Hormonal signaling shapes plant architecture and salt stress responses, but its effects on root architecture and ion accumulation remain unclear. Here, we conducted a detailed analysis of how individual hormone treatments affect root architecture and ion accumulation under salt stress in tomato. The study focused on three tomato accessions with varying responses to salt stress. Our findings revealed distinct, species-specific hormonal effects. Auxin, ethylene, and gibberellin promoted lateral root development, yet their impacts on ion accumulation, particularly in Na+/K+ ratio, varied considerably. To explore the molecular basis of these differences, we examined Arabidopsis mutants for ethylene- and auxin-related genes, revealing novel components of hormone signaling involved in the salt stress response. Further, analysis of tomato mutants with impaired ethylene perception demonstrated that the nr mutant exhibits increased root growth and a higher shoot Na+/K+ ratio, largely due to reduced K+ retention. Our integrated physiological and genetic analysis reveals species-specific hormonal strategies can boost crop performance under salt stress.

Salinity, projected to impact over 50% of arable land by 2050, threatens tomato-a crop of major agronomic and nutritional value. While salt stress effects on tomato shoot and fruit traits are well studied, the genetic basis of root development under salinity remains underexplored. Roots are the primary sensors of salt stress, making them central to plant adaptation. To uncover the genetic regulators of root system architecture (RSA) under salt, we analyzed a natural diversity panel consisting of 220 wild- and 25 cultivated-tomato varieties. We identified distinct RSA strategies, favouring either lateral root elongation or emergence. An F1 hybrid with superior root architecture under salt stress was used to generate an F2 population for Bulk Segregant Analysis (BSA), and a parallel GWAS was performed across the diversity panel. Integrating BSA and GWAS results yielded 22 candidate genes. RNA-seq analysis of contrasting accessions prioritised four candidates, including an l-ascorbate peroxidase involved in ROS homoeostasis. Further functional analysis revealed genotype-specific H₂O₂ dynamics, and exogenous ascorbate improved K⁺ retention under salt. Together, these results uncover a genetic link between lateral root development, ROS signalling, and ion homoeostasis under salinity, offering new targets for engineering salt-resilient tomato.

Plant responses to salt stress involve regulatory networks integrating ion transport, hormonal signaling, and root system architecture remodeling. A key adaptive mechanism is the regulation of sodium (Na⁺) transport by Class 1 HKT1 transporters, which compertamentalize Na⁺ in non-photosynthetic tissues. High HKT1 expression reduces Na+ accumulation in shoots, leading to increased salt tolerance, but simultaneously results in reduced lateral root development. In this study, we explored transcriptional responses that are altered by high HKT1 expression in root stelle in two Arabidopsis backgrounds, Col-0 and C24. We identified TMAC2, a negative ABA regulator, and TIP2:2, a tonoplast aquaporin, as key modulators of root development under salt stress. While TIP2:2 function was conserved, TMAC2 exhibited genotype-specific effects on ABA accumulation and HKT1-mediated salt sensitivity. Co-expression of TMAC2 and HKT1 in Col-0 upregulated ABI4 and ABI5, linking Na⁺ transport to ABA signaling. Our findings underscore genetic context in shaping salt responses and provide molecular targets for enhancing root plasticity under stress.

Heat stress poses a serious threat to plant survival and productivity, and has a direct influence on crop yield stability. Plants response to high temperature is tightly controlled by complex genetic networks. Plants can be acclimated through gradual pre-exposure to increasing temperatures and that in turn causes higher survival in subsequent and otherwise lethal heat stress conditions. To investigate the physiological and molecular processes underlying heat acclimation and recovery, we examined changes in Arabidopsis thaliana transcriptome throughout the acclimation and the subsequent heat shock treatment. Groups of differentially expressed genes and enriched biological pathways that constitute the heat transcriptional memory were identified. The function of flavonoids in plant heat stress were further explored experimentally. In addition, we observed altered stomata density and aperture responses in heat acclimated plants, and this might be partially controlled by AGAMOUS-LIKE16 ( AGL16 ) transcription factor and its negative regulator microRNA824 ( miR824 ).

