Sains Malaysiana 54(2)(2025): 449- 460

http://doi.org/10.17576/jsm-2025-5402-11

 

Genetic Diversity of Garut Mutant (Maranta arundinacea L.) (M3) with Random Amplified Polymorphic DNA (RAPD) Analysis

(Kepelbagaian Genetik Mutan Garut (Maranta arundinacea L.) (M3) dengan Analisis DNA Polimorfik Diperkuat Rawak (RAPD))

 

Yashanti Berlinda Paradisa¹, Puspita Deswina^2,*, Dodi Priadi², Yuliana Galih Dyan Anggraheni¹, Santi Nurbaeti³, Liberty Chaidir³ & Noladhi Wicaksana⁴

 

¹Research Center for Genetic Engineering, Research Organization for Life Sciences and Environment, National Research and Innovation Agency Indonesia
²Research Center for Horticulture, Research Organization for Agriculture and Food, National Research and Innovation Agency Indonesia
³Department of Agrotechnology, Faculty of Science and Technology, UIN Sunan Gunung Djati Bandung, Indonesia
⁴Faculty of Agriculture, Padjadjaran University, Jalan Raya Bandung-Sumedang KM 21, Jatinangor, Sumedang 45363 West Java, Indonesia

 

Received: 4 June 2024/Accepted: 6 November 2024

 

Abstract

Arrowroot is a type of tuber that is rich in carbohydrates. This plant can grow well in various parts of Indonesia. However, arrowroot has a low level of genetic diversity, making it difficult to obtain superior varieties with high productivity. Mutation treatment with gamma-ray radiation is expected to increase the diversity of arrowroot to produce superior-quality plants. This study aimed to determine the genetic diversity of arrowroot mutants resulting from the 4th generation of gamma-ray radiation (M3). The research analysed molecular markers using Random Amplified Polymorphic DNA (RAPD). A total of 30 samples of arrowroot M3 DNA were amplified using 11 selected primers. The results of the analysis show that there are six specific primers selected from the selection, which have the potential to produce high polymorphism bands that can be used for diversity analysis. The similarity index of arrowroot mutant is 0.69 to 0.99, which means that it still has a high similarity between arrowroot mutant. Based on genetic similarity of 84%, mutant arrowroot (M3) can be divided into 7 clusters.

 

Keywords: DNA; Garut mutant; genetic diversity; RAPD

 

Abstrak

Ubi garut adalah sejenis ubi yang kaya dengan karbohidrat. Tumbuhan ini boleh tumbuh dengan baik di pelbagai tempat di Indonesia. Walau bagaimanapun, ubi garut mempunyai tahap kepelbagaian genetik yang rendah, menjadikannya sukar untuk mendapatkan varieti unggul dengan produktiviti tinggi. Rawatan mutasi dengan sinaran sinar gamma dijangka meningkatkan kepelbagaian anak panah untuk menghasilkan tumbuhan berkualiti tinggi. Kajian ini bertujuan untuk menentukan kepelbagaian genetik mutan ubi garut yang terhasil daripada sinaran sinar gamma (M3) generasi ke-4. Penyelidikan menganalisis penanda molekul menggunakan DNA Polimorfik Diperkuat Rawak (RAPD). Sebanyak 30 sampel DNA M3 anak panah telah dikuatkan menggunakan 11 primer terpilih. Hasil analisis menunjukkan terdapat enam primer khusus yang dipilih daripada pemilihan yang berpotensi menghasilkan jalur polimorfisme tinggi yang boleh digunakan untuk analisis kepelbagaian. Indeks kesamaan mutan ubi garut adalah 0.69 hingga 0.99, yang bermaksud ia masih mempunyai persamaan yang tinggi antara mutan ubi garut. Berdasarkan persamaan genetik sebanyak 84%, anak panah mutan (M3) boleh dibahagikan kepada 7 kelompok.

 

Kata kunci: DNA; kepelbagaian genetik; mutan garut; RAPD

 

REFERENCES

Abdullah, S., Kamaruddin, N.Y. & Harun, A.R. 2018. The effect of gamma radiation on plant morphological characteristics of Zingiber officinale Roscoe. International Journal on Advanced Science, Engineering and Information Technology 8(5): 2085-2091. doi:10.18517/ijaseit.8.5.4641

Ali, H., Ghori, Z., Sheikh, S. & Gul, A. 2015. Effects of gamma radiation on crop production. In Crop Production and Global Environmental Issues, edited by Hakeem, K.R. Springer, Cham. pp. 27-78. doi:10.1007/978-3-319-23162-4

