BACKGROUND: Soft rot caused by Botryosphaeria dothidea is a common disease in postharvest kiwifruit. Kiwifruit cultivars show varying susceptibility, but the molecular mechanisms underlying these differences are poorly understood. RESULTS: This study revealed that the ‘Jinyan’ (JY) kiwifruit cultivar exhibited greater resistance to B. dothidea and higher contents of total phenolics, flavonoids, and lignin compared to ‘Jinkui’ (JK). Transcriptome analysis revealed that 4011 genes were differentially expressed, with 1892 being upregulated and 2119 downregulated, between the resistant (JY) and susceptible (JK) kiwifruit cultivars on the first day post‐inoculation. GO and KEGG enrichment analyses indicated that differentially expressed genes (DEGs) were primarily associated with defense response functions and metabolic pathways. The DEGs related to phenylalanine metabolism ( DHQS , ADT , TAT , GOT2 , 4CL , CHS , CHI , CCR , F5H , BGLU , BGLU2 , BGLU4 , POD12 , POD55 ), calcium (Ca ²⁺ ) signaling pathway ( CALM2 , CML23 ), transcription factors ( WRKY22 , MYC2 ), plant hormone signaling pathway ( ATP7 , ETR , EBF1_2 , PP2C16 , SAPK2 ), and MAPK signaling pathway ( MKK4_5 ) were identified as key markers of resistance to B. dothidea . The expression patterns of these genes related to the key pathways were further validated by real‐time quantitative polymerase chain reaction; most of these genes show higher expression levels in JY than in JK. In total, these candidate genes and their associated pathways were found to be associated with kiwifruit resistance to B. dothidea ‐induced soft rot. CONCLUSION: This study revealed the functional genes and defense pathways involved in governing soft rot resistance in kiwifruit against B. dothidea . These results contribute to understanding the molecular differences in disease resistance between resistant and susceptible kiwifruit cultivars. © 2026 Society of Chemical Industry.

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