Pelagic Sargassum forms extensive floating populations, which expand across the tropical North Atlantic without spatial restrictions. Its ecological drivers and the dominance of three genetic variants remain poorly understood. Here, we characterized their optical (absorptance and specific absorption coefficient) and photosynthetic traits under variable light and temperature regimes, revealing distinct light absorption and photosynthetic efficiencies, and a metabolic adaptation to temperature. Two variants, S. natans-VIII and S. fluitans-III, showed reduced thallus respiration rates, enhancing photosynthetic production at elevated temperature, and explaining their dominance in warmer tropical regions. Conversely, the smallest variant, S. natans I, exhibited superior light-harvesting and photosynthetic efficiencies and lower nutrient demands, aligning with its previous dominance in the Sargasso Sea oligotrophic conditions. These functional differences, combined with increased nutrient availability from ocean fertilization and rising temperatures due to global warming, can explain the massive proliferation of Sargassum in the tropical Atlantic. Our findings stress the role of physiological and optical traits in explaining variant dominance within algal populations and provide a foundation for predictive models and management strategies addressing large-scale algal blooms. They also highlight the potential of pelagic Sargassum as a potential model for studying adaptive traits in asexual lineages through metabolic tuning.

Plants in natural and agricultural environments are continuously exposed to multiple simultaneous abiotic stresses whose combined effects markedly differ from those of individual stresses. Despite this, our mechanistic understanding of plant stress biology still largely relies on reductionist frameworks based on single or pairwise interactions. Here, we argue that plant responses to increasing stress complexity are fundamentally non-additive and involve emergent molecular, metabolic, and physiological states that require a shift towards integrative and predictive approaches. We synthesize recent advances showing how signaling and metabolic networks are rewired under multifactorial stress combination (MFSC), leading to nonlinear behaviors and context-dependent regulation. We highlight the central role of multi-omics integration in uncovering system-level responses and discuss how emerging computational frameworks, including machine learning, can transform high-dimensional datasets into predictive models linking molecular states to plant performance. We further evaluate the limitations of current experimental systems, emphasizing the gap between controlled-environment studies and field conditions, where stress dynamics, microbiome interactions, and genotype × environment complexity shape plant responses. Together, we propose a roadmap towards a predictive science of plant resilience under MFSC, with direct implications for crop improvement in the context of climate change.

Life has undergone profound transformations since its origin approximately 3.5 billion years ago. These evolutionary milestones, most notably terrestrialization, have left indelible marks on all extant land plants. A prime example is the sesquiterpenoid compound abscisic acid (ABA), which transitioned from a metabolic byproduct into a major phytohormone orchestrating stress responses and development in the green lineage. In this review, we examine the shaping of ABA metabolism, signaling, and downstream responses through the lens of gene family evolution and transcriptional regulation. By exploring the integration of ABA with core cellular and metabolic processes and comparing seed-free lineages and spermatophytes, we highlight the fundamental conservation and divergence of ABA-mediated responses in plant evolution.

Successful soil emergence requires apical hook establishment during skotomorphogenesis. Soil salinity disrupts this process, but the mechanisms linking environmental stress to hook growth remain unclear. Here, we employed a genome-wide association study (GWAS) across Arabidopsis thaliana accessions to identify a locus associated with variation in the salt-induced reduction of apical hook curvature. Fine mapping reveals genetic variation in the promoter of 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE (DXR), encoding the first committed enzyme of the plastid-localized methylerythritol phosphate (MEP) pathway. Accessions carrying an alternative promoter haplotype exhibit elevated DXR expression and a stronger hook bending under salt. Salt treatment and loss of transcriptional repressor PHYTOCHROME INTERACTING FACTOR1 (PIF1) additively increase DXR transcript levels, and pif1-2 seedlings exhibit higher apical hook angles under salt stress. This phenotype is suppressed by inhibition of DXR activity, indicating that an increased MEP pathway flux reduces salt sensitivity in pif1-2 seedlings. Across accessions, DXR expression positively correlates with hook curvature under salt stress, further strengthening the link between DXR and modulation of hook bending under salt stress. Together, these findings identify plastid metabolism as a regulatory layer linking environmental stress to altered skotmomorphogenis, and raise important questions about how etioplast-derived signals interact with growth-control networks in the dark.

