Transcriptomic Profiling of Panicle Development Uncovers Key Regulators in Foxtail Millet

Deciphering the molecular regulatory networks of panicle development is essential for the genetic improvement of crop yield. However, to date, no systematic studies of gene expression across different panicle developmental stages have been performed in foxtail millet. In this study, a transcriptome analysis of foxtail millet panicle was conducted in four stages of development spanning from the initiation of primary branches to floral organ differentiation. A total of 20,377 expressed genes were identified, including 10,647 differentially expressed genes. Fuzzy C-means clustering detected stage-specific expressed homologs of key transcription regulators, which may be involved in plant organ morphogenesis. Moreover, 1215 transcription factors of 55 families were identified. Members of the MADS-box and GRAS transcription factors showed stage-specific expression patterns, whose conservation was useful in discovering genes related to foxtail millet panicle development. Our analysis was further substantiated by the functional characterization of SiSOC1, whose expression exhibited a gradual upregulation across the four developmental stages. SiSOC1 was identified and validated, which revised the annotation of the reference genome. Overexpression of SiSOC1 markedly accelerated the heading of foxtail millet under long-day and short-day conditions, validating its function in regulating the heading date. In summary, this study systematically identified the transcriptomic landscape of foxtail millet panicle development, and elucidated key regulatory genes. These results provide a theoretical foundation and gene resources for facilitating the molecular breeding of foxtail millet.