Soil salinity is one of the major threats to agricultural productivity worldwide. Salt stress exposure alters root and shoots growth rates, thereby affecting overall plant performance. While past studies have extensively documented the effect of salt stress on root elongation and shoot development separately, here we take an innovative approach by examining the coordination of root and shoot growth under salt stress conditions. Utilizing a newly developed tool for quantifying the root:shoot ratio in agar-grown Arabidopsis seedlings, we found that salt stress results in a loss of coordination between root and shoot growth rates. We identify a specific gene cluster encoding domain-of-unknown-function 247 (DUF247), and characterize one of these genes as Salt Root:shoot Ratio Regulator Gene (SR3G). Further analysis elucidates the role of SR3G as a negative regulator of salt stress tolerance, revealing its function in regulating shoot growth, root suberization, and sodium accumulation. We further characterize that SR3G expression is modulated by WRKY75 transcription factor, known as a positive regulator of salt stress tolerance. Finally, we show that the salt stress sensitivity of wrky75 mutant is completely diminished when it is combined with sr3g mutation. Together, our results demonstrate that utilizing root:shoot ratio as an architectural feature leads to the discovery of a new stress resilience gene. The study’s innovative approach and findings not only contribute to our understanding of plant stress tolerance mechanisms but also open new avenues for genetic and agronomic strategies to enhance crop environmental resilience.

Plant responses to salt stress involve complex processes integrating short- and long-term adaptations, including changes in ion transport, systemic signaling, root architecture, and biomass distribution. A key adaptive mechanism involves the regulation of sodium (Na+) and potassium (K+) ion transport via Class 1 HKT1 transporters, which reduce Na+ accumulation in shoots, thereby enhancing salinity tolerance but at the expense of lateral root development. In this study, we identified differential roles of TMAC2 in modulating ABA accumulation and lateral root development under salt stress in two distinct Arabidopsis genotypes, Col-0 and C24. Overexpression of TMAC2 in the Col-0 background increased ABA accumulation, resulting in reduced lateral root development, suggesting a positive feedback loop involving HKT1, TMAC2, and ABA signaling. In contrast, TMAC2 overexpression in C24 reduced ABA accumulation in lines overexpressing HKT1, indicating genotype-specific differences in the TMAC2-HKT1 interaction. Additionally, we observed that the co-expression of TMAC2 and HKT1 in Col-0 induced ABI4 and ABI5 transcription factors, which are known to mediate salt sensitivity. These findings reveal a regulatory network where TMAC2 and HKT1 modulate salt stress responses through genotype-dependent feedback mechanisms. Our results highlight the complexity of root remodeling under salt stress and the crucial role of genetic background in shaping these adaptive responses. ### Competing Interest Statement The authors have declared no competing interest.

Tomatoes are crucial for global food security and agricultural economies. With over 50% of arable land projected to become saline by 2050, understanding tomato responses to saline environments is essential. Soil salinization, prevalent in arid regions, leads to salt stress. Roots are primary salinity sensors and integrate stress responses like nutrient deficiency. Understanding the molecular processes maintaining root growth is vital for crop resilience. While salt stress impacts on tomato seed germination, shoot growth, and fruit yield are documented, root development remains underexplored. Most studies have focused on a limited number of cultivars and their physiological responses, not the genetic basis of salt resilience. Wild tomato relatives, such as Solanum pimpinellifolium , offer traits that are beneficial for breeding resilient crops. However, few studies have examined the genetics of salinity tolerance in S. pimpinellifolium . This study characterizes salt stress-induced changes in root system architecture (RSA) using a natural diversity panel of 220 wild tomato accessions. We identified natural variation in lateral root development and several candidate loci through Genome-Wide Association Study (GWAS). Bulk segregant analysis (BSA) revealed 22 candidate genes overlapping with GWAS findings. Exploring root transcriptome reprogramming in two accessions with differing lateral root responses highlighted genotype-specific changes. Integrating GWAS, BSA, and RNA sequencing data identified four key genes underlying differential lateral root development under salt stress. These findings offer novel genetic targets for improving salt resilience in tomatoes, providing opportunities for future research and breeding programs to enhance crop sustainability and productivity. ### Competing Interest Statement The authors have declared no competing interest.

