Variasi Genetik dan Filogeografi Pisang Raja (Musa spp.) di Pulau Jawa Berdasarkan Sekuen Internal Transcribed Spacer

  • Didik Wahyudi Universitas Islam Negeri Maulana Malik Ibrahim Malang
    (ID)
  • Lutfiana Hasanah Gusmiati Universitas Islam Negeri Maulana Malik Ibrahim Malang
    (ID)
  • Lia Hapsari Pusat Riset Konservasi Tumbuhan, Kebun Raya dan Kehutanan, Badan Riset dan Inovasi Nasional, Cibinong
    (ID)
Keywords: haplotype, phylogenetic, Pisang Raja, polymorphism, sequencing

Abstract

Pisang Raja is an important banana cultivar for the Javanese people since ancient times, with many morphological variations and local names. This study aims to determine the genetic variation and phylogeography of Pisang Raja based on Internal Transcribed Spacer (ITS) sequences. The results of the research can be used as a reference for developing superior Pisang Raja cultivars that are resistant to disease and make farmers easier to choose Pisang Raja cultivars that suit with geographical conditions on Java Island. This study used 9 samples of Pisang Raja (in-group) and 2 samples of wild bananas (out-group). The research method started with DNA isolation, qualitative and quantitative tests, ITSL and ITS4 primer amplification, and sequencing. Data analysis performed included polymorphism, phylogenetics (MP, ML, NJ and BI) and haplotype. The results showed that the ITS sequences in Pisang Raja was amplified with a length of 600-700 bp and GC content of 61.70%. Polymorphism analysis showed that the genetic variation of Pisang Raja in Java was very high. Phylogenetic analysis resulted in 4 phylogenetic trees with relatively same topologies, where the in-groups were divided into 2 clades, namely clade I (AAA and AAB) and clade II (AAA and ABB). The highest genetic similarity was showed by Raja Brentel and Raja Bali (89.43%) and the least was Raja Gareng and Raja Seribu (56.82%). Haplotype analysis formed 11 haplotypes which grouped into 4 groups. Pisang Raja evolution comes from two ancestors, i.e. M. acuminata and M. balbisiana. The phylogeography of ITS gene flow in Pisang Raja originates from Central Java then spread to East Java and Jakarta. This is presumably due to the high utilization followed by the planting of Pisang Raja by the people of Central Java for ritual and ceremonial events in the past which influenced the domestication process. The results of this study can served as the reference for genetic conservation strategy of Pisang Raja.

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References

Ahrens, D., Fujisawa, T., Krammer, H. J., Eberle, J., Fabrizi, S. & Vogler, A. P. (2016). Rarity and incomplete sampling in DNA-Based species delimitation. Systematic Biology, 65(3), 478–494. https://doi.org/10.1093/sysbio/syw002

Almutairi, Z. (2021). Molecular identification and phylogenetics of local pearl millet cultivars using Internal Transcribed Spacers of nuclear ribosomal DNA. Plant Genetic Resources, 19(4), 339-346. https://doi.org/10.1017/S1479262121000393

Arruum, Z.S. & Waluyo, B. (2021). Keberhasilan dan kompatibilitas penyerbukan sendiri dan silang pada hibridisasi interspesifik ciplukan (Physalis spp). Jurnal Agro, 8(1), 84-99. https://doi.org/10.15575/9368

Baurens, F. C., Martin, G., Hervouet, C., Salmon, F., Yohomé, D., Ricci, S., Rouard, M., Habas, R., Lemainque, A., Yahiaoui, N. & D'Hont, A. (2019). Recombination and large structural variations shape interspecific edible bananas genomes. Molecular Biology and Evolution, 36(1), 97–111. https://doi.org/10.1093/molbev/msy199

BPS. Badan Pusat Statistik. (2023). Statistik Hortikultura 2022. Badan Pusat Statistik Republik Indonesia. https://www.bps.go.id/publication/2023/06/09/03847c5743d8b6cd3f08ab76/statistik-hortikultura-2022.html

De Langhe, E., Vrydaghs, L., de Maret, P., Perrier, X. & Denham, T. (2009). Why bananas matter: An introduction to the history of banana domestication. Ethnobotany Research and Application, 7, 165-177. https://ethnobotanyjournal.org/index.php/era/article/view/356/229

Drummond, A.J., Suchard, M.A., Xie, D., Rambaut, A (2012). Bayesian phylogenetics with BEAUti and the BEAST 1.7. Molecular Biology and Evolution. 29(8), 1969-73. doi: 10.1093/molbev/mss075

Ekayanti, N.L.F., Megawati, F. & Dewi, N.L.K.A.A. (2023). Artikel review: pemanfaatan tanaman pisang (Musa paradisiaca L.) sebagai sediaan kosmetik. USADHA: Jurnal Integrasi Obat Tradisional, 2(2), 1-6. https://doi.org/10.36733/usadha.v2i2.6217

Fiani, A. (2015). Review: Strategi konservasi sumber daya genetik aren (Arenga pinnata). Prosiding Seminar Masyarakat Biodiversitas Indonesia, 1(3), 687-690. https://doi.org/10.13057/psnmbi/m010350

Forster, M. (2020). Network 10.2.0.0. user guide. Fluxus Technology Ltd. All rights reserved.

