonesian Archipelago

Yıl 2024, Cilt: 21 Sayı: 4, 844 - 853, 20.09.2024

Dindin Hidayatul Mursyidin , Muhammad Riyan Firnanda

https://doi.org/10.33462/jotaf.1247037

Öz

The native Phalaenopsis is valuable germplasm for future orchid breeding programs and for its conservation because it provides many beneficial traits or genes. This study aimed to determine and analyze the molecular diversity and phylogeny of Indonesian native Phalaenopsis by a DNA barcoding (matK) marker. A total of 19 samples of Phalaenopsis orchids were used in this study. All leaf samples of orchid were extracted and purified using a commercial DNA isolation kit from Geneaid Biotech Ltd., Taiwan (GP100). The DNAs were then amplified by specific matK primers: Forward (5’-CGTACAGTACTTTTGTGTTTACGAG-3’) and Reverse (5’-ACCCAGTCCATCTGGAAATCTTGGTTC-3’). The DNA targets or products (matK) were purified and sequenced by the Sanger-bidirectional method at 1st Base Ltd., Malaysia. Before further analysis, the matK sequences of Phalaenopsis were edited, reconstructed, and aligned with the assistance of Clustal W in the MEGA 11 software. Its genetic diversity was determined using the nucleotide diversity index (π%), and the phylogenetic analysis was performed using the maximum likelihood (ML) method with a statistical bootstrap. The phylogenetic relationship was also assessed using principal component analysis (PCA). Based on this marker, the native Phalaenopsis has a high genetic diversity (π% = 1.70). In addition, the phylogenetic analysis revealed that this germplasm was separated into seven clades, where P. pantherina has the closest relation to P. cornu-cervi and P. gigantea. Conversely, the highest genetic distance was to P. amabilis from South Kalimantan and to P. celebensis from Sulawesi, at a coefficient divergence of 0.084. Our findings provide an essential foundation for supporting future orchid breeding practices, including conservation, on local and global scales.

Anahtar Kelimeler

Breeding program, Genetic diversity, Moth orchid, Ornamental plant, Phylogenetic relationship

