BMC Plant Biology

Barley yellow dwarf virus (BYDV), transmitted by the bird cherry-oat aphid (Rhopalosiphum padi L.), is among the most damaging viral diseases of barley, but the mechanisms underlying resistance to both the virus and its vector remain poorly understood. Here, we investigated resistance associated with the Hordeum bulbosum-derived Ryd4 introgression in the barley hybrid SY Kestrel by integrating behavioural, electrophysiological, physiological and multi-omics analyses with functional validation of defence metabolites. SY Kestrel exhibited constitutive volatile-mediated antixenosis together with strong post-settlement antibiosis characterised by impaired phloem feeding, reduced aphid fitness and suppression of BYDV gene expression 10 days after transmission. Integrated transcriptomic, metabolomic and small RNA analyses revealed coordinated immune activation, chloroplast remodelling and defence metabolism associated with the resistance introgression. Candidate immune regulators were identified both within the refined Ryd4 interval and the surrounding introgressed region. Maintenance of photosystem II function was accompanied by reprogramming of -linolenic acid-derived oxylipin metabolism, while phenylpropanoid and branched-chain amino acid/lysine pathways generated metabolites that directly reduced aphid survival. We demonstrate that the Ryd4 introgression coordinates constitutive vector deterrence with host defence reprogramming to restrict aphid colonisation and suppress BYDV establishment. These results provide a mechanistic framework for improving durable resistance to aphid-transmitted viruses in cereals.

Heavy metals act as essential metalloprotein cofactors in numerous physiological processes but can become toxic when non-essential metals accumulate or when essential metals are in excess. As plants continuously encounter heavy metals through their roots, they have evolved complex homeostatic mechanisms to regulate metal uptake and distribution. The Heavy Metal ATPase (HMA) gene family encodes a group of heavy metal transporting P-type ATPases that have been linked to stress resistance and nutrient supply. Here, we used a bioinformatics approach to identify and characterise 13 HMA genes containing characteristic P1B-type ATPase domains and motifs in the barley Morex V3 reference genome. The genes are located on five of the seven barley chromosomes. Phylogenetic analysis revealed that they cluster into five sub-clades, including one clade unique to barley. Expression profiling across multiple datasets showed distinct temporal and tissue-specific expression patterns among HvHMAs, with several members exhibiting significant transcriptional responses to specific biotic and abiotic stresses. By utilising recently available pan-transcriptomic and pan-genomic resources, we have identified substantial allelic diversity and inter-accession variation in HvHMAs. Our findings suggest that HvHMAs have functions extending beyond canonical heavy metal homeostasis and warrant further investigation for their potential roles in broader physiological and stress-related processes.

Rafflesiaceae, known for producing the largest flowers in the world, are obligate parasites that exclusively infect Tetrastigma sp. (Vitaceae). Despite their unique biology, the interactions between parasitic tissues and host roots remain poorly understood, particularly during the flower morphogenesis phase, where parasitic tissue erupts through the host root. Here, we performed dual transcriptome analyses of two Rafflesiaceae species and their respective Tetrastigma hosts: Sapria himalayana with T. cauliflorum and Rafflesia speciosa with T. magnum. Our findings reveal species-specific transcriptional responses in Tetrastigma, suggesting divergent parasitism strategies between Rafflesia and Sapria. Moreover, we identify molecular signatures of parasitism that parallel plant gall formation, particularly in genes governing cell wall modification and host tissue reorganization. Unlike bacterial or insect-induced galls, these mechanisms may involve fungal symbionts, highlighting the unique nature of these interactions. Together, our results demonstrate that Rafflesiaceae parasitism represents a complex tripartite relationship among host, holoparasite, and associated microbes, offering new insights into the hidden biology of these remarkable parasitic plants.

In plant breeding and genetics, recent advances in high-throughput phenotyping are beginning to meet the growing demand for large-scale, high-quality phenotypic data that emerged after the development of next-generation sequencing technologies. Recent developments in phenomics have been incorporated into almond breeding programs, facilitating the large-scale acquisition of quantitative phenotypes and the dissection of the genetic architecture underlying morphological and quality-related traits. The implementation of a high-throughput phenotyping platform integrating RGB and hyperspectral imaging with genotyping using the 60K almond SNP array enabled the large-scale characterization of almond populations and the identification of 567 robust marker-trait associations across 66 traits. These analyses revealed two major genomic hotspots on chromosomes 2 and 5 associated with morphological and quality-related traits. These regions harbored biologically relevant candidate genes, including genes associated with OVATE family proteins, brassinosteroid signaling, protein ubiquitination, and acyl-CoA metabolism, as well as other regulators of organ growth, cell proliferation, hormone signaling, and seed development. Furthermore, a novel candidate gene encoding a COMT-like O-methyltransferase involved in lignin biosynthesis was identified and proposed to contribute to shell hardness, a major genetically controlled trait in almond. Together, these findings demonstrate the potential of integrating high-throughput phenomics and genomics to dissect complex traits, identify candidate genes, and accelerate genomics-informed breeding in almond.

