The genes in question encode proteins from the BRI1 EMS SUPPRESSOR 1/BRASSINAZOLE RESISTANT 1 family, usually abbreviated BES1/BZR1. These transcription factors sit at the very end of the brassinosteroid signaling pathway, the cascade that carries instructions from steroid hormones at the cell surface down to the DNA in the nucleus. When brassinosteroids are abundant, BES1 and BZR1 proteins accumulate in the nucleus and switch large sets of genes on or off, promoting stem elongation, leaf expansion, flowering, and other growth processes. When the hormone signal is absent or when stress conditions demand a change of priorities, the proteins are phosphorylated and retained in the cytoplasm, effectively putting growth on hold. Because of this dual role, BES1/BZR1 factors have become a major focus for researchers trying to breed crops that grow vigorously while still tolerating hostile environments.

Despite their importance in the model plant Arabidopsis thaliana and in major cereals, the BES1/BZR1 family had not been systematically cataloged in flowering Chinese cabbage. A team led by Haobo Yang, Jinpeng Lu, Jia Li, and Hongyong Shi of Guangzhou University set out to close that gap. Using the recently available genome annotation of the crop, they searched the entire genome for sequences encoding the characteristic BES1-type DNA-binding motif, the molecular signature that allows these proteins to recognize their target genes. The search returned ten genes, which the team named BraBES1, each carrying the conserved motif that defines the family. That number fits the general pattern seen across the Brassica genus, whose genomes expanded through an ancient whole-genome triplication event that left many gene families larger than their counterparts in Arabidopsis.

Identifying the genes was only the first step. To understand how the ten BraBES1 proteins relate to one another and to their relatives in other species, the researchers carried out phylogenetic analysis, constructing an evolutionary tree of BES1/BZR1 proteins. The analysis sorted the wider family into six groups, designated A through F. The ten BraBES1 proteins from flowering Chinese cabbage fell into five of those groups, namely A, C, D, E, and F, with no member assigned to group B. This distribution matters because group membership often predicts function: proteins that cluster together tend to share DNA-binding preferences, interaction partners, and expression patterns inherited from a common ancestor. The absence of a group B representative suggests that whatever ancestral gene gave rise to that lineage was lost or diverged beyond recognition in this species.

The team also examined where the genes sit on the chromosomes and how their neighborhoods compare with those of Arabidopsis. The ten BraBES1 genes were distributed across seven chromosomes, and synteny analysis revealed strong conservation of genomic context with the BES1/BZR1 homologs of Arabidopsis. Synteny, the preservation of gene order across chromosomes of different species, is a powerful clue to evolutionary history. It indicates that the BraBES1 family members are true orthologs, descended from the same ancestral genes as their Arabidopsis counterparts rather than arising through unrelated duplications. For breeders and molecular biologists, this conserved synteny is practical good news, because it means that decades of functional knowledge accumulated in Arabidopsis can serve as a reasonable starting hypothesis for interpreting how the Brassica genes behave.

Subcellular localization provided the next layer of insight. Transcription factors must enter the nucleus to do their work, so where a protein accumulates within the cell often hints at how it is regulated. Using transient expression in tobacco leaves, the researchers found that BraBES1 proteins from groups A, E, and F localized to both the nucleus and the cytoplasm, while proteins from groups C and D were found predominantly in the nucleus. The cytoplasmic fraction in the first group is consistent with the canonical brassinosteroid logic, in which the GSK3-like kinase BIN2 phosphorylates BES1 and BZR1 in the absence of hormone, holding them outside the nucleus until brassinosteroid signaling releases them. The predominantly nuclear behavior of the C and D groups hints at a different regulatory logic, one that may not depend so heavily on hormone-controlled shuttling.

That interpretation gained support from protein interaction assays. Using yeast two-hybrid tests, which detect physical binding between two proteins inside yeast cells, the team showed that all ten BraBES1 proteins interact with BraSK21, a SHAGGY-LIKE KINASE 21 in the crop. In Arabidopsis, the equivalent kinase family, which includes BIN2, acts as the central brake on brassinosteroid signaling, phosphorylating BES1 and BZR1 to inactivate them. The finding that every BraBES1 member binds BraSK21 points to a conserved BR-associated regulatory module: a kinase-and-transcription-factor circuit that has been maintained across hundreds of millions of years of evolution and across the divergence of the Brassica and Arabidopsis lineages. Conservation at this level underscores how fundamental the pathway is to plant life, and it gives researchers an immediate entry point for manipulating the pathway in the vegetable.

