MUTASI GENETIK Pepper yellow leaf curl Indonesia virus PENYEBAB PENYAKIT KUNING-KERITING DAUN TANAMAN CABAI RAWIT (Capsicum frutescens L.)

OZIE AKBAR PRATAMA, Prof. Dr. Budi Setiadi Daryono, M.Agr.Sc., Dr. Ir. Sedyo Hartono, M.P.

2020 | Tesis | MAGISTER BIOLOGI

Penyakit kuning keriting daun yang menginfeksi tanaman cabai rawit (Capsicum frutescens L.) disebabkan oleh Pepper yellow leaf curl Indonesia virus (PepYLCIV). Infeksi virus mengakibatkan daun mengecil, menguning (klorosis), serta helai daun menjadi keriting. Tanaman menjadi kerdil dan mengalami kerontokan bunga. Gen AV1 berperan dalam mengkode coat protein. Gen AC1/Rep mengkode protein yang berperan dalam replikasi virus. Penelitian ini bertujuan untuk mendeteksi mutasi gen AV1 (Coat Protein) dan AC1/Rep pada virus wild type dan mild strain yang ditemukan di lapangan. Sampel tanaman cabai rawit terinfeksi PepYLCIV didapatkan di area persawahan Umbulmartani, Sleman, Yogyakarta. Identifikasi virus awal dilakukan di lapangan dengan mengamati gejala yang muncul pada tanaman cabai rawit. Identifikasi virus secara molekular menggunakan primer universal Begomovirus (PALIc1960/PARIv722) dilakukan di Laboratorium Genetika dan Pemuliaan Fakultas Biologi UGM. Sequencing gen AV1 dan AC1/Rep metode Sanger untuk mendeteksi adanya mutasi dilakukan di FirstBase Malaysia. Hasil penelitian menunjukkan bahwa terdapat 10 mutasi silent dan satu mutasi missense pada gen AV1. Mutasi ini menyebabkan valin ditranslasikan menjadi alanin. Gen AC1/Rep ditemukan 4 mutasi silent dan dua mutasi missense dalam satu kodon yang sama, menyebabkan valin ditranslasikan menjadi alanin. Berdasarkan ENC-Plot Analysis tiga query sekuens DNA virus, kedua sampel sekuens virus gen AV1 mild (2 query) memiliki codon usage yang dipengaruhi oleh tekanan mutasi. Hanya query 5 (wild type) saja yang memiliki codon usage akibat seleksi alam. ENC-Plot Analysis kedua sampel sekuens virus gen AC1/Rep wild type dan mild (2 query) memiliki codon usage yang dipengaruhi oleh tekanan mutasi.

Yellow leaf curl disease which infects the cayenne pepper (Capsicum frutescens L.) plant is caused by the Pepper yellow leaf curl Indonesia virus (PepYLCIV). Viral infections cause the leaves to shrink, turn yellow (chlorosis), and become curly. Plants become stunted and experience flower loss. The AV1 gene plays a role in coding the coat protein. The AC1/Rep gene encodes a protein that plays a role in viral replication. This study was aimed to detect AV1 and AC1/Rep gene mutations in wild type and mild strain viruses found in the plantation area. Samples of cayenne pepper infected with PepYLCIV were obtained from Umbulmartani plantation area, Sleman, Yogyakarta. Early virus identification was carried out in the field by observing the symptoms that appear in cayenne pepper plants. Molecular identification of viruses using the Begomovirus universal primer (PALIc1960 / PARIv722) was conducted at the Genetic and Breeding Laboratory of the Faculty of Biology UGM. Sanger sequencing method for detecting AV1 and AC1/Rep gene mutations was carried out in FirstBase Malaysia. The results showed that there were 10 silent mutations and one missense mutation in the AV1 gene, causing valine to be translated into alanine. In the AC1/Rep gene, 4 silent mutations and two missense mutations were found in the same codon, causing valine to be translated into alanine. Based on the ENC-Plot Analysis of three viral DNA sequence queries, both AV1 mild (2 queries) gene virus sequences have codon usage which is affected by pressure mutation. Only query 5 (wild type) has codon usage due to natural selection. ENC-Plot Analysis of the two AC1/Rep wild type gene virus sequence samples and mild (2 queries) gene virus sequences have codon usage which is influenced by pressure mutation.

Kata Kunci : Capsicum frutescens L., ENC-Plot analysis, mutation, sequencing, PepYLCIV