Yarrowia lipolytica is a versatile cell factory widely used in bioprocesses for producing lipids, organic acids, and other high-value compounds. Historically, its genetic engineering was constrained by low homologous recombination (HR) efficiency and the predominance of non-homologous end joining (NHEJ), limiting strain development and metabolic pathway optimization. The advent of CRISPR-Cas technologies has revolutionized genome editing in Y. lipolytica, enabling precise, efficient, and multiplexed modifications. Innovations such as pCAS1yl and pCRISPRyl plasmids, along with genomic Cas9 integration, have enhanced targeted editing efficiency. CRISPR applications now extend to metabolic engineering for lipids, itaconic acid, erythritol, and other compounds. Beyond canonical Cas9, alternative systems, including CRISPRa, Cas12a, base editors, and sgRNA libraries, provide increased flexibility and functional diversity. Central to these approaches is the rational design of guide RNAs (gRNAs), supported by bioinformatics platforms such as CHOPCHOP v3, CRISPOR, CCTop, and Cas-OFFinder, which assist in target site selection, off-target prediction, and editing optimization. This review summarizes the main CRISPR/Cas9 applications in Y. lipolytica, highlighting key engineered strains and emphasizing the critical role of bioinformatics in improving editing strategies. We also propose a pipeline for systematic gRNA design based on published evidence and discuss future perspectives, including the integration of machine learning, artificial intelligence, and emerging CRISPR variants to further advance yeast metabolic engineering.

Leaf mesophyll traits influence the architecture and mechanical properties of plant tissue and are often assumed to shape plant–herbivore interactions. For example, homobaric leaves have a relatively continuous mesophyll, whereas heterobaric leaves possess vascular bundle sheath extensions (BSEs) that partition the mesophyll into discrete compartments, thereby increasing structural heterogeneity. Based on this contrast, we hypothesized that heterobaric leaves could impose a mechanical barrier to leafminer caterpillars, potentially raising foraging costs and causing immediate, effort-related changes in chewing behavior. To test this, we compared the feeding behavior of tomato pinworm caterpillars, Phthorimaea absoluta (Lepidoptera: Gelechiidae), using Solanum lycopersicum wild-type (WT) tomato and isogenic lines harboring the obscuravenosa (obv) mutation. These tomato isolines differ in mesophyll architecture by the presence (heterobaric, WT) or absence (homobaric, obv) of vascular BSEs. Larval feeding activity was recorded using synchronized high-resolution video and laser Doppler vibrometry. The resulting vibratory output was used as a proxy for mandibular closure events, allowing quantification of fine-scale temporal and spectral features of feeding activity. Contrary to our predictions, mesophyll architecture did not appear to influence larval chewing motor patterns, as no differences were detected in event duration, dominant frequency, amplitude, or mandibular rhythm. These results suggest that larval chewing motor control is remarkably robust and largely insensitive to this specific type of substrate variation, possibly reflecting biomechanical or behavioral adaptations in tomato pinworm that maintain feeding efficiency across structurally heterogeneous tissues. From an applied perspective, the lack of an immediate biomechanical cost indicates that management strategies that rely solely on modifying mesophyll traits are unlikely, on their own, to deter this specialized pest. These points highlight the need to integrate anatomical traits with other plant defense mechanisms for effective pest management.

The Capsicum genus shows remarkable phenotypic diversity, making it an excellent system to study non-climacteric fruit ripening. Unlike climacteric model species, such as tomato (Solanum lycopersicum), the regulatory networks linking transcriptome and metabolome to fruit quality traits remain poorly understood in non-climacteric crop species. To address this gap, we selected four contrasting C. chinense accessions and performed integrated transcriptomic and metabolomic analyses to investigate the regulation of total soluble solids (TSS) accumulation. We profiled 16 922 genes and 63 metabolic features across two fruit developmental stages (immature and mature), including sugars, organic acids, capsaicinoids, and other secondary metabolites. We identified more than 3800 differentially expressed genes and detected strong correlations between gene expression and metabolite levels. Some metabolites, including chlorophylls, carotenoids, and starch, showed consistent temporal trends across genotypes, while others showed genotype-dependent variation. Our results demonstrate that pepper fruit ripening involves a transcriptional shift toward soluble sugar accumulation, characterized by upregulation of starch-hydrolyzing enzymes (CaAMY1/2, CaBAM1), invertases (CaINV1, CaCWINV3), sucrose synthase (CaSUS2), and the sugar transporter CaSWEET10, alongside downregulation of the starch biosynthetic gene CaSBE1. Among these, CaSUS2, CaSWEET10, and CaBAM1 emerged as key candidate regulators. These results suggest that coordinated starch degradation and sucrose transport primarily drive TSS increase, while secondary metabolism undergoes independent shifts that characterize other aspects of the ripening process.