Where the family truly diverges is in its regulatory wiring. The researchers found sequence variation among the ten genes, and their promoter regions, the stretches of DNA upstream of each gene that control when and where it is switched on, carried divergent cis-elements, the short motifs that bind other regulatory proteins. Consistent with that promoter diversity, the genes showed distinct expression profiles across tissues and conditions. When the team exposed plants to a panel of hormones, including brassinolide, the active brassinosteroid, along with gibberellic acid, the auxin indole-3-acetic acid, abscisic acid, and salicylic acid, each BraBES1 gene responded in its own characteristic pattern. The same held true under abiotic stresses: cold and heat, drought, high light, and salt each elicited gene-specific changes in expression. This is the signature of a gene family that has undergone subfunctionalization, in which duplicated copies shed redundant roles and each specialized for particular signals, tissues, or conditions.

One pattern stood out from the stress and hormone experiments. Genes in group A showed especially strong responsiveness to hormones and to high temperature in the cultivar Sijiu-19, a traditional variety of flowering Chinese cabbage. Given that heat stress is an increasingly serious constraint on vegetable production in southern China, a transcription factor family member that couples brassinosteroid signaling with heat responsiveness is an obvious candidate for further study. If group A BraBES1 genes turn out to mediate the well-documented role of brassinosteroids in thermotolerance, they could become targets for marker-assisted selection or genome editing aimed at producing varieties that hold their yield through heat waves. The authors position the whole dataset as a resource for exactly this kind of functional analysis of BR-linked development and stress adaptation.

The study is a reminder of how much modern crop improvement depends on cataloging the parts list before tinkering with the machine. By combining genome-wide identification, evolutionary classification, chromosomal synteny, protein localization, interaction mapping, and expression profiling under a dozen different treatments, the Guangzhou University team has built a multi-layered picture of a single transcription factor family in a crop that had been largely invisible to this kind of analysis. The conserved features, the shared DNA-binding motif, the interaction with BraSK21, the syntenic anchors to Arabidopsis, give the field confidence that established brassinosteroid biology transfers to flowering Chinese cabbage. The divergent features, the split localization patterns, the varied promoters, and the gene-specific responses to hormones and stresses, show where the interesting specialization lies. The next step, functional validation of individual BraBES1 genes in the crop itself, will determine whether this catalog becomes a toolkit for breeding leafy vegetables that grow fast, flower on schedule, and shrug off the stresses of a warming climate.

Subject of Research: BES1/BZR1 transcription factor gene family identification and brassinosteroid signaling in flowering Chinese cabbage

Article Title: Genome-wide identification of BraBES1 genes reveals conserved BR-module features and differential hormone/stress responsiveness in Brassica rapa var. parachinensis

Article References: Yang, H., Lu, J., Li, J., & Shi, H. (2026). Genome-wide identification of BraBES1 genes reveals conserved BR-module features and differential hormone/stress responsiveness in Brassica rapa var. parachinensis. BMC Plant Biology. https://doi.org/10.1186/s12870-026-10215-3

Image Credits: AI Generated

DOI: 10.1186/s12870-026-10215-3

Keywords: Brassica rapa, flowering Chinese cabbage, BES1/BZR1, brassinosteroid, transcription factors, gene family, phylogenetics, synteny, abiotic stress, hormone signaling, plant biotechnology, Guangzhou University

The research team focused on two formulations drawn from a commercial biostimulant platform: fulvic acid alone, designated BLG, and a mixture of fulvic acid with quillaja extract, designated BLGQ. Fulvic acid is a humic substance known for its ability to chelate nutrients and modulate plant metabolism, while quillaja extract, derived from the soapbark tree, is rich in saponins and is often included in biostimulant blends for its surfactant and signaling properties. By comparing these two treatments against untreated controls, the researchers could isolate not only what each formulation does, but what the quillaja component adds to the mixture. Leaf tissue was collected at two carefully chosen time points, three hours and twenty-seven hours after application, capturing what the authors describe as the early signaling phase and the later transcriptional and metabolic adjustment phase of the plant response.

