Keragaman Genetik Aksesi Tanaman Kunyit ( Curcuma longa  L.) Berdasarkan Penanda Molekuler  Simple Sequence Repeat  (SSR)

Muthia Hanin Afidani; Noor Farid; Eka Oktaviani

doi:10.22146/veg.99927

Keragaman Genetik Aksesi Tanaman Kunyit (Curcuma longa L.) Berdasarkan Penanda Molekuler Simple Sequence Repeat (SSR)

https://doi.org/10.22146/veg.99927

Muthia Hanin Afidani⁽¹⁾, Noor Farid⁽²⁾, Eka Oktaviani^(3*)

(1) Department of Agrotechnology, Faculty of Agriculture, Universitas Jenderal Soedirman
(2) Department of Agrotechnology, Faculty of Agriculture, Universitas Jenderal Soedirman
(3) Department of Agrotechnology, Faculty of Agriculture, Universitas Jenderal Soedirman
(*) Corresponding Author

Abstract

A plant breeding program for turmeric (Curcuma longa L.) development is required to fulfil the pharmaceutical industry's demand. Understanding genetic diversity is the initial step in selecting the parents in plant breeding. Selection assisted by molecular markers, specifically Simple Sequence Repeat (SSR), can be used to obtain genetic information. However, genetic information on turmeric based on SSR markers in Indonesia is still limited. This study aimed to determine the genetic diversity and relationship of six accessions of turmeric using 4 (four) SSR primers. This study was conducted from October 2023 to January 2024 at the Laboratory of Plant Breeding and Biotechnology, Faculty of Agriculture, Universitas Jenderal Soedirman. The result showed that the CuMiSat-19, CuMiSat-20, and CuMiSat-29 primers were informative based on the electrophoresis band polymorphism. The CuMiSat-19 primer generated the highest PIC value (0,88), followed by CuMiSat-20 (0,80) and CuMiSat-29 (0,74). While CuMiSat-23 did not produce polymorphism, the PIC value was 0. The dendrogram classified six turmeric accessions into the two clusters with a Jaccard correlation coefficient range of 0.11-0.33. Cluster I consisted of accession A (Ponorogo), accession C (Gresik), accession D (Indramayu), and accession B (Semarang). Cluster II grouped accession E (Banyumas) and accession F (Bogor). Based on the polymorphism and similarity coefficient, turmeric accessions have a wide range of genetic diversity. Turmeric in different clusters is a potential germplasm that can be utilized to broaden genetic diversity in plant breeding programs.

Keywords

CuMiSat; genetic diversity; microsatellites; molecular markers; Simple Sequence Repeat (SSR); turmeric

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References

Adisa, S.D., Tripatmasari, M., Suryawati, S., & Wasonowati, C. 2022. Identifikasi morfologi dan rendemen kunyit (Curcuma domestica Val.) di Kecamatan Kamal dan Kecamatan Bangkalan, Kabupaten Bangkalan. Agromix, 13(2): 209–216. Doi: 10.35891/agx.v13i2.2883.

Anindita, P.A., Putri, T.K., Ustari, D., Maulana, H., Rachmadi, M., Concibido, V., Suganda, T., & Karuniawan, A. 2020. Dataset of agromorphological traits in early population of turmeric (Curcuma longa L.) local accessions from Indonesia. Data in Brief, 33: 1–8. Doi: 10.1016/j.dib.2020.106552.

Aswathi, A.P., Baghav, S.B., & Prasath, D. 2022. Assessment of genetic variation in turmeric (Curcuma longa L.) varieties based on morphological and molecular characterization. Genet Resour Crop Evol, 70: 147–158. Doi: 10.1007/s10722-022-01417-3.

Badan Pusat Statistik. 2024. (On-line), Produksi Tanaman Biofarmaka (Obat) 2021-2023. https://www.bps.go.id/id/statistics-table/2/NjMjMg==/produksi-tanaman-biofarmaka--obat-.html diakses 30 November 2024.

