The review, led by Ikram Ullah and Naveed Ahmad, who contributed equally, together with Aashaq Hussain Bhat, Adil Hussain, Fan Wei, and Wu Hongzhi, draws together evidence spanning cold stress perception, signal transduction, transcriptional regulation, metabolic reprogramming, and phytohormone interactions in pepper. Its central argument is that pepper’s intrinsic cold tolerance has been constrained not by the absence of defensive machinery, but by its incomplete deployment. The crop possesses endogenous cold-responsive regulators such as CaNAC035 and CabHLH035, along with antioxidant defense systems, yet these remain insufficiently activated when temperatures drop, leaving plants exposed to damage they are nominally equipped to resist.

At the heart of the problem lies a cluster of biological complications that conventional breeding has struggled to disentangle. Key cold-response regulators show low transcriptional activation under stress, meaning the genetic instructions for defense are present but poorly executed. Functional redundancy among cold-responsive genes further complicates matters: multiple genes can substitute for one another, so knocking out or enhancing a single factor often produces negligible phenotypic change. Cold tolerance itself is polygenic, governed by many genes of small effect scattered across the genome. Layered on top of these complexities are low genetic diversity within elite pepper germplasm and linkage drag, the troublesome tendency of undesirable traits to hitchhike along with desirable ones during crossing. Together, these obstacles have stymied decades of conventional cold-resistance breeding.

To overcome them, the authors champion what they call Precision Breeding 2.0, an integrated innovation that couples multi-omics-based target identification with next-generation genome-editing techniques. Rather than editing one gene at a time, this approach allows precise and multiplex engineering of complex, interconnected regulatory networks. The distinction matters because cold tolerance is not a switch but a symphony: calcium signatures, phosphorylation cascades, hormone signals, and transcriptional circuits must all be tuned in concert. By mapping these networks through transcriptomics, proteomics, and metabolomics before editing, breeders can identify the highest-leverage nodes and modify several of them simultaneously.

Among the most promising strategies highlighted in the review is the engineering of the DREB/CBF pathway, the canonical cold-response cassette first characterized in Arabidopsis and now recognized across crops. In pepper, cold-inducible CBF transcription factors interact with homeodomain leucine zipper proteins, and genome-wide analyses of the C-repeat binding factor family in related Capsicum species have revealed functional diversity in low-temperature responses. The review also outlines allele-specific editing, which lets researchers swap inferior versions of genes for superior ones without altering anything else in the genome, and targeted disruption of negative regulators, transcriptional brakes that suppress cold responses and whose removal can unlock latent tolerance.

The molecular detail underpinning these strategies is impressive. Recent work has shown that CaSnRK2.4-mediated phosphorylation of CaNAC035 regulates abscisic acid synthesis in pepper under cold stress, linking the ABA hormone pathway directly to cold acclimation. The bHLH transcription factor CabHLH035 promotes cold resistance and reactive oxygen species homeostasis, while the NAC factor CaNAC064 has been identified as a cold tolerance regulator, and CaMYB80 enhances cold tolerance by directly targeting CaPOA1. Newer discoveries continue to expand the toolkit: CaPDX1, a novel protein that positively regulates cold tolerance through interaction with CaSnRK2.4, and CaDoF10, a DNA-binding-with-one-finger transcription factor recently shown to act as a positive regulator of cold stress tolerance. CBL-interacting protein kinase CaCIPK13 reinforces defense mechanisms against cold, and the dehydrin CaDHN3 contributes to membrane stabilization, while CaPIF8 links light and cold signaling through phytochrome-interacting factors.

Beyond transcription factors, the review emphasizes metabolic reprogramming as a critical dimension of cold adaptation. Soluble sugars, glycine betaine, proline, and antioxidant flavonoids accumulate under chilling conditions to protect membranes and scavenge reactive oxygen species. Comparative transcriptomic and metabolomic analyses of cold-tolerant and cold-sensitive pepper species have pinpointed essential metabolic pathways that distinguish resilient genotypes from vulnerable ones. Melatonin application has been shown to bolster photosynthetic performance and redox homeostasis in cold-stressed pepper seedlings, and exogenous glycine betaine improves tolerance of combined low-temperature and low-light stress by enhancing antioxidant capacity. These findings suggest that editing genes governing compatible solute biosynthesis and flavonoid accumulation could complement transcription-factor engineering.