The sequencing data showed that the earliest hours after treatment are anything but quiet. Within three hours, both formulations triggered rapid activation of genes involved in hormone signaling, ion transport, proteostasis, and transcription factor networks, the cellular machinery a plant needs to reprogram itself quickly in response to an external cue. What stood out most was the difference in amplitude: the quillaja-containing mixture, BLGQ, induced broader and stronger transcriptional changes than fulvic acid alone. This suggests that the saponin-rich extract acts as an amplifier of sorts, widening the set of genes that respond and pushing the early signaling cascade harder than the humic component can achieve on its own.

Among the most prominently upregulated genes in that early window were members of several major transcription factor families, including ERF, NAC, C2H2, WRKY, and MYB-related factors. These families are well known to science as master regulators of stress responses, growth, and developmental pathways in plants. ERF factors, for example, sit downstream of ethylene signaling and orchestrate responses to stress and senescence, while WRKY and NAC factors coordinate defenses against pathogens, drought, and other challenges. Their rapid mobilization within three hours indicates that the biostimulant treatments are perceived by maize not as passive nutrition but as genuine biological signals that engage the plant’s own regulatory architecture, priming pathways associated with both stress adaptation and growth promotion.

By twenty-seven hours, the picture had shifted in revealing ways. The fulvic acid treatment, BLG, predominantly reinforced broad metabolic, redox, and transcriptional regulatory networks, consistent with a formulation whose effects radiate outward into general adaptive processes: energy metabolism, oxidative balance, and wide-ranging gene regulation. The quillaja mixture, by contrast, emphasized signaling integration, vesicle trafficking, and secondary metabolism at the later time point. Vesicle trafficking, the cellular logistics system that moves proteins and signaling molecules between compartments, is an intriguing target for biostimulant action, as it underpins cell wall modification, hormone transport, and defense signaling. The secondary metabolism signal hints at the production of specialized compounds that may bolster the plant’s defensive and adaptive chemistry over longer timescales.

The transcription factor analysis added a further layer of nuance, showing that each formulation deploys its own regulatory strategy over time. Fulvic acid sustained the upregulation of MYB-related, NAC, GRAS, and ERF transcription factors across the response window, maintaining pressure on pathways tied to general adaptation. The quillaja mixture took a more surgical approach, selectively balancing upregulation and downregulation of NF-YB, HSF, and bZIP families. This push-and-pull pattern suggests a fine-tuning function, in which the mixture modulates heat shock responses, abiotic stress signaling, and specialized metabolic pathways with greater precision rather than simply turning them up. The authors interpret these contrasting patterns as evidence of stimulus- and time-specific strategies, meaning the plant’s response depends on both what is applied and when you look.

Taken together, the findings reframe how biostimulants should be understood at the molecular level. Rather than acting as generic tonics, these formulations appear to engage distinct, overlapping but separable regulatory programs. The fulvic acid response was associated with broader transcriptional changes in genes involved in general adaptive processes, while the quillaja-containing mixture was associated with more specific signaling and regulatory pathways. For growers and agronomists, this has practical implications: the choice between formulations, and the timing of their application, could be optimized based on which physiological outcome is desired, whether broad metabolic support or targeted signaling priming. For biostimulant developers, the study provides a mechanistic roadmap for designing products with defined molecular targets rather than relying on empirical field trial results alone.

The study also carries a methodological lesson that extends well beyond biostimulants. Had the researchers sampled only a single time point, they would have captured a misleadingly static snapshot and missed the fundamental shift in response character between three and twenty-seven hours. The early phase is dominated by rapid signaling and transcription factor activation, while the later phase reflects downstream metabolic and regulatory consolidation. The authors explicitly underline the importance of time-resolved analyses for understanding plant growth and stress adaptation, a point that applies equally to studies of fertilizers, elicitors, and stress treatments across crop science. Dynamic processes demand dynamic measurement, and this work demonstrates how RNA sequencing at multiple time points can expose the temporal architecture of a plant’s response to agricultural inputs.

