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 (Secale cereale L.) remain unclear. Here, 26 ScTCP genes were identified from the reference rye genome. Phylogenetic and collinearity analyses with six representative cereals (Secale cereale, H. vulgare, O. sativa, T. aestivum, Z. mays, and A. tauschii Coss) revealed that segmental duplication, rather than tandem repetition, drove ScTCP expansion, with ScTCP2 located in a conserved syntenic block shared across the Poaceae family. Promoter analysis identified numerous hormone- and stress-responsive cis-elements, while a predicted protein-protein interaction network indicated extensive cross-talk with ERF and MYB transcription factors. Expression profiling of 12 representative ScTCP genes using qRT-PCR across different organs, developmental stages, six abiotic stress conditions, and three hormone treatments showed that ScTCP6 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 TCP gene family in rye and contributes to a broader understanding of the evolution and functional diversification of the TCP superfamily in higher plants.