Karakterisasi Genom Pepper Yellow Leaf Curl Indonesia Virus dan Mekanisme Ketahanan Biokimiawi Beberapa Spesies Cabai Terhadap Infeksi Virus.

Abstract

Penyakit daun keriting kuning pada cabai yang disebabkan oleh Pepper yellow leaf curl Indonesia virus (PepYLCIV) merupakan ancaman serius bagi produksi cabai di Indonesia. Virus ini termasuk anggota genus Begomovirus dan ditularkan oleh vektor kutukebul (Bemisia tabaci). Sampai saat ini belum diperoleh genotipe cabai yang benar-benar tahan terhadap infeksi virus tersebut. Penelitian ini bertujuan untuk mengidentifikasi genom lengkap PepYLCIV isolat Bogor, melakukan skrining ketahanan berbagai genotipe cabai terhadap infeksi PepYLCIV, mengevaluasi aktivitas enzim antioksidan pada genotipe terpilih, serta menganalisis profil senyawa metabolit daun cabai akibat interaksi dengan kutukebul. Metode yang digunakan meliputi identifikasi genom lengkap dilakukan menggunakan teknologi Oxford Nanopore Technologies (ONT), skrining ketahanan 32 genotipe, pengukuran aktivitas enzim antioksidan (APX, CAT, POD, PPO) pada 6 genotipe terpilih, serta analisis profil metabolit menggunakan teknik GC-MS headspace dan derivatisasi. Hasil penelitian menunjukkan bahwa tiga isolat Begomovirus yang menginfeksi cabai diidentifikasi sebagai PepYLCIV dengan tingkat kesamaan nukleotida DNA-A >93% dan DNA-B >92% terhadap isolat lain di Asia Tenggara. Analisis evolusi menunjukkan bahwa DNA-A berada di bawah tekanan seleksi purifikatif kuat (? = 0,049–0,111), sedangkan DNA-B menunjukkan tekanan negatif lebih lemah, menandakan diferensiasi adaptif antar segmen genom. Skrining terhadap 32 genotipe cabai dari empat spesies (Capsicum annuum, C baccatum, C. chinense, dan C. frutescens) dengan metode inokulasi massal menunjukkan tidak ada genotipe yang sepenuhnya resisten terhadap infeksi PepYLCIV. Namun, tiga genotipe (‘F6 LDxBS-4-7-4-3’, ‘Red Bhut Jolokia’, dan ‘Red Chupetinho’) menunjukkan kategori agak rentan dengan tingkat keparahan dan titer virus rendah. Variasi masa inkubasi (5–28 hari setelah inokulasi) dan perbedaan titer virus antar genotipe menunjukkan adanya mekanisme pertahanan parsial yang berhubungan dengan dinamika enzimatik dan metabolik tanaman. Skrining ketahanan 6 genotipe cabai terpilih menunjukkan bahwa genotipe ‘Bara’ memiliki periode inkubasi paling pendek dan respons ketahanan yang rentan, sedangkan ‘Red Habanero’ memiliki periode inkubasi paling panjang dengan respons agak rentan. Studi aktivitas enzim antioksidan mengungkapkan bahwa aktivitas enzim CAT, POD dan PPO dipengaruhi oleh waktu pengujian. Aktivitas enzim POD juga dipengaruhi oleh perlakuan dan genotipe. Inokulasi kutukebul viruliferous memicu peningkatan aktivitas enzim pertahanan, terutama pada genotipe yang responsif seperti ‘Lemon Drop’ dan ‘Bara’. Aktivitas POD secara khusus meningkat pada genotipe dengan ketahanan baik, menunjukkan mekanisme pertahanan sistemik jangka panjang terhadap tekanan biotik. Aktivitas PPO meningkat seiring waktu, namun tidak dipengaruhi oleh perlakuan atau genotipe. Profil metabolit daun cabai menunjukkan perubahan signifikan akibat infeksi virus dan interaksi serangga, termasuk akumulasi gula sederhana, polyol, pektin, serta aktivasi jalur pentosa fosfat, metabolisme asam amino, dan siklus sitrat. Senyawa 1-hexanol dan methyl salicylate (MeSA) merupakan penanda penting respons tanaman terhadap infeksi dan interaksi serangga. Selain itu, temuan baru berupa identifikasi senyawa kunci seperti D-ribose, L-arabinitol, pektin, serta penurunan proline dan L-glutamic acid, mengindikasikan adanya realokasi nitrogen dan pool asam amino selama infeksi. Implikasi penelitian ini adalah memperkuat pemahaman mekanisme pertahanan molekuler dan metabolik tanaman cabai terhadap infeksi PepYLCIV dan gangguan serangga, serta memberikan dasar ilmiah bagi pengembangan varietas cabai yang lebih tahan dan strategi pengelolaan penyakit berbasis metabolit di masa mendatang.

