Studi In Silico Sekuen NONEXPRESSOR OF PATHOGENESIS-RELATED GENES 1 (NPR1) pada Jeruk yang Terkait dengan Resistensi Huanglongbing
DOI:
https://doi.org/10.70158/buitenzorg.v2i2.25Abstrak
Evaluasi ketahanan jeruk terhadap penyakit Huanglongbing (HLB) masih menjadi tantangan karena bakteri penyebabnya tidak dapat dikultur secara murni pada media buatan, metode inokulasi yang kompleks, serta waktu pengamatan fenotipe yang sangat lama. Oleh karena itu, penggunaan penanda molekuler menjadi salah satu alternatif untuk mengatasi permasalahan tersebut. Fokus penelitian ini adalah melakukan analisis in silico terhadap variasi nukleotida pada sekuens gen NONEXPRESSOR OF PATHOGENESIS-RELATED GENES 1 (NPR1) di antara beberapa genotipe jeruk yang informasi ketahanannya terhadap HLB telah diketahui sebelumnya, serta melakukan analisis filogenetik di antara genotipe-genotipe tersebut. Sekuens gen NPR1 dari 20 genotipe, yang terdiri atas 14 genotipe jeruk dan enam genotipe kerabatnya, dikumpulkan secara in silico dari Citrus Genome Database dan dianalisis menggunakan program multiple sequence alignment. Sebanyak enam SNP menarik yang dapat membedakan antara genotipe jeruk yang rentan dan yang tahan terhadap HLB berhasil terdeteksi dalam penelitian ini. Lima SNP bersifat nonsinonim, sedangkan satu SNP sinonim yang tidak menyebabkan perubahan asam amino juga teridentifikasi. Analisis filogenetik menunjukkan adanya pemisahan antara genotipe jeruk yang rentan dan yang toleran/tahan dalam dua klaster utama. SNP yang ditemukan dalam penelitian ini diharapkan dapat berguna untuk merancang penanda fungsional baru sebagai alat seleksi pada studi-studi selanjutnya.
Kata kunci: in silico, penanda molekuler, analisis filogenetik, alat seleksi, SNP
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