Anshori, S.R., Aisyah, S.I. & Darusman, L.K. 2014. Induksi mutasi fisik dengan iradiasi sinar gamma pada kunyit (Curcuma domestica Val.). Jurnal Hortikultura Indonesia 5(03): 84-94. doi:10.29244/jhi.5.2.84-94

Carsono, N., Lukman, P.N., Damayanti, F., Susanto, U. & Sari, S. 2014. Identifikasi polimorfis marka-marka molekuler yang diduga berkaitan dengan karakter daya hasil tinggi pada 30 genotip padi. Chimica et Natura Acta 2(1): 91-95. doi:10.24198/cna.v2.n1.9141

Chatterjee, S. & Raval, I.H. 2019. Pathogenic microbial genetic diversity with reference to health. In Microbial Diversity in the Genomic Era, edited by Das, S. & Dash, H.R. Elsevier Inc. pp. 559-578. doi:10.1016/B978-0-12-814849-5.00032-0

Choi, H., Han, S.M., Jo, Y.D., Hong, M.J., Kim, S.H. & Kim, J. 2021. Effects of acute and chronic gamma irradiation on the cell biology and physiology of rice plants. Plants 10(3): 439. doi:10.3390/plants10030439

Deswina, P., Prihastuti, L. & Saputra, A. 2019. Cytomorphological characteristics evaluation of the third generation of arrowroot plant (Maranta arundinacea L.) radiated by gamma ray. Jurnal Agro 6(2): 181-195. doi:10.15575/6104

Dhakshanamoorthy, D., Selvaraj, R. & Chidambaram, A. 2015. Utility of RAPD marker for genetic diversity analysis in gamma rays and ethyl methane sulphonate ( EMS ) - treated Jatropha curcas plants. Comptes Rendus Biologies 338(2): 75-82. doi:10.1016/j.crvi.2014.12.002

Doyle, J. & Doyle, J. 1990. Isolation of plant DNA from fresh tissue. Focus 12: 13-15.

Du, Y., Feng, Z., Wang, J., Jin, W., Wang, Z., Guo, T., Chen, Y., Feng, H., Yu, L., Li, W. & Zhou, L. 2022. Frequency and spectrum of mutations induced by gamma rays revealed by phenotype screening and whole-genome re-sequencing in Arabidopsis thaliana. International Journal of Molecular Sciences 23(2): 654. doi:10.3390/ijms23020654

Dwivedi, S., Singh, S., Chauhan, U.K. & Tiwari, M.K. 2018. Inter and intraspecific genetic diversity (RAPD) among three most frequent species of macrofungi (Ganoderma lucidum, Leucoagricus sp. and Lentinus sp.) of tropical forest of Central India. Journal of Genetic Engineering and Biotechnology 16(1): 133-141. doi:10.1016/j.jgeb.2017.11.008

Effendi, Y. & Palupi, E.A. 2013. Uji produksi bioetanol sebagai bahan bakar dari umbi garut (Maranta arundinacea Linn) menggunakan katalisator pupuk urea sebagai exstender premium. Jurnal Teknik Mesin 02(2): 36-43. https://docplayer.info/44377494-Arundinacea-linn-menggunakan-katalisator-pupuk-urea-sebagai-exstender-premium.html

Ghasemi-Soloklui, A.A., Kordrostami, M. & Karimi, R. 2023. Determination of optimum dose based of biological responses of lethal dose (LD_{25, 50, 75}) and growth reduction (GR_{25, 50, 75}) in ‘Yaghouti’ grape due to gamma radiation. Scientific Reports 13: 2713. doi:10.1038/s41598-023-29896-z

Grema, M.N., Ismail, H.Y. & Muhammad, S. 2022. Comparative study on the effect of biofertilizer, organic and inorganic fertilizers on chlorophyll and moisture contents of Pennisetum typhoides. UMYU Scientifica 2(1): 1-7. doi:10.56919/usci.2123.001

Guseva, J., Smolina, G. & Torshin, S. 2022. Effect of γ-radiation of lettuce seeds (Lactuca sativa L.) for the yield and removal of macronutrients by plants. BIO Web of Conferences. doi: 10.1051/bioconf/20224705008

Gusmiaty, G., Restu, M., Asrianny & Larekeng, S.H. 2016. Polimorfisme penanda RAPD untuk analisis keragaman genetik Pinusmerkusii di Hutan Pendidikan Unhas. Jurnal Natur Indonesia 16(2): 47-53. doi:10.31258/jnat.16.2.47-53

Hong, M.J., Kim, D.Y., Ahn, J., Kang, S., Seo, Y.W. & Kim, J. 2018. Comparison of radiosensitivity response to acute and chronic gamma irradiation in colored wheat. Genetics and Molecular Biology 41(3): 611-623. doi:10.1590/1678-4685-GMB-2017-0189

