ANALISIS FILOGENETIK BEBERAPA KLON KARET DENGAN MARKA AFLP (AMPLIFIED FRAGMENT LENGTH POLYMORPHISM)
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Abstract
Produktivitas karet nasional masih lebih rendah dibanding dengan negara-negara penghasil karet lainnya di dunia. Diperlukan program pemuliaan tanaman karet yang berbasis marka DNA untuk meningkatkan produksi lateks serta karakter unggul lainnya. Proses pemuliaan untuk mengidentifikasi keragaman genetik bisa dilakukan dengan marka AFLP. Tujuan studi ini adalah untuk menganalisis filogenetik enam klon karet berdasarkan produktivitasnya. Proses pre-amplifikasi dan amplifikasi dilakukan dengan menggunakan 64 kombinasi pasangan primer yang dilanjutkan dengan analisis hasil elektroforesis pada gel poliakrilamid 6%. Sebanyak 2806 pita AFLP telah dihasilkan. Kekerabatan keenam klon menunjukkan kemiripan genetik sebesar 60%. Pohon filogenetik membentuk dua kelompok, yang memisahkan GT 1 dengan klon-klon lainnya. Sub-kelompok pada puncak filogenetik terdiri dari klon IRR 104 dan RRIM 600 dengan kemiripan genetik sebesar 74%. Informasi yang diperoleh telah menunjukkan keragaman genetik keenam klon karet yang bersifat polimorfis. Diperoleh pita-pita unik dari pasangan primer tertentu yang dapat berperan sebagai marka spesifik dan dapat digunakan untuk mengidentifikasi klon.
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References
Bakhtiar Y, Yahya S, Sumaryono W, Sinaga MS, Budi SW, Tajuddin T (2010) Isolation and identification of Mycorrhizosphere bacteria and their antagonistic effects towards Ganoderma boninense in vitro. Microbiol Indones 4:96-102. doi: 10.5454/mi.4.2.9
Barril P, Nates S (2012) Introduction to agarose and polyacrylamide gel electrophoresis matrices with respect to their detection sensitivities, Gel Electrophoresis – Principles and Basics, Magdeldin S (Ed). ISBN: 978-953-51-0458-2. Intech. doi: 10.5772/38573
Bintang M (2010) Biokimia: Teknik Penelitian. Erlangga, Jakarta
Bueche F (1957) Mechanical properties of natural and synthetic rubbers. J Polym Sci 25: 305-324. doi: 10.1002/pol.1957.1202511005
Chial H (2008) DNA fingerprinting using amplified fragment length polymorphisms (AFLP): No genome sequence required. Nat Educ 1:176
Collard BCY, Mackill DJ (2008) Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Phil Trans R Soc B 363: 557–572. doi: 10.1098/rstb.2007.2170
Damanik S, Syakir M, Tasma M, Siswanto (2010) Budidaya dan pasca panen karet. Pusat Penelitian dan Pengembangan Perkebunan, Bogor
Daslin A (2005) Kemajuan pemuliaan dan seleksi dalam menghasilkan kultivar karet unggul. Hlm: 26-37. Prosiding Lokakarya Nasional Pemuliaan Tanaman Karet, 22-23 November 2005. Balai Penelitian Sungei Putih, Pusat Penelitian Karet, Medan
Daslin A (2013) Produktivitas klon karet pada berbagai kondisi lingkungan di perkebunan. Agrium 18: 1-6
Daslin A (2014) Perkembangan penelitian klon karet unggul IRR seri 100 sebagai penghasil lateks dan kayu. Warta Perkaretan 33:1-10
Daslin A, Pasaribu SA (2015) Uji adaptasi klon karet IRR seri 100 pada agroklimat kering di kebun Sungei Baleh Kabupaten Asahan Sumatera Utara. J Penelitian Karet 33: 25-34
Dirjenbun (2015) Rencana Strategis Direktorat Jenderal Perkebunan Tahun 2015-2019. Direktorat Jenderal Perke-bunan Kementerian Pertanian. Jakarta
Dirjenbun (2016) Statistik Perkebunan Indonesia Karet 2015-2017. Direktorat Jenderal Perkebunan, Kementerian Pertanian, Jakarta
Doyle JJ (1990) Isolation of plant DNA from fresh tissue. Focus 12:13-15
Evenson WE, Boden LM, Muzikar KA, O’Leary DJ (2012) 1H and 13C NMR assignments for the cyanine dyes SYBR safe and thiazole orange. J Org Chem 77:10967-10971. doi: 10.1021/jo3021659
