The team began by charting where and when VvbHLH10 switches on. Under laboratory conditions, its transcription was rapidly and strongly induced by both salt and alkali treatments, a pattern consistent with a gene recruited into the front line of the stress response. Intriguingly, the gene is also predominantly expressed in actively growing tissues, including latent buds, young stems and young tendrils, placing it at the intersection of stress defense and development. Using a VvbHLH10-GFP fusion protein, the researchers confirmed that the protein localizes to the nucleus, the expected working address for a transcription factor that binds promoter regions and orchestrates the expression of downstream target genes.

To test function rather than mere correlation, the researchers deployed two complementary experimental systems. The first was homologous overexpression in grape callus cultures, an in vitro system derived from the plant itself. When grape calli engineered to overexpress VvbHLH10 were challenged with salt and alkali stress, they survived and grew significantly better than control calli. Biochemical assays pointed to the mechanism behind that resilience: the engineered tissues accumulated markedly lower levels of reactive oxygen species (ROS) and malondialdehyde (MDA), two classic signatures of oxidative damage. Because salt and alkali stress disrupt photosynthesis and electron transport, plants typically respond with bursts of ROS that damage membranes, proteins and DNA; reducing that oxidative burden is a central goal of stress-resilience breeding.

The second system took the gene out of grapes altogether. In a heterologous expression approach, the team introduced VvbHLH10 into tomato, a widely used surrogate that allows plant scientists to ask whether a gene’s function is conserved across species. The answer was a clear yes. Transgenic tomato lines overexpressing VvbHLH10 showed markedly improved tolerance to salt-alkali treatment compared with wild-type controls, again with reduced oxidative damage and better overall growth. Cross-species validation of this kind matters for breeders because it suggests the underlying regulatory module is not a grape-specific quirk but a portable stress-protection circuit that could, in principle, be engineered into other horticultural crops facing the same soil chemistry problems.

Then came the surprise. Beyond its protective function, ectopic expression of VvbHLH10 in tomato promoted axillary bud outgrowth and altered the plants’ vegetative architecture. Axillary buds are the embryonic shoots that sit in the angle between leaf and stem, and whether they remain dormant or break out into branches is governed by a tight hormonal and transcriptional network involving strigolactones, auxin and cytokinin. A transcription factor that simultaneously modulates this developmental switch and the stress response is unusual, and it hints that VvbHLH10 belongs to a growing group of bHLH proteins whose roles have diversified beyond single functions. In practical terms, the same gene that helps a vine survive degraded soil could also be tuned to change how the plant allocates its growth, a lever for shaping canopy structure and productivity.

The dual identity of VvbHLH10 fits into a broader emerging picture of the bHLH family. With hundreds of members in most plant genomes, bHLH transcription factors have been implicated in everyone’s favorite processes, from iron uptake and flavonoid biosynthesis to light signaling and hormone crosstalk. Group 9 bHLH factors, the subclass to which VvbHLH10 belongs, have drawn particular interest for their roles in abiotic stress responses. What this study adds is evidence that in a woody perennial crop of global economic importance, one group 9 member can be rapidly mobilized by salinity and alkalinity cues, act in the nucleus to dampen oxidative injury, and at the same time remodel shoot architecture by freeing axillary buds from dormancy.

For viticulture, the implications are concrete. Salt-alkali soils are expanding in many grape-growing regions as irrigation, climate change and intensive cultivation push pH and sodium levels upward, and vineyards on marginal land often suffer stunted vines, poor bud break and yield losses. A gene that improves survival under both saline and alkaline conditions, verified in both homologous and heterologous systems, offers a candidate target for marker-assisted selection or genome editing. Because VvbHLH10 is naturally expressed in latent buds, breeders could also exploit its developmental role to improve bud fertility and branching in varieties where shy bud break limits yield. The authors position VvbHLH10 as a promising candidate for the genetic improvement of both salt-alkali tolerance and plant architecture in grapevine.

