In Arabidopsis thaliana, BIRD nuclear factors, also known as the INDETERMINATE DOMAIN (IDD) protein family, regulate asymmetric cell division and tissue patterning in the root meristem. The BIRD protein JACKDAW (JKD) forms a regulatory complex with the GRAS transcription factors SHORT-ROOT (SHR) and SCARECROW (SCR) to maintain the stem cell niche and stabilize tissue boundaries. While BIRD protein functions are well characterized in Arabidopsis, their role in other plant species remains unclear. Here, we show that in rice, the JKD ortholog NUTCRACKER (NUC) restricts cell division in the root meristem. nuc knockout mutants display ectopic divisions in the ground tissue and vasculature, a loss of quiescence in the quiescent center, and premature differentiation of columella stem cells. NUC associates with SHR and SCR and regulates the expression of SCR and QUIESCENT CENTER-SPECIFIC HOMEOBOX (QHB/WOX5). NUC is expressed in the ground tissue and exodermis and complements the nuc mutant when driven by its native promoter. These findings reveal a role for the BIRD protein NUC in controlling cell division and maintaining the stem cell niche in the rice root meristem.

Phoenix dactylifera L. is an economically, nutritionally, and culturally important fruit crop in the arid and semi-arid regions of the Middle East and North Africa. Here, we present a gap-free, telomere-to-telomere reference genome of the variety Ajwa, along with 19 additional high-quality assemblies (18 female and 1 male). These assemblies reveal updated, corrected chromosome assemblies validated through cytogenetics, Hi-C and optical mapping. Chromosome numbering was revised based on average lengths across all sequenced genomes. The Sex Determination Region (SDR) was inferred on chromosome 14, spanning approximately 15.2 Mb. Nucleolar organizing regions (NORs) were localized on chromosome 10, where a large 45S rDNA locus displayed unique repeat spacer motifs containing transposon-like sequences. In some accessions, a second NOR was identified on the female sex chromosome. This collection of date palm assemblies, anchored by the Ajwa reference genome, provides a fundamental resource for advancing breeding strategies aimed at enhancing the genetic resilience and productivity of date palm.

Rice roots develop aerenchyma, which transports oxygen from shoots to roots, facilitating adaptation to waterlogged conditions. This oxygen oxidizes ferrous ions into ferric compounds, forming iron plaque that mitigates iron toxicity. However, the molecular mechanisms linking aerenchyma and iron plaque formation remain poorly understood. Here we identified a rice mutant (AZ1302) defective in both aerenchyma and iron plaque formation, with the causal mutation mapped to the PHYTOENE SYNTHASE 2 (OsPSY2) gene. CRISPR-Cas9-induced psy2 mutants exhibited reduced levels of carotenoid-derived hormones, strigolactones and abscisic acid, in roots. In psy2 mutants, exogenous application of strigolactones rescued aerenchyma formation, while abscisic acid restored iron plaque deposition, providing evidence for distinct hormonal regulatory functions in the two processes. These findings revise the current understanding by dissociating the roles of aerenchyma and iron plaque formation, establishing a role for OsPSY2 in integrating hormonal signalling to drive root plasticity and offering new insights into plant adaptation under environmental stress.

The activation of immune Mitogen Activated Protein Kinases (MAPKs) is one of the earliest cellular responses following pathogen attack leading to the phosphorylation of appropriate cytosolic or nuclear targets to regulate cellular processes. In this work, we show that the Arabidopsis nuclear protein DEK2 is a target of MPK6 and regulator of plant defense against bacterial and fungal plant pathogens. Transcriptomic analysis unveils that AtDEK2 modulates transcription of defense-related genes, as well as genes associated with hormone synthesis and signaling. Chromatin immunoprecipitation sequencing (ChIP-Seq) analysis reveals that DEK2 potentially binds to TGGGC(C/T) motifs of ZNF, bZIP, WRKY and TCP transcription factors. DEK2 orchestrates diverse chromatin-related processes. Our findings suggest that DEK2 is recruited to specific chromatin regions by transcription factors and functions as a reader of the bivalent histone mark H3K4me3K27me3.

