Integrated transcriptomic and metabolomic analysis of Korla fragrant pear responses to black spot disease caused by Alternaria alternata

Black spot disease, which manifests as early defoliation and fruit rot, causes significant economic losses in the production of Korla fragrant pear ( Pyrus sinkiangensis ), a perennial fruit tree indigenous to Xinjiang, China. To date, the molecular mechanisms underlying the response of pear species to Alternaria alternata infection remain poorly understood, impeding progress in the breeding of disease-resistant pear trees. We employed transcriptome (RNA-seq) and metabolome profiling to analyze Korla fragrant pear leaves at multiple time points following black spot disease inoculation. Comparative analysis revealed 17,362 differentially expressed genes (DEGs) relative to the pre-inoculation baseline (0 h) and 9840 DEGs relative to the time-matched mock-inoculated controls. A core set of 9008 DEGs common to both comparisons was identified and clustered into six distinct expression profiles, with pathway enrichment performed for each cluster. Metabolomic analysis revealed 2596 differentially regulated metabolites (DRMs) versus the 0 h baseline and 2616 DRMs versus time-matched mock controls, yielding 2017 common DRMs. Integrated transcriptomic and metabolomic analyses highlighted flavonoid biosynthesis, photosynthesis-related processes, and plant hormone signal transduction as major response-associated pathways. Weighted gene co-expression network analysis (WGCNA) further identified 12 candidate hub genes, including six transcription factors and three flavonoid-pathway genes for subsequent functional validation. Collectively, these results provide an integrated overview of transcriptomic and metabolic changes associated with the Korla fragrant pear response to A. alternata infection and prioritize candidate genes for future functional validation.