Molecular Characteristics of Cassava Carvita 25 Somaclonal Variant Using SSR Marker
Abstract
Cassava is one of the most important food commodities besides rice and corn. Carvita 25 is a somaclonal variation that was induced from Adira IV cassava variety. Our study aimed to analyze the genetic differences of Carvita 25 compared to Adira IV by using SSR markers. Two cassava varieties, Carvita 25 and Adira IV, were used as plant materials and eleven SSRY primers were used to amplifythe fragments of cassava DNA. The results showed that SSRY 151 primer produced the highest polymorphic band (85.71%) where 6 out of 7 alels were polymoprphics with the length size from 120 to 600 bp. Of the total 56 of polymorphic bands, 26 alels were previously present in Adira IV but then it can not be found in Carvita 25, while 30 other bands were new fragments that were previously not present in Adira IV but then were present in Carvita 25. These genetic differencesof both Adira IV and Carvita 25 were also strengthened by the Jacard similarity value. The Jaccard similarity between Carvita 25 and Adira IV were 0.40-0.50, while the similarity between plants of Carvita 25 were 0.79-0.87, and in plants of Adira IV were 0.98- 1.These values showed thewide genetic difference between Adira IV and a somaclonal variation of Carvita 25.
Keywords: cassava, Carvita 25, polymorphic, somaclonal variation, SSR Marker.
References
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Sharp MJ & Hayden P. 2001. Targeted development of informative SSR (SSR) markers. Nucleic Acids Research.29 (8): 44.
Suryana A. 2006. Kebijakan penelitian dan pengembangan ubikayu untuk agroindustri dan ketahanan pangan. Lokarya Pengembangan Ubikayu di Balitkabi, Malang, 7-8 September 2006.
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Wargiono J, Hasanuddin A & Suyamto.2006. Teknologi produksi ubi kayu mendukung industri bioetanol. Puslitbangtan. Bogor.
Widiastuti A, Sobir M & Suhartanto R. 2013. Analisis Keragaman Genetik Manggis (Garcinia Mangostana) Diiradiasi Dengan Sinar Gamma Berdasarkan Penanda SSR.Bioteknologi.10 (1): 15-22.
Yunita R. 2009. Pemanfaatan Variasi Somaklonal dan Seleksi in Vitro dalam Perakitan Tanaman Toleran Cekaman Abiotik. Jurnal Litbang Pertanian. 28(4): 142-148.
Zhang S, Ma P, Wang H, Lu C, Chen X, Xia Z, Zou M, Zhou X & Wang W. 2014. Genomics Approaches to Unlock the Heigh Yield Potential of Cassava, a Tropical Model Plant. Front. Agr. Scie. Eng. 1(4):259-266.
Anil VA, Bennur S & Lobo S. 2018. Somaclonal Variations for Crop Improvement: Selection for Disease Resistant Variants in Vitro. Plant Science Today. 5(2): 44-54.
Azrai M. 2006. Sinergi Teknologi Marka Molekuler dalam Pemuliaan Tanaman Jagung. Jurnal Litbang Pertanian. 25(3) : 81-89.
Balitkabi. 2004. Balai Penelitian Tanaman Kacang-kacangan dan Umbi-umbian. Malang.
Balitkabi. 2005. Teknologi produksi kacang-kacangan dan umbi-umbian. Balai Penelitian Tanaman Kacang-kacangan dan Umbi-umbian Malang, Kementerian Pertanian.
Basuki TMD. 2018. Aanlisis Keragama Genetik Sepuluh Aksesi Cabai Merah (Capsicum annuum L.) Indonesia Menggunakan Marka Random Amplified Polymorphic DNA. [Skripsi]. Jurusan Pertanian. Fakultas Pertanian. Universitas Jendral Soedirman, Purwokerto
Cao Z, Sui S, Cai X, Yang Q & Deng Z. 2016. Somaclonal Variation in Red Flash Caladium morphological, Cytological and Molecular Characterization. Plant Cell, Tissue and Organ Culture. 126(2): 269-279.
Delgarado-Paredes GE, Rojas-Idrogo C, Chaneme-Cespedes J, Floh EIS & Handro W. 2017. Development and Agronomic Evaluation of in Vitro Somaclonal Variation in Sweet Potato Regenerated Plants from Direct Organogenesis of Roots. Asian Journal of Plant Science and Research.7(1): 39-48.
Ferguson M, Rabbi I, Jin Kim D, Gedil M, Lopez-Lavalle LAB & Okogbenin E. 2012. Molecular Markers and Their Application to Cassava Breeding: Past, Present and Future. Tropical Plant Biol. 5:95–109.
Fitriani H, Supatmi & Sudarmonowati E. 2018. Induksi embriogenesis somatik untuk perbanyakan bibit dan perbaikan mutu genetik ubi kayu. Dalam: Sudarmonowati E, Hartati NS, Hartati. Biodiversitas, Perakitan Klon Unggul dan Pemanfaatan bioresources ubi kayu untuk mendukung ketahanan pangan. LIPI Press, Jakarta.
Hammer O, Tarper DAT & Ryan PD. 2001. Paleontological Statistics Software Package for Education and Data Analysis. Palaentologia Electronica. 4 (1):9-18.
