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ANALISIS KERAGAMAN GENETIK ISOLAT Ganoderma Boninense DARI KELAPA SAWIT (Elaeis Guineensis Jacq.) PT SOCFIN INDONESIA DENGAN METODE SIMPLE SEQUENCE REPEATS (SSR)

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ANALISIS KERAGAMAN GENETIK ISOLAT Ganoderma Boninense DARI KELAPA SAWIT (Elaeis Guineensis Jacq.) PT SOCFIN INDONESIA DENGAN METODE SIMPLE SEQUENCE REPEATS (SSR) ANALISIS KERAGAMAN GENETIK ISOLAT Ganoderma boninense DARI KELAPA SAWIT (Elaeis guineensis Jacq.) PT SOCFIN INDONESIA DENGAN METODE SIMPLE SEQUENCE REPEATS (SSR) TESIS Oleh AGUSTIAMAN PURBA 157001008 PROGRAM STUDI MAGISTER AGROTEKNOLOGI FAKULTAS PERTANIAN UNIVERSITAS SUMATERA UTARA 2020 ANALISIS KERAGAMAN GENETIK ISOLAT Ganoderma boninense DARI KELAPA SAWIT (Elaeis guineensis Jacq.) PT SOCFIN INDONESIA DENGAN METODE SIMPLE SEQUENCE REPEATS (SSR) TESIS Oleh AGUSTIAMAN PURBA 157001008 Tesis Sebagai Salah Satu Syarat Untuk Dapat Mendapatkan Gelar Magister di Program Studi Magister Agroteknologi Fakultas Pertanian Universitas Sumatera Utara PROGRAM STUDI MAGISTER AGROTEKNOLOGI FAKULTAS PERTANIAN UNIVERSITAS SUMATERA UTARA 2020 ABSTRACT AgustiamanPurba. 2020. “ANALYSIS OF GENETIC DIVERSITY OF Ganoderma boninense ISOLATES FROM OIL PALM (Elaeis guineensis Jacq.) of PT SOCFIN INDONESIA WITH SIMPLE SEQUENCE REPEATS (SSR) METHODS, guided by Mohammad Basyuni and Revandy I. M. Damanik. This study aims to identify the genetic diversity of Ganoderma boninense from several oil palm (Elaeis guineensis Jacq) PT Socfin Indonesia and the other host plants. This research was carried out at the Pathology Laboratory of PT Socfin Indonesia in Kebun Tanah Gambus, Lima Puluh, Batu Bara District and DNA Laboratory at SSPL (Socfindo Seeds Production and Laboratories) Bangun Bandar, Dolok Masihul, Serdang Bedagai District. This research was conducted using the SSR (Simple Sequence Repeats) method and DNA sequence analysis. The results showed that the most informative primer was the KT124399 primer with a PIC value of 1.0. Based on the number of specific primers amplifying, the lontar basal stem rot of fruit body isolate has a tendency of similarity with G.boninense is greater (83%) compared to the rubber basal stem rot of fruit body isolate (50%) the palm rot basal stem rot of fruit body isolate (33%) %). Genetic diversity of G.boninense isolates obtained from several oil palm plantations of PT Socfin Indonesia are low but has high gene flow potential. Key words : Basal Stem Rot, Ganoderma boninense, genetic diversity, Simple Sequence Repeats i ABSTRAK AgustiamanPurba. 2020. “ANALISIS KERAGAMAN GENETIK ISOLAT Ganoderma boninense DARI KELAPA SAWIT (Elaeis guineensis Jacq.) PT SOCFIN INDONESIA DENGAN METODE SIMPLE SEQUENCE REPEATS (SSR), dibimbing oleh Mohammad Basyuni dan Revandy I. M. Damanik. Penelitian ini bertujuan untuk mengidentifikasi keragaman genetik Ganoderma boninense dari kelapa sawit (Elaeis guineensis Jacq) PT Socfin Indonesia dan tanaman inang lainnya. Penelitian ini dilaksanakan di Laboratorium Patologi PT Socfin Indonesia di Kebun Tanah Gambus Kecamatan Lima Puluh Kabupaten Batu Bara dan Laboratorium DNA di SSPL (Socfindo Seeds Production and Laboratories) Bangun Bandar Kecamatan Dolok Masihul Kabupaten Serdang Bedagai. Penelitian ini dilakukan menggunakan metode SSR (Simple Sequence Repeats) dan analisis sequence DNA. Hasil penelitian menunjukkan bahwa primer yang paling informatif adalah primer KT124399 dengan nilai PIC adalah 1,0. Berdasarkan banyaknya primer spesifik yang mengamplifikasiI, isolat tubuh buah basal stem rot lontar memiliki kecenderungan kemiripan dengan G.boninense lebih besar (83%) dibandingkan dengan isolat tubuh buah basal stem rot karet (50%) isolat tubuh buah basal stem rot kelapa nyiur (33%). Keragaman genetik isolat G.boninense yang diperoleh dari beberapa kebun kelapa sawit PT Socfin Indonesia adalah rendah namun memiliki potensi aliran gen yang tinggi. Kata kunci : Basal Stem Rot, Ganoderma boninense, keragaman genetik, Simple Sequence Repeats ii KATA PENGANTAR Puji dan syukur penulis ucapkan kepada Tuhan Yang Maha Esa karena atas berkat dan rahmat-Nya penulis dapat menyelesaikan tesis ini tepat pada waktunya. Adapun judul dari tesis ini adalah “Analisis Keragaman Genetik Isolat Ganoderma boninense dari Kelapa Sawit (Elaeis guineensis Jacq.) PT SOCFIN INDONESIA dengan Metode Simple Sequence Repeats (SSR)” yang merupakan salah satu syarat untuk mendapatkan gelar Magister Program Studi Agroteknologi Fakultas Pertanian Universitas Sumatera Utara, Medan. Pada kesempatan ini penulis mengucapkan terima kasih kepada dosen pembimbing yaitu Mohammad Basyuni, S.Hut., M.Si., Ph.D., sebagai Ketua Komisi Pembimbing dan Ir. Revandy I.M. Damanik, M.Sc., Ph.D., sebagai Anggota Komisi Pembimbing yang telah membantu dan membimbing dalam menyelesaikan tesis ini. Penulis juga mengucapkan terima kasih kepada orang tua, keluarga, staf pengajar dan pegawai di Program Studi Magister Agroteknologi, direksi/manajemen, pegawai Laboratorium Patologi