Feng S, Wu Y, Li W, Yu F, Wang J (2012) Analysis of genetic diversity and SSR allelic variation in rubber tree (Hevea brasilensis). The Molecular Basic of Plant Genetic Diversity. Caliskan M (Ed). 7:136-150. ISBN: 978-953-51-0157-4
Feng SP, Li WG, Huang HS, Wang JY, Wu YT (2009) Development, characterization and cross-species/ genera transferability of EST-SSR markers for rubber tree (Hevea brasiliensis) Mol Breeding 23:85–97. doi: 10.1007/s11032-008-9216-0
Ghosh S, Majumder PB, Sen Mandi S (2011) Species-specific AFLP markers for identification of Zingiber officinale, Z. montanum and Z. zerumbet (Zingiberaceae). Genet Mol Res 10:218-29. doi: 10.4238/vol10-1gmr1154
Gouvea LRL, Rubiano LB, Chioratto AF, Zucchi MI, Goncalves PS (2010) Genetic divergence of rubber tree estimated by multivariate techniques and microsatellite markers. Genet Mol Biol 33:308-318. doi: 10.1590/S1415-47572010005000039
Gregory TR (2008) Understanding evolutionary trees. Evo Edu Outreach 1: 121-137. doi: 10.1007/s12052-008-0035-x
Hamzah P (2014) Evaluasi marka Simple Sequence Repeat (SSR) untuk identifikasi genotip klon karet (Hevea brasiliensis). Skripsi, Institut Pertanian Bogor
Healey A, Furtado A, Cooper T, Henry RJ (2014) Protocol: a simple method for extracting next-generation sequencing quality genomic DNA from recalcitrant plant species. Plant Methods 10:21. doi: 10.1186/1746-4811-10-21
Heru DS, Andoko A (2008) Petunjuk Lengkap Budi Daya Karet. Agromedia Pustaka, Jakarta
Jiang GL (2013) Molecular markers and marker-assisted breeding in plants Pp 45-83. Andersen SB (Ed.) Plant breeding from Laboratories to Fields. ISBN 978-953-51-1090-3. InTech. doi: 10.5772/52583
Kementerian Pertanian (2007) Klon karet unggul untuk 2006-2010. Tabloid Sinar Tani Edisi 28 Maret-3 April 2007
Kementerian Pertanian (2015) Outlook Karet – Komoditas Pertanian Subsektor Perkebunan. Pusat Data dan Sistem Informasi Pertanian, Sekretariat Jenderal
Kubota C, Tajuddin T, Kozai T (1998) Photoautotrophic micropropagation of mangosteen plantlets. Jap J Trop Agr 42:31-32
Kück P, Greve C, Misof B, Gimnich F (2012) Automated masking of AFLP markers improves reliability of phylogenetic analyses. PLoS One 7:e49119. doi: 10.1371/journal.pone.0049119
Lasminingsih M, Sipayung HH (2012) Petunjuk Praktis Pembibitan Karet. ISBN: 979-006-402-0. AgroMedia Pustaka, Jakarta
Le Guen V, Gay C, Xiong TC, Souza LM, Rodier-Goud M, Seguin M (2011) Development and characterization of 296 new polymorphic microsatellite markers for rubber tree (Hevea brasiliensis). Plant Breeding 130: 294–296. doi: 10.1111/j.1439-0523.2010.01774.x
Li D, Xia Z, Deng Z, Liu X, Feng F (2013) Development, characterization, genetic diversity and cross-species/genera transferability of ILP markers in rubber tree (Hevea brasiliensis). Genes Genom 35:719-731. doi: 10.1007/s13258-013-0122-4
Misra A, Shasany AK, Shukla AK, Darokar M, Singh S, Velusamy S, Singh J, Bagchi GD, Jain SP, Saikia D, Khanuja SPS (2010) AFLP markers for identification of Swertia species (Gentianaceae). Genet Mol Res 9:1535-1544. doi: 10.4238/vol9-3gmr785
NanoDrop Technologies Inc (2007) ND-1000 Spechtrophotometer V3.5 user’s manual
Novalina, Sagala AD (2011) Studi segregasi dan pewarisan marka-marka RAPD pada tanaman karet hasil persilangan PB 260 dengan PN. Biospecies 4:18-26
Nurhaimi-Haris, Aswidinnoor H, Toruan-Mathius N, Purwantara A (2003) Kemiripan genetik klon karet (Hevea brasiliensis Muell. Arg.) berdasarkan metode Amplified Fragment Length Polymorphisms (AFLP). Menara Perkebunan 71:1-15
