Zhang Ju, Chen Can, Yang Qihang, Xu Jie, Han Zizhuo, Ma Wei, Zhang Xiaomeng, Xu Kedong, Zhao Jianjun, Chen Xueping
State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, Hebei, China.
Key Laboratory of Plant Genetics and Molecular Breeding, Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, Henan International Joint Laboratory of Translational Biology, Zhoukou Normal University, Zhoukou, Henan, China.
Front Plant Sci. 2025 Apr 3;16:1583110. doi: 10.3389/fpls.2025.1583110. eCollection 2025.
The HD-ZIP protein, a unique class of transcription factors in plants, plays a crucial role in plant growth and development. Although some HD-ZIP transcription factors have been associated with leafy head formation in Chinese cabbage, their regulatory mechanisms remain poorly understood.
This study identified the HD-ZIP family using HMM and TBtools, constructed a phylogenetic tree with OrthoFinder, and analyzed gene family expansion and contraction using CAFE. Conserved features were analyzed with MAFFT, MEME, and TBtools; regulatory networks were predicted using ATRM and PlantTFDB; and gene expression was validated by qRT-PCR.
In this study, gene sequences from 87 species were analyzed to explore the evolutionary history of this gene family. Despite significant variation in gene family expansion and contraction across species, our findings indicated that HD-ZIP family proteins were conserved in both lower (Charophyta) and higher plants, where they were potentially involved in root, stem, and leaf differentiation. In our analysis of 22 Brassica species, HD-ZIP III protein sequences and domains were conserved. However, within the pan-genome A of 18 species, differences were observed in auxin-related cis-elements within the HD-ZIP III promoter regions between heading and non-heading cabbage varieties. RNA-seq analysis of wild-type A03 (heading) and mutant (non-heading) revealed that 131 genes formed a protein interaction network or clustered in the same branch as family genes. Through GO enrichment and qRT-PCR, several key candidate genes of ssp. A03 associated with leafy head formation in cabbage were identified. These findings established a foundation for understanding the molecular mechanisms by which the gene family regulated head growth in Chinese cabbage.
HD-ZIP蛋白是植物中一类独特的转录因子，在植物生长发育中起关键作用。尽管一些HD-ZIP转录因子与大白菜叶球形成有关，但其调控机制仍知之甚少。
本研究使用HMM和TBtools鉴定HD-ZIP家族，用OrthoFinder构建系统发育树，用CAFE分析基因家族的扩张和收缩。用MAFFT、MEME和TBtools分析保守特征；用ATRM和PlantTFDB预测调控网络；通过qRT-PCR验证基因表达。
本研究分析了87个物种的基因序列，以探索该基因家族的进化历史。尽管不同物种间基因家族的扩张和收缩存在显著差异，但我们的研究结果表明，HD-ZIP家族蛋白在低等植物（轮藻门）和高等植物中都保守，可能参与根、茎和叶的分化。在对22个芸苔属物种的分析中，HD-ZIP III蛋白序列和结构域是保守的。然而，在18个物种的泛基因组A中，结球和不结球甘蓝品种的HD-ZIP III启动子区域内生长素相关顺式元件存在差异。对野生型A03（结球）和突变体（不结球）的RNA-seq分析表明，131个基因形成了一个蛋白质相互作用网络，或与家族基因聚集在同一分支。通过GO富集和qRT-PCR，鉴定了几个与大白菜叶球形成相关的关键候选基因。这些发现为理解基因家族调控大白菜叶球生长的分子机制奠定了基础。