dan Laboratorium DNA PT Socfin Indonesia, dan semua teman yang telah memberi dukungan dan membantu penulis dalam menyelesaikan tesis ini. Akhir kata penulis mengucapkan terima kasih. Semoga tesis ini bermanfaat bagi seluruh pihak yang membutuhkan. Medan, Januari 2020 Agustiaman Purba iii DAFTAR ISI Halaman ABSTRACT ........................................................................................................ i ABSTRAK ......................................................................................................... ii KATA PENGANTAR ....................................................................................... iii DAFTAR ISI ...................................................................................................... iv DAFTAR TABEL.............................................................................................. vi DAFTAR GAMBAR ......................................................................................... vii PENDAHULUAN .............................................................................................. 1 Latar Belakang ........................................................................................... 1 Tujuan Penelitian ....................................................................................... 4 Kegunaan Penelitian .................................................................................. 4 TINJAUAN PUSTAKA .................................................................................... 5 Taksonomi Ganoderma boninense ............................................................ 5 Morfologi dan Ekologi Ganoderma boninense ......................................... 5 Penyebaran Ganoderma ............................................................................ 9 Keragaman Genetik Ganoderma spp......................................................... 11 Simple Sequence Repeats (SSR)................................................................. 11 METODE PENELITIAN ................................................................................. 16 Tempat dan Waktu Penelitian .................................................................... 16 Bahan dan Alat Penelitian ......................................................................... 16 Metode Penelitian ...................................................................................... 23 Pelaksanaan Penelitian............................................................................... 23 Persiapan Isolat .................................................................................. 23 Ekstraksi DNA Ganoderma spp. ........................................................ 24 Uji kualitas DNA ................................................................................ 25 Uji kuantitas DNA .............................................................................. 25 Amplifikasi PCR................................................................................. 26 Visualisasi Hasil Amplifikasi DNA dengan Penanda SSR ............... 27 Analisis Sekuens DNA ....................................................................... 27 Analisis Data....................................................................................... 28 HASIL DAN PEMBAHASAN ......................................................................... 29 Hasil…… ................................................................................................... 29 Uji Kuantitas DNA ............................................................................. 29 Uji Kualitas DNA ............................................................................... 33 Analisis Molekuler ............................................................................. 35 Amplifikasi PCR dengan Primer KT 124397 ..................................... 35 Amplifikasi PCR dengan Primer KT 124402 ..................................... 39 Amplifikasi PCR dengan Primer KT 124403 ..................................... 44 Amplifikasi PCR dengan Primer KT 124399 ..................................... 48 iv Amplifikasi PCR dengan Primer KT 124400 ..................................... 53 Amplifikasi PCR dengan Primer KT 124394 ..................................... 57 Analisis Sekuens DNA ....................................................................... 62 Uji Statistik dan Migrasi Alel ..................................................... 62 Profil Lokus Mikrosatelit ............................................................ 62 Analisis Varian Molekuler .......................................................... 64 Uji BLASTX ............................................................................... 64 Analisis Filogenetik Isolat Ganoderma boninense ..................... 66 Pembahasan ............................................................................................... 67 Amplifikasi PCR................................................................................
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