The word 'descriptive' in the reviewer's comment often forebodes manuscript rejection due to insufficient mechanistic insights provided. Mechanistic studies are indispensable for understanding cause and effect within the studied biological systems. Nevertheless, descriptive research is foundational for the development of new hypotheses that can lead our science in new and exciting directions. Although big data sets are often generated with a specific question in mind, they can be reused in multiple fashions, by performing alternative data analysis, to the benefit of scientific progress. Reference genomes (Sun et al., 2022), pangenomes (Bayer et al., 2020), transcriptional atlas (Papatheodorou et al., 2019), metabolite atlas (Kranawetter et al., 2021) and interactomes (Cao et al., 2019; Osborne et al., 2023) have been serving for a long time as the footing for developing the mechanistic hypotheses to be tested. For this footing to be reliable, there are certain conditions to be met, as flawed input oftentimes leads to nonsensical output (often referred to as 'garbage in, garbage out'). Thus, for the descriptive data set to be of high value to the community, it requires solid experimental design, high data quality and well-documented annotation of scripts and pipelines used for data processing. Data reusability guidelines have been developed over the last two decades, resulting in a wide array of community standards for FAIR (Findable, Accessible, Interoperable and Reproducible) deposition of various data sets (Considine & Salek, 2019; Ćwiek-Kupczyńska et al., 2016; Wilkinson et al., 2016). Data Insights is a new category of manuscripts developed over the past year within the Plant, Cell and Environment, to welcome descriptive research papers that focus on large and exciting datasets that can be explored for hypothesis development and data-driven discoveries. To exemplify our expectation for this category regarding the question addressed, experimental design, data analysis and presentation, I highlight below three papers that we have accepted in the Data Insights category in 2023. The manuscript by King et al. (2023) sets out to explore the differences in microbial communities between various functional units of fine roots, namely, absorptive and transportive fine roots. The major motivation for this research was to provide proof of concept that limiting the analysis to the macroscopic plant boundaries, such as root diameter, is confounding our understanding of discrete processes and communities taking place in the rhizosphere. The authors indeed found that functional characteristics of fine roots were important and second only to the tree species samples. The combination of microbial community sequencing within this paper, combined with the metabolome data, provides insight into give-and-take dynamics that take place within the rhizosphere and highlights the role of sugar transport, urea and peptidases. This data set not only teaches us to dissect our samples based on function rather than size but also can be further mined for species-specific differences in transportive and absorptive microbial communities, or looking for your favourite microbe within this experiment. The study by Yamashita et al. (2023) focuses on exploring physiological and transcriptional responses to light across 14 genotypes of lettuce. The team explored transcriptional and phytochemical changes in response to various light regimes, thereby characterizing G × E interactions, and used transcriptional modelling to identify putative mechanisms that underlie the accumulation of phytochemicals of interest. While the team's goal was to identify the varieties of lettuce that are suitable for indoor agriculture, with a specific focus on light-regulated production of flavonoids, the data set can be further explored for other genes showing G × E interactions, or conserved transcriptional responses to light. Moreover, the transcriptome-based modelling approach used in this study is well documented and can serve as an educational and inspirational resource for future transcriptome explorations in highly dimensional data sets. Genomics is an integral part of the resources that are fundamental for scientific progress; however, the gaps in phylogenetics are acting as inhibitors to exploring various evolutionary hypotheses. Guerreiro et al. (2023) generated missing genomes for 19 closely related Brassicaceae species. The authors discovered that C3–C4 intermediate photosynthesis evolved five independent times during the evolution of studied taxa. The generated high-quality genomes of previously unsequenced Brassicaceae species serve as important resources for future forward genetic studies and expand the opportunities for evolutionary hypotheses within the Brassicaceae. Moreover, the identification and grouping of orthologs within Brassicaceae will further facilitate the genomic comparisons between gene families. The highlighted papers show only a fraction of insights generated through Data Insights over the past year. The studies published in this category vary in their topic, experimental approaches and analysis methods. We encourage the authors to combine information from different data types and to extract solid scientific insight while avoiding the discussion of hypothetical gene functions. Our main mission is that the shared data sets are a valuable resource for the community. The review process therefore focuses on the quality of the experimental design as well as data analysis, presentation and accessibility (see Guidelines for Authors). I highly encourage readers to explore Data Insights, and authors to consider submitting their descriptive research to PC&E. My hope for the future is that Data Insights will continue to provide exciting new data sets in an accessible format for PC&E readership to mine, explore and inspire.