Seed coat and hilum pigmentation represent commercially and nutritionally significant traits in soybean, determined by anthocyanin and proanthocyanidin accumulation. Despite their agricultural importance, the spatial regulatory mechanisms governing these flavonoid deposition patterns are not fully understood. In this study, we identified soybean TT8a/b as central bHLH transcription factors coordinating soybean seed coloration through integrative transcriptomic co-expression network analysis. TT8a/b exhibit specific spatiotemporal expression restricted to early seed developmental stages. CRISPR-generated soybean tt8a/b double mutants displayed complete hilum depigmentation and a significant reduction in anthocyanins, firmly establishing these transcription factors as master regulators of pigmentation in soybean seeds. Conversely, TT8a/b overexpression using their endogenous promoters significantly enhanced pigmentation intensity, demonstrating their dosage-dependent regulation. Transcriptomic analysis revealed near-complete suppression of key flavonoid biosynthetic genes in tt8a/b mutants, further validating direct regulatory influence. Population genetic analyses revealed that TT8a underwent strong selection during soybean domestication, and this selection gave rise to light-colored seed coats and hila. Our discovery of the decisive role of TT8a/b in seed coat and hilum pigmentation yields fundamental insights into plant flavonoid patterning and provides precision tools for breeding nutritionally enhanced and visually distinct soybean cultivars.

Apocarotenoids are a structurally diverse group of specialized metabolites produced by oxidative cleavage of carotenoids, which perform important physiological, ecological, and interspecific communication roles in plants. Pigmented apocarotenoids form a distinctive yet insufficiently explored subgroup within this class. This review critically resumes current knowledge on apocarotenoid pigments, emphasizing their organ specific distribution, the biosynthetic pathways controlling their accumulation, and their adaptive significance. Particular attention is devoted to carotenoid cleavage dioxygenases (CCDs), the key enzymes driving their formation, including their substrate specificity and tissue dependent activity. Selected case studies focus on ethnobotanically relevant species, in which these pigments contribute to pollinator attraction, tolerance to abiotic and biotic stress, and possible allelopathic interactions. Traditional applications as natural colorants, food ingredients, and nutraceuticals are also considered. Interestingly, several neglected species produce rare apocarotenoids with potential industrial value but remain still poorly characterized. Because functional data are still fragmentary for many taxa, deeper characterization of these compounds represents a promising avenue for understanding the evolution of specialized metabolism and for advancing applications in food, cosmetics, and pharmaceuticals. Similarly, identification of regulatory networks and biosynthetic enzymes is essential to enable sustainable biotechnological production of high value apocarotenoids in heterologous systems through targeted metabolic engineering strategies.

Water deficit is a major constraint on pepper (Capsicum annuum) yield, yet the genetic architecture of reproductive-stage drought tolerance remains poorly resolved. We phenotyped a Balkan C. annuum diversity panel (n = 133) and an interspecific backcross inbred line (BIL) population (n = 76) under well-watered (WW) and water-stress (WS) conditions. WS was applied from anthesis of the second truss as a stepwise reduction in irrigation volume relative to WW (30% for 7 days, then 60% thereafter), maintained for 90 days across the reproductive period. We assessed yield components, soluble solids, and stress-tolerance (STI) and stress-susceptibility (SSI) indices. Genome-wide association study (GWAS) identified 104 SNP-trait associations (P < 1×10-5), and QTL mapping detected 38 significant QTLs (1,000 permutations, α = 0.01), with the QTL intervals defined at LOD ≥ 8. Integrating GWAS and QTL mapping under WS revealed overlapping loci on chromosomes 5 and 6, harboring two consensus intergenic SNPs associated with yield components and soluble solids. Haplotype analysis linked chromosome 5 alleles to higher fruit number and soluble solids. At chromosome 6, the G allele at SNP 6_28348737 was enriched in tolerant lines for fruit number. These regions harbor candidate genes for reproductive development and stress response, including GREEN RIPE-LIKE1 (GRL1), CYP77A19, Endoglucanase-like, and FLOWERING PROMOTING FACTOR 1 (FPF1), possibly through cis-regulatory variation. Together, these results advance understanding of the genetic basis of pepper yield under drought and identify candidate breeding markers.