The research, led by Rui Xu and Huiping Liu as co-first authors and corresponding author Ke Li, was published open access on 12 September 2026 after acceptance on 9 September, and was supported by the Key Research and Development Project of Shandong Province, the National Natural Science Foundation of China, the Shandong Provincial Natural Science Foundation and several programs at the Shandong Academy of Agricultural Sciences. The team also released transcriptomic datasets from VvbHLH10-overexpressing tomato as supplementary material, giving the community a resource to trace which downstream pathways the transcription factor rewires, from antioxidant defenses to branching hormones.

What remains to be resolved is the direct target repertoire of VvbHLH10 and how its stress-protective and developmental outputs are mechanistically linked. If the same set of bound promoters underlies both ROS quenching and bud release, that would suggest an elegant coupling in which growth resumption under stress is actively licensed rather than merely permitted. If the two functions run through separate downstream circuits, breeders may be able to dial in salt tolerance without unwanted changes in vine shape. Either outcome broadens understanding of the functional diversification of bHLH transcription factors in horticultural crops and brings grape growers one gene closer to vines that thrive where the soil fights back.

Subject of Research: Functional characterization of the VvbHLH10 transcription factor in grapevine salt-alkali stress tolerance and axillary bud growth regulation

Article Title: VvbHLH10 promotes axillary bud growth and salt-alkali tolerance in grapevine

Article References: Xu, R., Liu, H., Mu, Q., Li, A., Wang, F., & Li, K. (2026). VvbHLH10 promotes axillary bud growth and salt-alkali tolerance in grapevine. BMC Plant Biology. https://doi.org/10.1186/s12870-026-09949-x

Image Credits: AI Generated

DOI: 10.1186/s12870-026-09949-x

Keywords: grapevine, VvbHLH10, bHLH transcription factor, salt-alkali stress, axillary bud growth, reactive oxygen species, abiotic stress tolerance, Vitis vinifera, plant architecture, viticulture, plant molecular biology, transgenic plants

The study, published in Plant Cell Reports, set out to answer two intertwined questions. First, where did a family of plant stress genes known as ERF-VII come from in the deep history of plant evolution? Second, what do these genes actually do in the tea plant when the temperature drops? To resolve both, the researchers combined broad comparative genomics across 14 plant lineages with detailed analyses of 20 tea plant cultivars, creating one of the most comprehensive portraits of this gene family in any woody beverage crop.

The ERF-VII family belongs to the larger AP2/ERF superfamily of transcription factors, master regulators that bind specific DNA sequences and switch suites of target genes on or off. In the model plant Arabidopsis thaliana, ERF-VII proteins are famous for their role in oxygen sensing: they carry a conserved N-terminal motif, the MCGGA/I motif, that tags them for destruction by the oxygen-dependent branch of the N-degron protein degradation pathway. When oxygen is scarce, as during flooding or submergence, these proteins escape degradation, accumulate in the nucleus and activate survival programs. The new work shows that this regulatory architecture is ancient and evolutionarily telling.

By reconstructing phylogenetic trees of ERF-VII proteins across lineages ranging from algae to flowering plants, the team found that the family originated after the divergence of vascular plants, and that its emergence coincided precisely with the appearance of the MCGGA/I motif linked to oxygen-dependent degradation. This suggests that the oxygen-sensing capacity of ERF-VII factors was built into the family at its inception. Gymnosperms, the conifers and their relatives, retained only a few conserved members, while angiosperms underwent dramatic, lineage-specific expansion. Monocots, the grasses and their kin, expanded the family extensively, apparently driven by whole-genome duplication events, whereas eudicots showed more moderate expansion accompanied by functional diversification, with duplicated genes taking on specialized roles in stress and development.

With the evolutionary framework established, the researchers turned to the tea plant itself. A pan-genome analysis, comparing genome sequences from 20 different tea cultivars, revealed that the ERF-VII gene complement is not identical across varieties. Some cultivars carry genes that others lack, and the family members fall into categories that differ in number and distribution between accessions. This varietal variation is significant because it provides raw material for breeders: genes present in hardy landraces but absent or divergent in elite cultivars could underpin differences in freezing tolerance that breeders can exploit through marker-assisted selection.

