IDENTIFICATION OF THEOBROMA CACAO L. MIRNA AS POTENTIAL BIOCONTROL AGENTS AGAINST PHYTOPHTHORA PALMIVORA

• Main Author: Pramesti, Yonadita
• Format: Theses
• Language: Indonesia
• Online Access: https://digilib.itb.ac.id/gdl/view/76084
• Institution: Institut Teknologi Bandung

<p align="justify"> Cacao (Theobroma cacao L.) is a highly valuable commodity in both domestic and international markets. Cacao farmers, on the other hand, frequently suffer difficulties due to the Phytophthora palmivora infection, which causes black pod disease (BPD). This disease significantly reduces cacao production by more than 50%. Fungicides are commonly used to control P. palmivora, but their application can have detrimental effects on the environment. Cross-kingdom RNA interference (RNAi) has emerged as a promising plant defense mechanism against pathogen infections to address this issue. By transferring small regulatory RNAs into the pathogen, RNAi can silence the virulence genes and suppress pathogen infections. In this study, a miRNA transcriptomic analysis of cacao fruits infected with P. palmivora was conducted to explore the potential of RNAi-based biocontrol. Cacao pods from resistant and susceptible varieties of BPD were obtained from the Cacao Plantation at the Indonesian Coffee and Cacao Research Institute in Jember, East Java. Subsequently, miRNAs from the resistant and susceptible cacao pods were isolated, yielding isolates with purity ranging from 1.87 to 2.00 and concentrations ranging from 37.9 to 81 ng/?L. These miRNA isolates were sequenced using the Illumina/Novoseq 6000 platform, resulting in a total of 9 to 12 million raw reads. After removing adapter contamination using Trimmomatic, 4 to 10 million clean reads were obtained with lengths ranging from 18 to 28 nucleotides. The clean reads were then mapped to the cacao genome and quantified using Rsubread. Known miRNA identification was done based on pmiREN and miRBase database and identified 54 known miRNA while identification and analysis of novel miRNA were conducted using Mirdeep2 and identified 67 novel miRNA. Differential expression analysis of miRNA with Deseq2 identified 17 differentially expressed miRNAs in P. palmivora-infected cacao pods, with 9 miRNAs being up-regulated and 8 miRNAs down-regulated. Target analysis in P. palmivora unveiled that tcc-miR156b, Novel-miR6, and Novel-miR18 target effector proteins, which serve as virulence factors triggering hypersensitive responses in the host plant. Additionally, several miRNAs were found to target P. palmivora genes involved in crucial processes such as glycolysis, respiration, and the cell cycle. These findings highlight the potential of these miRNAs as RNAi-based biocontrol agents. This research represents a significant step towards controlling P. palmivora infections in cacao pods and supporting national cacao production. By harnessing the power of RNAi, we can potentially develop sustainable and environmentally friendly strategies to combat this devastating pathogen. Continued research in this field will contribute to the advancement of biocontrol approaches, improving crop protection and ensuring the cacao industry’s long-term survival.