BMC Plant Biology

Heavy-metal accumulation in cereal grains is becoming critical for European food safety, regulation and plant breeding. In the EU, Cd maximum levels in certain foodstuffs have been revised, including lowering or establishing limits for relevant food categories, while new maximum levels for nickel (Ni) have recently been introduced for several foodstuffs, including cereal categories, with limits for oats and selected cereals applying from 2026. Together, these developments create an urgent need to identify genetic and physiological mechanisms that reduce Cd and Ni accumulation in cereal grains while maintaining crop quality and productivity. Against this regulatory and food-safety background, our broader RNA-seq experiment investigates early transcriptional responses to Cd and Ni in oat F2 segregants contrasting for metal accumulation. The full dataset includes low- and high-accumulating segregants, roots and developing caryopses sampled at 3 h and 7 h after treatment. In the present pilot analysis, we focus on the Cd response in developing caryopses of the low-Cd accumulating segregant AS131 to identify candidate processes associated with reduced grain Cd accumulation. The strongest transcriptional responses were not dominated by canonical Cd-detoxification pathways. At 3 h after Cd exposure, differentially expressed transcripts were mainly associated with cell-wall functions, endosperm transfer-cell-specific PR60 proteins, DUF239-containing proteins and cysteine proteinase inhibitors, whereas several dehydration-, pathogen-, defence-, cell-wall-loosening- and ROS- related genes were repressed. By 7 h, the response suggested a shift towards homeostatic acclimation, with induction of TIP2 aquaporins, thiamine thiazole synthases, EF-Tu proteins, coatomer-related genes and carbohydrate metabolism-associated genes, together with repression of LEA/SMP/dehydrin genes, FRO7-like genes, EF-hand calcium-binding proteins and stress-regulatory transcription factors. Pathway-level analyses were broadly consistent with these transcript-level patterns, highlighting structural, nucleosome-associated, translation-related, metabolic and developmental processes. Several Cd-responsive transcripts were also associated with broader abiotic-stress responses, suggesting recruitment of shared stress-regulatory modules rather than Cd-specific detoxification pathways alone. Overall, these results support a working hypothesis in which low Cd accumulation in developing oat grain may involve regulation of solute-transfer interfaces, cellular protection, intracellular homeostasis, trafficking pathways and caryopsis developmental programmes. These findings provide candidate processes for future comparison with high-Cd accumulating segregants, root tissues and Ni responses in the broader dataset.

Photosynthesis is acknowledged as a potential target to increase crop yield. Improved photosynthesis may be achieved by conventional breeding, exploiting the available natural genetic variation for photosynthesis traits. This approach is challenging for crops due to limitations in high-throughput photosynthesis phenotyping, the highly polygenic nature of photosynthesis, and its strongly dynamic response to environmental changes. Recent advancements in phenomics make accurate and detailed photosynthesis phenotyping more feasible, with the model species Arabidopsis thaliana paving the way for applications in crops. In this study, we examined photosynthesis parameters over time in the global Arabidopsis HapMap diversity panel exposed to three conditions: optimal nutrient supply, low phosphorus supply and low nitrogen supply. Combined with two previous studies on photosynthesis in response to low temperature, and to a one-step change in irradiance from low light to high light, five high-quality datasets were systematically analysed using the same approach (with one million-maker set, uni- and multi-variate analyses). Our findings emphasize the genetic complexity of photosynthesis, detecting hundreds of significant quantitative trait loci, only a small number of which are robust, and of which most are condition specific. Robust loci, found in multiple conditions, exemplify those suited for conferring higher all-round photosynthesis, and targets for marker-assisted selection, contributing to environmental resilience, while the multitude of small-effect conditional loci suggest that genomic selection approaches may be more suited to improve crop photosynthesis.