Kaynakça

• Acquaah, G. (2015). Conventional Plant Breeding Principles and Techniques. In Advances in Plant Breeding Strategies: Breeding, Biotechnology and Molecular Tools, Eds. J. M. Al Khayri, S. M. Jain, D. V., Johnson, Springer International Publishing, Cham.
• Aesomnuk, W., Ruengphayak, S., Ruanjaichon, V., Sreewongchai, T., Malumpong, C., Vanavichit, A., Toojinda, T., Wanchana, S. and Arikit, S. (2021). Estimation of the genetic diversity and population structure of Thailand’s rice landraces using SNP markers. Agronomy, 11(5): 1–14.
• Allier, A., Teyssèdre, S., Lehermeier, C., Moreau, L. and Charcosset, A. (2020). Optimized breeding strategies to harness genetic resources with different performance levels. BMC Genomics, 21(1): 1–16.
• Bahar, E., Korkutal, I., Şahin, N., Saǧir, F. S., Kök, D., Ergönül, O., Uysal, T. and Özalp, Z. O. (2019). Molecular and ampelographic characterization of grapevine (Vitis vinifera L.) genetic materials collected in natural flora of Ganos Mountains. Journal of Tekirdag Agricultural Faculty, 16(1): 92–102.
• Barthet, M. M., Pierpont, C. L. and Tavernier, E. K. (2020). Unraveling the role of the enigmatic matK maturase in chloroplast group IIA intron excision. Plant Direct, 4(3): 1–17.
• Besi, E. E., Nikong, D., Mus, A. A., Nelson, H. V., Mohamad, N. N., Ombokou, R., Rusdi, A., David, D., Aziz, Z. A. and Go, R. (2021). A species checklist of wild orchids in selected sites in Kadamaian, Kota Belud, Sabah. Journal of Tropical Biology and Conservation, 18: 131–147.
• Căprar, M., Copaci, C. M., Chende, D. M., Sicora, O., Şumălan, R. and Sicora, C. (2017). Evaluation of genetic diversity by DNA barcoding of local tomato populations from North-Western Romania. Notulae Botanicae Horti Agrobotanici Cluj-Napoca, 45(1): 276–279.
• CBOL Plant Working Group. (2009). A DNA barcode for land plants. PNAS, 106 (31), 12794–12797.
• Chen, J. R. and Shiau, Y. J. (2015). Application of internal transcribed spacers and maturase K markers for identifying Anoectochilus, Ludisia, and Ludochilus. Biologia Plantarum, 59(3): 485–490.
• Clegg, M. T. (1993). Chloroplast gene sequences and the study of plant evolution. PNAS, 90: 363–367.
• Deng, H., Zhang, G. Q., Liu, Z. J. and Wang, Y. (2015). A new species and a new combination of Phalaenopsis (Orchidaceae: Epidendroideae: Aeridinae): Evidence from morphological and DNA analysis. Phytotaxa, 238(3): 243–254.
• Fatimah, F. and Sukma, D. (2011). Development of sequence-based microsatellite marker for Phalaenopsis Orchid. HAYATI Journal of Biosciences, 18(2): 71–76.
• Govindaraj, M., Vetriventhan, M. and Srinivasan, M. (2015). Importance of genetic diversity assessment in crop plants and its recent advances: An overview of its analytical perspectives. Genetics Research International, 2015: 1–14.
• Hinsley, A., De Boer, H. J., Fay, M. F., Gale, S. W., Gardiner, L. M., Gunasekara, R. S., Kumar, P., Masters, S., Metusala, D., Roberts, D. L., Veldman, S., Wong, S. and Phelps, J. (2018). A review of the trade in orchids and its implications for conservation. Botanical Journal of the Linnean Society, 186: 435–455.
• Hsu, C. C., Chen, H. H.and Chen, W. H. (2018). Phalaenopsis. In: Ornamental Crops, Ed. J. Van Huylenbroeck, Springer International Publishing AG, Cham.
• Huang, W., Zhao, X., Zhao, X., Li, Y. and Lian, J. (2016). Effects of environmental factors on genetic diversity of Caragana microphylla in Horqin Sandy Land, northeast China. Ecology and Evolution, 6(22): 8256–8266.
• Jheng, C. F., Chen, T. C., Lin, J. Y., Chen, T. C., Wu, W. L. and Chang, C. C. (2012). The comparative chloroplast genomic analysis of photosynthetic orchids and developing DNA markers to distinguish Phalaenopsis orchids. Plant Science, 190: 62–73.
• Kar, P., Goyal, A. K. and Sen, A (2015). Maturase K gene in plant DNA barcoding and phylogenetics. In: Plant DNA Barcoding and Phylogenetics, Eds: Ajmal Ali, M., Gábor, G., Al-Hemaid, F., Lambert Academic Publishing, Germany.
• Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16: 111–120.
• Kwon, Y. E., Yu, H. J., Baek, S., Kim, G. B., Lim, K. B. and Mun, J. H. (2017). Development of gene-based identification markers for Phalaenopsis ‘KS Little Gem’ based on comparative genome analysis. Horticulture Environment and Biotechnology, 58(2): 162–169.
• Lafarge, D. (2015). Phalaenopsis: A Complete Guide.
• Le, D. T., Zhang, Y. Q., Xu, Y., Guo, L. X., Ruan, Z. P., Burgess, K. S. and Ge, X. J. (2020). The utility of DNA barcodes to confirm the identification of palm collections in botanical gardens. PLoS ONE, 15: 1–14.
• Lee, S. C., Wang, C. H., Yen, C. E. and Chang, C. (2017). DNA barcode and identification of the varieties and provenances of Taiwan’s domestic and imported made teas using ribosomal internal transcribed spacer 2 sequences. Journal of Food and Drug Analysis, 25 (2): 260–274.
• Li, C., Dong, N., Zhao, Y., Wu, S., Liu, Z. and Zhai, J. (2021). A review for the breeding of orchids: Current achievements and prospects. Horticultural Plant Journal, 7(5): 380–392.
