Decoding the shading effect in cigar tobacco leaf development through transcriptomic and physiological insights

Shading or low light is a key agronomic practice affecting the growth, physiology, and quality of cigar tobacco wrapper leaves, yet the physiological and molecular mechanisms underlying shading responses remain poorly characterized. This study investigated the physiological, transcriptomic, and agronomic responses of the cultivar QX103 under three light regimes: full light (CT), moderate shading (MT, 70–80 % transmittance), and heavy shading (LT, 50–60 % transmittance). Shading significantly enhanced wrapper yield (LT>MT>CT), with moderate shading promoting optimal plant height, leaf expansion, SPAD values, and photosynthetic efficiency. Transcriptome analysis revealed distinct gene expression changes, with MT upregulating AMY, UGP2, TREH, WAXY, and SPS genes to enhance starch degradation and sucrose synthesis, whereas LT upregulated TPS, GN1_2_3, and ISA, indicating starch catabolism under low light. Circadian genes (PRR5, CO, CDF1) were activated under MT, while LT disrupted clock entrainment (TOC1, LHY, CRY1/2, COP1). Hormone profiling validated that MT enhanced ICAId and TZR, supporting growth, whereas, LT increased IAA, GA1, GA7, and IPA while reducing SAG, DHJA, and SA, indicating stress. qRT-PCR confirmed that MT promoted primary metabolism, while LT altered hormonal profiles driving a shade-avoidance-like response mediated by altered IAA/GA and JA/SA dynamics. Collectively, these results demonstrate that moderate shading balances growth, metabolism, and stress responses, improving wrapper leaf quality and yield, providing a mechanistic basis for precision shading in cigar tobacco cultivation.