Lu Yao, Ma Rongqun, Wu Kunhao, Sun Jilu, Li Yutong, Zhao Jiawei, Qi Zhenbao, Sha Guangli, Ge Hongjuan, Shi Yanjing
College of Biological Engineering, Qingdao University of Science and Technology, Qingdao, China.
Qingdao Academy of Agricultural Science, Qingdao, China.
PeerJ. 2025 Aug 18;13:e19741. doi: 10.7717/peerj.19741. eCollection 2025.
Class III peroxidases (PRXs) play a crucial role in maintaining reactive oxygen species (ROS) homeostasis, thereby influencing plant growth, development, and defense responses. To date, the roles of PRXs in apple branch development and the control of rootstock growth vigor remain poorly understood. This research aimed to exhaustively annotate and analyze the Class III PRX family in the apple genome. Ninety-nine PRX proteins were identified from the genome. Phylogenetic analysis revealed that the PRXs from and were classified into six groups. McSCAN analysis indicated that tandem duplication events played a dominant role in the expansion of peroxidases (MdPRXs), thus purifying selection maintained their function. Most genes contained cis-elements responsive to light and plant hormones such as abscisic acid (ABA) and methyl jasmonate (MeJA), as well as various stress factors. Although most MdPRXs possess N-terminal signal peptides, in contrast to the majority of Arabidopsis PRX gene family members that are primarily localized in the apoplast, 50 MdPRXs are localized in the chloroplasts, with only one-third predicted to be apoplastic. Analysis of their spatiotemporal expression patterns, based on transcriptome data, revealed extensive involvement in apple tissue and organ development, demonstrating distinct and specialized expression profiles. These variations are primarily attributed to differences in cis-elements within the promoter regions and their three-dimensional structural variations, rather than to their phylogenetic relationships. In rootstock-scion composite trees, the expression patterns of MdPRXs were influenced by both rootstock species and scion varieties. Unlike previous studies relying on zymogram analysis, our findings reveal that the transcriptional expression of MdPRXs is not inherently negatively correlated with the dwarfing capacity of apple rootstocks. Notably, we identified that high expression of is specifically associated with vigorous rootstocks. A set of such as , , and may affect the ROS status in stem cell niche of the axillary buds and promote the differentiation of branches. This systematic analysis provides a foundation for the further functional characterization of genes, with the aim of improving apple rootstock dwarfing ability and branching characteristics.
III类过氧化物酶（PRXs）在维持活性氧（ROS）稳态中起关键作用，从而影响植物的生长、发育和防御反应。迄今为止，PRXs在苹果枝条发育和砧木生长势调控中的作用仍知之甚少。本研究旨在全面注释和分析苹果基因组中的III类PRX家族。从基因组中鉴定出99个PRX蛋白。系统发育分析表明，苹果和其他植物的PRXs被分为六组。McSCAN分析表明，串联重复事件在苹果过氧化物酶（MdPRXs）的扩增中起主导作用，因此纯化选择维持了它们的功能。大多数苹果基因含有对光和植物激素（如脱落酸（ABA）和茉莉酸甲酯（MeJA））以及各种胁迫因子有响应的顺式作用元件。虽然大多数MdPRXs具有N端信号肽，但与大多数主要定位于质外体的拟南芥PRX基因家族成员不同，50个MdPRXs定位于叶绿体，只有三分之一预计定位于质外体。基于转录组数据对其时空表达模式的分析表明，它们广泛参与苹果组织和器官的发育，显示出独特和专门的表达谱。这些差异主要归因于启动子区域内顺式作用元件的差异及其三维结构变异，而不是它们的系统发育关系。在砧木-接穗复合树中，MdPRXs的表达模式受砧木种类和接穗品种的影响。与以往依赖酶谱分析的研究不同，我们的研究结果表明，MdPRXs的转录表达与苹果砧木的矮化能力并非固有负相关。值得注意的是，我们发现MdPRX10的高表达与旺盛的砧木特异性相关。一组如MdPRX28、MdPRX33和MdPRX34可能影响腋芽干细胞龛中的ROS状态并促进枝条分化。这种系统分析为进一步功能表征MdPRX基因奠定了基础，目的是提高苹果砧木的矮化能力和分枝特性。
