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Background <p>Trehalose 6-phosphate (Tre6P) synthase (TPS) and Tre6P phosphatase (TPP) are two key enzymes involved in the trehalose synthesis pathway in plants. However, the identification and research of <i>TPS</i> and <i>TPP</i> gene families in rye are still limited.</p> Results <p>In this study, a total of 10 <i>TPS</i> genes and 9 <i>TPP</i> genes were identified based on the Lo7 genome database. According to phylogenetic analysis, ScTPS and ScTPP proteins from rye were more closely related to wheat, barley and other <i>Triticeae</i> species, and the fragment replication events might be the main driver of gene family expansion and new function generation during <i>ScTPS</i> and <i>ScTPP</i> genes evolution. Cis-element analysis revealed that <i>ScTPS</i> and <i>ScTPP</i> genes showed more stress-related cis-element distribution in rye, and some members of the ERF, MYB, bZIP, and C2H2 transcription factor families may play potential regulatory roles. Protein–protein interaction network analysis revealed that <i>ScTPS07</i>, <i>ScTPS08</i>, <i>ScTPS09</i> and <i>ScTPS10</i> might be hub genes in the rye trehalose synthesis pathway. RNA-seq and qRT-PCR analyses show that low temperature induces <i>ScTPS</i> and <i>ScTPP</i> expression; most genes reach maximal expression at 12–24&#xa0;h; expression differs between roots and leaves of rye seedlings.</p> Conclusions <p>This study provided a molecular basis for trehalose synthesis in rye by identifying members of the <i>ScTPS</i> and <i>ScTPP</i> gene families, provided insights into the mechanism of cold stress tolerance of this substance in rye by preliminary analysis of the expression patterns of these genes under low temperature stress.</p>

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Genome-wide identification and expression analysis of Trehalose 6-phosphate (Tre6P) synthase (TPS) and Tre6P phosphatase (TPP) genes under cold stress in winter Rye (Secale cereals L.)

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年2月21日

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  • Dan Wang,
  • Wei Ren,
  • Xianguo Wang

摘要

Background

Trehalose 6-phosphate (Tre6P) synthase (TPS) and Tre6P phosphatase (TPP) are two key enzymes involved in the trehalose synthesis pathway in plants. However, the identification and research of TPS and TPP gene families in rye are still limited.

Results

In this study, a total of 10 TPS genes and 9 TPP genes were identified based on the Lo7 genome database. According to phylogenetic analysis, ScTPS and ScTPP proteins from rye were more closely related to wheat, barley and other Triticeae species, and the fragment replication events might be the main driver of gene family expansion and new function generation during ScTPS and ScTPP genes evolution. Cis-element analysis revealed that ScTPS and ScTPP genes showed more stress-related cis-element distribution in rye, and some members of the ERF, MYB, bZIP, and C2H2 transcription factor families may play potential regulatory roles. Protein–protein interaction network analysis revealed that ScTPS07, ScTPS08, ScTPS09 and ScTPS10 might be hub genes in the rye trehalose synthesis pathway. RNA-seq and qRT-PCR analyses show that low temperature induces ScTPS and ScTPP expression; most genes reach maximal expression at 12–24 h; expression differs between roots and leaves of rye seedlings.

Conclusions

This study provided a molecular basis for trehalose synthesis in rye by identifying members of the ScTPS and ScTPP gene families, provided insights into the mechanism of cold stress tolerance of this substance in rye by preliminary analysis of the expression patterns of these genes under low temperature stress.