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<p>Trehalose is a typical stress metabolite that plays a crucial role in plant metabolism, growth development, and the tolerance to abiotic stress. Two key enzymes involved in trehalose synthesis are trehalose-6-phosphate synthase (TPS) and trehalose-6-phosphate phosphatase (TPP). To date, research on genes related to low-temperature response in the trehalose gene families in foxtail millet (<i>Setaria italica</i>) has not been reported. In this study, we identified 10 SiTPS genes (SiTPSs) and 10 SiTPP genes (SiTPPs) from the foxtail millet genome. Based on analyses of phylogenetic relationships, domains, motifs, and gene structures, SiTPSs were classified into two subfamilies, while SiTPPs were divided into three subfamilies. Numerous cis-acting elements responsive to light and hormones were found in both SiTPSs and SiTPPs. In addition, low-temperature response elements were identified in <i>SiTPS3</i>, <i>SiTPS4</i>, <i>SiTPS6</i>, <i>SiTPS7</i>, <i>SiTPS8</i>, <i>SiTPP4</i>, and <i>SiTPP5</i>. Collinearity analysis revealed three pairs of gene duplications (<i>SiTPS2</i> and <i>SiTPS9</i>, <i>SiTPS3</i> and <i>SiTPS8</i>, <i>SiTPS6</i> and <i>SiTPS7</i>) in foxtail millet. Expression pattern analysis indicated that both SiTPSs and SiTPPs exhibit spatiotemporal specificity and can be induced by low temperatures. The protein–protein interaction (PPI) network demonstrated strong interactions between SiTPSs and SiTPPs. Furthermore, weighted gene co-expression network analysis (WGCNA) identified several candidate genes that are co-expressed with genes related to low-temperature responses. Haplotype analysis suggested that <i>SiTPS1</i>, <i>SiTPS9</i>, and <i>SiTPS10</i> are involved in the response to low-temperature stress in foxtail millet. This study highlights the significant contributions of SiTPSs and SiTPPs to the plant’s responses to low-temperature stress. These genes offer crucial genetic resources for low-temperature breeding in foxtail millet. Moreover, the exploitation of these resources in low-temperature tolerance research is essential for ensuring the yield and quality of foxtail millet.</p>

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Identification and Functional Analysis of Trehalose Synthesis Genes in Foxtail Millet: Insights into Low-Temperature Stress Response

  • 期刊论文

  • 发表日期：

    2025年7月17日

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  • Yueyue Wang,
  • Yajun Li,
  • Yidan Luo,
  • Yuhua Xu,
  • Bo Zhao,
  • Rong Sun,
  • Juan Zhao,
  • Xukai Li,
  • Yijuan Zhang,
  • Yuanhuai Han,
  • Hongying Li,
  • Hui Zhang

摘要

Trehalose is a typical stress metabolite that plays a crucial role in plant metabolism, growth development, and the tolerance to abiotic stress. Two key enzymes involved in trehalose synthesis are trehalose-6-phosphate synthase (TPS) and trehalose-6-phosphate phosphatase (TPP). To date, research on genes related to low-temperature response in the trehalose gene families in foxtail millet (Setaria italica) has not been reported. In this study, we identified 10 SiTPS genes (SiTPSs) and 10 SiTPP genes (SiTPPs) from the foxtail millet genome. Based on analyses of phylogenetic relationships, domains, motifs, and gene structures, SiTPSs were classified into two subfamilies, while SiTPPs were divided into three subfamilies. Numerous cis-acting elements responsive to light and hormones were found in both SiTPSs and SiTPPs. In addition, low-temperature response elements were identified in SiTPS3, SiTPS4, SiTPS6, SiTPS7, SiTPS8, SiTPP4, and SiTPP5. Collinearity analysis revealed three pairs of gene duplications (SiTPS2 and SiTPS9, SiTPS3 and SiTPS8, SiTPS6 and SiTPS7) in foxtail millet. Expression pattern analysis indicated that both SiTPSs and SiTPPs exhibit spatiotemporal specificity and can be induced by low temperatures. The protein–protein interaction (PPI) network demonstrated strong interactions between SiTPSs and SiTPPs. Furthermore, weighted gene co-expression network analysis (WGCNA) identified several candidate genes that are co-expressed with genes related to low-temperature responses. Haplotype analysis suggested that SiTPS1, SiTPS9, and SiTPS10 are involved in the response to low-temperature stress in foxtail millet. This study highlights the significant contributions of SiTPSs and SiTPPs to the plant’s responses to low-temperature stress. These genes offer crucial genetic resources for low-temperature breeding in foxtail millet. Moreover, the exploitation of these resources in low-temperature tolerance research is essential for ensuring the yield and quality of foxtail millet.