Genetic Diversity and Phylogenetic Relationships of Pometia pinnata Variants from South Sumatra Using RAPD Markers
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Laila Hanum , Sandra Novira , Yadi OktariansyahDOI:
10.29303/jbt.v25i4b.10536Published:
2025-11-30Issue:
Vol. 25 No. 4b (2025): Special IssueKeywords:
Biodiversity, Matoa, Phylogenetic relationship, RAPD, Pometia pinnataArticles
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Abstract
Matoa (Pometia pinnata J.R. & G. Forst) is a tropical tree of the Sapindaceae family widely distributed in Southeast Asia, yet the genetic diversity and evolutionary relationships among its variants in South Sumatra remain poorly understood. This study aimed to clarify the genetic structure of four local variants forest, red, yellow, and green matoa using Random Amplified Polymorphic DNA (RAPD) markers. Leaf samples representing each variant were collected across different regions of South Sumatra and analyzed through standard molecular procedures, including DNA extraction and RAPD amplification using five primers. Cluster analysis based on Jaccard’s coefficient and UPGMA revealed two major genetic groups, indicating substantial variation among the studied variants. Red and yellow matoa showed the closest genetic affinity, whereas forest matoa was the most distinct from the others. These findings demonstrate considerable intraspecific diversity within matoa populations in South Sumatra. The study provides essential baseline information that strengthens conservation strategies, supports potential breeding programs, and enhances understanding of the species’ evolutionary patterns within tropical ecosystems.
References
Adjebeng-Danquah, J., Manu-Aduening, J., Asante, I. K., Agyare, R. Y., Gracen, V., & Offei, S. K. (2020). Genetic diversity and population structure analysis of Ghanaian and exotic cassava accessions using simple sequence repeat (SSR) markers. Heliyon, 6(1). DOI: https://doi.org/10.1016/j.heliyon.2019.e03154
Alsaffar, R. S. (2023). Analysis of the genetic distance of several generations of barley (Hordeum vulgare L.) by RAPD–PCR technique. Bionatura, 8(1), 23. DOI: https://doi.org/10.21931/RB/2023.08.01.23
Arsyad, M. A., Irwan, I., Boer, D., Cahyaningsih, Y. F., Larekeng, S. H., & Iswanto, I. (2022). Polimorfisme primer RAPD pada tanaman jambu mete asal tiga kabupaten di Sulawesi Tenggara. Jurnal Galung Tropika, 11(2), 124–131. DOI: https://doi.org/10.31850/jgt.v11i2.888
Aydın, F., Özer, G., Alkan, M., & Çakır, İ. (2022). Start codon targeted (SCoT) markers for the assessment of genetic diversity in yeast isolated from Turkish sourdough. Food Microbiology, 107, 104081. DOI: https://doi.org/10.1016/j.fm.2022.104081
Azizah, U. D. L., Yulianti, F., Adiredjo, A. L., & Sitawati. (2019). Analisis kekerabatan plasma nutfah tanaman stroberi (Fragaria sp.) berdasarkan karakter morfologi dan random amplified polymorphic DNA (RAPD). Plantropica Journal of Agricultural Science, 4(1), 77–85. DOI: https://doi.org/10.21776/ub.jpt.2019.004.1.9
Azzahra, F., Nurfajriya, S., Putri, K. K., Fadhilah, H., Putrizalda, H., Achyar, A., & Ahda, Y. (2024). Karakteristik profil DNA isolat bakteri dari sampel air galon di kantin Laboratorium Kimia FMIPA UNP menggunakan primer OPE 12 dan OPE 14 dengan teknik RAPD. Prosiding SEMNASBIO, Universitas Negeri Padang, 781–787. DOI: https://doi.org/10.24036/prosemnasbio/vol4/954