Hormonal crosstalk emerges as another central theme. Abscisic acid and low temperatures act synergistically to induce CBF/DREB1 expression in other species, and ABA core signaling components are active in pepper seed responses. The review situates cold responses within a broader web of phytohormone interactions involving jasmonic acid, cytokinins, and brassinosteroids, each modulating stress outcomes in tissue- and timing-specific ways. Circadian regulation adds yet another layer, since cold responses are gated by the clock, meaning that the same genetic intervention may yield different results depending on the time of day it is deployed, a consideration the authors argue should inform both experimental design and field deployment.

Accelerating the pipeline from discovery to delivery, the review proposes integrating transcriptomics, proteomics, metabolomics, high-throughput phenomics, and speed breeding to compress the identification, validation, and deployment of superior alleles into a fraction of the traditional timeline. High-throughput phenomics allows researchers to quantify chilling injury, membrane leakage, chlorophyll fluorescence, and recovery kinetics across thousands of seedlings, while speed breeding shortens generation cycles so that edited lines can be advanced and field-tested rapidly. Epigenetic memory and systemic priming, through which plants retain a trained state after mild stress exposure, offer an additional lever: chromatin-level modifications could potentially be exploited or engineered to keep cold-response genes in a poised, readily activated configuration.

The practical stakes are considerable. Cold snaps damage seedlings in open fields and greenhouses alike, and postharvest chilling injury degrades fruit quality during cold storage, imposing losses across the entire supply chain. As climate volatility increases, the window of safe cultivation for a crop with such narrow thermal tolerance is shrinking in key production regions. By connecting functional genomics with precision genome engineering, the authors contend, pepper breeders can move beyond the incremental gains of conventional crossing and build cultivars with fundamentally rewired stress responses. The review’s roadmap, spanning DREB/CBF pathway engineering, multiplex editing of regulatory networks, negative-regulator disruption, and omics-guided allele deployment, positions Capsicum annuum as a test case for how Precision Breeding 2.0 could reshape the resilience of horticultural crops more broadly, ensuring that one of humanity’s favorite spices keeps thriving in a colder, less predictable world.

Subject of Research: Functional genomics and precision genome-editing strategies for engineering cold stress resilience in Capsicum annuum

Article Title: Engineering cold stress resilience in capsicum annuum through functional genomics and precision breeding

Article References: Ullah, I., Ahmad, N., Bhat, A. H., Hussain, A., Wei, F., & Hongzhi, W. (2026). Engineering cold stress resilience in capsicum annuum through functional genomics and precision breeding. Plant Cell Reports, 45(10), Article 288. https://doi.org/10.1007/s00299-026-03965-9

Image Credits: AI Generated

DOI: 10.1007/s00299-026-03965-9

Keywords: Capsicum annuum, cold stress, chilling tolerance, CRISPR/Cas, Precision Breeding 2.0, DREB/CBF pathway, multi-omics, transcriptional regulation, abscisic acid signaling, climate resilience, plant biotechnology, genome editing

Long non-coding RNAs are RNA transcripts longer than about 200 nucleotides that do not encode proteins. Long dismissed as transcriptional noise, they are now recognized as versatile regulators that can modulate chromatin, stabilize or destabilize messenger RNAs, and—critically—serve as competing endogenous RNAs, or ceRNAs, that sponge up microRNAs and thereby protect the genes those microRNAs would otherwise silence. In plants, individual lncRNAs have been linked to drought tolerance, cold acclimation, and pathogen defense, but the field has lacked a systematic answer to a fundamental question: which lncRNAs integrate several stress signals at once, and do they actually do anything? The new study set out to answer both parts.