Hartati NS, Fitriani H, Supatmi & Sudarnonowati E. 2012. Karakter umbi dan nutrisi tujuh genotip ubi kayu(Manihot esculenta). Jurnal Agricola. 2(2): 101-110.
Hartati, Fathoni A, Kurniawati S, Hartati NS & Sudarmonowati E. 2017. Technological Innovation in The Protection of Beta Carotene on Mocaf Production which is Rich in Beta Carotene. Nusantara Bioscience. 9(1): 6-11.
Karihaloo LJ. 2015. DNA Fingerprinting Techniques for Plant Identification. In: Plant Biology and Biotechnology. Springer. India
Krishna H, Alizadeh M, Singh D, Singh U, Chauhan N, Eftekhari M & Sadh RK. 2016. Somaclonal Variations and Their Applications in Horticultural Crops Improvement. 3 Biotech. 6(1):54.
Lestari EG, Dewi IS, Yunita R & Sukmadjaja D. 2010. Induksi Mutasi dan Keragaman Somaklonal untuk Meningkatkan Ketahanan Penyakit Blas Daun pada Padi Fatmawati. Buletin Plasma Nutfah.16(2): 96-102
Manchanda P, Kaur A & Gosal SS. 2018. Somaclonal Variation for Sugarcane Improvement. Dalam Gosal SS & Wani SH (eds.). Biotechnologies of Crop Improvement, 1: 299-326. Springer International Publishing AG.
Mba REC, Stephensen P, Edwards K, Melzer S, Nkumbira J, Gullberg U, Apel K, Gale M, Tohme J & Fregene M.2001. Simple Sequence Repeat (SSR) Markers Survey of the Cassava (Manihot esculenta Crantz) Genome: Towards and SSR-based Molecular Genetik Map of Cassava. Theor Appl Genet. 102:21–31.
Mulsanti IW, Surahman M, Wahyuni S & Utami DW. 2013. Identifikasi Galur Tetua Padi Hibrida dengan Marka SSR Spesifik dan Pemanfaatannya dalam Uji Kemurnian Benih. Penelitian Pertanian Tanaman Pangan. 32 (1) : 1-8.
Podwyszynska M, Niedoba K, Korbin M& Marasek A. 2006. Somaclonal Variation In Micropropagated Tulips Determined By Phenotype And DNA Markers. Acta Hortic. 714: 211-220.
Poerba YS & Martanti D. 2008. Keragaman genetik berdasarkan marka random amplified polymorphic DNA pada Amorphophallus muelleri Blume di Jawa. Biodiversitas. 9(4): 245-249.
Raji A, Anderson J, Kolade O, Ugwu C, Dixon A & Ingelbrecht I.2009. Gene-based SSRs for cassava (Manihot esculenta Crantz): prevalence, polymorphisms, and cross-taxa utility. BMC Plant Biol. 9:118.
Sato M, Hosokawa M & Doi M. 2011. Somaclonal variation is induced de novo via the tissue culture process: a study quantifying mutated cells in Saintpaulia. PLoS ONE. 6:e23541.
Sharp MJ & Hayden P. 2001. Targeted development of informative SSR (SSR) markers. Nucleic Acids Research.29 (8): 44.
Suryana A. 2006. Kebijakan penelitian dan pengembangan ubikayu untuk agroindustri dan ketahanan pangan. Lokarya Pengembangan Ubikayu di Balitkabi, Malang, 7-8 September 2006.
Sraphet S, Boonchanawiwat A, Thanyasiriwat T, Boonseng O, Tabata S, Sasamoto S, Shirasawa K, Isobe S, Lightfoot D, Tangphatsornruang S & Triwitayakorn K. 2011. SSR and EST-SSR-based genetik linkage map of cassava (Manihot esculenta Crantz). Theor Appl Genet.122:1161–1170.
Wargiono J, Hasanuddin A & Suyamto.2006. Teknologi produksi ubi kayu mendukung industri bioetanol. Puslitbangtan. Bogor.
Widiastuti A, Sobir M & Suhartanto R. 2013. Analisis Keragaman Genetik Manggis (Garcinia Mangostana) Diiradiasi Dengan Sinar Gamma Berdasarkan Penanda SSR.Bioteknologi.10 (1): 15-22.
Yunita R. 2009. Pemanfaatan Variasi Somaklonal dan Seleksi in Vitro dalam Perakitan Tanaman Toleran Cekaman Abiotik. Jurnal Litbang Pertanian. 28(4): 142-148.
Zhang S, Ma P, Wang H, Lu C, Chen X, Xia Z, Zou M, Zhou X & Wang W. 2014. Genomics Approaches to Unlock the Heigh Yield Potential of Cassava, a Tropical Model Plant. Front. Agr. Scie. Eng. 1(4):259-266.
Published
2020-07-03
How to Cite
HARTATI, Hartati et al.
Molecular Characteristics of Cassava Carvita 25 Somaclonal Variant Using SSR Marker.
Jurnal ILMU DASAR, [S.l.], v. 21, n. 2, p. 87-96, july 2020.
ISSN 2442-5613.
Available at: <https://jurnal.unej.ac.id/index.php/JID/article/view/9396>. Date accessed: 06 nov. 2024.
doi: https://doi.org/10.19184/jid.v21i2.9396.
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