ABSTRACT Climate change affects the productive performance of tomato plants. Limited information is available on the use of dwarfing genes in tomato breeding to address these challenges. This study evaluated the photosynthetic efficiency and agronomic performance of tomato plants with different genetic backgrounds (dwarf, wild, and domesticated). The study was conducted using 25 genotypes arranged in a randomized block design, with three replicates and six plants per plot. Hybrids showed higher acylsugar content compared to the cultivar Santa Clara, except for hybrids 1, 2, 6, and 8. According to the dendrogram, Group III comprised hybrids 1, 2, 3, 5, 6, 7, 8, 9, 10, 13, 14, and 15, which exerted a strong influence on yield and fruit number per plant. Meanwhile, according to the Kohonen Self-Organizing Map, Group V included hybrids 11 and 12, which showed genetic similarity, highlighting their close relationship in agronomic characteristics. Hybrid 12 stood out for variables related to yield, average fruit weight, and number of fruits per plant demonstrating photosynthetic efficiency and agronomic potential. The dwarf donor parent, UFU MC TOM 1, showed photosynthetic efficiency similar to that of the wild accession, Solanum pennellii. Therefore, it can be concluded that the use of dwarf male parents to develop hybrids with standard architecture provides advances in tomato cultivation.

Anthocyanins are specialized plant metabolites with significant dietary value due to their anti-inflammatory properties. Research indicates that dietary intake of these phenolic compounds contributes to preventing various chronic diseases. As the most consumed vegetable worldwide, tomato (Solanum lycopersicum) is an excellent candidate for anthocyanin-enrichment strategies. In tomato, the activation of anthocyanin biosynthesis is light-dependent, but this mechanism has yet to be entirely characterized. We investigated the role of light in anthocyanin biosynthesis in purple tomato fruits generated by combining the Anthocyanin fruit (Aft), atroviolacea (atv), and high-pigment 2 (hp2) mutations into cv. Micro-Tom (MT). MT-Aft/atv/hp2 starts accumulating anthocyanins early during fruit development, but this accumulation is restricted to the peel (exocarp and epicarp). By manipulating light incidence in different fruit tissues, we determined that the absence of anthocyanin accumulation in the flesh results from the sun-blocking effect of the cyanic epicarp on the flesh (mesocarp), thus preventing light from penetrating deeper into the fruits. Comparative transcriptional analyses of the fruit peel and flesh indicated that the bHLH transcription factor SlAN1 (Solyc09g065100) may be the limiting factor for light-dependent anthocyanin accumulation in both tissues. This research enhances our comprehension of the genetic and environmental regulation of anthocyanin accumulation in fruit tissues, offering valuable insights into plant breeding for human nutrition.

Abstract The sequencing of the Capsicum genus pangenome has stimulated interest in biotechnological strategies aimed at modulating pungency levels. While promising, such approaches require a comprehensive understanding of the ecological and physiological roles of capsaicinoids—the alkaloids responsible for pepper pungency. Although traditionally considered a defense against mammalian seed predators, accumulating evidence indicates that capsaicinoid biosynthesis is integrated into broader stress-response networks. Capsaicinoid production is influenced by genetic, ecological, and environmental factors, including light intensity, temperature, drought, and mineral nutrition, which dynamically regulate the biosynthetic pathway. Beyond defense, capsaicinoids perform internal physiological functions such as antioxidant protection, redox buffering, and nitrogen assimilation, framing pungency as a component of a coordinated metabolic strategy rather than a singular defensive trait. By connecting ecological pressures with molecular regulation, the dual ecological and physiological roles of capsaicinoid biosynthesis are emphasized, while knowledge gaps remain, particularly regarding non-Directed Deterrence Hypothesis (DDH) functions and tissue-specific expression of capsaicinoid genes. This integrated perspective provides a foundation for biotechnological interventions that modulate pungency without compromising plant resilience or metabolic homeostasis.

