Variasi Genetik dan Filogeografi Pisang Raja (Musa spp.) di Pulau Jawa Berdasarkan Sekuen Internal Transcribed Spacer
Abstrak
Pisang Raja adalah kultivar pisang penting bagi masyarakat Jawa sejak zaman dahulu, dengan banyak variasi morfologi dan nama daerah. Penelitian ini bertujuan untuk mengetahui variasi genetik dan filogeografi Pisang Raja di Pulau Jawa berdasarkan sekuen Internal Transcribed Spacer (ITS). Hasil penelitian ini diharapkan dapat digunakan sebagai acuan pengembangan kultivar Pisang Raja unggul yang tahan terhadap penyakit serta memudahkan petani dalam memilih kultivar Pisang Raja yang sesuai dengan kondisi lokal daerah yang ada di pulau Jawa. Penelitian ini menggunakan 9 sampel Pisang Raja (in-group) dan 2 sampel pisang liar (out-group). Metode penelitian diawali dengan isolasi DNA, uji kualitatif dan kuantitatif, amplifikasi primer ITSL dan ITS4, dan sekuensing. Analisis data yang dilakukan meliputi polimorfisme, filogenetik (MP, ML, NJ dan BI) dan haplotipe. Hasil menunjukkan bahwa sekuen ITS pada pisang Raja teramplifikasi dengan panjang 600-700 bp dan konten GC 61.70%. Analisis polimorfisme menunjukkan variasi genetik Pisang Raja di Pulau Jawa sangat tinggi. Analisis filogenetik menghasilkan 4 pohon filogenetik dengan topologi yang kurang lebih sama, dimana in-group terbagi menjadi 2 klad yaitu klad I (AAA dan AAB) dan klad II (AAA dan ABB). Similaritas genetik tertinggi dimiliki oleh Raja Brentel dengan Raja Bali (89,43%) dan terendah oleh Raja Gareng dengan Raja Seribu (56,82%). Analisis haplotipe menghasilkan 11 haplotipe yang mengelompok menjadi 4 grup. Evolusi Pisang Raja berasal dari dua tetua yaitu M. acuminata dan M. balbisiana. Filogeografi aliran gen ITS pada Pisang Raja berasal dari wilayah Jawa Tengah kemudian menyebar ke Jawa Timur dan Jakarta. Hal ini diduga karena tingginya pemanfaatan yang diikuti oleh penanaman Pisang Raja oleh masyarakat Jawa Tengah untuk acara ritual dan seremonial pada masa lampau yang berpengaruh pada proses domestikasi. Hasil dari penelitian ini dapat menjadi dasar untuk strategi konservasi genetik Pisang Raja.
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Referensi
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
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