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.

Background. DNA-based molecular markers underpin plant genetic diversity assessment, germplasm characterisation, and conservation prioritisation. Four marker systems dominate the field: Amplified Fragment Length polymorphisms (AFLPs), simple sequence repeats (SSRs), single nucleotide polymorphisms (SNPs), and random amplified polymorphic DNA (RAPDs). No quantitative meta-analysis had pooled their performance on the canonical diversity metrics: polymorphism information content (PIC), expected heterozygosity (He), and resolution power, across plants. Existing reviews are narrative, marker-restricted, or qualitatively conclusive of infeasibility. Methods. A PRISMA 2020-compliant systematic review (registered at the Open Science Framework) was executed. Eligible studies were within-study paired comparisons genotyping the same accession panel with at least two of {SNP, SSR, AFLP, RAPD} and reporting at least one diversity metric. Effect sizes were paired standardised mean differences (Hedges' g) computed under the Bernoulli-variance approximation. Random-effects REML meta-analysis used metafor 5.0.1 with Knapp-Hartung adjustment, leave-one-out, and r-sensitivity. Results. Fifteen within-study paired contrasts were eligible, distributed across three pools. Pool 2 (SSR vs SNP, He, k = 5) yielded a pooled Hedges' g of 0.494 (95% CI: -0.078 to 1.066, p = 0.075; I-squared = 90.2%; 95% PI [-0.82, 1.81]). SSRs exceeded SNPs on He in 4 of 5 studies; leave-one-out removal of the panel-size-asymmetric outlier raised the estimate to g = 0.644 (p = 0.025). Pool 3a (dominant-marker stratum, k = 6) yielded g = 0.419 (95% CI: -0.121 to 0.960, p = 0.103; I-squared = 56.5%); five of six contrasts showed SSR or AFLP exceeding RAPD on per-locus PIC. Pool 1 (PIC, k = 3, exploratory) gave a consistent direction (g = 0.453). All three pools point in the same direction: codominant or AFLP markers carry more per-locus information than the alternative being compared. Conclusions. SSR markers reported higher per-locus diversity than SNP and RAPD markers in plant within-study paired comparisons, mechanistically grounded in the SNP biallelic ceiling and the multi-allelic richness of SSRs. The effect attenuated or reversed in selfing/low-diversity panels and at the per-panel level when SNP panels exceeded approximately 1000 loci. RAPDs show the lowest per-locus information content of the four classes.

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.

Starch is the primary carbohydrate reserve in potato (Solanum tuberosum L.) tubers and a critical determinant of their industrial value. The rate of starch degradation during postharvest storage directly influences key traits such as endodormancy (ED) duration and cold-induced sweetening (CIS), which affect sprouting behavior. In this study, we used CRISPR/Cas9 genome editing to knockout StAMY23, a gene encoding -amylase involved in starch breakdown. stamy23 plants exhibited higher yield and extended tuber ED postharvest, without significantly altering CIS or starch granule content. To further reduce CIS, we knockout StAMY23 in VACUOLAR INVERTASE knockout (stvinv) backgrounds, generating stamy23/stvinv double-knockouts plants. These lines showed significantly reduced CIS, prolonged ED, and elevated starch content, along with altered starch granule content. Collectively, our findings demonstrate that simultaneous downregulation of StAMY23 and StVINV can additively enhance desirable postharvest traits, providing a promising strategy for improving potato storage quality through precision genome editing.

Floods cause significant crop losses worldwide. Plant response mechanisms to flooding have been extensively studied, particularly the ethylene-meditated mechanisms of perception and initiation of the response. However, other mechanisms are often studied more marginally, and it is difficult to determine which are species-specific and which are part of a conserved angiosperm response to hypoxia. Here, we performed a meta-analysis of transcriptomic data under hypoxic or flooding conditions across 11 angiosperm species and identified 259 homologous gene clusters that constitute the core response to hypoxia in angiosperms. These include the previously identified main mechanisms linked to ethylene, as well as numerous novel genes whose role in the hypoxia response is often poorly characterized. In particular, many previously overlooked genes associated with oxidative stress were identified as part of the core response, such as HRU1, TIP1-2, OZF1, and OZF2. Our results reveal many new candidate genes with strong potential for improving plant resilience to flooding.

