Identification of auxin response factor in the pan-genome and their expression pattern analysis in cucumber

Auxin response factors (ARFs) are important transcription factors that regulate the expression of early genes in response to auxin. Auxin is a crucial phytohormone that controls plant growth and development. Even though ARF genes have been identified in the cucumber (Cucumis sativus) genome version 3.0, the features of this gene family are unclear in the cucumber pan-genome and in the newly assembled genome v4.0. We identified a total of 18 CsARF genes, including two CsARF13s in Gy14. All ARF proteins, except ARF5 and 7, showed differences in protein length; all of them showed amino acid variation in the cucumber pan-genome, including 13 accessions. We also analyzed their organ-specific expression and their expression patterns in fruit development and in response to biotic stresses. Importantly, we found that the overexpression of CsARF12 significantly enhanced the resistance of cucumber cotyledons to gray mold infection. Therefore, this study lays a foundation for understanding the biological functions of CsARF genes and provides CsARF12 as a candidate gene to improve the cucumber resistance to gray mold.