To identify which ERF-VII members respond to cold, the team mined transcriptome data from the Tea Plant Information Archive, a public repository of gene expression profiles. One member, named CsRAP2.2, stood out. Its expression was strongly induced by low temperature and, crucially, remained sustained throughout cold treatment rather than flickering briefly and fading. The name is telling: CsRAP2.2 is an ortholog of Arabidopsis RAP2.2, a factor previously implicated in hypoxia survival and low-oxygen, oxidative and osmotic stress responses. The tea version appears to have been recruited into the cold-response network, hinting at an evolutionary link between oxygen sensing and chilling tolerance in this species.

Correlation alone does not prove function, so the researchers ran a series of direct tests. When they silenced CsRAP2.2 in tea leaves, the plants became measurably more vulnerable to cold. Conversely, when they overexpressed the gene in tea leaves and introduced it heterologously into Arabidopsis, both systems showed enhanced cold tolerance. The physiological basis of this protection was traced to three pillars of cellular defense. Transgenic and overexpressing material maintained photosystem II efficiency, the quantum engine of photosynthesis that cold typically damages; they suffered less membrane lipid peroxidation, the oxidative rancidity of cellular membranes that accompanies freezing injury; and they showed improved antioxidant capacity, the enzymatic and chemical scavenging of reactive oxygen species that otherwise accumulate as toxic byproducts of cold stress.

To place CsRAP2.2 within the wider regulatory landscape, the team applied weighted gene co-expression network analysis, a computational method that clusters thousands of genes into modules based on coordinated expression across samples and conditions. This analysis positioned CsRAP2.2 as a hub, a highly connected node integrating cold signaling, hormone pathways and oxygen-sensing machinery. Gene Ontology enrichment of its co-expressed network highlighted processes ranging from protein transport to the detection of oxygen and hypoxia, consistent with the idea that cold, hormone and low-oxygen signals converge on ERF-VII factors in tea. In practical terms, CsRAP2.2 may act less like a lone switch and more like a control tower, coordinating multiple stress-response programs simultaneously.

The broader implications extend well beyond tea biology. Global tea production is concentrated in subtropical and highland regions where frost events are becoming increasingly erratic as the climate shifts. A validated cold-tolerance gene with demonstrated function in both tea and a heterologous model gives breeders a concrete molecular target. Marker-assisted breeding or genome editing approaches could introduce or amplify favorable CsRAP2.2 alleles in susceptible cultivars, potentially protecting harvests without the long timelines of conventional crossing. The pan-genome perspective adds another layer: because ERF-VII gene content varies among cultivars, screening germplasm collections for the most protective variants becomes a tractable strategy.

The study also enriches our understanding of transcription factor family evolution. By anchoring the origin of ERF-VII genes to the rise of vascular plants and tying it to a specific protein motif, the work illustrates how a single molecular innovation, a degron recognized by the N-end rule pathway, can seed an entire regulatory system that plants later repurposed for drought, flooding, hypoxia and now cold tolerance. For the humble tea bush, it seems, survival in the cold may hinge on an ancient oxygen-sensing trick repurposed by millions of years of evolution. For the scientists and growers betting on climate-resilient agriculture, CsRAP2.2 offers a promising lead, and possibly the genetic key to keeping the world’s favorite infusion flowing through frosts to come.