Globe artichoke (Cynara cardunculus var. scolymus L.) comprises a broad range of local ecotypes and varietal groups whose genetic diversity has been investigated through different molecular markers. However, recent advances in next-generation sequencing and pangenomics approaches provide new opportunities to capture genome-wide variation at higher resolution and to develop practical tools for varietal discrimination, traceability, and germplasm conservation. In this study, we developed the first pangenomic framework for cultivated artichoke and evaluated pangenome-informed SNP markers for varietal fingerprinting. Whole-genome resequencing data from the Italian local ecotype Asti Sori were integrated with publicly available genomic data from representative globe artichoke and cultivated cardoon accessions to construct and annotate a pangenome. Genome-wide SNP and presence/absence variation (PAV) analyses were combined with pangenome-anchored genotyping-by-sequencing (GBS) data from 45 accessions representing the main cultivated varietal groups. The pangenome revealed a largely conserved core gene repertoire alongside a smaller accessory component, with gene accumulation curves suggesting a tendency toward saturation within the sampled cultivated germplasm. SNP- and PAV-based analyses provided complementary views of accession relationships and consistently resolved the principal cultivated groups. Across the broader germplasm panel, pangenome-anchored GBS-derived SNPs identified well-supported phylogenetic clusters corresponding to recognized varietal types. A reduced panel of 50 SNPs, selected through iterative random subsampling, retained at least 90% of the genetic diversity captured by the full dataset and reproduced its main population structure. This compact pangenome-anchored marker set provides a practical foundation for varietal fingerprinting, DUS-oriented applications, traceability, and conservation of traditional globe artichoke germplasm. Validation across independent collections will be required before routine deployment.

Provitamin A biofortification of cassava (Manihot esculenta) is constrained by a negative genetic correlation between total carotenoid (TC) and dry matter (DM) contents, but its underlying biological mechanism remains unclear. We examined this relationship in 24 African, Latin American, and hybrid cassava genotypes by measuring gene expression and metabolites in inner and outer storage root layers that varied spatially in carotenoid accumulation, enabling comparisons across and within genotypes. TC, and particularly upstream cis-carotenes, were negatively associated with DM after accounting for genotype, and this relationship strengthened across developmental timepoints, consistent with a physiological component of the trade-off. Gene-metabolite co-expression networks constructed from genetic, non-genetic, and overall phenotypic trait components showed no significant topological overlap between carotenoid- and starch-related gene sets, indicating that the TC/DM relationship is not driven by transcriptional co-regulation of the main pathways, although individual associations between carotenoids and carbohydrate-related genes suggested possible indirect metabolic links. Instead, TC accumulation was most strongly associated with regulatory, stress-, redox-, and plastid-related genes, enriched for heme-binding and oxidoreductase functions. These findings suggest that the TC/DM trade-off is not a fixed constraint, and identify candidate regulators of carotenoid content for future functional validation to support cassava provitamin A biofortification. HighlightGenetic, spatial, and developmental variation in cassava storage roots implicate cis-carotenes, but not direct transcriptional regulation of the carotenoid and starch pathways, in the trade-off between carotenoids and dry matter.

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.