Das, A., Gaur, M., Barik, D.P., & Subudhi, E. 2016. Genetic diversity analysis of 60 ginger germplasm core accessions using ISSR and SSR markers. Plant Biosystems, 151: 1–11. Doi: 10.1080/11263504.2016.1211197

Doyle, J. 1991. DNA Protocols for Plants. In: Hewitt, G.M., Johnston, A.W.B., Young, J.P.W. (Eds). Molecular Techniques in Taxonomy. NATO ASI Series, vol 57. Springer, Berlin, Heidelberg. Doi: 10.1007/978-3-642-83962-7_18.

Dudekula, M.V., Kandasamy, V., Balaraman, S.S., Selvamani, S.B., Muthurajan, R., Adhimoolam, K., Manoharan, B., & Natesan, S. 2022. Unlocking the genetic diversity of Indian turmeric (Curcuma longa L.) germplasm based on rhizome yield traits and curcuminoids. Front. Plant Sci., 13 (1036592): 1–15. Doi: 10.3389/fpls.2022.1036592.

Effendy, Respatijarti, & Waluyo, B. 2018. Keragaman genetik dan heritabilitas karakter komponen hasil dan hasil ciplukan (Physalis sp.). Jurnal Agro, 5(1): 30–38. Doi: 10.15575/1864.

Elfianis, R., Warino, J., Rosmaina, Suherman, & Zulfahmi. 2021. Analisis kekerabatan genetik tanaman padi (Oryza sativa L.) di Kabupaten Kampar dengan menggunakan penanda Random Amplified Polymorphic DNA (RAPD). Jurnal Agroteknologi, 11(2): 75–84. Doi: 10.24014/ja.v11i2.10013.

Gogoi, A., Munda, S., Paw, M., Begum, T., Siddiqui, M.H., Gaafar, A.Z., Kesawat, M.S., & Lal, M. 2023. Molecular genetic divergence analysis amongst high curcumin lines of golden crop (Curcuma longa L.) using SSR marker and use in trait‑specifc breeding. Scientific Reports, 13(19690): 1-18. Doi: 10.1038/s41598-023-46779-5.

Gunardi, D.V. 2023. Aktivitas Antioksidan Ekstrak Kloroform dan Etanol dari Beras Putih (Oryza sativa L.) dan Beras Merah (Oryza nivara). Skripsi. Fakultas Kedokteran, Universitas Kristen Indonesia, Jakarta. Retrieved from: http://repository.uki.ac.id/10505/.

Heryanto, R. & Syahid, S.F. 2021. Preliminary study on genetic diversity and relationship of 12 white turmeric (Curcuma zedoaria (Christm.) Roscoe) accessions based on morphological traits. IOP Conf. Series: Earth and Environmental Science 762 (012019): 1–9. Doi: 10.1088/1755-1315/762/1/012019.

Ilahi, A.K. 2020. Keragaman fenotipe dan kemiripan morfologis hanjeli (Coix larcyma-jobi L.) di Kabupaten Lima Puluh Kota. Jurnal Ilmu-Ilmu Pertanian Indonesia, 22(2): 129–135. Doi: 10.31186/jipi.22.2.129-135.

Ilyas, S., Naz, S., Javad, S., & Shahzadi, K. 2018. Genetic divergence among Curcuma longa L. (turmeric) germplasm from Pakistan using RAPD markers. The Journal of Animal & Plant Sciences, 28(2): 597–603. Retrieved from: https://www.thejaps.org.pk/docs/v-28-02/31.pdf.

Ismail, N.A., Rafii, M.Y., Mahmud, T.M.M., Hanafi, M.M., & Miah, G. 2019. Genetic diversity of torch ginger (Etlingera elatior) germplasm revealed by ISSR and SSR markers. BioMed Research Article, 2019 (1): 1–14. Doi: 10.1155/2019/5904804.

