Genome-wide characterization of XBMD3 genes in apple and the role of XBMD32 in response to drought stress

Abstract

The XANTHOMONAS RESISTANCE 21-binding protein 3 (XB3) gene family, encoding proteins with RING-finger or U-box domains, primarily functions as E3 ubiquitin ligases that are crucial for ubiquitin-mediated protein degradation and stress responses. This study presents the first genome-wide identification and characterization of the XB3 family in apple (Malus domestica), revealing 10 members named XBMD3s. Comprehensive analyses of phylogenetic relationships, chromosomal distribution, gene structures, conserved motifs, and promoter cis-acting elements revealed the evolutionary conservation and regulatory complexity of the XBMD3 family. The tissue-specific expression data revealed that XBMD31/31-1/31-2/31-3 and XBMD35 predominantly expressed in roots, whereas XBMD32/32-1, XBMD33/33-1, and XBMD34 exhibited preferential expression in leaves. Furthermore, all XBMD3 genes responded to drought stress, in which XBMD32 showing the strongest transcriptional induction, with an increase by more than 4.3 folds. Functional characterization demonstrated that overexpression of XBMD32 enhanced drought tolerance in transgenic tobacco plants increasing antioxidant enzyme activities and reducing reactive oxygen species (ROS) accumulation. In addition, we obtained XBMD32-overexpressing and XBMD32-silenced apple plants by Agrobacterium-mediated transient genetic transformation. The overexpression plants were more drought tolerant, whereas the silenced plants showed more sensitive phenotypes. Taken together, these findings underscore the role of the XBMD3 family in apple adaptation to drought stress, providing a basis for future functional studies and the improvement of drought tolerance.

Keywords

XBMD3 / Apple genome / Expression patterns / Drought stress / ROS accumulation

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Funding

Postdoctoral Fellowship Program of China Postdoctoral Science Foundation(GZC20231871)

Special Project for the Double Support Plan of Discipline Construction at Sichuan Agricultural University(2024ZYTS021)

Sichuan Province Science and Technology Department Projects(2025ZNSFSC0190)

RIGHTS & PERMISSIONS

The Author(s)