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<p>To investigate the characteristics of the homeobox (<i>HB</i>) gene family in quinoa and its expression patterns under flooding stress, this study systematically identified <i>HB</i> gene family members based on the quinoa whole-genome data. Phylogenetic tree construction, cis-acting element analysis, and physicochemical property prediction of proteins were conducted to elucidate their evolutionary relationships, regulatory features, and functional divergence. Transcriptomic data under flooding stress were integrated to analyze the expression regulatory network of <i>HB</i> genes during the grain-filling stage. The results revealed that 44 <i>HB</i> genes were identified in the quinoa genome, classified into five evolutionary subfamilies, with uneven chromosomal distribution and significant divergence in physicochemical properties of encoded proteins. Promoter cis-acting element analysis showed that a large number of <i>HB</i> genes contain light-responsive, low-temperature, and drought-stress-related elements. Tissue-specific expression analysis indicated differential expression of <i>HB</i> genes in roots, stems, leaves, and flowers. Under flooding stress and recovery treatments, <i>HB</i> gene expression levels exhibited significant differences. Correlation analysis with physiological parameters identified 10 key <i>HB</i> genes potentially involved in flooding stress response during the grain-filling stage, with 8 belonging to the HD-ZIP I subfamily. GO enrichment analysis demonstrated their functional enrichment in terms such as “response to stimulus” and “regulation of biological process.” This study provides the first systematic characterization of the evolutionary features and expression regulatory patterns of the <i>HB</i> gene family in quinoa, offering critical candidate genes for deciphering its flooding tolerance mechanisms.</p>

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Identification of homeobox gene family in Chenopodium quinoa and expression patterns in response to flooding stress during the filling stage

  • 期刊论文

  • 发表日期：

    2025年6月25日

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  • Guofei Jiang,
  • Li Li,
  • Yutao Bai,
  • Xuqin Wang,
  • Lingyuan Zhang,
  • Ping Zhang,
  • Junna Liu,
  • Hanxue Li,
  • Liubin Huang,
  • Shan Zhang,
  • Peng Qin

摘要

To investigate the characteristics of the homeobox (HB) gene family in quinoa and its expression patterns under flooding stress, this study systematically identified HB gene family members based on the quinoa whole-genome data. Phylogenetic tree construction, cis-acting element analysis, and physicochemical property prediction of proteins were conducted to elucidate their evolutionary relationships, regulatory features, and functional divergence. Transcriptomic data under flooding stress were integrated to analyze the expression regulatory network of HB genes during the grain-filling stage. The results revealed that 44 HB genes were identified in the quinoa genome, classified into five evolutionary subfamilies, with uneven chromosomal distribution and significant divergence in physicochemical properties of encoded proteins. Promoter cis-acting element analysis showed that a large number of HB genes contain light-responsive, low-temperature, and drought-stress-related elements. Tissue-specific expression analysis indicated differential expression of HB genes in roots, stems, leaves, and flowers. Under flooding stress and recovery treatments, HB gene expression levels exhibited significant differences. Correlation analysis with physiological parameters identified 10 key HB genes potentially involved in flooding stress response during the grain-filling stage, with 8 belonging to the HD-ZIP I subfamily. GO enrichment analysis demonstrated their functional enrichment in terms such as “response to stimulus” and “regulation of biological process.” This study provides the first systematic characterization of the evolutionary features and expression regulatory patterns of the HB gene family in quinoa, offering critical candidate genes for deciphering its flooding tolerance mechanisms.