Maize, as one of the world’s most important cereal crops and a staple grown across diverse and increasingly unpredictable climates, stands to benefit considerably from this kind of mechanistic insight. As agriculture confronts pressure to reduce synthetic inputs while maintaining yields under heat, drought, and disease stress, biostimulants are likely to play an expanding role, and understanding their molecular modes of action will be essential for credible, effective deployment. This transcriptomic study provides a foundation for that understanding, mapping the temporal layers of biostimulant action in a major crop and showing that the mixture of quillaja extract with fulvic acid is more than the sum of its parts. The next steps for the field will involve connecting these transcriptional signatures to measurable agronomic traits, but the study makes clear that the conversation between biostimulant and plant begins within hours and unfolds along distinct, formulation-specific paths that science is only now beginning to read.

Subject of Research: Temporal transcriptomic responses of maize to fulvic acid and quillaja extract biostimulants

Article Title: Temporal and stimulus-specific transcriptional responses of maize to a biostimulant mixture of quillaja extract and fulvic acid

Article References: Hesami, M., Rahbari, M., & Salzman, R. A. (2026). Temporal and stimulus-specific transcriptional responses of maize to a biostimulant mixture of quillaja extract and fulvic acid. PLOS One, 21(10), e0360081. https://doi.org/10.1371/journal.pone.0360081

Image Credits: AI Generated

DOI: 10.1371/journal.pone.0360081

Keywords: maize, biostimulants, fulvic acid, quillaja extract, transcriptomics, RNA sequencing, transcription factors, plant stress response, hormone signaling, secondary metabolism, time-resolved gene expression, PLOS One

The research team, led by Yuanqian Ni and supervised by Zhaosen Xie and Youmei Li, took advantage of a natural contrast between two grapevine cultivars. ‘Einset Seedless’, abbreviated ENT in the study, tends to produce inflorescences at the lower tendril nodes of its lateral shoots, while ‘Pinot Noir’, or PN, overwhelmingly produces true tendrils at the equivalent positions. By comparing these two varieties node by node, the researchers could ask a precise question: when the same meristem faces the same choice, what is different inside the cells of a plant that flowers versus a plant that climbs?

The homology of tendrils and inflorescences in grapevine is well established. Classical anatomical work showed that both organs arise from the same uncommitted primordia on lateral shoots, and earlier molecular studies found that floral meristem identity genes are expressed even in developing tendrils, as if the tendril were an inflorescence that never quite committed to flowering. Decades ago, pioneering experiments by Srinivasan and Mullins demonstrated that isolated tendrils could even be coaxed into forming inflorescences in vitro, hinting that the switch between the two fates is chemically malleable. What the new study adds is a genome-wide, node-resolved map of the transcriptional landscape in which that switch is thrown.

The team first quantified the anatomical difference, confirming that ENT achieved a markedly higher flowering rate at tendril nodes one through four than PN did. They then harvested tissue from specific tendril nodes in both cultivars and performed RNA sequencing, using an intersection and exclusion strategy to isolate 549 differentially expressed genes that distinguish inflorescence-prone from tendril-prone tissue. When those genes were subjected to Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis, two signaling systems rose to the top: plant hormone signal transduction and mitogen-activated protein kinase cascades. In other words, the decision between flower and tendril appears to be broadcast through the cell by hormonal and phosphorylation-based communication channels rather than by a single master switch.

To move beyond a static snapshot, the researchers applied Mfuzz clustering, a computational method that groups genes according to the shape of their expression trajectories across a developmental series. This revealed that multiple expression programs rise and fall in patterns that track the flowering gradient running along the shoot, from the most inflorescence-prone basal nodes to the tendril-dominated upper nodes. Across every dynamic cluster, plant hormone signal transduction emerged as the predominantly enriched pathway, underscoring that phytohormones are not merely participants in this process but sit at its very center.

