Identifikasi Morfologis dan Analisis Filogenetik Berdasarkan Internal Transcribed Spacer pada Cabai Introduksi (Capsicum chinense L. 'Suriname Merah')

Siti Yulianingsih, Prof. Dr. Budi Setiadi Daryono, M.Agr.Sc.

2026 | Skripsi | BIOLOGI

Cabai 'Suriname Merah' merupakan salah satu kultivar introduksi yang memiliki potensi sebagai sumber daya genetik untuk pengembangan tanaman cabai. Namun, identitas spesies kultivar ini masih belum diketahui secara pasti karena memiliki karakter morfologis yang mirip dengan beberapa spesies Capsicum. Oleh karena itu, penelitian ini bertujuan mengidentifikasi dan menganalisis keragaman Cabai 'Suriname Merah' berdasarkan karakterisasi morfologis dan molekuler menggunakan penanda Internal Transcribed Spacer (ITS), serta menentukan variasi genetik, jarak genetik, dan hubungan filogenetiknya dengan beberapa spesies Capsicum domestikasi. Penelitian dilaksanakan pada periode Maret 2025 hingga Juni 2026 di Greenhouse Jamusan, dengan proses analisis molekuler dilakukan di Laboratorium Genetika dan Pemuliaan Tanaman, Universitas Gadjah Mada serta sekuensing di Integrated Genome Factory (IGF). Penelitian dilakukan melalui pengamatan karakter morfologis, isolasi DNA, amplifikasi daerah ITS menggunakan Polymerase Chain Reaction (PCR), sekuensing DNA, dan analisis filogenetik. Hasil penelitian menunjukkan bahwa cabai 'Suriname Merah' memiliki karakter morfologis yang didominasi oleh ciri-ciri Capsicum chinense, antara lain mahkota bunga berwarna putih kehijauan, antera berwarna hitam, bunga menggantung, buah berwarna merah saat masak, serta terdapat annular constriction pada pertemuan tangkai buah dan kelopak. Amplifikasi daerah ITS menghasilkan fragmen DNA berukuran sekitar 700 pb yang berhasil disekuensing untuk analisis lebih lanjut. Analisis sekuens menunjukkan kandungan GC lebih tinggi daripada AT serta adanya variasi nukleotida yang membedakan cabai 'Suriname Merah' dari spesies pembanding. Analisis jarak genetik menunjukkan bahwa cabai 'Suriname Merah' memiliki kedekatan genetik tertinggi dengan C. chinense dan C. annuum, sedangkan rekonstruksi pohon filogenetik menempatkan cabai 'Suriname Merah' dalam satu clade dengan C. chinense dengan dukungan nilai bootstrap yang tinggi. Berdasarkan karakter morfologis dan analisis molekuler menggunakan penanda ITS, cabai 'Suriname Merah' diidentifikasi sebagai kultivar yang termasuk dalam spesies Capsicum chinense.

'Suriname Merah' pepper (Capsicum sp.) is an introduced cultivar with potential as a genetic resource for chili pepper improvement. However, its taxonomic identity remains uncertain due to its morphological similarity to several Capsicum species. Therefore, this study aimed to identify and analyze the diversity of the 'Suriname Merah' chili pepper based on morphological characterization and molecular analysis using the Internal Transcribed Spacer (ITS) marker, as well as to determine its genetic variation, genetic distance, and phylogenetic relationship with several domesticated Capsicum species. The study was conducted from March 2025 to May 2026 at the Jamusan Greenhouse, while molecular analyses were carried out at the Laboratory of Genetics and Plant Breeding, Gadjah Mada University, and DNA sequencing was performed at the Integrated Genome Factory (IGF). The study was conducted through morphological observations, DNA isolation, amplification of the ITS region using Polymerase Chain Reaction (PCR), DNA sequencing, and phylogenetic analysis. The results showed that the 'Suriname Merah' chili pepper exhibited morphological characteristics predominantly consistent with Capsicum chinense, including greenish-white corollas, black anthers, pendant flowers, red ripe fruits, and the presence of an annular constriction at the junction between the fruit pedicel and calyx. Amplification of the ITS region produced a DNA fragment of approximately 700 bp, which was successfully sequenced for further analysis. Sequence analysis revealed a higher GC content than AT content and identified nucleotide variations that distinguished the 'Suriname Merah' chili pepper from the reference species. Genetic distance analysis indicated that the 'Suriname Merah' chili pepper was most closely related to C. chinense and C. annuum, while phylogenetic reconstruction placed it within the same clade as C. chinense with high bootstrap support. Based on both morphological characteristics and molecular analysis using the ITS marker, the 'Suriname Merah' chili pepper was identified as a cultivar belonging to Capsicum chinense.

Kata Kunci : Capsicum, filogenetik, ITS, ‘Suriname Merah’