Cassava (Manihot esculenta Crantz) is a major staple crop across tropical and subtropical regions. Despite advances in genomic selection, delayed, non-flowering, and asynchronous flowering remain key bottlenecks in breeding programs. To better understand the molecular basis of flowering-time variation, we performed RNA sequencing across three genotypes with contrasting flowering phenotypes (early, late, and non-flowering) sampled at three developmental stages under contrasting light regimes in field conditions (natural light and three-hour night-break with white light). Comparative transcriptomic analysis revealed distinct gene expression patterns associated with flowering responses. Genotype comparisons with no light supplementation revealed stage-specific enrichment of biological processes. Light supplementation was associated with changes in the expression of key components of photoperiodic and circadian regulation, as well as pathways involved in flowering-time integration and hormone and sugar-related signaling. These findings suggest that coordinated changes across multiple biological pathways regulate flowering behavior in cassava. The candidate genes and expression patterns reported provide a foundation for functional studies and advance our understanding of molecular mechanisms governing flowering-time regulation in cassava.

Bluebunch wheatgrass (Pseudoroegneria spicata) exhibits substantial variation in its response to salt stress, making it a valuable model for studying salinity-tolerance mechanisms for use in crop improvement. In this study, we identified two P. spicata genotypes with contrasting responses to salt stress: the tolerant W6 56551, which maintained growth with green foliage under saline conditions, and the susceptible PI693916, which exhibited severe leaf chlorosis and stunted growth. To better understand the molecular basis of salt tolerance in blue-bunch wheatgrass, we conducted RNA-sequencing at 0, 1, and 4 days (D0, D1, and D4) after salt treatment at 160 mM level to examine changes in gene expression of salt-tolerant and salt-susceptible genotypes. Comparative analysis across time points identified 6,154 and 1,086 differentially expressed genes (DEGs) at D4 and D1 in PI693916, and 4,638 and 3,302 DEGs at D4 and D1 in W6 56551, respectively, relative to control (D0). Functional analysis of these DEGs showed that the salt-tolerant geno-type displayed an early and broad transcriptional reprogramming, including induction of photosynthesis, carbon metabolism, and flavonoid biosynthesis pathways, whereas the salt-susceptible genotype exhibited delayed and less coordinated responses, with enrichment of cyanoamino acid metabolism and repression of antioxidant-associated pathways. Notably, calcium signaling, ion transporter regulation, and osmolyte biosynthesis genes showed contrasting expression between genotypes, highlighting distinct strategies for ionic and osmotic homeostasis. Collectively, these results demonstrate that salt tolerance in P. spicata is associated with rapid metabolic adjustment, enhanced photosynthetic stability, and differential regulation of ion transport and osmoprotectant pathways.

Polyploidization can profoundly affect plant metabolite biosynthesis, yet its influence on chemodiversity remains poorly understood, despite the central role of chemodiversity in mediating plant interactions with the environment. The coexistence of facultative apomictic and sexual reproductive systems across ploidy levels in Hypericum provides an excellent model for investigating the evolution of chemodiversity following polyploidization. We analyzed ploidy levels and leaf metabolic fingerprints across selected populations of three Hypericum taxa, H. maculatum, H. perforatum subsp. perforatum and H. perforatum subsp. veronense. Polyploidization was common across all three taxa. Leaf metabolic fingerprints were more pronouncedly differentiated by the ploidy level of the mother plant (F0) than that of the offspring (F1). Although unique metabolic features emerged in plants of most ploidy levels, diploid plants exhibited fewer metabolic features than polyploid plants. Higher Shannon diversity, functional Hill diversity, and intensities of features belonging to specific chemical families were associated with higher F0 ploidy levels in H. perforatum subsp. perforatum, but not in H. maculatum and H. perforatum subsp. veronense. Our findings demonstrate that polyploidization can lead to rapid shifts in chemodiversity across generations in Hypericum. The fast divergence in chemodiversity associated with polyploidization in H. perforatum may contribute to its remarkable invasive potential.