Guided by that transcriptional evidence, the team measured the endogenous levels of two key hormones directly in the nodal tissues: zeatin, the classic cytokinin that generally promotes reproductive meristem activity and flowering, and gibberellin GA3, which is more often associated with stem elongation and vegetative growth. The striking result was that the ratio between the two, rather than the absolute level of either hormone alone, paralleled the flowering gradient across nodes and correlated with the gene expression trajectories identified by clustering. A high zeatin-to-GA3 ratio accompanied the inflorescence-prone state, while a lower ratio accompanied tendril formation. This provides concrete physiological support for a cytokinin-gibberellin interaction model in which the balance between these two antagonistic hormones helps determine whether a lateral meristem matures into a flower-bearing branch or an elongating, climbing tendril.

The hormone story dovetails with a long history of viticultural observation. Growth retardants that suppress gibberellin synthesis have been known since the 1960s to influence fruitfulness in grapes, and cytokinin treatments have been shown to convert tendril primordia into inflorescences, with the success of that conversion depending on the genotype. The famous ‘green revolution’ dwarfing mutation in grapevine, which links reduced gibberellin response with enhanced floral induction, fits the same pattern. What the new transcriptomic work contributes is the mechanistic scaffolding: it shows that the endogenous hormone ratio in the organ itself, not just externally applied chemicals, tracks the developmental outcome, and that the downstream transcriptional response is organized into coherent, flowering-correlated trajectories.

Within the pool of differentially expressed transcription factors, one gene stood out. A MADS-box gene named FRUITFULL-LIKE, or VvFUL-L, was markedly upregulated in PN tendrils compared with inflorescence-prone ENT tissue. MADS-box transcription factors are the celebrated architects of floral development, and the FRUITFULL lineage in particular is known from arabidopsis and tomato to regulate meristem identity, flowering time, and inflorescence architecture. To probe what VvFUL-L might be doing, the team overexpressed it heterologously in arabidopsis. The transgenic plants flowered earlier than normal and produced inflorescences with reduced branching, phenotypes consistent with a role in steering lateral meristem development. The authors suggest that VvFUL-L may help tip the uncommitted grapevine lateral meristem toward the tendril program, although confirming that function in grapevine itself will require further work in the crop.

The agronomic implications are immediate and tangible. Excessive tendril growth increases vineyard management costs because tendrils must be removed or redirected by hand or machine, and they can girdle shoots and interfere with canopy machinery. If the cytokinin-to-gibberellin ratio and regulators like VvFUL-L can be manipulated, whether through breeding, targeted gene editing, or growth regulator programs, growers could eventually favor inflorescence formation at the basal nodes where fruit is wanted and suppress the runaway tendril production that wastes the vine’s resources. The study’s authors frame their findings as a foundation for future molecular and breeding studies aimed at managing tendril growth, and the identification of a small set of hormone-responsive genes and a candidate transcriptional regulator is exactly the kind of entry point such efforts require.

There is also a broader evolutionary resonance in the result. Across the grape family, the Vitaceae, tendrils and inflorescences are thought to be variations on a single ancestral organ, and expression studies of APETALA1, FRUITFULL, FLOWERING LOCUS T, and LEAFY orthologs throughout the family support that homology. The Yangzhou study now supplies a quantitative, node-by-node account of how that shared developmental potential is partitioned within a single plant, showing that the fate of each primordium is written in the language of hormone ratios and read out by MADS-box transcription factors. A curling tendril on a Pinot Noir vine, in this light, is not a failed flower but an alternative interpretation of the same instructions, and researchers are learning to read, and perhaps one day to rewrite, the grammar behind that choice.

Subject of Research: Molecular regulation of tendril versus inflorescence development in grapevine lateral shoots

Article Title: Comparative transcriptomics reveals hormone signaling and MADS-box genes in divergent development of inflorescences and tendrils in grapevine lateral shoots

Article References: Ni, Y., Bian, Y., Xie, Z., & Li, Y. (2026). Comparative transcriptomics reveals hormone signaling and MADS-box genes in divergent development of inflorescences and tendrils in grapevine lateral shoots. Plant Cell Reports, 45(9), Article 270. https://doi.org/10.1007/s00299-026-03957-9

Image Credits: AI Generated

DOI: 10.1007/s00299-026-03957-9

Keywords: grapevine, Vitis vinifera, tendrils, inflorescences, cytokinin, gibberellin, MADS-box, VvFUL-L, transcriptomics, hormone signaling, flowering, viticulture