Transcriptome reveals effects of low red/far-red ratio and shade on soybean seedlings

ABSTRACT Light intensity and spectral composition regulate plant photomorphogenesis, with far-red light (FR) playing a vital role in shade avoidance. Soybean (Glycine max (L.) Merr.), a globally significant crop, is vulnerable to canopy shade, which decreases the red/far-red (R/FR) ratio and causes adaptive responses. We explored how FR supplementation modifies soybean seedling responses under shade stress using morphological, physiological, and transcriptome analysis. Four light treatments were applied: Normal light (NL, R = 125.62 μmol·m-2·s-1, FR = 91.68 μmol·m-2·s-1), normal light + FR (NF, R = 124.57 μmol·m-2·s-1, FR = 161.77 μmol·m-2·s-1), shade (SL, R = 4.62 μmol·m-2·s-1, FR = 4.58 μmol·m-2·s-1), and shade + FR (SF, R = 4.58 μmol·m-2·s-1, FR = 16.35 μmol·m-2·s-1). Key characteristics assessed included plant height, stem thickness, chlorophyll concentration (SPAD), soluble sugars, antioxidant enzymes (superoxide dismutase SOD, peroxidase POD, catalase CAT), and transcriptome profiles at 7 and 15 d post-treatment. Results demonstrated that SF caused the most significant shade avoidance phenotype, with the highest plant height (22.7 cm), hypocotyl elongation (7.75 cm), and stem thinning (1.46 mm), associated with reduced chlorophyll concentration (SPAD: 25.3). The NF enhanced soluble sugar accumulation (2.66 g) and antioxidant enzyme activity (SOD: +38%, CAT: +29%), whereas SL/SF decreased these features compared to NL treatment group. Transcriptomic study showed 15 762 differentially expressed genes (DEGs) under SF, largely enriched in photosynthesis-antenna proteins, porphyrin-chlorophyll metabolism, and phytohormone signaling (abscisic acid, ethylene). These data indicate that FR possibly amplifies shade avoidance by coordinating photoreceptor signaling, hormonal dynamics, and photosynthetic repression. Shade avoidance is often characterized by stem and hypocotyl elongation, leaf expansion, and reduced chlorophyll content. These molecular insights are crucial for developing shade-resilient soybean cultivars.