Genome-wide identification and integrative analysis of the WRKY gene family reveal candidate regulators involved in biotic stress responses in Hass avocado

Background Avocado ( Persea americana Mill.) is a significant fruit crop in tropical and subtropical regions. However, its growth, yield, and fruit quality are substantially impacted by biotic stresses, such as insect herbivory and pathogen infections. WRKY transcription factors are crucial in regulating plant growth, development, hormone signaling, and stress responses. Despite their importance, comprehensive genome-wide identification and characterization of the WRKY gene family, particularly in response to various biotic stresses, remain largely uninvestigated in Hass avocado. This study aims to identify the WRKY gene family at the genome-wide level and to explore its evolutionary characteristics, gene structures, tissue-specific expression patterns, and responses to biotic stresses in Hass avocado. Results A total of 70 PaWRKY genes were identified within the Hass avocado genome, exhibiting an uneven distribution across 12 chromosomes. Through analyses of phylogenetic relationships and conserved domain composition, these PaWRKY genes were categorized into three principal groups, with Group II further subdivided into five subgroups. Segmental duplication emerged as the primary mechanism driving the expansion of the PaWRKY gene family, with most duplicated gene pairs appearing to have undergone purifying selection. Investigations into gene structure, conserved motifs, cis -regulatory elements, and protein interaction networks indicated that PaWRKY members maintained relative conservation within subgroups, while also demonstrating potential for functional diversification. Transcriptomic analyses revealed distinct tissue-specific expression patterns and differential responses of PaWRKY genes to insect-infested leaves, diseased leaves, and insect-bored fruits. Compared to insect feeding, diseased leaves elicited more extensive and robust defense responses, which were further linked to tissue damage and senescence-related processes. Through integrative analyses employing K-means clustering, weighted gene co-expression network analysis (WGCNA), differentially expressed genes (DEG) screening, and UpSet plots, several candidate core PaWRKY genes implicated in biotic stress responses were identified. The predicted three-dimensional protein structures revealed that these core PaWRKY proteins exhibit localized structural variations while maintaining highly conserved WRKY domains. Conclusion This study systematically characterizes the WRKY gene family in Hass avocado, emphasizing its evolutionary diversification and differential responses to biotic stresses. These findings offer valuable candidate genes and theoretical support for future resistance breeding and molecular enhancement of avocado to combat biotic stresses.