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<p>Zinc/iron-regulated transporter-like protein (ZIP) gene family plays a key role in the transport of metals, such as cadmium (Cd), which is critical for various plant functions. Although there has been extensive research on this gene family across multiple species, detailed exploration with respect to <i>Malus</i> crabapple is still lacking. In this study, we identified 23 <i>McZIP</i> genes from the <i>Malus</i> crabapple genome, categorizing them into four distinct subfamilies. Our analysis of gene structure and conserved motifs revealed notable evolutionary conservation, suggesting functional diversification within the family. Chromosomal mapping and synteny analysis revealed that the expression of the <i>McZIP</i> genes was unevenly distributed, with five pairs showing tandem duplication and three pairs exhibiting segmental duplication. Promoter region analysis revealed several cis-elements that are potentially involved in responses to environmental stressors, such as cold and hypoxia, as well as in hormone pathways, including those mediated by methyl jasmonate and abscisic acid. Transcriptome profiling revealed that 15 <i>McZIP</i> genes were differentially expressed in response to cadmium treatment in crabapple roots. Among them, <i>McZIP5/6</i> expression was consistently upregulated with increasing Cd exposure, whereas <i>McZIP3/12/13/17</i> expression initially increased but then decreased with increasing Cd concentration. Weighted gene co-expression network analysis (WGCNA) further revealed that <i>McZIP13</i>, with a yellow module, was significantly correlated with 50 µmol/L CdCl₂ treatment. Genes within this module were enriched primarily in pathways such as glutathione metabolism, MAPK signaling, and flavonoid biosynthesis, indicating its involvement in various detoxification and signaling processes. Based on these findings, a significant co-expression regulatory network comprising 26 transcription factors (including MYB, WRKY, NAC, etc.) and <i>McZIP13</i> was constructed. Furthermore, the promoter region of <i>McZIP13</i> contains two WRKY binding sites and two MYB binding sites, suggesting that its expression may be regulated by WRKY and MYB transcription factors. These results provide valuable insights into the potential role of the <i>McZIP</i> gene family in heavy metal stress responses in <i>Malus</i> crabapple.</p>

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Genome-wide identification and characterization of the McZIP gene family in Malus crabapple and its response to cadmium stress

  • 期刊论文

  • 发表日期：

    2026年5月14日

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  • Yupei Song,
  • Wenjing Wu,
  • Yihao Wei,
  • Xin Wen,
  • Jiaqi Zhang,
  • Tengxun Zhang,
  • Kaiming Zhang,
  • Weichao Liu

摘要

Zinc/iron-regulated transporter-like protein (ZIP) gene family plays a key role in the transport of metals, such as cadmium (Cd), which is critical for various plant functions. Although there has been extensive research on this gene family across multiple species, detailed exploration with respect to Malus crabapple is still lacking. In this study, we identified 23 McZIP genes from the Malus crabapple genome, categorizing them into four distinct subfamilies. Our analysis of gene structure and conserved motifs revealed notable evolutionary conservation, suggesting functional diversification within the family. Chromosomal mapping and synteny analysis revealed that the expression of the McZIP genes was unevenly distributed, with five pairs showing tandem duplication and three pairs exhibiting segmental duplication. Promoter region analysis revealed several cis-elements that are potentially involved in responses to environmental stressors, such as cold and hypoxia, as well as in hormone pathways, including those mediated by methyl jasmonate and abscisic acid. Transcriptome profiling revealed that 15 McZIP genes were differentially expressed in response to cadmium treatment in crabapple roots. Among them, McZIP5/6 expression was consistently upregulated with increasing Cd exposure, whereas McZIP3/12/13/17 expression initially increased but then decreased with increasing Cd concentration. Weighted gene co-expression network analysis (WGCNA) further revealed that McZIP13, with a yellow module, was significantly correlated with 50 µmol/L CdCl₂ treatment. Genes within this module were enriched primarily in pathways such as glutathione metabolism, MAPK signaling, and flavonoid biosynthesis, indicating its involvement in various detoxification and signaling processes. Based on these findings, a significant co-expression regulatory network comprising 26 transcription factors (including MYB, WRKY, NAC, etc.) and McZIP13 was constructed. Furthermore, the promoter region of McZIP13 contains two WRKY binding sites and two MYB binding sites, suggesting that its expression may be regulated by WRKY and MYB transcription factors. These results provide valuable insights into the potential role of the McZIP gene family in heavy metal stress responses in Malus crabapple.