Subject of Research: Evolution and cold-stress function of the ERF-VII gene family in tea plant (Camellia sinensis)

Article Title: Genome-wide identification and evolutionary analysis of the ERF-VII gene family in the tea plant (Camellia sinensis) and functional characterization of CsRAP2.2 in response to cold stress

Article References: Huang, Q., Pan, R., Wu, L., Chen, S., Hu, J., Long, Z., Zhao, J., Hao, X., & Tang, H. (2026). Genome-wide identification and evolutionary analysis of the ERF-VII gene family in the tea plant (Camellia sinensis) and functional characterization of CsRAP2.2 in response to cold stress. Plant Cell Reports, 45(10), Article 290. https://doi.org/10.1007/s00299-026-03973-9

Image Credits: AI Generated

DOI: 10.1007/s00299-026-03973-9

Keywords: tea plant, Camellia sinensis, ERF-VII, CsRAP2.2, cold stress, transcription factors, pan-genome, oxygen sensing, N-degron pathway, plant evolution, molecular breeding, abiotic stress

PERK genes belong to the vast superfamily of receptor-like kinases, the molecular sentinels that stud plant cell membranes and translate external signals into internal biochemical commands. A typical PERK protein is a modular device: an extracellular region rich in proline and reminiscent of extensin—a structural cell-wall protein—sits outside the membrane, linked through a single membrane-spanning segment to an intracellular serine/threonine protein kinase domain. When an appropriate cue is perceived at the cell surface, the kinase domain can become activated through phosphorylation, launching cascades of downstream signalling. Previous work in other species had already linked PERK proteins to important processes: the Arabidopsis PERK4 protein, for example, was shown to regulate calcium signalling and abscisic acid responses, while PERK1 in bean is rapidly induced by wounding. Genome-wide analyses in crops such as wheat, cotton, maize and Brassica rapa have likewise suggested roles in development and environmental response. Tomato, however, had remained comparatively unexplored for this family until now.

The research team worked from the SL4.0/ITAG4.0 genome assembly, the latest and most refined annotation of the tomato genome, to locate and verify every member of the PERK family. Their search yielded six genes, designated SlPERK1 through SlPERK6, and every one of them was confirmed to carry the conserved serine/threonine protein kinase domain that defines the family’s catalytic function. The modest size of the family compared with the expansions seen in some polyploid crops makes tomato an unusually clean system for dissecting what each gene does, since redundancy among close relatives is limited.

To understand how these six genes had evolved, the researchers performed phylogenetic and structural comparisons. One of the most informative measures in evolutionary genetics is the ratio of non-synonymous to synonymous substitution rates, known as Ka/Ks. Non-synonymous substitutions change the amino acid sequence of a protein, while synonymous substitutions do not, so a Ka/Ks value below 1 indicates purifying selection—evolutionary pressure to preserve the protein sequence because changes are typically harmful. In the case of the SlPERK genes, Ka/Ks values were consistently below 1, indicating strong purifying selection and suggesting that the functions of these kinases are so important to the plant that damaging mutations are weeded out over generations. The team also examined exon-intron architecture, the pattern of coding regions and intervening non-coding sequences within each gene, and found distinct organizational differences among family members—a feature often associated with functional divergence, where genes that arose from a common ancestor have taken on specialized roles.

Because gene activity is regulated not only by the gene itself but by the DNA elements that control it, the researchers scanned the promoter regions upstream of each SlPERK gene for cis-regulatory elements—short DNA motifs that serve as binding sites for transcription factors. Their analysis uncovered an abundance of stress-responsive and hormone-responsive elements, including motifs associated with responses to abscisic acid, drought, cold and salinity. This finding is significant because it suggests the genes are wired at the regulatory level to respond to exactly the kinds of environmental challenges the researchers would go on to test experimentally. In effect, the promoters of the SlPERK genes carry built-in switches tuned to adverse conditions.

The team went a step further by exploring regulation after transcription. Using computational prediction, they identified 57 microRNAs—small regulatory RNAs that can bind complementary sequences in messenger RNAs and either cleave them or block their translation—as potential post-transcriptional regulators of the SlPERK genes. They also constructed protein-protein interaction networks, revealing that the PERK proteins are predicted to connect with a broader web of signalling components. Together, these analyses sketch a picture of a small gene family embedded in multiple layers of control, from transcriptional regulation through microRNA-mediated tuning to network-level interactions with other signalling proteins.

