Aziz Rana Badar, Wei Ji, Wu Qiqi, Song Siyan, Yang Hui, Chen Xinpeng, Wang Ying, Chao Ruiqiang, Baz Naila Mir, Chen Haitao, Song Yuxuan, Fang Jinggui, Wang Chen
College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
College of Horticulture, Shanxi Agricultural University, Taigu 030031, China.
Int J Mol Sci. 2025 Jan 27;26(3):1102. doi: 10.3390/ijms26031102.
Paclobutrazol (PAC) is a significant inhibitor of gibberellin biosynthesis that profoundly influences grape seed development (GSD) through the modulation of key molecular pathways. Here, we identified 6659 differentially expressed genes (DEGs) in GSD under PAC treatment, with 3601 up-regulated and 3058 down-regulated. An analysis of hormone-associated DEGs revealed that auxin-related genes (16) were the most up-regulated, followed by genes associated with brassinosteroid and ABA. In contrast, cytokinin- and gibberellin-related genes exhibited a suppressive response. PAC treatment also triggered extensive reprogramming of metabolic pathways, including 44 genes involved in starch and sucrose metabolism (24 up-regulated, 20 down-regulated), 101 cell wall-related genes (53 up-regulated, 48 down-regulated), and 110 transcription factors (77 up-regulated, 33 down-regulated). A cis-element analysis of the promoters of 76 hormone-responsive genes identified 14 types of hormone-responsive cis-elements, with ABRE being the most prevalent. Genes responsible for inactivating active hormones, such as ABA-, and , were also identified. Concurrently, PAC negatively regulated hormone-active genes, including , , and , leading to reduced levels of these hormones. PAC modulates GSD by mediating the dynamic balance of multi-hormone accumulations. Furthermore, development-related cis-elements such as the AACA-motif, AAGAA-motif, AC-I, AC-II, O2-site, as-1, CAT-box, CCAAT-box, circadian, GCN4-motif, RY-element, HD-Zip 1, HD-Zip 3, MSA-like, MYB-like sequence, MYB-binding site, and MYB recognition site, were found in key DEGs involved in starch and sucrose metabolism, cell wall remodeling, and epigenetic regulation. This indicates that these pathways are responsive to PAC modulation during GSD. Finally, we developed a comprehensive regulatory network to illustrate the PAC-mediated pathways involved in GSD. This network integrates multi-hormonal signaling, cell wall remodeling, epigenetic regulation, and transcription factors, highlighting PAC's pivotal role in GSD. Our findings provide new insights into the complex mechanisms underlying PAC's effects on grapevine development.
多效唑（PAC）是赤霉素生物合成的重要抑制剂，它通过调节关键分子途径深刻影响葡萄种子发育（GSD）。在此，我们鉴定出在PAC处理下GSD中的6659个差异表达基因（DEG），其中3601个上调，3058个下调。对激素相关DEG的分析表明，生长素相关基因（16个）上调最为明显，其次是与油菜素内酯和脱落酸相关的基因。相比之下，细胞分裂素和赤霉素相关基因表现出抑制反应。PAC处理还引发了代谢途径的广泛重编程，包括44个参与淀粉和蔗糖代谢的基因（24个上调，20个下调）、101个细胞壁相关基因（53个上调，48个下调）和110个转录因子（77个上调，33个下调）。对76个激素响应基因启动子的顺式元件分析鉴定出14种激素响应顺式元件，其中ABRE最为普遍。还鉴定出负责使活性激素失活的基因，如ABA - 等。同时，PAC负向调节激素活性基因，包括等，导致这些激素水平降低。PAC通过介导多激素积累的动态平衡来调节GSD。此外，在参与淀粉和蔗糖代谢、细胞壁重塑和表观遗传调控的关键DEG中发现了与发育相关的顺式元件，如AACA - 基序、AAGAA - 基序、AC - I、AC - II、O2 - 位点、as - 1、CAT - 框、CCAAT - 框、昼夜节律、GCN4 - 基序、RY - 元件、HD - Zip 1、HD - Zip 3、MSA - 样、MYB - 样序列、MYB - 结合位点和MYB识别位点。这表明这些途径在GSD过程中对PAC调节有响应。最后，我们构建了一个综合调控网络来说明PAC介导的参与GSD的途径。该网络整合了多激素信号传导、细胞壁重塑、表观遗传调控和转录因子，突出了PAC在GSD中的关键作用。我们的研究结果为PAC对葡萄发育影响的复杂机制提供了新的见解。