The computational core of the work is ambitious in scale. Rather than generating new sequencing data, the team mined 447 publicly available RNA-seq datasets from Arabidopsis samples treated with abscisic acid, subjected to drought, or exposed to methyl jasmonate, a volatile derivative of jasmonic acid that the plant deploys when attacked by herbivores and necrotrophic pathogens. Because these datasets came from different laboratories and experimental designs, the researchers applied batch-effect correction using ComBat-seq before reconstructing transcriptomes with StringTie, aligning reads with HISAT2, and systematically filtering candidate transcripts to remove anything with protein-coding potential, as assessed by tools including PLEK, CPAT, and the machine-learning classifier LncDC. The result was a catalogue of 4,176 lncRNAs responsive to abscisic acid, 4,890 to methyl jasmonate, and 4,190 to drought. Strikingly, 54.33 percent of these transcripts had never been annotated before, underscoring how much of the plant transcriptome remains uncharted.

From this raw catalogue, differential expression analysis identified 2,318 abscisic acid-responsive, 2,603 jasmonate-responsive, and 1,788 drought-responsive lncRNAs. The team then intersected the lncRNA loci across all three conditions, a deliberately stringent procedure designed to isolate transcripts whose genomic positions were recovered under every treatment. After filtering, 287 high-confidence multi-stress-responsive lncRNAs emerged—the study’s headline number. Functional enrichment analysis of the protein-coding genes located near these transcripts in the genome, so-called cis-neighboring genes, revealed that the lncRNAs cluster around genes involved in pathogen defense, phytohormone signaling, and abiotic stress responses. In other words, the lncRNAs appear to be embedded in precisely the genomic neighborhoods where a plant would need rapid regulatory control when multiple threats coincide.

To understand how these transcripts might exert their influence, the researchers constructed competing endogenous RNA networks. Using miRBase and plant microRNA databases alongside the PsRobot prediction tool, they identified 232 endogenous target mimics—lncRNAs capable of binding and sequestering specific microRNAs—interacting with 118 distinct microRNAs. The messenger RNA targets of those microRNAs were themselves enriched in hormone signaling, stress response, and core metabolic pathways. This architecture is the classic signature of ceRNA regulation: an lncRNA rises in response to stress, absorbs the microRNA that normally restrains a defensive gene, and the defensive gene’s expression consequently climbs. Under this model, mslncRNAs function not as passive byproducts of stress but as molecular nodes—relay points through which the abscisic acid, drought, and jasmonate pathways can communicate with one another.

Computational predictions, however, are only hypotheses until they survive contact with living plants. The team selected two candidates, mslncRNA-84 and mslncRNA-189, for experimental validation. Quantitative reverse-transcription PCR confirmed that both transcripts were induced by abscisic acid, drought, and methyl jasmonate, matching the in silico expression predictions with gratifying fidelity. The researchers then took a decisive step that many lncRNA studies omit: they obtained T-DNA insertion lines in which the genes encoding these transcripts are disrupted, allowing direct functional tests rather than correlation-based inference.

The mutant assays spanned the full breadth of the three stress pathways. In germination assays, seeds carrying disruptions in the candidate lncRNAs displayed altered sensitivity to abscisic acid, a hormone that normally arrests germination to prevent seedlings from emerging into dry soil. In jasmonate-dependent growth inhibition assays, which measure the root-growth restraint characteristic of jasmonate signaling, the mutants again behaved differently from wild type, implicating the lncRNAs in jasmonate responsiveness. Biotic stress experiments using the bacterial pathogen Pseudomonas syringae pv. tomato DC3000—a workhorse of plant immunity research—included diaminobenzidine staining to visualize hydrogen peroxide accumulation, trypan blue staining to detect cell death, and colony-forming unit counts to quantify bacterial growth. Drought survival assays completed the picture, testing whether the lncRNAs contribute to the plant’s capacity to withstand water deprivation. Collectively, these results support the conclusion that mslncRNA-84 and mslncRNA-189 are genuine candidate regulators associated with phytohormone signaling, defense responses, and drought adaptation.

