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Universitas Negeri Semarang 2020 ANALISIS FILOGENI DURIAN PULAU KUNDUR KEPULAUAN RIAU BERDASARKAN SEKUEN trnL-F INTERGENIC SPACER Skripsi Disusun sebagai salah satu syarat untuk memperoleh gelar Sarjana Sains Program Studi Biologi oleh Anang Ma’ruf 4411415038 JURUSAN BIOLOGI FAKULTAS MATEMATIKA DAN ILMU PENGETAHUAN ALAM UNIVERSITAS NEGERI SEMARANG 2020 ii iii MOTTO “Segala perbuatan dan tindakan yang diniati baik, Insyallah akan mendapatkan hasil yang baik” PERSEMBAHAN Untuk Ibu, Bapak dan segenap keluarga iv PRAKATA Puji syukur ke hadirat Allah SWT atas segala rahmat dan hidayah-Nya sehingga penulis dapat menyelesaikan tugas akhir ini dengan baik. Penulis telah banyak menerima bantuan, kerjasama, dan sumbangan pikiran dari berbagai pihak. Oleh karena itu, penulis mengucapkan terima kasih kepada: 1. Rektor Universitas Negeri Semarang atas kesempatan yang diberikan untuk menempuh pendidikan di UNNES. 2. Dekan Fakultas Matematika dan Ilmu Pengetahuan Alam (FMIPA), UNNES yang telah memberikan izin penelitian. 3. Ketua dan Sekretaris Jurusan Biologi, Fakultas Matematika dan Ilmu Pengetahuan Alam, UNNES yang membantu kelancaran administrasi dalam penyelesaian skripsi. 4. Prof. Dr. Ir. Amin Retnoningsih, M.Si. selaku pembimbing dan ketua tim penelitian durian yang telah membiayai penelitian ini, memberikan ilmu, saran, arahan, dan masukan dalam menyelesaikan tugas akhir. 5. Ibu Talitha Widyatningrum, M.Si.,Ph.D. selaku penguji yang telah memberikan kritik dan saran untuk menyelesaikan tugas akhir. 6. Dr. Yustinus Ulung Anggraito, M.Si. selaku penguji yang telah memberikan kritik dan saran untuk menyelesaikan tugas akhir 7. Dr. Niken Subekti, M.Si. selaku dosen wali penulis atas segala dukungan, masukan, dan doa selama menempuh pendidikan di UNNES. 8. Ibu Elis Sumiati, Bapak Suparman, Bagas Dwi Satrio dan segenap keluarga penulis atas seluruh doa, dukungan, dan segala jerih payah pengorbanannya. 9. Anggi Angeliena kawan seperjuangan penelitian durian yang selalu memberikan dukungan, motivasi, dan saling mendoakan dalam keadaan senang maupun susah. 10. Rekan tim penelitian durian yang memberikan bantuan dan arahan selama penelitian. Teman-teman yang mendukung dan membantu dalam pelaksanaan penelitian, serta segenap tim yang bertugas. v Penulis menyadari sepenuhnya bahwa tugas akhir ini masih jauh dari kesempurnaan. Namun demikian, semoga tugas akhir ini dapat bermanfaat bagi pembaca di masa yang akan datang. Semarang, 30 April 2020 Penulis vi ABSTRAK Ma’ruf, A. (2020). Analisis Filogeni Durian Pulau Kundur Kepulauan Riau Berdasarkan Sekuen trnL-F Intergenic Spacer. Skripsi, Jurusan Biologi Fakultas Matematika dan Ilmu Pengetahuan Alam Universitas Negeri Semarang. Prof. Dr. Ir. Amin Retnoningsih, M.Si. Kata kunci: trnL-F intergenic spacer, filogeni, Pulau Kundur, durian Durian Pulau Kundur memiliki variasi genetik tinggi. Letak geografis yang berdekatan menjadikan komoditas perdagangan diantara Pulau Kundur dan Malaysia. Peran masyarakat memungkinkan bibit dan buah durian Malaysia masuk ke Pulau Kundur, mengakibatkan variasi genetik durian di Pulau Kundur tinggi. Analisis filogeni penting dilakukan untuk menjelaskan hubungan keturunan dan kekerabatan durian di Pulau Kundur. Sekuen trnL-F intergenic spacer memiliki sifat haploid, diwariskan maternal, dan laju evolusi tinggi dilaporkan sesuai untuk mengkaji filogeni pada takson rendah. Tujuan penelitian ini adalah menganalisis filogeni durian Pulau Kundur berdasarkan sekuen trnL-F intergenic spacer Dua puluh sembilan sekuen DNA sebagai ingroup yang terdiri atas 23 varietas Kundur, 4 varietas lokal Indonesia, dan 2 varietas Malaysia. Sekuen Heritiera fomes dari GenBank digunakan sebagai outgroup. Sebanyak 29 sekuen varietas durian dan 1 sekuen outgroup dianalisis menggunakan primer trnL-F intergenic spacer. Hasil phylogram berdasarkan sekuen trnL-F intergenic spacer menunjukkan percabangan yang parafiletik, artinya seluruh varietas durian berasal dari keturunan nenek moyang yang berbeda. Varietas Matahari (B11) diduga menjadi common ancestor karena memiliki umur molekuler yang lebih tua daripada varietas lain. Filogeni durian Pulau Kundur berdasarkan sekuen trnL-F intergenic spacer tidak bisa dikaitkan dengan karakter morfologi. Hal ini disebabkan perbedaan pewarisan sifat dari karakter morfologi (paternal) dan sekuen trnL-F (maternal). vii DAFTAR ISI Halaman HALAMAN .................................................................................................... i PERNYATAAN KEASLIAN ......................................................................... ii PENGESAHAN .............................................................................................. iii MOTTO DAN PERSEMBAHAN .................................................................. iv PRAKATA ...................................................................................................... v ABSTRAK ...................................................................................................... vii DAFTAR ISI .................................................................................................... viii DAFTAR GAMBAR ....................................................................................... x DAFTAR TABEL ........................................................................................... xi DAFTAR LAMPIRAN ................................................................................... xii BAB I. PENDAHULUAN 1.1 Latar Belakang Penelitian .......................................................................... 1 1.2 Rumusan Masalah Penelitian ..................................................................... 3 1.3 Tujuan Penelitian ....................................................................................... 3 1.4 Manfaat Penelitian .................................................................................... 4 1.5 Ruang Lingkup Penelitian ......................................................................... 4 II. TINJAUAN PUSTAKA 2.1 Deskripsi Durio zibethinus ………………………………………………. 5 2.2 Penanda Molekuler DNA Kloroplas untuk Analisis Filogeni.................... 6 2.3 Kerangka Berfikir Penelitian ..................................................................... 10 III. METODE PENELITIAN 3.1 Waktu dan Tempat Penelitian .................................................................... 11 3.2 Subjek Penelitian ........................................................................................ 11 3.3 Alat dan Bahan .......................................................................................... 12 3.4 Prosedur Penelitian..................................................................................... 13 3.5 Analisis Filogeni ........................................................................................ 15 IV. HASIL DAN BAHASAN 4.1 Hasil Penelitian ......................................................................................... 16 4.2 Bahasan ..................................................................................................... 24 viii Halaman V. SIMPULAN DAN SARAN 5.1 Simpulan ................................................................................................... 33 5.2 Saran .......................................................................................................... 33 DAFTAR PUSTAKA RUJUKAN .................................................................. 34 LAMPIRAN .................................................................................................... ix DAFTAR GAMBAR Gambar Halaman 1.1 Letak geografis Pulau Kundur Kepulauan Riau (merah) dengan negara Malaysia dan Singapura yang berdekatan ................................... 2 2.1 Karakter morfologi Durio zibethinus (Dokumentasi pribadi) ................ 6 2.2 Peta genom kloroplas pada Hibiscus rosa-sinensis (Malvaceae) ........... 8 2.3 Lokasi gen trnL-F intergenic spacer yang digunakan sebagai primer untuk analisis filogeni tumbuhan durian kundur .................................... 9 2.4 Kerangka berfikir penelitian analisis filogeni durian Pulau Kundur ...... 10 4.1 Elektroforegram hasil isolasi DNA genom 23 varietas Pulau Kundur Kepulauan Riau, 4 varietas durian lokal Indonesia dan 2 varietas durian Malaysia ...................................................................................... 17 4.2 Elektroforegram optimasi suhu annealing primer trnL-F dengan suhu 48ºC; 49,1ºC; 50,3ºC; 51,4ºC; 52,6ºC; 53,7ºC; 54,9ºC .................. 19 4.3 Elektroforegram hasil amplifikasi primer trnL-F reverse dan forward pada semua sampel uji ............................................................................ 20 4.4 Rekonstruksi pohon filogeni Neighboor-Joining dengan bootstrap 1000 kali ulangan sekuen trnL-F intergenic spacer ........................................ 24 x DAFTAR TABEL Tabel Halaman 3.1 Daftar varietas durian ............................................................................ 11 3.2 Alat dan bahan Penelitian ...................................................................... 12 3.3 Primer trnL-F intergenic spacer yang digunakan .................................. 14 3.4 Komposisi master mix PCR primer trnL-F intergenic spacer................ 14 3.5 Tahapan amplifikasi DNA primer trnL-F intergenic spacer ................. 15 4.1 Data kuantitas DNA genom sampel uji .................................................. 18 4.2 Persentase basa konten AT dan GC dari alignment sekuen trnL-F intergenic spacer sampel uji durian sepanjang 493 bp .......................... 21 4.3 Matriks jarak genetik hasil
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