Gusmiati, L.H., Hapsari, L. & Wahyudi, D. (2018). Morphological diversity and clustering of 10 cooking bananas (Musa cv. Group ABB) collection of Purwodadi Botanic Garden - LIPI. Floribunda, 5(8), 299-314. https://www.ptti.or.id/journal/index.php/Floribunda/article/view/220

Hapsari, L., Lestari, D.A. & Probojati, R.T. (2020). Haplotype network analysis of wild banana relatives Ensete glaucum, Musa acuminata and Musa balbisiana based on cpDNA rbcL sequences in ex-situ collection. Indian Journal of Genetics and Plant Breeding, 80(3), 301-307. https://doi.org/10.31742/IJGPB.80.3.9

Hapsari, L., Azrianingsih, R. & Arumingtyas, E.L. (2018). Genetic variability and relationship of banana cultivars (Musa L.) from East Java, Indonesia based on the Internal Transcribed Spacer region nrDNA sequences. Journal of Tropical Biology and Conservation 15:101-120. https://doi.org/10.51200/jtbc.v15i0.1482

Hapsari, L., Kennedy, J., Lestari, D.A., Masrum, A. & Lestarini, W. (2017). Ethnobotanical survey of bananas (Musaceae) in six districts of East Java, Indonesia. Biodiversitas, 18(1), 160‒174. https://doi.org/10.13057/biodiv/d180122

Hapsari, L. (2015). Keragaman dan kekerabatan genetik pisang (Musa L.) di Jawa Timur berdasarkan sekuen daerah Internal Transcribed Spacer. Tesis. Program Magister Biologi, Jurusan Biologi, Fakultas Matematika dan Ilmu Pengetahuan Alam, Universitas Brawijaya, Malang. http://repository.ub.ac.id/id/eprint/157810/

Hariyanto, S., Ainiyah, R.K., Utami, E.S.W. & Hapsari, L. (2021). Genetic diversity and network within dessert bananas (Musa acuminata cv. AA and AAA) inferred by newly designed matK marker. International Journal of Conservation Science, 12, 585‒598. https://ijcs.ro/public/IJCS-21-44_Hariyanto.pdf

Hiariej, A., Arumingtyas, E.L., Widoretno, W. & Azrianingsih, R. (2015). Genetic kinship of tongkat langit banana (Musa troglodytarum L.) from Moluccas based on rbcL gene sequence. Indian Journal of Genetics and Plant Breeding, 75(4), 526-528. https://doi.org/10.5958/0975- 6906.2015.00085.1

Hřibová, E., Ćίžková, J., Christelová, P., Taudin, S., de Langhe, E. & Doleźel, J. (2011) The ITS1- 5.8S-ITS2 sequence region in the Musaceae: structure, diversity and use in molecular phylogeny. PLoS ONE, 6(3): e17863. https://doi.org/10.1371/journal.pone.0017863

Janssens, S. B., Vandelook, F., De Langhe, E., Verstraete, B., Smets, E., Vandenhouwe, I. & Swennen, R. (2016). Evolutionary dynamics and biogeography of Musaceae reveal a correlation between the diversification of the banana family and the geological and climatic history of Southeast Asia. The New Phytologist, 210(4), 1453-1465. https://doi.org/10.1111/nph.13856

Kiktev, D.A., Sheng, Z., Lobachev, K.S. & Petes, T.D. 2018. GC content elevates mutation and recombination ratesin the yeast Saccharomyces cerevisiae. PNAS, 115(30), E7109-E7118. www.pnas.org/cgi/doi/10.1073/pnas.1807334115

Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. ( 2018). MEGA X: Molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution, 35, 1547-1549. https://doi.org/10.1093%2Fmolbev%2Fmsy096

Kurnianto, B.K., Lestari, M.D. & Dewi, E. (2023). Metode pemasaran Pisang Raja (Musa paradisiaca L) menjadi olahan nuget melalui media online. KOMITMEN: Jurnal Imilah Manajemen, 4(1), 30-36. https://doi.org/10.15575/jim.v4i1.23512.g8341

Lamare, A., Arman, M.O. & Satyawada, R.R. (2017). Phylogenetic implications of the internal transcribed spacers of nrDNA and chloroplast DNA fragments of Musa in deciphering the ambiguities related to the sectional classification of the genus. Genetic Resources Crop and Evolution, 64, 1241-1251. https://doi.org/10.1007/s10722-016-0433-9

Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R., Thompson, J.D., Gibson, T.J. & Higgins, D.G. (2007). Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948. https://doi.org/10.1093/bioinformatics/btm404

Leitwein, M., Duranton, M., Rougemont, Q., Gagnaire, P. A. & Bernatchez, L. (2020). Using haplotype information for conservation genomics. Trends in Ecology and Evolution, 35(3), 245-258. https://doi.org/10.1016/j.tree.2019.10.012