Babu, K. N., Sheeja, T. E., Minoo, D., Rajesh, M. K., Samsudeen, K., Suraby, E. J., & Kumar, I. P. V. (2020). Random amplified polymorphic DNA (RAPD) and derived techniques. In Molecular plant taxonomy: Methods and protocols (pp. 219–247). New York, NY: Springer US. DOI: https://doi.org/10.1007/978-1-0716-0346-8_13
Ballo, A., & Nge, S. T. (2020). Analisis keragaman genetik pada tanaman kelor (Moringa oleifera) berdasarkan penanda molekuler random amplified polymorphic DNA (RAPD). Jurnal Biotropikal Sains, 17(1), 35–44. URL: https://ejurnal.undana.ac.id/index.php/biotropikal/issue/view/173/5-AB-STN
Choudhury, D. R., Kumar, R., Maurya, A., Semwal, D. P., Rathi, R. S., Gautam, R. K., Trivedi, A. K., Bishnoi, S. K., Ahlawat, S. P., Singh, K., Singh, N. K., & Singh, R. (2023). SSR and SNP Marker-Based Investigation of Indian Rice Landraces in Relation to Their Genetic Diversity, Population Structure, and Geographical Isolation. Agriculture, 13(4), 823. https://doi.org/10.3390/agriculture13040823
Dewanata, P. A., & Mushlih, M. (2021). Perbedaan uji kemurnian DNA menggunakan spektrofotometer UV–Vis dan spektrofotometer Nanodrop pada pasien diabetes melitus tipe 2. Indonesian Journal of Innovation Studies, 15, 1–10. DOI: https://doi.org/10.21070/ijins.v15i.553
Dias, A. C. C., Serra, A. C., Sampaio, D. S., Borba, E. L., Bonetti, A. M., & Oliveira, P. E. (2018). Unexpectedly high genetic diversity and divergence among populations of the apomictic Neotropical tree Miconia albicans. Plant Biology, 20(2), 244–251. DOI: https://doi.org/10.1111/plb.12654
Ebert, A. W., & Engels, J. M. M. (2020). Plant biodiversity and genetic resources matter! Plants, 9(12), 1706. DOI: https://doi.org/10.3390/plants9121706
Emelianova, K., Riaño-Pachón, D. M., & Jiménez, M. F. (2023). Making sense of complexity: Advances in bioinformatics for plant biology. Applications in Plant Sciences, 11(4), e11538. DOI: https://doi.org/10.1002/aps3.11538
Fitriyanti, R. I., Yuniastuti, E., & Nandariyah, N. (2023). Hubungan kekerabatan genetik rambutan (Nephelium lappaceum L.) berdasarkan lima marka RAPD (Random Amplified Polymorphic DNA). Jurnal Agrikultura, 34(2), 264–273. DOI: https://doi.org/10.24198/agrikultura.v34i2.41258
Hajar, S., Rahmah, W., Maharani E., Septian, R. S., & Hamzah, H. (2021). Potensi ekstrak buah matoa (Pometia pinnata) sebagai sumber antioksidan: Literatur review. Jurnal Farmasi Sains dan Praktis, 7(1), 59–66. DOI: https://doi.org/10.31603/pharmacy.v7i1.4240
Hanum, L., Wardana, S., A., Windusari, Y., Aminasih, N., & Patriono, E. (2020). Analysing South Sumatra red rice polymorphism using random amplified polymorphic DNA (RAPD) markers. Journal of Physics: Conference Series, 1480(1), 012069. DOI: https://doi.org/10.1088/1742-6596/1480/1/012069
Hibbins, M. S., Breithaupt, L. C., & Hahn, M. W. (2023). Phylogenomic comparative methods: Accurate evolutionary inferences in the presence of gene tree discordance. Proceedings of the National Academy of Sciences of the United States of America, 120(22), e2220389120. DOI: https://doi.org/10.1073/pnas.2220389120
Hikmatyar, M. F., Royani, J. I., & Dasumiati. (2015). Isolasi dan amplifikasi DNA keladi tikus (Typhonium flagelliform) untuk identifikasi keragaman genetik. Jurnal Bioteknologi & Biosains Indonesia, 2(2), 42–48. URL: http://ejurnal.bppt.go.id/index.php/JBBI
