Integrating transcriptomics and network biology to identify candidate genes against Conopomorpha cramerella in Theobroma cacao

Abstract Cocoa pods suffer significant damage from the cocoa pod borer (CPB, Conopomorpha cramerella ), a major pest affecting cocoa ( Theobroma cacao ) crops in Southeast Asia, severely diminishing yield. The mechanisms underlying the genetic resistance of cocoa varieties to this pest are not yet fully elucidated. This study aims to identify key candidate genes associated with cocoa responses to CPB infestation through an integrative approach combining de novo transcriptomic profiling and gene co-expression network analysis to evaluate the genetic basis of CPB resistance in two contrasting T. cacao cultivars: KKM22 (CPB-moderately resistant; ADSI = 1.45) and PBC123 (CPB-susceptible; ADSI = 2.98). The de novo sequencing of husks and pulps from control and CPB-infested plants produced 70,073 transcripts. Functional annotation identified genes in diverse biological processes and pathway-related categories. For WGCNA, gene-level expression data were used following low-expression filtering and variance-stabilizing transformation (VST). Co-expression analysis identified 32 modules, from which key modules were prioritized based on module size, eigengene expression patterns, and functional enrichment. bisque4 was associated with cell-wall-related functions, including plant-type secondary cell wall biogenesis, while chocolate4 showed enrichment of defense-associated functions. Network analysis further identified highly connected genes within these key modules as candidate genes associated with the cocoa response to CPB infestation. These findings provide an exploratory framework for understanding tissue and cultivar-associated transcriptional responses to CPB and for prioritizing candidate genes for future functional validation.