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<p>Black pod disease, caused by <i>Phytophthora palmivora</i>, severely constrains cacao production, necessitating the identification of resistance-related genes. This study employed high-throughput RNA sequencing (RNA-seq) using the Illumina platform to investigate transcriptomic responses associated with disease resistance in cacao. Transcriptome sequencing generated 185,984,548 raw reads, of which 106,456,430 high-quality reads were retained after filtering. Following reference-guided assembly, 29,452 non-redundant transcripts were obtained, with an average length of 1,833&#xa0;bp. Gene Ontology (GO) annotation classified transcripts into biological processes (59%), molecular functions (55%), and cellular components (67%), with cellular components being the most represented category. Differential expression analysis using edgeR identified 57 differentially expressed (DE) transcripts across comparisons between resistant (Sca-12) and susceptible (DR-1) genotypes under control and pathogen-treated conditions. Notably, 42 DE transcripts were identified between resistant and susceptible genotypes under control conditions, while 2 and 13 transcripts were detected in untreated and treated Sca-12 and DR-1 genotypes, respectively. Seven candidate genes associated with defense responses were selected for validation, and five (glycine-rich protein, plantacyanin, expansin-like B1, cysteine proteinase, and ACC oxidase 1) were confirmed by qRT-PCR, showing expression patterns consistent with RNA-seq data. These findings provide valuable insights into transcripts that may play crucial roles in the cacao plant’s defense mechanisms against <i>Ppal</i>.</p>

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Transcriptome analysis of cacao reveals differentially expressed genes associated with resistance to Phytophthora palmivora

  • 期刊论文

  • 发表日期：

    2026年5月25日

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  • Nur Kholilatul Izzah,
  • Murukarthick Jayakodi,
  • Sang-Choon Lee,
  • Khaerati,
  • Cici Tresniawati,
  • Widi Amaria,
  • Faizal Maulana,
  • Jee Young Park,
  • Tae-Jin Yang

摘要

Black pod disease, caused by Phytophthora palmivora, severely constrains cacao production, necessitating the identification of resistance-related genes. This study employed high-throughput RNA sequencing (RNA-seq) using the Illumina platform to investigate transcriptomic responses associated with disease resistance in cacao. Transcriptome sequencing generated 185,984,548 raw reads, of which 106,456,430 high-quality reads were retained after filtering. Following reference-guided assembly, 29,452 non-redundant transcripts were obtained, with an average length of 1,833 bp. Gene Ontology (GO) annotation classified transcripts into biological processes (59%), molecular functions (55%), and cellular components (67%), with cellular components being the most represented category. Differential expression analysis using edgeR identified 57 differentially expressed (DE) transcripts across comparisons between resistant (Sca-12) and susceptible (DR-1) genotypes under control and pathogen-treated conditions. Notably, 42 DE transcripts were identified between resistant and susceptible genotypes under control conditions, while 2 and 13 transcripts were detected in untreated and treated Sca-12 and DR-1 genotypes, respectively. Seven candidate genes associated with defense responses were selected for validation, and five (glycine-rich protein, plantacyanin, expansin-like B1, cysteine proteinase, and ACC oxidase 1) were confirmed by qRT-PCR, showing expression patterns consistent with RNA-seq data. These findings provide valuable insights into transcripts that may play crucial roles in the cacao plant’s defense mechanisms against Ppal.