Bioinformatics alone, however convincing, cannot establish a role in stress tolerance, so the researchers validated their predictions in the greenhouse. They selected two tomato cultivars with different genetic backgrounds—GMOTL-1 and Roma—and exposed them to three abiotic stresses: cold, heat and salinity. They then measured gene expression using quantitative reverse-transcription PCR, a laboratory technique that converts messenger RNA into complementary DNA and amplifies it to quantify how active each gene is under different conditions. Expression levels were normalized using established relative-quantification methods, allowing precise comparison of gene activity between stressed and unstressed plants and between the two cultivars.

The qRT-PCR results revealed cultivar-specific expression dynamics that matched the computational predictions in compelling ways. SlPERK4 showed strong transient induction under cold and heat stress, meaning its activity spiked rapidly in response to temperature extremes before subsiding—a pattern typical of genes involved in early stress signalling rather than long-term physiological adjustment. SlPERK6, by contrast, proved highly responsive to salinity, its expression climbing when plants were grown under salt treatment. Perhaps most striking was the difference between the cultivars. GMOTL-1 displayed significantly higher and broader stress-responsive expression across the SlPERK family than Roma, its genes responding more strongly and to a wider range of stresses. This pattern suggests that the more robust expression of PERK-mediated signalling could contribute to the superior stress tolerance observed in some tomato backgrounds, and it provides breeders with a molecular signature they might look for when screening germplasm for resilient lines.

The implications extend well beyond basic biology. Tomatoes are grown on every continent and are a cornerstone of global diets, yet they are notoriously sensitive to environmental extremes. Cold snaps damage membranes and photosynthetic machinery, heat waves impair pollen development and fruit set, and soil salinity—exacerbated by irrigation and climate change—suppresses growth and yield across millions of hectares. Conventional breeding for stress tolerance is slow, and the underlying genetics is often complex. Genomic resources like the one assembled here accelerate that process by pinpointing candidate genes whose regulation or sequence could be targeted by marker-assisted selection or, increasingly, by gene-editing tools such as CRISPR-Cas9, which has already been applied to enhance abiotic stress resilience in tomato. A compact, well-characterized gene family with clear stress-responsive members is precisely the kind of resource that functional validation and molecular breeding programmes need.

The study, supported by an ALP-funded project of the Pakistan Agricultural Research Council, also reflects the growing power of combining the newest genome assemblies with classical stress physiology. By anchoring their search in SL4.0/ITAG4.0, the researchers minimized the risk of missing genes or misannotating family members—an issue that has plagued earlier family-wide studies built on older assemblies. By pairing bioinformatics with experimental expression profiling in two cultivars, they moved from prediction to evidence, demonstrating that the SlPERK genes are not merely present in the genome but actively engaged in the plant’s response to its environment. As climate variability intensifies, understanding how sensor genes like PERKs tune a crop’s response to adverse conditions will become increasingly important. For now, the six SlPERK genes stand as both a genomic resource and a set of molecular leads: SlPERK4 for temperature stress, SlPERK6 for salinity, and the cultivar contrast between GMOTL-1 and Roma as a roadmap for breeding tomatoes that can thrive in a warming, salinizing world.

AP2/ERF transcription factors are critical regulatory proteins in plants, influencing a wide array of developmental processes as well as responses to environmental stimuli. The AP2/ERF gene family is known for its roles in the expression regulation of genes involved in responses to abiotic stresses like drought and salinity, as well as biotic stresses including pathogen attack. Characterizing this gene family in Cinnamomum camphora adds an important species to the existing database of plant genomic studies, which could lead to biotechnological applications aimed at improving crop resilience.

The identification process employed by the researchers involved comprehensive bioinformatics tools and methods to analyze the complete genome of Cinnamomum camphora. By executing a detailed annotation, the team meticulously categorized different members of the AP2/ERF family and elucidated their structures, including the conserved domains crucial for their functional activities. Advanced computational techniques were likely employed to align sequences, predict protein structures, and establish phylogenetic relationships amongst the identified transcription factors.