Anthocyanins are widespread specialized metabolites that provide pigmentation and antioxidant capacity, contributing to pollinator and seed-disperser attraction and to plant resistance to diverse environmental stresses. In human diets, anthocyanins are valued for their antioxidant and health-promoting properties. The biosynthetic pathway of anthocyanins is relatively conserved across plant species and is controlled by structural genes that encode the enzymes of the pathway along with regulatory genes, particularly transcription factors. This network integrates developmental and environmental signals, with light serving as a dominant cue: anthocyanins typically accumulate in light-exposed tissues and are repressed in darkness. A key node in this light-dependent switch is CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), an E3 ubiquitin ligase that, in the dark, promotes polyubiquitination and proteasome-mediated turnover of positive regulators of anthocyanin production. Although ELONGATED HYPOCOTYL 5 (HY5) is a canonical COP1 target and major activator of anthocyanin biosynthesis, COP1 control of this pathway extends well beyond HY5. Evidence from Arabidopsis and multiple horticultural crops, including apple, pear, eggplant, and tomato, indicates that COP1 also regulates anthocyanin accumulation through interactions with additional transcription factors and regulatory modules. Here, we synthesize recent advances in COP1-centered regulation of anthocyanin biosynthesis, with an emphasis on post-translational mechanisms and COP1 targets beyond HY5. We also discuss emerging opportunities to leverage this regulatory axis for nutritional improvement in horticultural species.

Gibberellins promote differentiated root and shoot responses in growth, morphology, and carbon allocation. Gibberellins (GAs) are plant hormones that are produced in young tissues and organs, acting locally in growing shoots and roots or being transported to other organs. The role of GAs in root development was first investigated decades ago using plants severely deficient in GA biosynthesis. However, only few studies have examined root metabolism in plants with reduced GA levels and evaluated its association with root growth and morphology. Furthermore, the signaling between the root and shoot systems plays a key role in coordinating plant growth and development. Therefore, this study aimed to assess the impact of endogenous alterations in GA levels on tomato mutants exhibiting mild (gibberellin deficient-3, gib3), intermediate (gib2), and high (gib1) GA deficiency on root and shoot growth, morphology, respiratory metabolism, and labeled carbon allocation. The low GA content exerted an effect on shoot growth and morphology, which, surprisingly, led to minor changes in the mutant roots. The gib2 and gib1 mutants exhibited higher proportions of thick roots than the wild-type and gib3, but the growth of roots with smaller diameters was most pronounced in these genotypes. The carbohydrate oxidation was influenced by a reduction in GA biosynthesis within mutant leaves and roots. In addition, the differential sensitivity to GA by each organ likely contributed to variations in sugar accumulation. Together, these results indicate that shoot tissues exhibit a distinct response compared to root tissues, suggesting a decoupling of root growth and carbon allocation from shoot growth and development in GA-deficient plants. This observation points to a key role for GA in orchestrating the growth of both shoots and roots.

Model organisms have been instrumental in advancing discoveries in plant biology. Tomato (Solanum lycopersicum) is distinguished as a prominent model system due to its well-characterized genetics and economic significance as a crop. Micro-Tom (MT), an ornamental dwarf tomato variety, was adopted by the tomato research community as a model plant due to its short stature, fast life cycle, ease of genetic transformation, and ample genomic resources. Over the last 30 years, the use of MT has illuminated various facets of plant development, including the control of growth habit, glandular trichomes, leaf anatomy, and the formation of arbuscular mycorrhizal symbioses. We briefly summarize these contributions and point to further potential advances in the future.

Leaf anatomical traits can play a pivotal role in mediating plant resistance to herbivory and shaping pest dynamics in agroecosystems. Understanding how leaf anatomical traits shape insect–plant interactions is essential to elucidate these relationships and to develop more sustainable pest management strategies. In this context, we investigated an underexplored leaf structural feature—the vascular bundle sheath extension (BSE). Using tomato (Solanum lycopersicum L.) isogenic lines harboring the obscuravenosa (obv) mutation, we assessed how the presence (+) or absence (−) of BSEs impacts interactions with the tomato pinworm, Phthorimaea (= Tuta) absoluta (Meyrick) (Lepidoptera: Gelechiidae), a major invasive pest of the tomato. The absence of BSEs did not influence oviposition preference or egg incubation time, but it significantly reduced larval leaf consumption and prolonged larval development, without affecting survival. Pupal development was also altered in BSE- plants, resulting in lower body mass and delayed adult emergence, while sex ratio remained unaffected. Phytohormonal profiling revealed differences between BSE+ and BSE- plants, particularly in jasmonate levels, suggesting that BSEs may influence plant defense signaling pathways. Together, these findings highlight the potential of BSEs as morphophysiological modulators of insect–plant interactions, emphasizing that internal leaf anatomical traits, alongside chemical defenses, contribute significantly to herbivory resistance.

Water supply constraints limit crop yield across seasons and locations, restricting food production under diverse climate scenarios. Irrigation schedules that align with plant water demand at specific times of the day have been proposed to overcome limitations in the water supply. Watering crops in the morning has been associated with reductions in productivity, although the mechanisms underlying this phenomenon remain poorly understood. Here, we demonstrate that watering tomato (Solanum lycopersicum) at different times of the day alters the transcriptional patterns of genes controlling flowering induction. Dawn watering (DAW) triggered a strong repression of the single flower truss (SFT) gene, leading to metabolite accumulation and delayed development. Dusk-watered plants showed increased fruit production compared to DAW-treated plants. Our findings highlight how metabolism and development in tomato are remodeled by the timing of watering, suggesting strategies to enhance tomato water-use efficiency by incorporating time-specific watering practices in agriculture.