Soil salinity is a major environmental stressor affecting agricultural productivity worldwide. Understanding plant responses to salt stress is crucial for developing resilient crop varieties. Wild relatives of cultivated crops, such as wild tomato, Solanum pimpinellifolium, can serve as a useful resource to further expand the resilience potential of the cultivated germplasm, S. lycopersicum. In this study, we employed high-throughput phenotyping in the greenhouse and field conditions to explore salt stress responses of a S. pimpinellifolium diversity panel. Our study revealed extensive phenotypic variations in response to salt stress, with traits such as transpiration rate, shoot mass, and ion accumulation showing significant correlations with plant performance. We found that while transpiration was a key determinant of plant performance in the greenhouse, shoot mass strongly correlated with yield under field conditions. Conversely, ion accumulation was the least influential factor under greenhouse conditions. Through a Genome Wide Association Study, we identified candidate genes not previously associated with salt stress, highlighting the power of high-throughput phenotyping in uncovering novel aspects of plant stress responses. This study contributes to our understanding of salt stress tolerance in S. pimpinellifolium and lays the groundwork for further investigations into the genetic basis of these traits, ultimately informing breeding efforts for salinity tolerance in tomato and other crops.

Nondestructive plant phenotyping forms a key technique for unraveling molecular processes underlying plant development and response to the environment. While the emergence of high-throughput phenotyping facilities can further our understanding of plant development and stress responses, their high costs greatly hinder scientific progress. To democratize high-throughput plant phenotyping, we developed sets of low-cost image- and weight-based devices to monitor plant shoot growth and evapotranspiration. We paired these devices to a suite of computational pipelines for integrated and straightforward data analysis. The developed tools were validated for their suitability for large genetic screens by evaluating a cowpea (Vigna unguiculata) diversity panel for responses to drought stress. The observed natural variation was used as an input for a genome-wide association study, from which we identified nine genetic loci that might contribute to cowpea drought resilience during early vegetative development. The homologs of the candidate genes were identified in Arabidopsis (Arabidopsis thaliana) and subsequently evaluated for their involvement in drought stress by using available T-DNA insertion mutant lines. These results demonstrate the varied applicability of this low-cost phenotyping system. In the future, we foresee these setups facilitating the identification of genetic components of growth, plant architecture, and stress tolerance across a wide variety of plant species.

Societal Impact Statement Rice farming is transitioning from transplanting rice seedlings towards the less labour‐intensive and less water‐demanding method of directly seeding rice. This, however, is accompanied by increased weed proliferation. To tackle this issue, this study seeks to identify how the crop itself can better suppress weeds, with a focus on light competition via shading. Using a rice diversity panel, traits were identified that contribute to enhanced shading capacity, and these traits were encapsulated into a single shading capacity metric. This was followed by the identification of the genetic loci underpinning variation in the core traits. The identified haplotypes can be used in breeding programmes to improve weed suppression by rice, thus contributing to sustainable agriculture. Summary In modern rice farming, one of the major constraints is weed proliferation and the entailed ecological impact of herbicide application. This requires increased weed competitiveness in current rice varieties, achieved via enhanced shade casting to limit the growth of shade‐sensitive weeds. To identify traits that increase rice shading capacity, we exhaustively phenotyped a rice diversity panel of 344 varieties at an early vegetative stage. A genome‐wide association study (GWAS) revealed genetic loci underlying variation in canopy architecture traits linked with shading capacity. The screen shows considerable natural variation in shoot architecture for 13 examined traits, of which shading potential is mostly determined by projected shoot area, number of leaves, culm height and canopy solidity. The shading rank, a metric based on these core traits, identifies varieties with the highest shading potential. Five genetic loci were found to be associated with canopy architecture, shading potential and early vigour. Identification of traits contributing to shading capacity and underlying allelic variation will serve future genomic‐assisted breeding programmes. Implementing the presented genetic resources for increased shading and weed competitiveness in rice breeding will make its farming less dependent on herbicides and contribute towards more environmentally sustainable agriculture.