Indow, L., Maturbongs, R. A., Prabawardani, S., & Hendri, H. (2022). Tree species used for fuelwood by remote indigenous communities in West Papua, Indonesia: Implication of empowerment program. Biodiversitas Journal of Biological Diversity, 23(7), 3507–3512. DOI: https://doi.org/10.13057/biodiv/d230725
Jacobs M. 1962. Pometia (Sapindaceae), a study in variability. Herbarium of Bogoriense, Bogor, Indonesia 6(2): 109–144. DOI: https://biologyjournal.brin.go.id/index.php/reinwardtia/issue/view/21
Kapli, P., Yang, Z., & Telford, M. J. (2020). Phylogenetic tree building in the genomic age. Nature Reviews Genetics, 21, 428–444. DOI: https://doi.org/10.1038/s41576-020-0233-0
Kardos, M., Armstrong, E. E., Fitzpatrick, S., Hauser, S., Hedrick, P. W., Miller, J., Tallmon, D., & Funk, W. C. (2021). The crucial role of genome-wide genetic variation in conservation. Proceedings of the National Academy of Sciences of the United States of America, 118, Article e2104642118. DOI: https://doi.org/10.1073/pnas.2104642118
Katad, P., Jadhav, A., Surbhaiyya, S., & Jagtap, K. (2024). Assessment of genetic diversity in tomato (Solanum lycopersicum) varieties by using RAPD markers. Journal of Advances in Biology & Biotechnology, 27(8), 260–267. DOI: https://doi.org/10.9734/jabb/2024/v27i81138
Kesari, V., & Rangan, L. (2011). Genetic diversity analysis by RAPD markers in candidate plus trees of Pongamia pinnata, a promising source of bioenergy. Biomass & Bioenergy, 35, 3123–3128. DOI: https://doi.org/10.1016/j.biombioe.2011.04.015
Khal, L. H., Tahir, N. A.-r., & Abdul-Razaq, R. T. (2023). Molecular variation in some taxa of genus Astragalus L. (Fabaceae) in the Iraqi Kurdistan Region. Horticulturae, 9(10), 1110. DOI: https://doi.org/10.3390/horticulturae9101110
Kundariati, M., Gani, A. R. F., & Pratiwi, J. S. (2021). Analisis hubungan kekerabatan Drosophila sp. (lalat buah) dari Tuban, Kediri, dan Tulungagung berdasarkan indeks similaritas dan dendogram. JBIO: Jurnal Biosains, 7(1), 10–17. DOI:https://doi.org/10.24114/jbio.v7i1.20448
Lukmanasari, P., Zulkifli, E., Ernita, & Wahyudi, R. U. (2024). Keragaman genetik kantong semar berdasarkan penanda Random Amplified Polymorphic DNA (RAPD). Vegetalika, 3(13), 290–307. DOI: https://doi.org/10.22146/veg.92938
Mahar, K. S., Palni, L. M. S., Ranade, S. A., Pande, V., & Rana, T. S. (2017). Molecular analyses of genetic variation and phylogenetic relationship in Indian soap nut (Sapindus L.) and closely related taxa of the family Sapindaceae. Meta Gene, 13, 50–56. DOI: https://doi.org/10.1016/j.mgene.2017.04.009
Massa, A. N., Sobolev, V. S., Faustinelli, P. C., Tallury, S. P., Stalker, H. T., Lamb, M. C., & Arias, R. S. (2024). Genetic diversity, disease resistance, and environmental adaptation of Arachis duranensis L.: New insights from landscape genomics. PLOS ONE, 19(4), e0299992. DOI: https://doi.org/10.1371/journal.pone.0299992
Nafisi, H., Kaveh, A., & Kazempour-Osaloo, S. (2023). Characterizing nrDNA ITS1, 5.8S and ITS2 secondary structures and their phylogenetic utility in the legume tribe Hedysareae with special reference to Hedysarum. PLOS ONE, 18(4), e0283847. DOI: https://doi.org/10.1371/journal.pone.0283847
Novira, S., & Hanum, L. (2025). Hubungan kekerabatan fenetik tanaman kungkil dan matoa (Pometia pinnata J.R. & G. Forst) berdasarkan marka Random Amplified Polymorphic DNA (RAPD) Undergraduate thesis, Sriwijaya University. Sriwijaya University Repository. URL: http://repository.unsri.ac.id/id/eprint/169900