The significance of the work extends well beyond Arabidopsis. As climate change intensifies, crops increasingly face combinations of stresses—heat plus drought, drought plus pathogen pressure—rather than single insults, and research has shown that plant responses to combined stresses are not simple sums of the individual responses. Hormone crosstalk lies at the heart of this complexity: abscisic acid governs stomatal closure and dehydration tolerance, while jasmonates orchestrate wound and pathogen defense, and the two pathways engage in reciprocal regulation that determines whether a plant prioritizes growth, defense, or survival. If lncRNAs such as mslncRNA-84 and mslncRNA-189 help arbitrate that arbitration itself, they represent attractive targets for engineering crops that maintain resilience without sacrificing yield. Previous work on individual lncRNAs—for example, DANA1, which promotes drought tolerance in Arabidopsis through histone deacetylation, or ARTA, which controls abscisic acid responses via nuclear trafficking of the transcription factor MYB7—demonstrated that manipulating single lncRNAs can have meaningful physiological consequences. The new study supplies a shortlist of 287 additional candidates, many of them entirely novel, for that kind of mechanistic dissection.

The methodological approach also offers a template for other systems. By leveraging hundreds of existing public datasets rather than generating new ones, the study shows how the ever-growing repositories of plant RNA-seq data can be repurposed for discovery, provided researchers carefully control for batch effects and apply rigorous coding-potential filtering. The strategy of intersecting genomic loci across treatments to define a high-confidence core set is conservative, which means the 287 mslncRNAs are likely the tip of the iceberg; transcripts responsive to only two of the three stresses, or those detected at lower abundance, were excluded. The authors’ ceRNA network analysis likewise provides a mechanistic framework that can be tested in other species where drought and jasmonate responses intersect, from staple cereals to horticultural crops.

Important questions remain. T-DNA insertion lines can have background mutations, and the precise molecular mechanisms by which mslncRNA-84 and mslncRNA-189 act—whether through microRNA sponging, chromatin modification, or direct interaction with other RNAs—will require targeted experiments such as microRNA co-immunoprecipitation, transcript localization studies, and rescue assays. The generalizability of the ceRNA model in plants, where small RNA targeting tends to be more direct than in animals, is still debated. Nevertheless, by combining genome-wide prediction, network modeling, and bona fide genetic validation in a single study, the Xi’an team has moved the field a substantial step closer to understanding how plants compute decisions at the intersection of drought and defense. For a world confronting increasingly unpredictable growing conditions, that computational and molecular map of 287 regulatory RNAs may prove to be one of the more consequential datasets in plant stress biology.

The PYL gene family encodes proteins that interact with abscisic acid (ABA), a plant hormone integral to stress response mechanisms. ABA helps plants navigate through periods of water scarcity by inducing stomatal closure, thus reducing water loss during drought conditions. The researchers meticulously analyzed the entire genome of Solanum melongena, identifying multiple PYL genes and characterizing their expression patterns under stress conditions. This comprehensive approach provides insights into how each member of the PYL family contributes to the overall stress resilience of eggplants and possibly other related species.

Utilizing cutting-edge genomic techniques, the research team conducted a detailed comparative analysis of the PYL gene family across different plant species. By aligning the sequences of PYL genes from Solanum melongena with those from other economically important crops and model organisms, the researchers were able to detect evolutionary conservation and divergence. This comparative approach not only reveals valuable insights into the evolutionary history of the PYL gene family but also highlights potential candidates for functional studies aimed at improving stress tolerance in crops.

The study found that PYL genes in Solanum melongena exhibit dynamic expression changes in response to abiotic stresses. For instance, certain PYL genes were significantly upregulated under conditions of salt and drought stress, indicating their pivotal role in the plant’s adaptive response. The differential expression of these genes suggests that specific members of the PYL family may have evolved specialized functions tailored to combat particular environmental challenges. This highlights the importance of targeted research aimed at dissecting the role of individual PYL genes in plant resilience.