Soil salinity is a major contributor to crop yield losses. To improve our understanding of root responses to salinity, we developed and exploited a real-time salt-induced tilting assay. This assay follows root growth upon both gravitropic and salt challenges, revealing that root bending upon tilting is modulated by Na+ ions, but not by osmotic stress. Next, we measured this salt-specific response in 345 natural Arabidopsis (Arabidopsis thaliana) accessions and discovered a genetic locus, encoding the cell wall-modifying enzyme EXTENSIN ARABINOSE DEFICIENT TRANSFERASE (ExAD) that is associated with root bending in the presence of NaCl (hereafter salt). Extensins are a class of structural cell wall glycoproteins known as hydroxyproline (Hyp)-rich glycoproteins, which are posttranslationally modified by O-glycosylation, mostly involving Hyp-arabinosylation. We show that salt-induced ExAD-dependent Hyp-arabinosylation influences root bending responses and cell wall thickness. Roots of exad1 mutant seedlings, which lack Hyp-arabinosylation of extensin, displayed increased thickness of root epidermal cell walls and greater cell wall porosity. They also showed altered gravitropic root bending in salt conditions and a reduced salt-avoidance response. Our results suggest that extensin modification via Hyp-arabinosylation is a unique salt-specific cellular process required for the directional response of roots exposed to salinity.

The nuclear lamina in plant cells is composed of plant-specific proteins, including nuclear matrix constituent proteins (NMCPs), which have been postulated to be functional analogs of lamin proteins that provide structural integrity to the organelle and help stabilize the three-dimensional organization of the genome. Using genomic editing, we generated alleles for the three genes encoding NMCPs in cultivated tomato (Solanum lycopersicum) to determine if the consequences of perturbing the nuclear lamina in this crop species were similar to or distinct from those observed in the model Arabidopsis thaliana. Loss of the sole NMCP2-class protein was lethal in tomato but is tolerated in Arabidopsis. Moreover, depletion of NMCP1-type nuclear lamina proteins leads to distinct developmental phenotypes in tomato, including leaf morphology defects and reduced root growth rate (in nmcp1b mutants), compared with cognate mutants in Arabidopsis. These findings suggest that the nuclear lamina interfaces with different developmental and signaling pathways in tomato compared with Arabidopsis. At the subcellular level, however, tomato nmcp mutants resembled their Arabidopsis counterparts in displaying smaller and more spherical nuclei in differentiated cells. This result argues that the plant nuclear lamina facilitates nuclear shape distortion in response to forces exerted on the organelle within the cell.

Plant architecture develops post-embryonically and emerges from a dialogue between the developmental signals and environmental cues. Length and branching of the vegetative and reproductive tissues were the focus of improvement of plant performance from the early days of plant breeding. Current breeding priorities are changing, as we need to prioritize plant productivity under increasingly challenging environmental conditions. While it has been widely recognized that plant architecture changes in response to the environment, its contribution to plant productivity in the changing climate remains to be fully explored. This review will summarize prior discoveries of genetic control of plant architecture traits and their effect on plant performance under environmental stress. We review new tools in phenotyping that will guide future discoveries of genes contributing to plant architecture, its plasticity, and its contributions to stress resilience. Subsequently, we provide a perspective into how integrating the study of new species, modern phenotyping techniques, and modeling can lead to discovering new genetic targets underlying the plasticity of plant architecture and stress resilience. Altogether, this review provides a new perspective on the plasticity of plant architecture and how it can be harnessed for increased performance under environmental stress.

