Genome-Wide Analysis Identifies ScTCP6 as a Stress Responsive Gene in Rye

Teosinte branched1/cycloidea/proliferating cell factor (TCP) transcription factors are key regulators of plant growth and stress adaptation. However, their evolutionary history and functional divergence in rye (<i>Secale cereale</i> L.) remain unclear. Here, 26 <i>ScTCP</i> genes were identified from the reference rye genome. Phylogenetic and collinearity analyses with six representative cereals (<i>Secale cereale</i>, <i>H. vulgare</i>, <i>O. sativa</i>, <i>T. aestivum</i>, <i>Z. mays</i>, and <i>A. tauschii Coss</i>) revealed that segmental duplication, rather than tandem repetition, drove <i>ScTCP</i> expansion, with <i>ScTCP2</i> located in a conserved syntenic block shared across the <i>Poaceae</i> family. Promoter analysis identified numerous hormone- and stress-responsive <i>cis</i>-elements, while a predicted protein-protein interaction network indicated extensive cross-talk with ERF and MYB transcription factors. Expression profiling of 12 representative <i>ScTCP</i> genes using qRT-PCR across different organs, developmental stages, six abiotic stress conditions, and three hormone treatments showed that <i>ScTCP6</i> plays an important role in rye development and in responses to hormonal signals and abiotic stresses. Therefore, this study provides the first genome-wide characterization of the <i>TCP</i> gene family in rye and contributes to a broader understanding of the evolution and functional diversification of the <i>TCP</i> superfamily in higher plants.