To further validate the functional significance of the identified PYL genes, the researchers employed advanced gene-editing technologies, such as CRISPR/Cas9. By knocking out specific PYL genes, they were able to observe the resulting phenotypic changes in Solanum melongena plants under stress conditions. This experimental approach not only confirms the functional relevance of the PYL genes but also provides a powerful tool for breeders seeking to enhance stress resistance in agricultural crops.

The implications of this research extend beyond the realm of basic science; they hold significant practical value for agriculture. With global climate challenges worsening, food security remains a pressing concern. As environmental stresses increasingly affect crop yield, understanding the genetic basis of stress tolerance becomes increasingly crucial. The insights gained from the study of the PYL gene family in Solanum melongena may guide future breeding programs aimed at developing crop varieties that are better equipped to withstand unfavorable conditions.

Moreover, the successful identification and characterisation of the PYL gene family in eggplant may have broader implications for other Solanaceae plants, a family that includes important crops such as tomato and potato. By establishing a model for PYL gene function in Solanum melongena, the research team lays a foundation for cross-species applications. Collaborative efforts across research institutions could expedite the application of these findings to other important crops, thus contributing to global agricultural sustainability.

The study also draws attention to the intricacies of plant stress signaling pathways. Understanding how plants perceive and respond to environmental cues is fundamental for creating resilient food systems. The findings on PYL gene expression dynamics provide a glimpse into the complex regulatory networks governing plant responses to abiotic stress. Such insights are essential for the development of molecular markers that can be used in selective breeding programs, ultimately leading to more resilient crop varieties.

In the face of ongoing climate change, the research conducted by Gong et al. significantly contributes to the body of knowledge required to tackle future agricultural challenges. As the frequency and intensity of environmental stresses increase, the demand for crops with enhanced resilience will only grow. Research such as this not only provides immediate benefits for eggplant cultivation but also serves as a reference point for future genomic and genetic studies aimed at improving other significant crops.

The comprehensive genome analysis of PYL genes in Solanum melongena represents an exciting advancement in plant molecular biology. As the field continues to evolve, researchers will undoubtedly employ these insights to explore new avenues for crop improvement. The innovative combination of genomic analysis and gene-editing technologies used in this study exemplifies the potential of modern science to drive sustainable agricultural practices.

The research is also a timely reminder of the importance of interdisciplinary approaches in tackling complex biological questions. By integrating genomics, molecular biology, and field trials, researchers are better equipped to address the multifaceted challenges posed by climate change. This collaborative spirit is essential for fostering innovation in agricultural research as well as for enhancing food security on a global scale.

Looking ahead, the collaborative spirit within the scientific community will be critical in translating research findings into practical applications. Continued investment in agricultural research, coupled with strong partnerships between academia and industry, will be essential for leveraging recent findings on the PYL gene family. As we edge closer to implementing these insights in real-world settings, it is imperative that we maintain our focus on sustainable agricultural practices that can withstand the tests of time and environmental pressures.

In conclusion, the work by Gong et al. lays foundational insights into the role of the PYL gene family in Solanum melongena, opening doors for future research that promises to enhance crop resilience to environmental stresses. By fortifying our understanding of plant genetics, this research holds the potential to usher in a new era of agricultural innovation, leading to improved food security and sustainable practices in the face of imminent global challenges.

Subject of Research: PYL gene family in Solanum melongena in response to abiotic stresses.

Article Title: Genome-wide identification and expression analysis of the PYL gene family in response to salt, drought and cold stresses in Solanum melongena L.

Article References:

Gong, F., Lan, Y., Zhang, T. et al. Genome-wide identification and expression analysis of the PYL gene family in response to salt, drought and cold stresses in Solanum melongena L.. BMC Genomics 26, 1007 (2025). https://doi.org/10.1186/s12864-025-12249-7

Image Credits: AI Generated

DOI: https://doi.org/10.1186/s12864-025-12249-7

Keywords: PYL gene family, Solanum melongena, abiotic stress, gene editing, crop resilience, plant biology.