Background Strigolactones (SLs) regulate diverse aspects of plant development and have been implicated in promoting leaf senescence. However, senescence phenotypes associated with SL deficiency have not been consistently observed across species, suggesting that this function may be species- or context-dependent. Moreover, the contribution of endogenous SL biosynthesis to senescence in leafy vegetable crops remains unclear. Here, we investigated the role of the SL biosynthetic gene MORE AXILLARY GROWTH1 (MAX1) in dark-induced leaf senescence in lettuce (Lactuca sativa). Results We found that endogenous SL biosynthesis plays a major role in dark-induced senescence in lettuce. SL pathway genes were induced during dark storage, while exogenous GR24 accelerated senescence and lettuce MAX1 (LsMAX1) complemented the delayed-senescence phenotype of the Arabidopsis max1 mutant. Consistent with these findings, CRISPR/Cas9-generated Lsmax1 mutants exhibited a pronounced stay-green phenotype during prolonged darkness, accompanied by strongly reduced induction of key senescence-associated genes. Despite this delayed visible senescence, Lsmax1 retained a substantial transcriptional response to dark storage. Strikingly, loss of LsMAX1 did not simply weaken the wild-type senescence program, but redirected part of the response toward a distinct stress-associated transcriptional state that was largely absent from wild type. Loss of LsMAX1 did not affect vegetative rosette architecture, although increased branching emerged after bolting. Conclusions Our findings establish MAX1-dependent SL biosynthesis as an important regulator of leaf senescence in lettuce and reveal a role that extends beyond controlling the rate of senescence. Rather than simply delaying the wild-type program, loss of LsMAX1 alters the transcriptional trajectory of senescence, favoring an alternative stress-associated state during prolonged darkness. The strong stay-green phenotype without detectable changes to vegetative rosette architecture further highlights SL biosynthesis as a potential target for extending postharvest longevity in lettuce and other leafy crops.

Utricularia gibba L. is an aquatic carnivorous plant with a diverse set of capabilities. Reddening of traps frequently occurs in old in vitro cultures. While anthocyanins are often responsible for red coloration in plants, not every plant turns red. Stress factors like high light or excess sucrose have previously been shown to induce the formation of anthocyanins. Here, we hypothesized the red trap formation to be dependent on nutrient deprivation and tested nitrogen deprivation. The results suggest, that only in combination with light, nitrogen deficiency leads to the activation of the complete anthocyanin biosynthesis pathway and visible red coloration. However, in darkness, anthocyanin biosynthesis appears generally less active compared to light conditions and expression of most anthocyanin biosynthesis genes is not significantly upregulated under nitrogen deficiency.

BackgroundThe capitulum of Asteraceae is a highly specialized inflorescence whose formation requires the coordinated regulation of multiple developmental processes, including floral organ identity and floral meristem determinacy. The LEAFY (LFY)-UNUSUAL FLORAL ORGANS (UFO) regulatory module is known to play an important role in flower development; however, naturally occurring mutations affecting this pathway have not been genetically characterized in gerbera (Gerbera hybrida). ResultsIn this study, we characterized a novel gerbera mutant identified during a commercial crossing program and named it marimo based on its green, spherical capitulum. Morphological observations revealed the repeated formation of secondary and tertiary floret-like organs within primary floret-like organs. Scanning electron microscopy showed that the epidermal structure of the green organs in marimo was similar to that of wild-type involucral bracts. RNA sequencing identified numerous differentially expressed genes between marimo and the wild type, and network and Gene Ontology analyses highlighted gene groups associated with flower development, reproductive organ differentiation, and tissue structure formation. RNA-seq analysis showed increased expression of LFY and reduced expression of GGLO1, a PISTILLATA/GLOBOSA-like B-class MADS-box gene, in the marimo mutant. RT-qPCR analysis of a segregating population further confirmed reduced GGLO1 expression in marimo-type individuals. In addition, a single-nucleotide deletion was identified in the coding region of UFO. This deletion was predicted to cause a frameshift and a premature stop codon. In selfed progeny of No. 251, the UFO genotype was fully associated with capitulum phenotype, and only individuals homozygous for the mutant allele exhibited the marimo phenotype. ConclusionsThese results indicate that the naturally occurring frameshift mutation in UFO is the strongest candidate variant underlying the marimo phenotype. RNA-seq analysis showed increased LFY expression and markedly reduced GGLO1 expression in the marimo mutant. Reduced activity of the LFY-UFO regulatory module may therefore have altered the expression of GGLO1 and other floral organ development-related genes despite the continued expression of LFY. These changes may have affected both floral organ identity and floral meristem determinacy, resulting in the formation of green involucral bract-like organs and the repeated production of floret-like organs. The marimo mutant provides a useful genetic resource for investigating capitulum development in Asteraceae and may also serve as breeding material for introducing novel ornamental traits into gerbera.