Kementerian Kesehatan Republik Indonesia. 2023. Laporan Kinerja 2022. Direktorat Jenderal Pencegahan dan Pengendalian Penyakit, Jakarta. Retrieved from: https://p2p.kemkes.go.id/wp-content/uploads/2023/03/Laporan-Kinerja-Direktorat-Jenderal-P2P-Tahun-2022.pdf.

Kusnadi, S., Novita, I., & Miftah, H. 2020. Analisis pendapatan usahatani dan efisiensi pemasaran kunyit (Curcuma domestica Val). Jurnal Agribsains, 6(1): 50–68. Doi: 10.30997/jagi.v6i1.2806.

Li, X., Qiao, L., Chen, B., Zheng, Y., Zhi, C., Zhang, S., Pan, Y., & Cheng, Z. 2022. SSR markers development and their application in genetic diversity evaluation of garlic (Allium sativum) germplasm. Plant Diversity, 44 (5): 481–491. Doi: 10.1016/j.pld.2021.08.001.

Liu, K. & Muse, S.V. 2005. PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics, 21(9): 2128–2129. Doi: 10.1093/bioinformatics/bti282.

Magar, S.G., Meetei, N.T., Singh, K.N., Khanna, V.K., & Chowdhury, V.K. 2021. Genetic variability of Curcuma sp. accessions of North East Hill region of India using ISSR and RAPD markers. The Pharma Innovation Journal, 10(11): 2781–2787. Retrieved from: https://www.thepharmajournal.com/archives/2021/vol10issue11S/PartAC/S-10-11-169-291.pdf.

Maharani, A.I., Riskierdi, F., Febriani, I., Kurnia, K.A., Rahman, N.A., Ilahi, N.F., & Farma, S.A. 2021. Peran antioksidan alami berbahan dasar pangan lokal dalam mencegah efek radikal bebas. Prosiding Seminar Nasional Biologi, 14 Desember 2021, Padang. Hal. 390–399. Doi: 10.24036/prosemnasbio/vol1/355.

Mehta, M.C., Raghuraman, M., & Srivastava, K. 2023. Student friendly approach of molecular data analysis for the evaluation of genetic diversity. The Pharma Innovation Journal, SP-12(10): 1622–1629. Retrieved from: https://www.thepharmajournal.com/archives/2023/vol12issue10S/PartU/S-12-10-127-765.pdf.

Mollah, A., Ashan, M.A., & Khatimah, A.H. 2022. Uji kualitas dan kuantitas DNA porang (Amorphophallus muelleri Blume) pada beberapa kawasan di Sulawesi Selatan. Agritechno Jurnal Teknologi Pertanian, 15 (1): 1-7. Doi: 10.20956/at.v15i1.688.

Nandakumar, K., Visnuvardhana, Fakrudin, B., Mohan, K.N.V., Brijesh, A., & Venkatesha, J. 2023. Genetic diversity in turmeric (Curcuma longa L.) genotypes using molecular markers. Biological Forum, 15(2):1229–1236. Retrieved from: https://www.researchtrend.net/bfij/pdf/Genetic%20Diversity%20in%20Turmeric%20(Curcuma%20longa%20L.)%20Genotypes%20using%20Molecular%20Markers-Nandakumar%20K-189.pdf.

Nugroho, K., Terryana, T.R., Reflinur, Lestari, P. 2019. Metode ekstraksi DNA tanaman tanpa presipitasi etanol untuk kegiatan Polymerase Chain Reaction (PCR). Jurnal Bioteknologi & Biosains Indonesia, 6(1): 29–38. Doi: 10.29122/jbbi.v6i1.3082.

Patel, P., Patel, R.K., Modha, K.G., Singh, T.J., & Singh, M. 2023. Genetic variability and molecular diversity analysis in turmeric (Curcuma longa L.). Indian Journal of Agricultural Research, 57(4): 500–506. Doi: 10.18805/IJARe.A-5800.