• Li, H. Q., Chen, J. Y., Wang, S. and Xiong, S. Z. (2012). Evaluation of six candidate DNA barcoding loci in Ficus (Moraceae) of China. Molecular Ecology Resources, 12(5): 783–790.
• Mitchell, C. (1993). MultAlin-multiple sequence alignment. Cabios Software Reviews, 9(5): 614–615.
• Mursyidin, D. H., Nazari, Y. A., Ahyar, G. M. Z. and Makruf, M. I. (2022). Molecular identity of native coconut (Cocos nucifera L.) germplasm from South Kalimantan, Indonesia. Australian Journal of Crop Science, 16(3): 424–430.
• Mursyidin, D. H., Ahyar, G. M. Z., Saputra, A. W. and Hidayat, A. (2021a). Genetic diversity and relationships of Phalaenopsis based on the rbcL and trnL-F markers: In silico approach. Biosaintifika: Journal of Biology & Biology Education, 13(2): 212–221.
• Mursyidin, D. H., Nazari, Y. A., Badruzsaufari, E. and Masmitra, M. R. D. (2021b). DNA barcoding of the tidal swamp rice (Oryza sativa) landraces from South Kalimantan, Indonesia. Biodiversitas Journal of Biological Diversity, 22(4): 1593–1599.
• Mursyidin, D. H. and Khairullah, I. (2020). Genetic evaluation of tidal swamp rice from South Kalimantan, Indonesia based on the agro-morphological markers. Biodiversitas Journal of Biological Diversity, 21(10), 4795–4803. https://doi.org/10.13057/biodiv/d211045
• Mustafa, K. M., Ewadh, M. J., Al-Shuhaib, M. B. S. and Hasan, H. G. (2018). The in silico prediction of the chloroplast maturase K gene polymorphism in several barley varieties. Agriculture, 64(1): 3–16.
• Nadeem, M. A., Nawaz, M. A., Shahid, M. Q., Doğan, Y., Comertpay, G., Yıldız, M., Hatipoğlu, R., Ahmad, F., Alsaleh, A., Labhane, N., Özkan, H., Chung, G. and Baloch, F. S. (2018). DNA molecular markers in plant breeding: current status and recent advancements in genomic selection and genome editing. Biotechnology and Biotechnological Equipment, 32(2): 261–285.
• Nei, M. and Li, W. H. (1979). Mathematical model for studying genetic variation in terms of restriction endonucleases (molecular evolution/mitochondrial DNA/nucleotide diversity). PNAS, 76(10): 5269–5273.
• Niknejad, A., Kadir, M.A., Kadzimin, S.B., Abdullah, N.A.P. and Sorkheh, K. (2009). Molecular characterization and phylogenetic relationships among and within species of Phalaenopsis (Epidendroideae: Orchidaceae) based on RAPD analysis. African Journal of Biotechnology, 8(20): 5225–5240.
• Ozer, M.O., Kar, H., Dogru, S.M. and Bekar, N.K. (2021). Morphological characterization of some hybrid red head cabbage (Brassica oleracea L. var. capitata subvar. rubra) varieties. Journal of Tekirdag Agricultural Faculty, 18(3): 428–435.
• Rahayu, M.E. Della, Sukma, D., Syukur, M., Aziz, S. A. and Irawati, D. (2015). In vivo polyploid ınduction using colchicine of moth orchid seedling (Phalaenopsis amabilis (L.) Blume). Buletin Kebun Raya, 18(1): 41–50.
• Singh, J., Kakade, D. P., Wallalwar, M. R., Raghuvanshi, R., Kongbrailatpam, M., Verulkar, S. B. and Banerjee, S. (2017). Evaluation of potential DNA barcoding loci from plastid genome: Intraspecies discrimination in rice (Oryza species). International Journal of Current Microbiology and Applied Sciences, 6(5): 2746–2756.
• Siregar, C. (2008). Exploration and inventory of native orchid germplasm in West Borneo, Indonesia. HortScience, 43(2): 554–557.
• Suriani, C., Prasetya, E., Harsono, T., Manurung, J., Prakasa, H., Handayani, D., Jannah, M. and Rachmawati, Y. (2021). DNA barcoding of andaliman (Zanthoxylum acanthopodium DC) from North Sumatra Province of Indonesia using maturase K gene. Tropical Life Sciences Research, 32(2): 15–28.
• Tamura, K., Stecher, G. and Kumar, S. (2021). MEGA11: Molecular evolutionary genetics analysis version 11. Molecular Biology and Evolution, 38(7): 3022–3027.
• Teixeira, J. C. and Huber, C. D. (2021). The inflated significance of neutral genetic diversity in conservation genetics. PNAS, 118(10): 1–10.
• Thakar, S. B., Dhanavade, M. J. and Sonawane, K. D. (2016). Phylogenetic, sequence analysis and structural studies of maturase K protein from mangroves. Current Chemical Biology, 10(2): 135–141.
• Tsai, C. C., Chiang, Y. C., Huang, S. C., Chen, C. H. and Chou, C. H. (2010). Molecular phylogeny of Phalaenopsis Blume (Orchidaceae) on the basis of plastid and nuclear DNA. Plant Systematics and Evolution, 288(1): 77–98.
• Tsai, C. C., Shih, H. C., Wang, H. V., Lin, Y. S., Chang, C. H., Chiang, Y. C. and Chou, C. H. (2015). RNA-Seq SSRs of moth orchid and screening for molecular markers across genus Phalaenopsis (Orchidaceae). PLoS ONE, 10(11): e0141761.
• Wu, F., Ma, S., Zhou, J., Han, C., Hu, R., Yang, X., Nie, G. and Zhang, X. (2021). Genetic diversity and population structure analysis in a large collection of white clover (Trifolium repens L.) germplasm worldwide. PeerJ, 9: 1–17.
• Yusop, M. S. M., Mohamed-Hussein, Z. A., Ramzi, A. B. and Bunawan, H. (2022). Cymbidium mosaic virus infecting orchids: What, how, and what Next? Iranian Journal of Biotechnology, 20(1):e3020.
• Zahara, M. and Win, C. C. (2019). Morphological and stomatal characteristics of two Indonesian local orchids. Journal of Tropical Horticulture, 2(2): 65.