Context. Barley production requires advanced knowledge of its response to changing environmental conditions in order to keep it competitive and sustainable. Aim. Advance in the understanding of barley phenology and foliar development under South American field conditions. Methods. 8 spring barley genotypes with differential phenology were studied in four field experiments under different temperature (through years and sowing dates) and photoperiod (through sowing dates) conditions. Time to anthesis, emergence to onset of stem elongation, stem elongation to anthesis, photoperiod response (PR) in these three traits, number of final leaves at anthesis (FLN) and phyllochron were measured. Key Results. Time to anthesis and its subphases were shorter in late plantings but under similar photoperiod, temperature increased them. Cultivars have differential responses but with magnitude interactions and not crossover ones. Cultivar effects defined PR with no interaction with year (temperature). Temperature and photoperiod affected FLN, phyllochron and their relationship with time to anthesis. Under the shorter photoperiod, FLN and phyllochron were negatively correlated, FLN was higher in the warmer year and positively correlated with time to anthesis while phyllochron was not affected by temperature and had no correlation with time to anthesis. Under longer photoperiod, phyllochron was higher in the warmer year and time to anthesis was positively correlated with both FLN and phyllochron. Conclusions. Cultivar basal thermal requirements and PR were consistent under the different studied conditions. Changes in temperature and photoperiod affected the relationship between time to anthesis, FLN and phyllochron suggesting that, although the three traits are arithmetically related, environmental conditions affect their balance.

Cocoa (Theobroma cacao L.) is grown in Cote d'Ivoire (the world's leading producer), almost always in association with trees, yet these cocoa-based agroforestry systems (cocoa AFS) remain characterized largely descriptively, without a robust inferential framework or modern diversity indices. We analyse a survey database covering 474 farms and 103 localities across the three main cocoa-producing zones of Cote d'Ivoire, locally known as " loops " (East/South-East, Centre/Centre-West, South/South-West; surveys 2013-2016), applying a renewed ecological and statistical framework: Hill numbers (q = 0, 1, 2), individual-based Hurlbert rarefaction, multiplicative alpha/beta/gamma diversity partitioning, ordination (PCoA) and PERMANOVA on Bray-Curtis matrices, Ward's hierarchical clustering for a data-driven floristic typology, multivariate MANOVA, and linear mixed models. Across 99 adequately sampled localities (>10 stems), mean taxonomic richness and the Shannon index differed significantly among zones (MANOVA: Wilks' = 0.350; F8,180 = 15.5; p < 0.001), including after standardizing sampling effort by rarefaction (F = 8.72; p < 0.001). Floristic composition differed significantly by zone (PERMANOVA, pseudo-F = 2.85; p = 0.001), though with uneven within-group dispersion (PERMDISP, p = 0.024) that calls for caution in interpretation. The Centre/Centre-West zone showed the highest beta diversity (inter-farm floristic turnover = 16.4, versus 7.2 and 2.2 in the other two zones), revealing a highly heterogeneous mosaic of individual agroforestry choices rather than a homogeneous regional system. A typological classification based on floristic composition distinguishes four cocoa-AFS profiles, ranging from dense, diverse stands to impoverished systems with low densities of associated trees, partially but not fully overlapping with the zonal boundaries. At the scale of the three loops (n = 409 farms with both age and yield recorded), cocoa yield varied significantly by orchard age class (Kruskal-Wallis, H = 18.2; p < 0.001), following a bell-shaped profile peaking around 20-35 years, consistent with the intermediate-age yield optimum suggested qualitatively by the source study; this relationship, robust to log-transformation of yield and to the exclusion of extreme values, nonetheless remains of small magnitude (R2=1.5%) and confers no out-of-sample predictive power under cross-validation, illustrating the need to distinguish statistical significance from predictive utility. This reanalysis provides a reproducible and transferable statistical framework for characterizing West African cocoa AFS, and highlights the potential value of high beta diversity as a possible indicator of landscape resilience.