Purnomo, H., Okarda, B., Puspitaloka, D., Ristiana, N., Sanjaya, M., Komarudin, H., & Brady, M. A. (2023). Public and private sector zero-deforestation commitments and their impacts: A case study from South Sumatra Province, Indonesia. Land Use Policy, 134, 106818. DOI: https://doi.org/10.1016/j.landusepol.2023.106818
Putri, A., Yuliana, T., Suzery, M., & Aminin, A. (2023). Total phenolic, flavonoid, and LC–MS analysis of the ethanolic extract of matoa (Pometia pinnata) leaves from Kudus, Central Java, Indonesia. Jurnal Kimia Sains dan Aplikasi, 26(12), 477–482. DOI: https://doi.org/10.14710/jksa.26.12.477-482
Radwan, K. H., Abdelfattah, G. A., Badawi, M. A., Zayedi, E. M., Tard M. M., El-Baghdady, M. M. S., & El-Maksoud, R. M. A. (2021). Genetic variations in some Egyptian Zea mexicana genotypes based on RAPD and AFLP markers. Journal of Bioscience and Applied Research, 7(2), 77–92. DOI: https://doi.org/10.21608/jbaar.2021.177577
Rojas-Cortés, Á. P., Gasca-Pineda, J., González-Rodríguez, A., & Ibarra-Manríquez, G. (2024). Genomic diversity and structure of a Neotropical microendemic fig tree. Ecology and Evolution, 14(3), e11178. DOI: https://doi.org/10.1002/ece3.11178
Saleky, D., & Dailami, M. (2021). Konservasi genetik ikan kakap putih (Lates calcarifer Bloch, 1790) melalui pendekatan DNA barcoding dan analisis filogenetik di Sungai Kumbe, Merauke Papua. Jurnal Kelautan Tropis, 24(2), 141–150. DOI: https://doi.org/10.14710/jkt.v24i2.10760
Salgotra, R., & Chauhan, B. (2023). Genetic diversity, conservation, and utilization of plant genetic resources. Genes, 14(1), 174. DOI: https://doi.org/10.3390/genes14010174
Shelke, R., Basak, S., & Rangan, L. (2020). Development of EST–SSR markers for Pongamia pinnata by transcriptome database mining: Cross–species amplification and genetic diversity. Physiology and Molecular Biology of Plants, 26, 2225–2241. DOI: https://doi.org/10.1007/s12298-020-00865-z
Sofiyanti, S., & Isda, M. N. (2019). Paku kawat Lycopodiella cernua (L.) Pic. Serm. (Lycopodiaceae–Lycopodiales) dari Provinsi Riau–kajian morfologi dan sekuen DNA berdasarkan primer rbcL. Jurnal Biologi Universitas Andalas, 7(1), 43–50. DOI: https://doi.org/10.25077/jbioua.7.1.43-50.2019
Song, S., Cameron, K., Wang, Y., Wang, S., Jin, X., Hina, F., Yang, Z., & Li, P. (2023). Phylogenomics and phylogeography of Menispermaceae. Frontiers in Plant Science, 14, 1280722. DOI: https://doi.org/10.3389/fpls.2023.1280722
Sutomo, S., Hasanah, N., Arnida, A., Sriyono, A. (2021). Standardisasi simplisia dan ekstrak daun matoa (Pometia pinnata J.R. Forst & G. Forst) asal Kalimantan Selatan. Jurnal Pharmascience, 8, 101–108. DOI: https://doi.org/10.20527/jps.v8i2.101
Suwardi, A. B., Navia, Z. I., Harmawan, T., Syamsuardi, S., & Mukhtar, E. (2022). Importance and local conservation of wild edible fruit plants in the East Aceh region, Indonesia. International Journal of Conservation Science, 13(1), 221–232. URL: https://ijcs.ro/public/IJCS-22-17_Suwardi.pdf
Suwardi, A., Navia, Z., Harmawan, T., Syamsuardi, S., & Mukhtar, E. (2020). Wild edible fruits generate substantial income for local people of the Gunung Leuser National Park, Aceh Tamiang Region. Ethnobotany Research and Applications, 20, 1–13. DOI: https://doi.org/10.32859/era.20.15.1-13
