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

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.

The online version contains supplementary material available at 10.1007/s13205-026-04875-z.