Arabidopsis Leucine-Rich Repeat-Malectin Receptor Kinase (LRR-MAL RK) genes have been previously implicated in the early stages of pollen-pistil interactions to support compatible pollen. One member, Receptor Kinase in Flowers 1 (RKF1), has been associated with roles in the stigma to support pollen hydration as well as pollen tube growth. To better understand the function of RKF1 in these processes, a yeast two-hybrid screen was conducted with the RKF1 cytosolic kinase domain. Two positive interactors identified from this screen were the Group VII Ethylene Response Factors (ERFVIIs), RELATED TO APETALA 2.12 (RAP2.12) and RAP2.3. Their putative roles in pollen-pistil interactions were investigated using the quintuple erfvii mutant, and novel pistil-mediated pollen tube callose deposition phenotypes were uncovered during the pollen tube growth stage. Loss of seven LRR-MAL RKs including RKF1 in the pistil was previously found to cause an unusual phenotype where shorter callose plugs were deposited in wildtype pollen tubes compared to that seen in wildtype Col-0 pistils. Contrary to this, wildtype pollen tubes growing through the quintuple erfvii mutant pistil deposited callose plugs that were more elongated than that seen in wildtype Col-0 pistils. Further analyses with the proteolysis 6 (prt6) mutant and RAP2.12 rescue constructs were consistent with these phenotypes providing support that RKF1 is a negative regulator of RAP2.12 and RAP2.3 in the pistil during pollen tube growth.

Flower opening is a complex developmental process involving coordinated changes in cell proliferation and cell expansion. Although several regulators of flower opening have been identified, how transcriptional programs are coordinated with the cellular and metabolic changes underlying petal expansion immediately before flower opening remains incompletely understood. Japanese morning glory (Ipomoea nil) is a suitable model for investigating these processes because its flowers open synchronously at a predictable time. This study aimed to identify transcriptional regulators involved in petal development and flower opening in Japanese morning glory. Temporal analyses of petal growth, sugar metabolism, and gene expression revealed that petal development was driven by both cell proliferation and cell expansion until approximately 48 h before flower opening, whereas cell expansion predominated thereafter. Weighted gene co-expression network analysis identified two genes encoding R2R3-MYB subgroup 19 transcription factors, InMYB21A and InMYB21B, as candidate regulators associated with petal development. CRISPR/Cas9-mediated knockout analysis revealed a prominent role for InMYB21B, whose loss markedly impaired petal cell expansion and prevented flower opening. InMYB21B knockout also impaired stamen and pistil development, resulting in male and female sterility. Starch degradation and glucose accumulation were impaired in InMYB21B knockout petals. Transcriptome analysis revealed delayed transcriptomic progression during petal development and reduced expression of genes associated with starch degradation, sucrose metabolism, cell wall remodeling, and water transport. These findings identify InMYB21B as a key regulator of petal cell expansion and flower opening in Japanese morning glory and show that loss of InMYB21B disrupts both metabolic and transcriptomic progression during late petal development.

Starch granule initiation involves the extension of maltooligosaccharide primers by glucosyltransferases. STARCH SYNTHASE 4 (SS4) plays a central role in almost all examined plant species, while the plastidial PHOSPHORYLASE 1 (Pho1) also plays an important role in some species, including rice and wheat. In Arabidopsis, an additional enzymatically inactive homolog of SS4, STARCH SYNTHASE 5 (SS5) contributes to starch granule initiation. To elucidate the mechanism of starch granule initiation in potato tubers, we used CRISPR/Cas9 to generate ss4, ss5, and pho1a knockout mutants in the commercial tetraploid 'Clearwater Russet', to systematically investigate their contribution to granule initiation. In ss4 and ss5 tubers, starch granule size and morphology were unaltered relative to the wild type, suggesting that SS4 and SS5 are dispensable for normal granule initiation in potato tubers. In contrast, pho1a tubers had compound starch granules that arose from multiple initiations, greatly reduced granule size, and highly variable granule morphologies. Affinity pull-down to find Pho1a interaction partners identified LIKE EARLY STARVATION (LESV), although yeast 2-hybrid assays did not show direct protein-protein binding. When expressed alone in Nicotiana benthamiana leaves, Pho1a located to the chloroplast stroma, but when expressed alongside LESV, both proteins co-located on starch granules. This co-localisation, alongside the similar accumulation of small starch granules when LESV is knocked out in tubers, suggest a possible functional interaction in planta. These findings position Pho1a as the central glucosyltransferase in starch granule initiation in Clearwater Russet tubers, where it acts together with LESV.