Suzuki, T., Nagata, M., Kagawa, N., Takano, S., & Nomura, J. (2021). Anti–obesity effects of matoa (Pometia pinnata) fruit peel powder in high–fat diet–fed rats. Molecules, 26(21), 6733. DOI: https://doi.org/10.3390/molecules26216733
Syamsuardi, S., Mukhtar, E., Nurainas, N., & Suwardi, A. (2022). Diversity and use of wild edible fruits in the Bukit Rimbang–Bukit Baling Wildlife Reserve, Kampar, Riau, Indonesia. Biodiversitas Journal of Biological Diversity, 23(10), 5035–5042. DOI: https://doi.org/10.13057/biodiv/d231025
Tamura, K., Stecher, G., & Kumar, S. (2021). MEGA11: Molecular evolutionary genetics analysis version 11. Molecular Biology and Evolution, 38(7), 3022–3027. DOI: https://doi.org/10.1093/molbev/msab120
Triandiza, T., Kusnadi, A., Sari, N., Pesilette, R. N., Ainarwoman, A., Suparno, & Sapulete, S. (2020). Keragaman genetik kimia kecil (Tridacna maxima) di Pulau Kur, Pulau Biak, dan Manado serta implikasinya untuk konservasi. Jurnal Penelitian Perikanan Indonesia, 26(3), 167–179. DOI: https://doi.org/10.15578/jppi.26.3.2020.167-179
Usman, S. G., & Hanum, L. (2025). Hubungan kekerabatan filogenetik tanaman kungkil dan matoa (Pometia pinnata J.R. & G. Forst) berdasarkan sekuen ITS rDNA. Undergraduate thesis, Sriwijaya University. Sriwijaya University Repository. URL: http://repository.unsri.ac.id/id/eprint/169953
Vankan, M., Ho, S., & Duchêne, D. (2021). Evolutionary rate variation among lineages in gene trees has a negative impact on species–tree inference. Systematic Biology, 71(3), 490–500. DOI: https://doi.org/10.1093/sysbio/syab070
Viana, J., Fang, Y., Avalos, A., Song, Q., Nelson, R., & Hudson, M. (2022). Impact of multiple selective breeding programs on genetic diversity in soybean germplasm. Theoretical and Applied Genetics, 135, 1591–1602. DOI: https://doi.org/10.1007/s00122-022-04069-7
Yoshida, R., Paul, L., & Nesbitt, P. (2022). Stochastic safety radius on UPGMA. Algorithms, 15(12), 483. DOI: https://doi.org/10.3390/a15120483
Yuniastuti, E., Masailla, A., Nandariyah, N., & Rahmah, N. (2023). Karyotyping of green, yellow and red matoa (Pometia pinnata J.R. Forst. & G. Forst.) from Central Java, Indonesia. Biodiversitas Journal of Biological Diversity, 24(1), 40–46. DOI: https://doi.org/10.13057/biodiv/d240107
Yuniastuti, E., Yuliana, A., Sukaya, & Nandariyah. (2023). Genetic diversity of matoa (Pometia pinnata) species based on RAPD markers. SABRAO Journal of Breeding and Genetics, 55(6), 1941–1949.
Yusvita, D., & Idami, Z. (2024). Teknik RAPD (Random Amplified Polymorphic DNA) untuk analisis keanekaragaman genetik pada tanaman ciplukan (Physalis angulata L.) di Kabupaten Labuhan Batu Utara. Bioscientist: Jurnal Ilmiah Biologi, 2(12), 1797–1809. DOI: https://doi.org/10.33387/bioscientist.v2i12.10453
Zhang, G., Huang, M. Z., Huang, W. C., Liu, D. K., Zhang, D., Hu, H., Downing, J. L., Liu, Z. J., & Ma, H. (2023). Comprehensive phylogenetic analyses of Orchidaceae using nuclear genes and evolutionary insights into epiphytism. Journal of Integrative Plant Biology, 65(6), 1204–1225. DOI: https://doi.org/10.1111/jipb.13497
Zulfahmi, Z., Pertiwi, S., Rosmaina, R., Elfianis, R., Gulnar, Z., Zhaxybay, T., Bekzat, M., & Zhaparkulova, G. (2023). Molecular identification of mother trees of four matoa cultivars (Pometia pinnata Forst & Forst) from Pekanbaru City, Indonesia using RAPD markers. Biodiversitas Journal of Biological Diversity, 24(3), 1524–1529. DOI: https://doi.org/10.13057/biodiv/d240318
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