Transcriptomic insights into the stress signaling and drought tolerance mechanisms in sea-island cotton (Gossypium barbadense)

Abstract

Drought stress significantly impacts plant growth and agricultural productivity. Elucidating the molecular mechanisms underlying drought stress response and plant tolerance is crucial for developing resilient crops. In Gossypium barbadense (G. barbadense), the specific genetic responses to drought stress remain underexplored. To provide insights into the transcriptomic dynamics and tolerance mechanisms in G. barbadense, we screened a diverse panel of G. barbadense accessions to identify drought-tolerant genotypes and investigate drought-stress responses across root and shoot tissues at two distinct time points. Differentially expressed genes (DEGs) analysis revealed diverse drought-responsive genes across tissue types and treatment time points. Functional enrichment and predictive protein-protein interaction (PPI) network analyses elucidated intricate patterns of drought-stress signaling pathways and transcriptional regulatory mechanisms. These upregulated DEGs were enriched in functional categories such as hormone signal transduction, phosphatidylinositol signaling system, ubiquitin-mediated proteolysis, phenylpropanoid biosynthesis, glutathione metabolism, and carbon metabolism pathways. The PPI network analysis underscores the activation of key signaling genes such as plant U-box E3 ubiquitin ligases (PUBs), protein phosphatase 2 C (PP2Cs), and F-Box genes, as well as transcriptional factors (CBF/NFYA) and various effector genes. These networks revealed the activation of effector genes involved in phenylpropanoid biosynthesis (Thioredoxin like 2–1, 1-Cys), glutathione metabolism (Thioredoxin, GPX6), and carbohydrate/sugar metabolism (GBSSI, AMY1.1). Gene silencing experiments validated the regulatory roles predicted for PUBs and PP2Cs in stress signaling and NFYA transcriptional factor in modifying the plant morphology and physiology to enhance drought tolerance. This research provides critical insights into the genetic signatures of stress signaling and regulatory pathways associated with drought tolerance in G. barbadense. The identified candidate genes are valuable for targeted breeding efforts to enhance drought tolerance and crop yield.