Permatasari, S., Ardiarini, N.R., & Kuswanto. 2018. Analisis hubungan kekerabatan antar galur kecipir (Psophocarpus tertragonolobus L.) lokal. Jurnal Produksi Tanaman, 6(11): 2923–2930. Retrieved from: https://protan.studentjournal.ub.ac.id/index.php/protan/article/view/1019/1037.

Prasath, D., Kandiannan, K., Leela, N.K., Aarthi, S., Sasikumar, B., & Babu, K.N. 2018. Turmeric: Botany and Production Practices. pp. 99–184. In: I. Warrington (Ed), Horticultural Reviews. John Wiley & Sons, Hoboken. Doi: 10.1002/9781119521082.ch3.

Prasetia, R.G.N., Suprayogi, Asnani, A., Oktaviani, E., & Nuryana, I. 2022. Microsatellite markers and metabolite profiles of salt-tolerant rice: Inpari Unsoed 79 Agritan. Caraka Tani: Journal of Sustainable Agriculture, 37(2): 223–232. Doi: 10.20961/carakatani.v37i2.57728.

Prasetiyo, A. & Sonia, N.R. 2021. Peningkatan ekonomi masyarakat melalui produksi dan pemasaran bubuk kunyit temu lawak di Dusun Ngagik, Pacitan. Prodimas, 1: 399–416. Retrieved from: https://prosiding.iainponorogo.ac.id/index.php/prodimas/article/cite/474/MlaCitationPlugin.

Purwoko, D., Pramono, Tajuddin, T., Rismayanti, & Dinuriah, I. 2021. Analisis homogenitas genetik klon apel (Malus spp.) hasil perbanyakan ex vitro berdasarkan penanda SSR. Jurnal Bioteknologi & Biosains Indonesia, 8(1): 57–67. Retrieved from: https://ejournal.brin.go.id/JBBI/article/view/1841.

Putri, T.K., Anindita, P.A., Wicaksana, N., Suganda, T., Concibido, V., & Karuniawan, A. 2020. Keragaman genetik 64 aksesi kunyit asal indonesia berdasarkan marka P450-based analogue (PBA). Buletin Penelitian Tanaman Rempah dan Obat, 31(2): 123–134. Doi: 10.21082/bullittro.v31n2.2020.123-134.

Rohlf, F.J. 2000. NTSYSpc: Numerical taxonomy and multivariate analysis system. Version: 2.1. Exeter Publishing Setauket, New York. Retrieved from: https://www.appliedbiostat.com/ntsyspc/update_NTSYSpc.html.

Senan, S., Kizhakayil, D., Sheeja, T.E., Sasikumar, B., Bhat.A.I., & Parthasarathy, V.A. 2013. Novel polymorphic microsatellite markers from turmeric, Curcuma longa L. (Zingiberaceae). Acta Bot. Croat, 72(2): 407–412. Doi: 10.2478/botcro-2013-0002.

Shan, C.Y. & Iskandar, Y. 2018. Studi kandungan kimia dan aktivitas farmakologi tanaman kunyit (Curcuma longa L.). Farmaka, 16(2): 547–555. Retrieved from: https://jurnal.unpad.ac.id/farmaka/article/view/17610/pdf.

Sholichah, L. 2019. Karakterisasi Genom Kultivar Pisang berdasarkan Marka Morfologi dan Marka Molekuler RAPD (Random Amplified Polymorphic DNA). Skripsi. Fakultas Sains dan Teknologi, Universitas Islam Negeri Maulana Malik Ibrahim, Malang. Retrieved from: http://etheses.uin-malang.ac.id/15232/1/15620111.pdf.

Singh, A.K., Nanda, P., Singh, A., & Singh, B. 2015. Genetic diversity analysis in turmeric (Curcuma longa L.) based on SSR markers. Journal of Biological Engineering Research and Review, 2(1): 20–24. Retrieved from: https://scispace.com/pdf/research-article-genetic-diversity-analysis-in-turmeric-3ac6a1eqf9.pdf.