Hybrid wheat breeding is constrained by the predominantly self-pollinating nature of wheat florets, which limits cross-pollination efficiency and increases grain production costs. Enhancing hybridization requires a better understanding of male reproductive traits, particularly pollen quantity and viability. Here, we combined developmental staging, environmental assays, and genetic mapping to dissect these traits in European winter bread wheat. Anther and pollen maturation, characterized using an enhanced high-resolution Waddington scale, followed a proximo-distal gradient across the spike and an acropetal gradient within spikelets, with W10 marking as peak pollen maturation and viability stage. Time-lapse imaging revealed that anthesis follows the same coordinated spatial pattern, indicating tightly synchronized reproductive development across the spike. Importantly, pollen viability was best maintained at room temperature (22 °C) for up to 8 h, but, unexpectedly, declined more rapidly under cooler storage conditions (15 °C and 8 °C). To test the genetic basis of pollen viability and pollen number we performed Quantitative Trait Locus (QTL) analysis and identified seven loci, including a major QTL for pollen number on chromosome 2A and a distinct QTL for pollen viability on 5A. In both cases alleles from cultivar Piko consistently conferred beneficial trait effects. These findings refine anther staging, highlight environmental sensitivity of wheat pollen, and identify genomic regions that can improve reproductive efficiency for hybrid wheat production and breeding.

Bolting time is critical for yield stability in spinach, a long-day Amaranthaceae crop whose photoperiod-dependent flowering pathway remains incompletely understood. We generated a chromosome-scale reference genome for an early-bolting spinach line (944.6 Mb; 97.9% BUSCO completeness) and used it to integrate QTL mapping, sequence variation, and transcriptome-based co-expression analysis. Remapping bolting-time QTLs on this improved reference retained qBt2.1, qBt3.1, and qBt3.2, while refining their physical intervals and candidate gene content. Candidate loci included SoCOL14/SoFL1 at qBt2.1, SoFT3 at qBt3.1, and SoLNK1/SoAGL21 at qBt3.2. Co-expression analysis identified ten modules, including a circadian-associated module M9 containing SoLNK1/2, SoGI, SoCOL5, SoPRR7, and SoBBX19, and a floral-initiation module M10 enriched for shoot-apex regulators. A predicted loss-of-function allele of SoLNK1 in the late-bolting line further supports its prioritization as a candidate regulator. Phylogenetic and network evidence suggest Amaranthaceae-specific remodelling of PRR-BBX-associated photoperiodic regulation in spinach. Together, this genome resource and integrative framework provide a basis for prioritizing bolting-associated genes and dissecting circadian-floral regulatory gene networks in spinach.

Effective plant disease phenotyping is crucial for resistance breeding, but traditional visual assessment is often inaccurate and inefficient. This is particularly challenging when breeding lettuce (Lactuca sativa) for resistance to downy mildew, given the obligate biotrophic lifestyle of the causal pathogen Bremia lactucae. We discovered that B. lactucae-infected lettuce exhibits patches of increased blue-green fluorescence (BGF) under UV-A excitation from 6 days post-inoculation, preceding visible symptoms. Co-localization of BGF with hyphae, visualized with trypan blue, indicates that BGF is induced by downy mildew colonization. We therefore investigated its potential for non-invasive disease detection and quantification, as well as the underlying physiological changes. Using a custom imaging system, we demonstrate that BGF leaf area correlates with downy mildew severity and can be automatically quantified via a U-Net-based convolutional neural network, enabling early, objective disease assessment. Exploring transcriptomic and metabolomic changes associated with BGF, we found that induction of the phenylpropanoid pathway led to accumulation of caffeoylquinic acids, whose fluorescence spectra overlap with that of BGF tissue, supporting the hypothesis that these compounds contribute to the fluorescence signal. BGF imaging offers a powerful tool for phenotyping in lettuce breeding and for identifying quantitative resistance traits that support durable downy mildew resistance.