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Integrated omics revealed regulatory mechanisms governing potato (Solanum tuberosum L.) seedling growth during shade avoidance syndrome

ABSTRACT: Background: Potato (Solanum tuberosum L.) is the fourth largest food crop worldwide with significant economic value and importance for food security. Shade avoidance syndrome (SAS) considerably affects crop architecture and productivity in high-density planting systems; however, its molecular mechanisms in potato remain poorly understood. Methods: Potato seedlings were subjected to four light treatments simulating different shade signals: white light (control, WL), low blue light (LBL, simulating blue light attenuation by plant canopies), low red:far-red ratio (WL+FR, simulating far-red reflection from neighboring plants), and their combination (LBL+FR, simulating complete plant shade environment). We conducted a comprehensive study integrating morphological characterization, leaf anatomical analysis, hormone quantification, transcriptome sequencing, and metabolite profiling. Results: Morphological analysis revealed that WL+FR primarily induced internode elongation (+20.0%) and leaf hyponasty, while LBL promoted stem elongation through increased node production (+36.3%). When combined, these signals (LBL+FR) synergistically enhanced stem elongation by 79.3%. Anatomical examination showed that LBL-treated leaves formed thickened palisade tissue layers (176.34 μm) with 6-7 layers of spongy tissue, whereas WL+FR resulted in thinner leaves (151.22 μm). Transcriptomic analysis identified 6,057 differentially expressed genes enriched in photosynthesis, hormone signaling, and carbohydrate metabolism pathways. A total of 1,168 differentially accumulated metabolites were detected across treatments, particularly organic acids and lipids associated with TCA (tricarboxylic acid) cycle and starch-sucrose metabolism. Weighted gene co-expression network analysis (WGCNA) identified PHYTOCHROME A (PHYA) as the central hub gene coordinating SAS responses under combined light stress, significantly diverging from the PHYB-centric model established in Arabidopsis.

ORGANISM(S): Solanum tuberosum

PROVIDER: GSE313166 | GEO | 2025/12/16

REPOSITORIES: GEO

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Project description:In dense plant stands, the ratio between red and far-red (R:FR) light declines and shade intolerant species will respond to this cue for future shade by inducing the shade avoidance syndrome (SAS), enabling them to outgrow their neighbours. Shade tolerant species from the forest understory are unable to outgrow neighbouring trees and will suppress SAS. Although the molecular mechanisms underlying SAS are well studied in various species, mechanisms of SAS-suppression in shade tolerant species have rarely been studied. We applied RNA sequencing on Geranium pyrenaicum and G. robertianum, two wild species with contrasting growth responses to low R:FR light. G. pyrenaicum strongly induces petiole elongation when exposed to low R:FR light, at any time of the photoperiod. Contrastingly, G. robertianum only induces this response early in the day, and suppresses petiole growth in low R:FR light at the end of the photoperiod, which results after 24 hours in a net difference with control treatments of zero. We compared expression patterns in the most apical (most responsive) part of the second petioles, in two-week-old Geranium plants (two leaf stage) after 2 and 11.5 hours of far-red light enrichment. This way, we identified a number of novel candidate regulators of shade avoidance, and differential phytochrome control of plant immunity genes in the two species. For de-novo assembly of the reference transcriptomes, we pooled petiole- and leaf lamina tissue exposed to normal white light (180 mol m-2 s-1 PAR, R:FR 1.8, Â± 60 mol m-2 s-1 blue light), low R:FR light (0.2), blue-depleted light (Â± 4 mol m-2 s-1 blue) and green shade (50 mol m-2 s-1 PAR, R:FR 0.45, Â± 13 mol m-2 s-1 blue) for 2, 11.5 and 24 hours. Libraries of these samples were normalized, Illumina sequenced, and together with sequences of non-normalized petiole samples of the expression analysis constructed into a reference transcriptome for each species, using the Trinity protocol. Transcripts were clustered into orthologue clusters using the ortho-MCL clustering technique. Non-normalized libraries of samples (control vs. low R:FR light, 2 and 11.5 hours after start of the treatment) were sequenced and aligned to the newly assembled transcriptomes. Read counts were summed per orthologue cluster before statistical analysis was proceeded.

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Integrated omics revealed regulatory mechanisms governing potato (Solanum tuberosum L.) seedling growth during shade avoidance syndrome

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