Jan, S., Parween, T. & Siddiqi, T.O. 2012. Effect of gamma radiation on morphological, biochemical, and physiological aspects of plants and plant products. Environmental Reviews 39: 17-39. doi:10.1139/A11-021

Lim, T.K. 2016. Edible Medicinal and Non-Medicinal Plants: Volume 11, Modified Stems, Roots, Bulbs. Springer International Publishing Switzerland. doi:10.1007/978-3-319-26062-4

Madineni, M.N., Faiza, S., Surekha, R.S., Ravi, R. & Guha, M. 2012. Morphological, structural, and functional properties of maranta (Maranta arundinacea L.) starch. Food Science and Biotechnology 21(3): 747-752. doi:10.1007/s10068-012-0097-y

Madrigal, K.B., Arias, C.Á., Cruz, R.M., Ramos, L.S., Murillo, R.P. & Vargas, P.H. 2018. Relation of chlorophyll and foliar nitrogen of Gmelina arborea Roxb. at the nursery and in the field. Revista Mexicana de Ciencias Forestales 9(46). doi:10.29298/rmcf.v9i46.124

Maoka, T. 2020. Carotenoids as natural functional pigments. Journal of Natural Medicines 74(1): 1-16. doi:10.1007/s11418-019-01364-x

Martida, V. & Pharmawati, M. 2016. Pemilihan primer RAPD (Random Amplified Polymorphic DNA) pada PCR (Polymerase Chain Reaction) tanaman kamboja (Plumeria sp.). Jurnal Simbiosis IV(1): 16-18. https://ojs.unud.ac.id/index.php/simbiosis/article/view/21226

Meliala, J.H.S., Basuki, N. & Seogianto, A. 2016. Pengaruh iradiasi sinar gamma terhadap perubahan fenotipik tanaman padi gogo (Oryza sativa L.). Jurnal Produksi Tanaman 4(7): 585-594.

Nurtjahjaningsih, I.L.G., Haryanti, T., Widyatmoko, A., Indrioko, S. & Rimbawanto, A. 2015. Keragaman genetik populasi Calophyllum inophyllum menggunakan penanda RAPD (Random Amplification Polymorphism DNA). Jurnal Pemuliaan Tanaman Hutan 9(2): 91-102. doi:10.20886/jpth.2015.9.2.103-115

Osakabe, Y., Watanabe, T., Sugano, S.S., Ueta, R., Ishihara, R., Shinozaki, K. & Osakabe, K. 2016. Optimization of CRISPR/Cas9 genome editing to modify abiotic stress responses in plants. Scientific Reports 6: 26685. doi:10.1038/srep26685

Padmalatha, K. & Prasad, M.N.V. 2006. Optimization of DNA isolation and PCR protocol for RAPD analysis of selected medicinal and aromatic plants of conservation concern from Peninsular India 5: 230-234. doi:10.5897/AJB05.188

Panigrahi, S., Velraj, P. & Rao, T.S. 2019. Functional microbial diversity in contaminated environment and application in bioremediation. In Microbial Diversity in the Genomic Era, edited by Das, S. & Dash, H.R. pp. 359-386. Elsevier Inc. doi:10.1016/B978-0-12-814849-5.00021-6

Paradisa, Y.B., Deswina, P. & Mulyaningsih, E.S. 2016. Keragaman genetik garut (Maranta arundinaceae) di kebun plasma nutfah Cibinong Science Centre dengan analisis marka Random Polymorphic DNA. Prosiding Kongres Teknologi Nasional 2016: Inovasi Teknologi untuk Kejayaan Bangsa dan Negara. Badan Pengkajian dan Penerapan Teknologi. pp. 533-540.

Perucka, I., Olszówka, K. & Chilczuk, B. 2013. Changes in the chlorophyll content in stored lettuce Lactuca sativa L. after pre-harvest foliar application of CaCl2. Acta Agrobotanica 66(4): 137-142. doi:10.5586/aa.2013.060

Reddy, P.P. 2015. Plant Protection in Tropical Root and Tuber Crops, 1st ed. New Delhi: Springer. doi:10.1007/978-81-322-2389-4

Respati, A.N., Umami, N. & Hanim, C. 2018. Growth and production of Brachiaria brizantha cv. MG5 in three difference regrowth phase treated by gamma radiation dose. Tropical Animal Science Journal 41(3): 179-184. doi:10.5398/tasj.2018.41.3.179

Roldan-Ruiz, I., Calsyn, E., Gilliland, T.J., Coll, R., Van Eijk, M.J.T. & De Loose, M. 2000. Estimating genetic conformity between related ryegrass (Lolium) varieties. 2. AFLP characterization. Molecular Breeding 6: 593-602. doi:10.1023/A:1011398124933