Adventitious root formation (ARF) is a critical trait for the cost-effective propagation of grapevines in commercial nurseries. Poor rooting ability can limit the use and adoption of new rootstocks derived from underutilized Vitis species, constraining breeding efforts largely to the traditional trio: Vitis riparia, V. rupestris, and V. berlandieri. Despite its agronomic relevance, the genetic basis of ARF remains poorly characterized across the broader Vitis genus. In this study, we evaluated 308 accessions representing 18 Vitis species over three growing seasons, quantifying rooting performance at two developmental stages, callus-stage and post-transplant, alongside root biomass, cutting weight, and a derived transplant-response index. We observed extensive phenotypic variation both within and across species, and species rankings depended on the trait considered. V. riparia, V. rupestris and V. californica ranked among the top five species for all four rooting traits, whereas V. cinerea and V. candicans ranked among the lowest for root weight and post-transplant rooting. V. arizonica and V. acerifolia rooted well at the callus stage but were intermediate after transplanting, and V. berlandieri was among the weakest at the callus stage yet intermediate for post-transplant rooting. Repeatability was moderate to high for root weight (0.74) and callus-stage rooting (0.66), and lower for post-transplant rooting (0.47), reflecting both genetic control and season-to-season variation. Between-species differences accounted for 68% of the genetic variance in callus-stage rooting but only 10% in cutting weight. Rooting was associated with the climate of each accession's wild site of origin: after removing differences among species, accessions originating from sites with lower dry-season precipitation rooted better and produced more root biomass. Genome-wide association analysis using 3.4 million SNPs identified 54 significant SNPs resolving into 18 independent loci across four traits, with root weight contributing 12 of them. Candidate genes in linkage with these loci include a mitogen-activated protein kinase, a SCARECROW-LIKE GRAS transcription factor, PASTICCINO1, expansin A1, an AP2/ERF-RAV1 transcription factor, a tandem array of caffeoyl-CoA O-methyltransferases, and several sugar, peptide and nitrate transporters, implicating auxin-linked cell proliferation, cell wall and lignin remodeling, and solute transport. Genomic and phenomic prediction models yielded moderate accuracies across traits and seasons; up to r = 0.67 for post-transplant rooting within a season and r = 0.65 for previously unevaluated accessions. Moreover, the integration of spectral and genotypic data further improved predictive performance. Prediction accuracy was essentially flat between 5,000 and 50,000 markers. This study establishes a foundational framework for the genetic improvement of grapevine rootstocks, promoting broader use of resilient, high-performing, and clonally-propagable germplasm in viticulture.

The rejection of self-incompatible (SI) Brassica pollen is mediated by three signaling branches that function in parallel in the stigma. The recognition of SI pollen by the stigma S-Receptor Kinase (SRK) results in activation of the ARM-Repeat-Containing 1 E3 ubiquitin ligase (ARC1) which mediates the degradation of compatibility factors, the FERONIA (FER) and ANJEA (ANJ) receptor kinases that induces ROS accumulation to inhibitory levels and the M Locus Protein Kinase (MLPK) which may also be connected to ROS production. Arabidopsis self-incompatibility is regulated by SRK as well, but the signaling events downstream of SRK following SI pollen perception are less well-understood. In this study, we evaluated the requirements of FER, ANJ and HERCULES RECEPTOR KINASE 1 (HERK1) for SI pollen rejection in the transgenic Arabidopsis thaliana SI-Col-0{psi} srka-1 line. The{psi} srka-1 T-DNA disrupting the expression of the endogenous{psi} SRKA gene was crossed into SI-Col-0 to prevent any potential SRK transgene silencing. T-DNA mutants for FER and ANJ/HERK1 were then crossed into the SI-Col-0{psi} srka-1 line. Using standard assays for pollen-stigma interactions, the SI phenotypes were assessed for the SI-Col-0 fer, SI-Col-0 anj-1 and SI-Col-0 anj-1 herk1-1 lines. Our results presented here indicated that FER and ANJ are not required in the stigma for Arabidopsis SI pollen rejection, further providing evidence for a divergence in the SI downstream signaling pathway in Arabidopsis.