AbstractSoil salinity is a major environmental stressor affecting agricultural productivity worldwide. Understanding plant responses to salt stress is crucial for developing resilient crop varieties. Wild relatives of cultivated crops, such as wild tomato,Solanum pimpinellifolium, can serve as a useful resource to further expand the resilience potential of the cultivated germplasm,S. lycopersicum. In this study, we employed high-throughput phenotyping in the greenhouse and field conditions to explore salt stress responses of aS. pimpinellifoliumdiversity panel. Our study revealed extensive phenotypic variations in response to salt stress, with traits such as transpiration rate, shoot mass, and ion accumulation showing significant correlations with plant performance. We found that while transpiration was a key determinant of plant performance in the greenhouse, shoot mass strongly correlated with yield under field conditions. Conversely, ion accumulation was the least influential factor under greenhouse conditions. Through a Genome Wide Association Study, we identified candidate genes not previously associated with salt stress, highlighting the power of high-throughput phenotyping in uncovering novel aspects of plant stress responses. This study contributes to our understanding of salt stress tolerance inS. pimpinellifoliumand lays the groundwork for further investigations into the genetic basis of these traits, ultimately informing breeding efforts for salinity tolerance in tomato and other crops.

Plants employ various molecular mechanisms to maintain primary root elongation upon salt stress. Identification of key functional genes, therein, is important for improving crop salt tolerance. Through analyzing natural variation of the primary root length of Arabidopsis natural population under salt stress, we identified NIGT1.4, encoding an MYB transcription factor, as a novel contributor to maintained root growth under salt stress. Using both T-DNA knockout and functional complementation, NIGT1.4 was confirmed to have a role in promoting primary root growth in response to salt stress. The expression of NIGT1.4 in the root was shown induced by NaCl treatments in an ABA-dependent manner. SnRK2.2 and 2.3 were shown to interact with and phosphorylate NIGT1.4 individually. The growth of the primary root of snrk2.2/2.3/2.6 triple mutant was shown sensitive to salt stress, which was similar to nigt1.4 plants. Using DNA affinity purification sequencing, ERF1, a known positive regulator for primary root elongation and salt tolerance, was identified as a target gene for NIGT1.4. The transcriptional induction of ERF1 by salt stress was shown absent in nigt1.4 background. NIGT1.4 was also confirmed to bind to the promoter region of ERF1 by yeast one-hybrid experiment and to induce the expression of ERF1 by dual-luciferase analysis. All data support the notion that salt- and ABA-elicited NIGT1.4 induces the expression of ERF1 to regulate downstream functional genes that contribute to maintained primary root elongation. NIGT1.4-ERF1, therefore, acts as a signaling node linking regulators for stress resilience and root growth, providing new insights for breeding salt-tolerant crops.

The GWAS performed on a population of +/- 199 accessions of wild tomato was screened by Dr. Mitchell Morton in the King Abdulazziz University at Hada Al Sham field site, Saudi Arabia. The details on data analysis and methodology are in Dr. Morton's PhD Thesis (KAUST). The GWAS was performed using the ASReml script similar to Awlia et al. (2021).

This experiment is describing the analysis of the root cross-sections. The roots were collected in the lab of Prof. Avat Shekoofa (Uni. of Tennessee), and the root samples were sent to Julkowska lab (BTI). Magda did hand cross-sections and stained them with toluidine blue to visualize the xylem vessels. The individual images were stitched into an ortho-mosaic using Photoshop.

Plant architecture develops post-embryonically and emerges from a dialogue between the developmental signals and environmental cues. Length and branching of the vegetative and reproductive tissues were the focus of improvement of plant performance from the early days of plant breeding. Current breeding priorities are changing, as we need to prioritize plant productivity under increasingly challenging environmental conditions. While it has been widely recognized that plant architecture changes in response to the environment, its contribution to plant productivity in the changing climate remains to be fully explored. This review will summarize prior discoveries of genetic control of plant architecture traits and their effect on plant performance under environmental stress. We review new tools in phenotyping that will guide future discoveries of genes contributing to plant architecture, its plasticity, and its contributions to stress resilience. Subsequently, we provide a perspective into how integrating the study of new species, modern phenotyping techniques, and modeling can lead to discovering new genetic targets underlying the plasticity of plant architecture and stress resilience. Altogether, this review provides a new perspective on the plasticity of plant architecture and how it can be harnessed for increased performance under environmental stress.