Saragih, S.H.Y., Aisyah, S.I. & Sobir. 2019. Induksi mutasi tanaman leunca (Solanum nigrum L.) untuk meningkatkan keragaman kandungan tanin. Jurnal Agronomi Indonesia 47(1): 84-89. doi:10.24831/jai.v47i1.19502

Shen, J., Jiang, C.Q., Yan, Y.F., Liu, B.R. & Zu, C.L. 2017. Effect of increased UV-B radiation on carotenoid accumulation and total antioxidant capacity in tobacco (Nicotiana tabacum L.) leaves. Genetics and Molecular Research 16(1): gmr16018438. doi:10.4238/gmr16018438

Shirley, B.W., Hanley, S. & Goodman, H.M. 1992. Effects of ionizing radiation on a plant genome: Analysis of two Arabidopsis transparent testa mutations. Plant Cell 4(3): 333-347. doi:10.1105/tpc.4.3.333

Side, T.H.R., Abdurrakhman, A., Djumali, D., Herwati, A., Yulaikah, S. & Supriyono, S. 2023. Developing determination of gamma irradiation dose to increase sugarcane growth and yield. E3S Web of Conferences 373: 03013. doi:10.1051/e3sconf/202337303013

Sobrizal. 2016. Potensi Pemuliaan Mutasi untuk Perbaikan Varietas Padi Lokal Indonesia. Jurnal Ilmiah Aplikasi Isotop dan Radiasi 12(1): 23-36. doi:10.17146/jair.2016.12.1.3198

Sudrajat, D.J., Rohandi, A., Yulianti, Nurhasybi, Rustam, E., Budiadi, Hardiwinoto, S. & Harmayani, E. 2023. Growth, tuber yield, and starch content of arrowroot (Maranta arundinacea) accessions on different altitudes and tree shades. Plant Physiology Reports 28(2): 221-230. doi:10.1007/s40502-023-00721-z

Suhartini, T. & Hadiatmi, N. 2016. Keragaman karakter morfologis garut (Marantha arundinaceae L.). Buletin Plasma Nutfah 17(1): 12-18. doi:10.21082/blpn.v17n1.2011.p12-18

Sumanta, N., Haque, C.I., Nishika, J. & Suprakash, R. 2014. Spectrophotometric analysis of chlorophylls and carotenoids from commonly grown fern species by using various extracting solvents. Research Journal of Chemical Sciences 4(9): 63-69.

Tanaka, A., Shikazono, N. & Hase, Y. 2010. Studies on biological effects of ion beams on lethality, molecular nature of mutation, mutation rate, and spectrum of mutation phenotype for mutation breeding in higher plants. Journal of Radiation Research 51(3): 223-233. doi:10.1269/jrr.09143

Tarique, J., Sapuan, S.M., Khalina, A., Sherwani, S.F.K., Yusuf, J. & Ilyas, R.A. 2021. Recent developments in sustainable arrowroot (Maranta arundinacea Linn) starch biopolymers, fibres, biopolymer composites and their potential industrial applications: A review. Journal of Materials Research and Technology 13: 1191-1219. doi:10.1016/j.jmrt.2021.05.047

Tilwari, A. & Sharma, R. 2021. Random amplified polymorphic DNA and inter simple sequence repeat markers reveals genetic diversity between micro propagated, wild and field cultivated genotypes of Gloriosa superba: An endangered medicinal plant. Molecular Biology Reports 48(3): 2437-2452. doi:10.1007/s11033-021-06278-0

Widyatmoko, A., Rimbawanto, A. & Chasani, A.R. 2013. Hubungan kekerabatan antar populasi jati (Tectona grandis Linn. F.) berdasarkan penanda RAPD (Random Amplified Polymorphic DNA). Jurnal Pemuliaan Tanaman Hutan 7(3): 151-166. doi:10.20886/jpth.2013.7.3.151-166

Yu, Q., Han, H., Vila-Aiub, M.M. & Powles, S.B. 2010. AHAS herbicide resistance endowing mutations: Effect on AHAS functionality and plant growth. Journal of Experimental Botany 61(14): 3925-3934. doi:10.1093/jxb/erq205

Zhang, Y., Huang, J., Wang, F., Blackburn, G.A., Zhang, H.K., Wang, X., Wei, C., Zhang, K. & Wei, C. 2017. An extended PROSPECT: Advance in the leaf optical properties model separating total chlorophylls into chlorophyll a and b. Scientific Reports 7: 6429. doi:10.1038/s41598-017-06694-y

 

*Corresponding author; email: pusp002@brin.go.id