Heat stress is one of the most damaging abiotic constraints on crop productivity, and its consequences are expected to intensify as extreme temperature events become more frequent and severe. Pepper (Capsicum annuum L.) is particularly vulnerable to sustained high temperatures, which can disrupt photosynthetic performance, cellular homeostasis, and redox regulation. However, the physiological and transcriptional dynamics underlying genotype-dependent responses to prolonged heat exposure remain insufficiently understood. We combined repeated physiological measurements with time-course RNA sequencing to compare GPC003240, previously identified as a candidate heat-tolerant accession, with two non-elite accessions, GPC010350 and GPC014930, which are phenotypically divergent from each other, under 40/30 {degrees}C Day/night temperatures for up to six days. GPC010350 maintained comparatively stable photosystem II performance and higher stomatal conductance, whereas GPC014930 showed progressive photochemical impairment and lower conductance; GPC003240 displayed a distinct, moderately responsive profile. Transcriptomic responses showed partial functional convergence during the early phase of stress exposure but diverged markedly after six days. When gene expression at day 6 was compared with the pre-treatment baseline separately within each genotype, 4,436 differentially expressed genes were detected in GPC010350, compared with 680 in GPC003240 and only 78 in GPC014930. The late response of GPC010350 was associated with enrichment of RNA- and ribosome-related, biosynthetic, DNA-repair, and genome-maintenance functions. By contrast, GPC014930 showed negative enrichment of photosynthesis, plastid organization, redox homeostasis, and translation-related processes. Global co-expression analysis identified a time-decreasing photosynthesis-associated module (ME5) and two time-increasing modules, ME12 and ME19, that were enriched in genes contributing to the late GPC010350 response. Integration of differential expressions, module membership, and functional annotation highlighted a heat shock transcription factor (Caz03g27980), HSP101 (Caz03g07770), and a dual-specificity phosphatase (Caz05g20970) as candidates for further investigation. Overall, the results suggest that genotype-dependent responses to prolonged heat exposure were associated not only with the magnitude of early transcriptional change, but also with differences in the temporal organization of stress-response, maintenance, and metabolic processes. The contrasting responses of the non-elite accessions GPC010350 and GPC014930 further highlight the value of phenotypically diverse germplasm for uncovering mechanisms relevant to future heat-tolerance breeding.

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.

Cassava is a major staple crop in tropical regions, and improving its root nutritional quality, particularly carotenoid and dry matter content (DMC), remains a central breeding goal. To elucidate the genetic basis of these traits by locating genomic regions associated with them, we analyzed 3,043 cassava clones from the Brazilian Agricultural Research Corporation (Embrapa) breeding program, phenotyped across 188 multi-environment trials conducted from 2011 to 2022 in Brazil. All clones were genotyped using Genotyping-by-Sequencing (27,045 Single Nucleotide Polymorphism - SNPs) and Diversity Arrays Technology - DArTseq (25,923 SNPs). Trait values were estimated using a two-stage mixed model to obtain deregressed BLUPs (Best Linear Unbiased Predictions), and genome-wide association analyses were performed using both the Mixed Linear Model (MLM) and Multi-Locus Mixed Model (MLMM). We detected six significant SNPs consistently associated with carotenoid content and DMC after Bonferroni correction. These SNPs mapped to six candidate genes involved in pathways relevant to root physiology, including Abscisic Acid ABA-related signaling, hydrolase activity affecting carotenoid conversion, fatty-acid biosynthesis within plastids, cell-wall remodeling, and glycolytic energy metabolism. The loci jointly explained 75.56 % of the phenotypic variance for carotenoids and 76.23 % for DMC, with individual SNP effects ranging from [~]17 % to [~]42 % PVE (Proportion of Variance Explained). Broad-sense heritability was H2 = 0.78 for carotenoids and H{superscript 2} = 0.34 for DMC, confirming substantial genetic control and suitability for molecular breeding. Haplotype analyses revealed four superior haplotypes for carotenoids and one key haplotype for DMC, each showing significantly higher trait values compared with other allelic combinations. These haplotypes represent promising targets for marker-assisted selection and genomic selection, with direct applicability for accelerating genetic gain in elite breeding populations. The results provide actionable genomic resources for breeding programs aiming to develop biofortified and high-root quality cultivars and establish a foundation for future multi-omics and functional validation studies.

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.

Branched-chain amino acids (BCAAs) are essential amino acids involved in protein synthesis and energy metabolism. Because animals cannot synthesize BCAA de novo, plant-derived BCAAs are important to human nutrition. Although mungbean sprouts are widely consumed as functional plant-based food materials, changes in individual BCAA accumulation and their transcriptional regulation during mungbean germination remain poorly understood. In this study, amino acid contents and transcriptomic profiles were analyzed at three germination stages, 8H, 24H, and 72H. Total BCAA content increased during germination, whereas individual BCAAs exhibited distinct temporal accumulation patterns. Isoleucine and valine increased until 72H, while leucine increased during early germination and decreased after 24H. Transcriptome analysis revealed time-dependent expression changes in BCAA biosynthesis and degradation genes associated with the leucine decrease after 24H. These findings suggest that 24H represents an important transition point for BCAA accumulation and compositional change during mungbean germination. This study provides molecular evidence for the regulation of BCAA metabolism during mungbean germination and supports the potential use of germinated mungbean as a plant-based amino acid resource.