Despite their agricultural potential, how bacterial-fungal consortia reshape root microbiomes and improve crop performance in sorghum remains poorly understood. Here, we investigated how individual and combined inoculation with Bacillus subtilis and Trichoderma afroharzianum influenced sorghum performance and root microbiome assembly. The in vitro co-culture assay demonstrated the compatibility of B. subtilis and T. afroharzianum as a microbial consortium. The B. subtilis-T. afroharzianum consortium demonstrated the highest CPPI (composite plant performance index) and shoot fresh weight in sorghum, while all inoculation treatments improved multiple growth and physiological traits. Split-root analysis demonstrated that bilateral root co-inoculation was necessary to maximize whole-plant growth benefits. Also, B. subtilis-T. afroharzianum co-inoculation increased carbon levels in both roots and leaves, accompanied by enhanced rhizosphere siderophore production consistent with improved nutrient status. In microbial community analysis, neither bacterial nor fungal alpha or beta diversity differed significantly among treatments; instead, inoculation selectively restructured root microbial communities. The B. subtilis-T. afroharzianum consortium selectively enriched plant growth-promoting Actinoplanes, siderophore-producing Enterobacter, and the plant-beneficial fungal genus Podospora. Co-occurrence network analysis identified Rhodoplanes, Serendipita, and Zopfiella among hub taxa associated with B. subtilis-T. afroharzianum co-inoculation, suggesting potential roles in microbial community connectivity and organization. Furthermore, the persistence of Streptomyces and Serendipita, particularly the latter, suggests the presence of a beneficial microbial core that may contribute to sustained rhizosphere functioning. In addition, Bacillus and Serendipita were among the indicator taxa associated with inoculated treatment combinations, suggesting that the inoculants selectively assembled a distinct plant-beneficial microbiome. Devosia was associated with chlorophyll content, siderophore production, and shoot height, whereas Serendipita correlated with shoot biomass under the B. subtilis-T. afroharzianum co-inoculation. Taken together, B. subtilis-T. afroharzianum consortium promotes sorghum growth by selectively reshaping the root microbiome, highlighting its potential as a next-generation microbial biofertilizer.

Tomato production, yield and fruit quality face major challenges due to several factors, including the complex polygenic inheritance of agronomically relevant traits, biotic and abiotic stresses, and increasingly stringent regulations limiting the use of phytosanitary products. In this context, bioinoculants have emerged as a sustainable strategy capable of enhancing yield without compromising fruit quality, conferring protection against different stresses and exerting a minimal or no impact on environment and human health. In this study, we evaluated the effects and the underlying mechanisms by which Streptomyces sp. N2A, an actinobacteria isolated from soybean rhizosphere, promotes seed germination, vegetative growth and yield in tomato, without modifying fruit quality. The obtained results demonstrated that the bacterial treatment significantly improved seedlin[g]s emergence and growth and development in vegetative stage. At harvest, yield was also significantly enhanced, mainly driven by increased individual fruit weight, which was positively correlated with a thicker pericarp in fruits from N2A-treated plants. Transcriptional analysis during fruit development revealed a coordinated induction of auxin and cytokinin signaling pathways before and after anthesis, providing a hormonal framework that underlies the promotion of pericarp growth. This study provides evidence of the beneficial effect of inoculation with Streptomyces sp. N2A on tomato yield and constitutes the first report describing the modification of fruit morphology and expression of genes involved in phytohormonal modulation during early growth and development, induced by a plant growth-promoting Streptomyces.