The brunt of climate change in the coming decades will be felt most acutely in the Global South, comprising Asia, Africa, and Latin America, where nearly two-thirds of the world's crop yield by volume is produced annually (Zsögön et al., 2022). Brazil, for instance, is the world's largest producer of soybeans, sugarcane, coffee, and orange juice (FAO, 2022). Training the next generation of crop physiologists is therefore essential to address these pressing challenges. At the Graduate Program in Plant Physiology at the Federal University of Viçosa, in Minas Gerais, Brazil, we are strongly committed to this mission. In line with this commitment, from 7 to 11 October 2024 we hosted the 19th Brazilian Congress of Plant Physiology (https://cbfv.sbfv.org.br/). This longstanding event brings together domestic and international students, researchers, and stakeholders from both academia and industry. This Special Issue features a diverse set of contributions, some of which were presented during the event, which was generously sponsored by the Journal of Experimental Botany (JXB).

Temperature may affect ethylene production in plant tissues. Due to temperature variations in the soil depth profile, planting depth can potentially affect ethylene production at the seed germination phase and postgermination growth phase. We hypothesized that in the field, altered ethylene biosynthesis in response to planting depth affect peanut growth and development. Ethylene production in peanut seedlings of the cultivars 'Tatu-53' and 'IAPAR 25' showed a positive correlation with soil temperature at different planting depth. In response to shallow (1.0-2.5 cm) planting depth, ethylene biosynthesis is increased, leading to low shoot/root ratio, whereas in in deep (10-15 cm) planting treatments, ethylene production is repressed, resulting in high shoot/root ratio. In both cases, peanut yield is lower than in the medium depth (5 cm) sowing treatment. These results indicate that ethylene alters shoot/root ratio in early postembryonic development in both shallow and depth planting, leading to negative effects in long-term adult plant development. Ethylene production in response to the 5-cm depth allows seedlings to balance shoot and root growth, avoiding the detrimental effects of planting depth response on yield. Moreover, sowing at 5 cm depth raises the concentration of Ca, S, and Zn in the seeds of the next generation. Together, these findings indicate that planting depth couples soil temperature with seedling ethylene production, and this plays a significant role in priming the future development of the peanut plant and conditioning its yield.

>Extreme temperatures have become an unavoidable reality across vast regions of the world. Heat waves can cause severe crop damage, intensify drought conditions, and severely impact agriculture, disrupting food systems and exacerbating food insecurity(Zs?g?n et al., 2022). Heat stress adversely affects reproductive development in plants, leading to grain or ovary abortion and causing significant yield losses(Li et al., 2012).

In the face of global climate change, several unprecedented challenges are currently faced by agriculture. To achieve food security, understanding the developmental program from seed formation and germination, through early seedling establishment until plant growth and crop yield, is required to increase agricultural production and ensure sustainability. Natural auxin, a heterogeneous group of aromatic carboxylic acids, is one of the most important plant hormones, mediating several endogenous developmental signals and exogenous environmental cues that profoundly affect virtually all plant growth and development processes. There must be a balance in endogenous auxin dynamics between synthesis, influx, efflux, degradation, receptor binding and downstream signaling to modulate plants responses. While the genes and biochemical reactions for endogenous auxin metabolism are well understood, the involvement of auxin in plant central metabolism (e.g. photosynthesis and respiration) remains poorly known. Nevertheless, it is already known that endogenous auxin acts as the main epigenetic regulator responsible for mesophyll cell expansion and thus, indirectly, for photosynthesis. Furthermore, endogenous auxin response factors have been identified that mediate sugar and starch metabolism, as well as abiotic stress tolerance, indicating that auxin should be further explored as a key molecule to improve plant performance under normal and stressful conditions in crops. Here, we summarize recent advances in dissecting auxin metabolism, their importance on central metabolism, and discuss the functions of endogenous auxin in the overall control of plant growth. We further provide an overview of the pivotal role of endogenous auxin and how mutations in different auxin signaling modulate photosynthetic and respiratory processes, which is likely crucial for coordinating cellular responses.

Abscisic acid (ABA) transport in plants is necessary to regulate developmental plasticity and responses to environmental signals. Plants use ABA exporter ATP-binding cassette G25 (ABCG25) to control ABA homeostasis. Three recent papers (Huang et al., Ying et al., and Xin et al.) have revealed the structure and transport mechanism of ABCG25.