Li, L.F., Wang, H.Y., Zhang, C., Wang, X.F., Shi, F.X., Chen, W.N. & Ge, X.J. (2013). Origins and domestication of cultivated banana inferred from chloroplast and nuclear genes. PLoS ONE, 8(11), e80502. https://doi.org/10.1371/journal.pone.0080502

Liu, A.Z., Kress, W.J. & Li, D.Z. (2010). Phylogenetic analyses of the banana family (Musaceae) based on nuclear ribosomal (ITS) and chloroplast (trnL-F) evidence. Taxon, 59 (1), 20-28. https://doi.org/10.1002/tax.591003

Martin, G., Carreel, F., Coriton, O., Hervouet, C., Cardi, C., Derouault, P., Roques, D., Salmon, F., Rouard, M., Sardos, J., Labadie, K., Baurens, F. C. & D'Hont, A. (2017). Evolution of the banana genome (Musa acuminata) is impacted by large chromosomal translocations. Molecular biology and evolution, 34(9), 2140–2152. https://doi.org/10.1093/molbev/msx164

Paradis E. 2018. Analysis of haplotype networks: The randomized minimum spanning tree method. Methods in Ecology and Evolution, 9, 1308-1317. https://doi.org/10.1111/2041-210X.12969

Perrier, X., De Langhe, E., Donohue, M., Lentfer, C., Vrydaghs, L., Bakry, F., Carreel, F., Hippolyte, I., Horry, J.p., Jenny, C. Lebot, V., Risterucci, A.M., Tomekpe, K., Doutrelepont, H., Ball, T., Manwaring, J., Maret, P.D. & Denham, T. (2011). Multidisciplinary perspectives on banana (Musa spp.) domestication. PNAS, 108(28), 2011, 11311-11318. https://doi.org/10.1073/pnas.1102001108

Probojati, R.T., Listyorini, D., Sulisetijono, S. & Wahyudi, D. (2021). Phylogeny and estimated genetic divergence times of banana cultivars (Musa spp.) from Java Island by maturase K (matK) genes. Bulletin of the National Research Centre, 45(33). https://doi.org/10.1186/s42269-021-00492-3

Probojati, R.T., Wahyudi, D. & Hapsari, L. 2019. Clustering analysis and genome inference of Pisang Raja local cultivars (Musa spp.) from Java Island by Random Amplified Polymorphic DNA (RAPD) Marker. Journal of Tropical Biodiversity and Biotechnology, 4(2),42-53. https://doi.org/10.22146/jtbb.44047

Safhi, F.A., Alshamrani, S.M., Alshaya, D.S., Hussein, M.A.A. & Abd El-Moneim, D. (2023). Genetic diversity analysis of banana cultivars (Musa sp.) in Saudi Arabia Based on AFLP Marker. Current Issues in Molecular Biology, 45, 1810–1819. https://doi.org/10.3390/cimb45030116

Sharma, S.K., Dkhar, J., Kumaria, S., Tandon, P. & Rao, S.R. (2012). Assessment of phylogenetic inter-relationships in the genus Cymbidium (Orchidaceae) based on internal transcribed spacer region of rDNA. Gene, 495(1), 10-15. https://doi.org/10.1016/j.gene.2011.12.052

Simmonds, N.W. & K. Shepherd. (1955). The taxonomy and origins of the cultivated banana. Journal of Linnean Society (Botany), 55, 302-312. https://doi.org/10.1111/j.1095-8339.1955.tb00015.x

Smith, M.R. (2019). Bayesian and parsimony approaches reconstruct informative trees from simulated morphological datasets. Biology Letters, 15, 20180632. http://dx.doi.org/10.1098/rsbl.2018.0632

Sultana, S., Lim, Y.P., Bang, J.W. & Choi, H.W. (2011). Internal transcribed spacer (ITS) and genetic variations in Lilium native to Korea. Horticulture, Environment, and Biotechnology, 52, 502–510. https://doi.org/10.1007/s13580-011-0050-7

Valmayor, R.V., Jamaluddin, S.H., Silayoi, B., Kusumo, S., Danh, L.D., Pascua, O.C. & R.R.C. Espino. (2000). Banana cultivar names and synonyms in Southeast Asia. International Network for the Improvement of Banana and Plantain – Asia and the Pacific Office. Los Banos, Laguna, Philippines. https://hdl.handle.net/10568/105378

Wahyudi, D., Nursita, D.C. & Hapsari L. (2022). Genetic diversity among and within genome groups of banana cultivars based on ISSR Markers. International Journal of Agriculture and Biology, 28, 366‒374. https://doi.org/10.17957/IJAB/15.1990

Published
2023-12-31
How to Cite
Wahyudi, D., Gusmiati, L. H., & Hapsari, L. (2023). Variasi Genetik dan Filogeografi Pisang Raja (Musa spp.) di Pulau Jawa Berdasarkan Sekuen Internal Transcribed Spacer. Jurnal Biotek, 11(2), 196-210. https://doi.org/10.24252/jb.v11i2.40807
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Articles
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