Moreover, the study is notable not just for the identification of genes, but also for the in-depth characterization of gene expression patterns. Gene expression profiling is essential in determining how these genes function under various conditions. By employing quantitative real-time polymerase chain reaction (qRT-PCR), the researchers assessed the expression levels of several AP2/ERF genes across different tissues and developmental stages of Cinnamomum camphora, providing insights into when and where these genes are activated within the plant’s lifecycle.

One of the study’s key findings is the identification of several novel AP2/ERF genes that may play roles specific to the metabolic pathways in Cinnamomum camphora, which is renowned for its essential oils and diverse bioactive compounds. This stretches the boundaries of traditional plant studies as the intersection between genomics and phytochemistry becomes more pronounced. By linking gene activity to the production of aromatic compounds, this study may pave the way for innovations in fragrance and flavor industries, potentially enhancing the economic value of Cinnamomum camphora.

The implications of this research extend far beyond Cinnamomum camphora alone. By enhancing the understanding of the AP2/ERF gene family, scientists can draw parallels and make predictions about the functionalities of similar genes in other economically important species, fostering advancements in crop breeding programs. The results could lead to the development of plants with enhanced resilience to climate change, resistance to pests, and optimization in the production of desired phytochemicals.

Importantly, this research highlights the advancements in genomic technologies that allow for swift and comprehensive exploration of plant genetics. The evolution of sequencing technologies, such as next-generation sequencing, has transformed the landscape of genomics, enabling researchers to generate vast datasets rapidly. Consequently, studies like this can accelerate our understanding of gene families across multiple species, some of which may have been previously understudied due to limitations in technology or funding.

Collaboration across disciplines is vital, and the team’s work exemplifies how genomics, bioinformatics, and molecular biology can converge to address complex biological questions. Understanding gene families at a genomic scale necessitates not just expert knowledge in plant biology, but also skilled proficiency in computational analysis and data interpretation. The collaborative nature of such research contributes to creating a well-rounded approach to studying biodiversity and gene functionalities.

Furthermore, the research contributes to conservation efforts for Cinnamomum camphora, which has been affected by habitat loss and over-exploitation. By understanding its genetic makeup and identifying key regulatory genes, conservationists and biotechnologists can devise strategies to preserve this valuable species while optimizing its cultivation for sustainable use, particularly in industries that benefit from its unique oil content.

Lastly, the implications of the novel findings on Cinnamomum camphora extend into the agricultural sector, opening doors for transgenic approaches that can enhance crops with desired traits. Employing techniques such as CRISPR/Cas9 gene editing to modify or activate specific AP2/ERF genes could lead to the creation of improved cultivars capable of withstanding environmental stressors or diseases. This aligns with the growing demand for sustainable agricultural practices aimed at ensuring food security in a rapidly changing world.

In conclusion, the research conducted on the AP2/ERF gene family in Cinnamomum camphora represents a significant advancement in plant genomics, providing valuable insights into the genetic underpinnings of essential traits. The findings have far-reaching implications, benefiting agriculture, conservation, and industry, and underscore the importance of continued research and innovation in plant genetics. Through collaborative efforts, scientists can deepen our understanding of plant biology and its relevance to global challenges.

Subject of Research: Genome-wide identification and characterization of the AP2/ERF gene family in Cinnamomum camphora.

Article Title: Genome-wide identification and characterization of the AP2/ERF gene family in Cinnamomum camphora.

Article References:

Yang, Z., Yang, X. & Zheng, X. Genome-wide identification and characterization of the AP2/ERF gene family in Cinnamomum camphora.
BMC Genomics 26, 972 (2025). https://doi.org/10.1186/s12864-025-12169-6

Image Credits: AI Generated

DOI: 10.1186/s12864-025-12169-6

Keywords: AP2/ERF gene family, Cinnamomum camphora, plant genomics, gene expression profiling, abiotic stress, biotic stress, bioinformatics, sustainable agriculture.