Accelerating photoprotective regulation to improve carbon assimilation is a promising strategy to increase crop productivity. Although rapid non-photochemical quenching (NPQ) relaxation has been validated as a target through metabolic engineering, it remains unclear whether conventional breeding has improved this trait. Here, we investigated whether more than a century of soybean breeding enhanced NPQ relaxation alongside light-saturated carbon assimilation and seed traits. We evaluated a historical panel of 24 soybean genotypes across vegetative and reproductive developmental stages by integrating NPQ relaxation, gas exchange parameters, xanthophyll-cycle pigment profiles, expression of key photoprotective genes (VDE, PsbS, and ZEP), seed number and seed weight. NPQ relaxation parameters were not consistently associated with genotype release year, seed number, or seed weight at either developmental stage. The only exception was the amplitude of the rapidly relaxing NPQ component (AqE), which was negatively correlated with all three variables during the reproductive stage. In contrast, genotype release year was positively associated with maximum net CO2 assimilation rate (Amax), maximum carboxylation rate of Rubisco (Vcmax), maximum electron transport rate (Jmax), seed number, and seed weight, while Amax and Vcmax were positively correlated with seed number and seed weight. These findings indicate that the greater photosynthetic capacity of modern genotypes was not accompanied by faster photoprotective response. Thus, photoprotective regulation has not kept pace with gains in photosynthetic capacity under field conditions. We conclude that rapid NPQ relaxation remains an important target for synchronizing photoprotection with the high photosynthetic capacity of modern soybean lines.

Concurrent exposure to heat and drought stress compromises legume productivity, yet their combined effects are rarely quantified systematically. We compiled a database of 18 studies covering seven legume species. From these, we extracted 929 physiological, biochemical, and yield-related traits and calculated actual-to-additive ratios to classify heat-drought interactions as antagonistic (ratio < 1), additive (ratio = 1), or synergistic (ratio > 1). Additive heat-drought relationships accounted for 59 % of all classifiable observations, 37% relationships were antagonistic, and 4% synergistic. The relationship varied with species, genotype, trait, and experimental conditions highlighting the complexity of combined abiotic stress effects. The results challenge the common assumption that concurrent stresses invariably exacerbate damage and underscore the need for more realistic, quantitatively defined stress treatments as well as frameworks that integrate trait-level responses into predictive models of crop growth and development. Our synthesis provides a quantitative foundation to understand legume phenotypes under the increasingly frequent co-occurrence of heat and drought stress and identifies research areas where further work is needed to improve insight into combined stress responses. HighlightsO_LICombined heat and drought responses were mainly additive or antagonistic. C_LIO_LIEvidence is biased toward few legumes and controlled environments. C_LIO_LIField-based, multi-species studies are needed to identify adaptive traits. C_LI

A strategy to improve agricultural water productivity is to increase water use efficiency (WUE) at the level of plant transpiration through genetic selection. This requires detectable genetic variability in WUE and the ability to phenotype and select plants with higher WUE within a population. A proxy for phenotyping leaf level WUE by measuring carbon isotope signature ({delta}13Cleaf) has been supported by theory and data in C4 species. However, the functional relationship of {delta}13Cleaf and WUE in C4 species can be driven by genetics and environment. Therefore, a wide survey of existing natural variation is needed to quantify the heritability and identify various genetic factors that influence {delta}13Cleaf and WUE. In this study a genome-wide association panel was used to quantify the heritability of {delta}13Cleaf. We measured {delta}13Cleaf across a population of 360 genetically diverse lines of the C4 species Sorghum bicolor with single nucleotide polymorphic (SNP) markers determined from whole-genome resequencing. This analysis was conducted on two independent field environments where heritability of {delta}13Cleaf was evident and was driven by small genetic effects from loci that were consistently identified across environments. Candidate genes are presented that offer insights on future targets to manipulate and explore the functional relationship between {delta}13Cleaf and WUEi in C4 plants.