Genome-Wide Identification and Abiotic Stress Response Analysis of C2H2 Zinc Finger Protein Genes in Foxtail Millet (<i>Setaria italica</i>)

Genome-Wide Identification and Abiotic Stress Response Analysis of C2H2 Zinc Finger Protein Genes in Foxtail Millet (<i>Setaria italica</i>)

C2H2 zinc finger proteins (C2H2-ZFPs) constitute one of the largest transcription factor families in plants, playing crucial roles in growth, development, and stress responses. Here, we performed a comprehensive genome-wide analysis of <i>C2H2-ZFPs</i> in foxtail millet (<i>Setaria...

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Main Authors: Qian Zhao, Yingxin Zhang, Xiangyu Xing, Shuyao Li, Ruidong Sun, Weilong Zhang, Jun Zhang, Liangyu Jiang, Zhenyuan Zang, Ming Gao, Jian Zhang
Format: Article
Language:English
Published: MDPI AG 2025-07-01
Series:Agronomy
Subjects:
<i>C2H2</i>
foxtail millet
phylogenetic analysis
expression profiles
abiotic stress
Online Access:https://www.mdpi.com/2073-4395/15/7/1618
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Summary:C2H2 zinc finger proteins (C2H2-ZFPs) constitute one of the largest transcription factor families in plants, playing crucial roles in growth, development, and stress responses. Here, we performed a comprehensive genome-wide analysis of <i>C2H2-ZFPs</i> in foxtail millet (<i>Setaria italica</i> v2.0), identifying 67 members that were unevenly distributed across all nine chromosomes. Most SiC2H2 proteins were predicted to be alkaline, stable, and nuclear-localized, with the exception of <i>SiC2H2-11</i> and <i>SiC2H2-66</i>, which were chloroplast-targeted. Phylogenetic analysis with <i>Arabidopsis thaliana</i> and <i>Oryza sativa</i> (rice) homologs classified these genes into seven distinct subfamilies, each containing the characteristic motif1 domain. Evolutionary studies revealed 14 segmental duplication events and strong syntenic conservation with <i>Triticum aestivum</i> (wheat, 163 orthologous pairs), suggesting conserved functions during evolution. Promoter analysis identified multiple cis-acting elements associated with light responsiveness, hormone signaling, and stress adaptation. Transcriptome profiling and qPCR validation in the YuGu 56 cultivar identified several stress-responsive candidates, including <i>SiC2H2-35</i> and <i>SiC2H2-58</i> (salt tolerance), as well as <i>SiC2H2-23</i> (5.19-fold induction under salt stress) and <i>SiC2H2-32</i> (5.47-fold induction under drought). This study provides some valuable insights into the <i>C2H2-ZFP</i> family in foxtail millet and highlights potential genetic markers for improving stress resilience through molecular breeding approaches.
ISSN:2073-4395

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