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All Journal Jurnal Agronomi Indonesia (Indonesian Journal of Agronomy) BIOTROPIA - The Southeast Asian Journal of Tropical Biology Jurnal Penelitian dan Pengembangan Pertanian Jurnal Tanaman Industri dan Penyegar Indonesian Journal of Disability Studies BERITA BIOLOGI JURNAL BIOLOGI INDONESIA Jurnal Biologi Tropis ANNALES BOGORIENSES AGROSAINSTEK: Jurnal Ilmu dan Teknologi Pertanian Journal La Lifesci Makara Journal of Science Buitenzorg: Journal of Tropical Science Annales Bogorienses
TRI JOKO SANTOSO
Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumberdaya Genetik Pertania
Agriculture, Biological Sciences & Forestry Humanities Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Decision Sciences, Operations Research & Management Earth & Planetary Sciences Economics, Econometrics & Finance Environmental Science Health Professions Immunology & microbiology Industrial & Manufacturing Engineering Medicine & Pharmacology Social Sciences Veterinary

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Studi In Silico Sekuen NONEXPRESSOR OF PATHOGENESIS-RELATED GENES 1 (NPR1) pada Jeruk yang Terkait dengan Resistensi Huanglongbing Nugroho, Kristianto; Santoso, Tri Joko; Kosmiatin, Mia; Sukma, Dewi; Purwito, Agus
Buitenzorg: Journal of Tropical Science Vol 2 No 2 (2025): Buitenzorg: Journal of Tropical Science
Publisher : Innovation Centre for Tropical Sciences

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.70158/buitenzorg.v2i2.25

Abstract

The evaluation of citrus resistance to Huanglongbing (HLB) disease is still challenging due to the incapability of the bacteria to be cultured purely in artificial medium, the complexity of inoculation methods, and the long duration required for phenotypic observation. Thus, the use of molecular markers is one of the alternatives to solve this problem. The focuses of this study were to perform in silico analysis of the nucleotide variations in NONEXPRESSOR OF PATHOGENESIS-RELATED GENES 1 (NPR1) gene sequence among several citrus genotypes whose resistance information to HLB have been known previously and to employ phylogenetic analysis among them. The NPR1 gene sequences from 20 genotypes which consisted of 14 citrus and six relative genotypes were collected in silico from Citrus Genome Database and analyzed using multiple sequence alignment program. A total of six interesting SNPs that could distinguish between susceptible and resistant citrus genotypes were detected in this study. As many as five SNPs were non-synonymous, while only one synonymous SNP that did not cause the amino acid change was identified in this study. The phylogenetic analysis also revealed the separation between susceptible and tolerant/resistant citrus genotypes in two main clusters. The SNPs found in this study are expected to be useful for designing new functional markers as a selection tool in future studies. Keywords: in silico, molecular marker, phylogenetic analysis, selection tool, SNP
Co-Authors A.A. Ketut Agung Cahyawan W Agus Purwito Agus Zainudin Akhdya, Alina Akhmad, Khabib Alia Ali Husni Andari Risliawati, Andari Andi Salamah Aniversari Apriana Anky Zannati Apriadi Situmorang Atmitri Sisharmini Bambang Sapta Purwoko Budi Martono Chaerani Chaerani Chaireni Martasari Dewi Sukma Dwi Astuti Dwi Widyajayantie DWINITA WIKAN UTAMI Eka Rosyida Enny Randriani Enung Sri Mulyaningsih Heri Syahrian, Heri Hilman Maulana Irshanty, Firdha Meidi KRISTIANTO NUGROHO, KRISTIANTO Kurniawan Rudi Trijatmiko, Kurniawan Rudi M. Khais Prayoga, M. Khais Maemunah Maemunah Mastur Mastur Mia Kosmiatin Nurul Hidayatun Pantouw, Carla F. Pantouw, Carla Frieda Priyono, Dika Migi PUJI LESTARI Rachmawati, Syamsidah Raden Mohamad Herdian Bhakti REFLINUR REFLINUR Samliok Ndobe Satya Nugroho Shabri Shabri, Shabri Sintho Wahyuning Ardie Solly Aryza Sri Indrayani, Sri Syafaruddin . Syamsidah Rahmawati, Syamsidah Trikoesoemaningtyas Triyani Dewi Vincentia Esti Windiastri, Vincentia Esti Vitria Puspitasari Rahadi Widyajayanti, Dwi Zakirah Raihani Ya’la