| Summary: | <i>Botrytis cinerea</i>, a pathogenic fungus that causes necrosis in plants, is one of the most destructive pathogens of hazelnuts. This fungus is responsible for causing Husk Brown Rot, a significant threat to hazelnut production. The plant’s defense mechanism against this pathogen, as well as other pathogens, is a complex biological process that involves changes at molecular, biochemical, and physiological levels. To better understand the molecular responses of hazelnut plants to <i>B. cinerea</i> infection, we conducted a comparative transcriptome profiling study between a <i>B. cinerea</i>-resistant Ping’ou hybrid hazelnut variety (Dawei; DW) and a susceptible variety (Qiuxiang; QX). Our study focused on the transcriptome profiles of DW and QX plants after three days of <i>B. cinerea</i> infection. The results of our study showed moderate changes in the defense strategies of both DW and QX plants in response to <i>B. cinerea</i> infection. Specifically, we observed that the expression of 14 disease-resistant genes was significantly different between DW and QX. Our comparative analysis revealed that DW had a higher number and expression of immunity-related differentially expressed genes compared to QX, which indicates that these genes play a crucial role in inducing innate resistance in DW plants against <i>B. cinerea</i> infection. This study highlights that plant resistance to pathogens like <i>B. cinerea</i> is a complex process that is controlled by multiple genes and biological pathways, each playing a specific role. Our findings provide new insights into the development of hazelnut varieties that are resistant to <i>B. cinerea</i> infection. By using the candidate genes identified in this study, it may be possible to enhance the resistance of hazelnut plants to <i>B. cinerea</i> and reduce the impact of Husk Brown Rot on hazelnut production.
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