Subositi, D., Kurnianingrum, N., Mujahid, R., & Widiyastuti, Y. 2020. Kaempferia galanga L. a medicinal plant used by Indonesian ethnic groups: genetic diversity based on Inter-Simple Sequence Repeats (ISSR). Agrivita Journal of Agricultural Science, 42(1): 45–52. Doi: 10.17503/agrivita.v42i1.1850.

Subositi, D., Widodo, H., Mujahid, R., Rahmawati, N., Mustofa, F.I., Haryanti, S., Sholikhah, I.Y.M., Maruzy, A., & Widiyastuti, Y. 2022. Genetic diversity and chemicals profile of ginger (Zingiber officinale Roscoe) in Indonesia. IJASEIT, 12(3): 929–936. Doi: 10.18517/ijaseit.12.3.15660.

Suprihatin, T. Rahayu, S., Rifa’i, M., & Widyarti, S. 2020. Senyawa pada serbuk rhizome powder (Curcuma longa L.) yang berpotensi sebagai antioksidan. Buletin Anatomi dan Fisiologi, 5(1): 35–42. Doi: 10.14710/baf.5.1.2020.35-42.

Terryana, R.T., Ningrum, N.D.S.A., Nugroho, K., Saptadi, D., Kurniawan, H., & Lestari, P. 2023. Analisis keragaman genetik dan pengembangan profil sidik jari DNA 20 varietas cabai lokal Indonesia berdasarkan marka SSR. Jurnal AgroBiogen, 16(2):45–58. Doi: 10.21082/jbio.v16n2.2020.p45-58.

Trimanto, Dwiyanti, D., & Indriyani, S. 2017. Morfologi, anatomi dan uji histokimia rimpang Curcuma aeruginosa Roxb; Curcuma longa L. dan Curcuma heyneana Valeton dan Zijp. Berita Biologi, 17(2): 123–133. Doi: 10.14203/beritabiologi.v17i2.3086.

Tsykun, T., Rellstab, C., Dutech, C., Sipos, G., & Prospero, S. 2017. Comparative assessment of SSR and SNP markers for inferring the population genetic structure of the common fungus Armillaria cepistipes. Heredity, 119: 371–380. Doi: 10.1038/hdy.2017.48.

Vasek, J., Cilova, D., Melounova, M., Svoboda, P., Vejl, P., Stikarova, R., Vostry, L., Kuchtova, P., & Ovesna, J. 2020. New EST-SSR Markers for individual genotyping of opium poppy cultivars (Papaver somniferum L.). Plants, 9(10): 1–15. Doi: 10.3390/plants9010010.

Verma, S., Singh, S., Sharma, S., Tewari, S.K., Roy, R.K., Goel, A.K., & Rama, T.S. 2015. Assessment of genetic diversity in indigenous turmeric (Curcuma longa) germplasm from India using molecular markers. Physiol Mol Biol Plants, 21(2): 233–242. Doi: 10.1007/s12298-015-0286-2.

Vieira, M.L.C., Santini, L., Diniz, A.L., Munhoz, C.F. 2016. Microsatellite markers: what they mean and why they are so useful. Genetics and Molecular Biology, 39(3): 312–328. Doi: 10.1590/1678-4685-GMB-2016-0027.

Wati, H.D., Ekawati, I. & Ratna, P. 2022. Keragaman genetik dan heritabilitas karakter komponen hasil jagung varietas lokal Sumenep. Cemara, 19(1): 85–94. Doi: 10.24929/fp.v19i1.1985.

Yuan, J., Zhang, X., Wang, M., Sun, Y., Liu, C., Li, S., Yu, Y., Gao, Y., Liu, F., Zhang, X., Kong, J., Fan, G., Zhang, C., Feng, L., Xiang, J., & Li, F. 2021. Simple sequence repeats drive genome plasticity and promote adaptive evolution in penaeid shrimp. Communications Biology, 4(186): 1–14. Doi: 10.1038/s42003-021-01716-y.

DOI: https://doi.org/10.22146/veg.99927