Differential co-expression modules underpin genotype-specific adaptation to shading in cigar tobacco: Linkages to sugar metabolism and leaf morphology

Shading is a common agronomic practice in cigar tobacco cultivation to improve wrapper leaf quality, yet its morphological and molecular effects across different cultivars remain underexplored. This study investigated morphological traits, sugar metabolism, and transcriptomic responses in three cigar tobacco cultivars (HN2, HY101, and HY103) under two treatments: no shading (NST) and shading (ST, 50–60% transparency). Morphological analysis revealed that shading reduced leaf thickness in HY103 without compromising chlorophyll content or structural integrity, traits desirable for wrapper leaf quality. Biochemical assays showed increased sucrose and total soluble sugars, particularly in HY103, along with elevated activities of sucrose phosphate synthase (SPS) and soluble starch synthase (SSS) enzymes. Transcriptome profiling and Weighted Gene Co-Expression Network Analysis (WGCNA) identified three key gene modules responsive to shading. The lightgreen module, enriched in nitrogen metabolism and signal transduction genes, displayed genotype-specific expression patterns. The midnightblue module, containing photosynthesis and reactive oxygen species (ROS) related genes, was highly expressed in HY103 under shading, indicating enhanced oxidative stress resilience and photosynthetic flexibility. The brown module was enriched in transcriptional regulators, potentially modulating leaf morphology. Together, these results demonstrate that HY103 employs a coordinated structural and molecular strategy to adapt to shaded environments, providing a basis for optimizing shade cultivation and breeding shade-tolerant cigar tobacco.