Nurhaimi-Haris, Suwanto A, Suhartono MT, Aswidinnoor H (2010) Isolation and cloning of cDNA fragments from rubber plant with resistant and susceptible characters to Corynespora cassiicola using cDNA-AFLP method. Menara Perkebunan 78:33-42
Perseguini JMKC, Romao LRC, Brinez B, Junior EJS, Goncalves PS, Benchimol LL (2012) Genetic diversity of cultivated accesions and wild species of rubber tree using EST-SSR markers. Pesq agropec bras 47:1087-1094
Priyadarshan PM (2011) Biology of Hevea Rubber. CABI, London
Reflinur, Lestari P (2015) Penentuan lokus gen dalam kromosom tanaman dengan bantuan marka DNA. J Litbang Pert 34:177-186
Roy CB, Ravindran M, Saha T (2012) Efficient screening of AFLP primer combinations for evaluating genetic diversity among cultivated rubber (Hevea brasiliensis) clones. Natural Rubber Research 25:21-30
Rubber Board (2016) Monthly Rubber Statistical News Vol 7 No 12 May 2016. Statistics & Planning Department, Rubber Board, Kottayam-686 002 Kerala, India
Shan C, Gu Z, Wang L, Li P, Song G, Gao Z, Yang X (2011) Preparation, characterization, and application of NR/SBR/Organoclay nanocomposites in the tire industry. J Appl Polym Sci 119: 1185-1194. doi: 10.1002/app.32773
Situmorang A, Sinaga MS, Suseno R, Hidayat SH, Siswanto, Darussamin A (2007) Virulensi isolat Corynespora cassiicola asal sentra perkebunan karet Indonesia terhadap beberapa klon karet anjuran. J Penelitian Karet 25:37-58
Syukur M, Sujiprihati S, Yunianti R (2012) Teknik Pemuliaan Tanaman. Penebar Swadaya, Jakarta
Tajuddin T, Cartealy IC, Safarrida A, Purwoko D, Zulaeha S, Ardiyani M (2012) Identification on Indonesian accessions of Curcuma xanthorrhiza Roxb. using AFLP markers. Biology, Medicine & Natural Product Chemistry 1:33-37
Tang C, Xiao X, Li H, Fan Y, Yang J, Qi J, Li H (2013) Comparative analysis of latex transcriptome reveals putative molecular mechanisms underlying super productivity of Hevea brasiliensis. PLoS One 8(9):e75307. doi: 10.1371/journal.pone.0075307
Toruan-Mathius N, Lalu Z, Soedarsono, Aswidinnoor H (2002) Keragaman genetik klon-klon karet (Hevea brasiliensis Muell. Arg.) yang resisten dan rentan terhadap Corynespora casiicola berdasarkan penanda RAPD dan AFLP. Menara Perkebunan 70:35-49
Townsend JP, Su Z, Tekle YI (2012) Phylogenetic signal and noise: Predicting the power of a data set to resolve phylogeny. Syst Biol 61:835-849. doi: 10.1093/sysbio/sys036
Vuylsteke M, Peleman JD, van Eijk MJ (2007) AFLP-based transcript profiling (cDNA-AFLP) for genome-wide expression analysis. Nat Protoc 2:1399-1413. doi: 10.1038/nprot.2007.174
Wibowo IY (2010) Analisis keragaman genetik tanaman karet hasil persilangan antara RRIM 600 dan PN 1546 dengan menggunakan teknik RAPD. Skripsi, Institut Pertanian Bogor
Woelan S, Sayurandi, Irwansyah E (2014) Keragaman genetik tanaman karet (Hevea brasiliensis Muell. Arg.) dari hasil persilangan interspesifik. J Penelitian Karet 32:109-121
Wooten JA, Tolley-Jordan LR (2009) Validation of phylogenetic signals in amplified fragment length data: testing the utility and reliability in closely related taxa. BMC Res Notes 2:26. doi: 10.1186/1756-0500-2-26
Xiao X, Li H, Tang C (2009) A silver-staining cDNA-AFLP protocol suitable for transcript profiling in the latex of Hevea brasiliensis (para rubber tree). Mol Biotechnol 42:91-99. doi: 10.1007/s12033-008-9139-3
Yu F, Wang BH, Feng SP, Wang JY, Li WG, Wu YT (2010) Development, characterization, and cross-species/ genera transferability of SSR markers for rubber tree (Hevea brasilien-sis) Plant Cell Rep. 30:335–344
Yuwono T (2007) Teori dan Aplikasi Polymerase Chain Reaction. Andi Publisher, Yogyakarta