Yellow leaf curl disease in chili peppers, caused by the Pepper yellow leaf curl Indonesia virus (PepYLCIV), is a serious threat to chili production in Indonesia. This virus belongs to the genus Begomovirus and is transmitted by the whitefly vector (Bemisia tabaci). To date, no chili pepper genotype has been found that is truly resistant to the virus infection. This research aims to identify the complete genome of PepYLCIV Bogor isolate, screen the resistance of various chili genotypes to PepYLCIV infection, evaluate the antioxidant enzyme activity in selected genotypes, and analyze the metabolic compound profile of chili leaves due to interaction with whiteflies. The methods used include whole genome identification using Oxford Nanopore Technologies (ONT) technology, screening for resistance in 32 genotypes, measurement of antioxidant enzyme activity (APX, CAT, POD, PPO) in 6 selected genotypes, and metabolite profile analysis using GC-MS headspace and derivatization techniques. The research results show that three Begomovirus isolates infecting chili peppers were identified as PepYLCIV with DNA-A nucleotide sequence similarity >93% and DNA-B >92% compared to other isolates in Southeast Asia. Evolutionary analysis showed that DNA-A was under strong purifying selection pressure (? = 0.049–0.111), while DNA-B showed weaker negative pressure, indicating adaptive differentiation between genome segments. Screening of 32 chili pepper genotypes from four species (Capsicum annuum, C. baccatum, C. chinense, and C. frutescens) using the mass inoculation method showed that no genotype was completely resistant to PepYLCIV infection. However, three genotypes ('F6 LDxBS-4-7-4-3', 'Red Bhut Jolokia', and 'Red Chupetinho') showed a moderately susceptible category with low severity and virus titer. Variations in incubation period (5–28 days after inoculation) and differences in viral titer between genotypes suggest the presence of a partial defense mechanism related to the enzymatic and metabolic dynamics of the plant. Screening for resistance in 6 selected chili genotypes showed that the 'Bara' genotype had the shortest incubation period and a susceptible resistance response, while 'Red Habanero' had the longest incubation period with a moderately susceptible response. Studies on antioxidant enzyme activity revealed that the activity of CAT, POD, and PPO enzymes was influenced by the testing time. The activity of the POD enzyme is also influenced by treatment and genotype. Inoculation with viruliferous whiteflies triggers increased activity of defense enzymes, particularly in responsive genotypes like 'Lemon Drop' and 'Bara'. POD activity specifically increased in genotypes with good resistance, indicating a long-term systemic defense mechanism against biotic stress. PPO activity increased over time but was not affected by treatment or genotype. The metabolite profile of chili pepper leaves shows significant changes due to viral infection and insect interaction, including the accumulation of simple sugars, polyols, and pectin, as well as the activation of the pentose phosphate pathway, amino acid metabolism, and the citric acid cycle. The compounds 1-hexanol and methyl salicylate (MeSA) are important markers of plant response to infection and insect interactions. Additionally, new findings, such as the identification of key compounds like D-ribose, L-arabinitol, and pectin, and the decrease in proline and L-glutamic acid, indicate a reallocation of nitrogen and amino acid pools during infection. The implications of this research are to strengthen the understanding of the molecular and metabolic defense mechanisms of chili plants against PepYLCIV infection and insect disturbances and to provide a scientific basis for the development of more resistant chili varieties and metabolite-based disease management strategies in the future.