In arid and semi-arid climates, native plants have developed unique strategies to survive challenging conditions. These adaptations often rely on molecular pathways that shape plant architecture to enhance their resilience. Date palms (Phoenix dactylifera) and mangroves (Avicennia marina) endure extreme heat and high salinity, yet the metabolic pathways underlying this resilience remain underexplored. Here, we integrate tissue imaging with spatial metabolomics to uncover shared and distinct adaptive features in these species. We found that mangrove roots accumulate suberin and lignin in meristematic tissues, this is unlike other plant species, where only the differentiation zones contain these compounds. Our metabolomic analysis shows that date palm roots are enriched in metabolites involved in amino acid biosynthesis, whereas compounds involved in lignin and suberin production were more abundant in mangrove roots. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) revealed tissue- and species-specific metabolite distributions in root tissues. We identified common osmoprotectants accumulating in the exodermis/epidermis of date palm and mangrove root meristems, along with a unique metabolite highly abundant in the inner cortex of date palm roots. These findings provide valuable insights into stress adaptation pathways and highlight key tissue types involved in root stress response.

The pomegranate (Punica granatum L.) is an ancient fruit-bearing tree known for its nutritional and antioxidant properties. They originated from the Middle East in regions having large farms including mountainous regions of Al-Baha in Saudi Arabia. Pomegranates can tolerate arid climates and are considered among the fruits that will play a major role in food security. However, the genomics resources of pomegranate growing in arid regions are scarce. Here, we present a high-quality chromosome-level reference genome using PacBio HiFi long reads. The final assembly was 384.65 Mb with N50 contig size of 43.11 Mb, with 353.42 Mb being anchored on the eight pseudo chromosomes. Annotation revealed that 48.79% of the genome comprises repetitive elements and contains 21,620 protein-coding genes. The new reference genome will contribute to identifying stress resistance traits in pomegranates thriving in arid environments as well as new dietary antioxidants and antimicrobial peptides with pharmaceutical and therapeutic applications.

Arak (Salvadora persica L.) is known as a toothbrush tree for its medicinal benefits for oral health and its antioxidant, analgesic, and anti-inflammatory properties. The plant has a remarkable ability to tolerate abiotic stress, especially drought and high salinity. The molecular mechanisms underlying this tolerance are yet to be determined. In this study, we show that salinity tolerance in the Arak plant is mediated by the ability of its roots to maintain a Na+/K+ balance when subjected to high salinity. Our proteome analysis of Arak leaves found an accumulation of proteins involved in energy metabolism pathways, indicating that Arak leaves maintain their energy-driving mechanisms under salinity stress conditions. While in roots the proteins involved in ROS scavenging and stress-related pathways were significantly differentially expressed. This suggests that the roots act as a first barrier to alleviating salinity-induced oxidative stress. Our study identifies key proteins and pathways that could have biotechnological importance and could be translated to crop species to improve their abiotic stress tolerance capacities.

In the root meristem of Arabidopsis, stem cell maintenance depends on the coordinated action of transcription factor networks. The transcriptional regulator EMBRYO DEFECTIVE 1579 (EMB1579), a protein that forms nuclear condensates, regulates plant growth. However, the molecular mechanisms through which it functions in the root meristem remain largely unclear. Here, we show that EMB1579 is required for stem cell maintenance and proper cell division orientation. EMB1579 modulates the function of two root stem cell regulatory modules, PLETHORAs and SCARECROW-SHORT-ROOT, through a process involving transcriptional regulation and RNA splicing. We show that EMB1579 acts as a catalyst for stem cell gene expression, and its activity is fine-tuned by its physical association with RNA splicing factors. The formation of nuclear condensates is essential for EMB1579 function in the root meristem. Our findings reveal a mechanism by which EMB1579 regulates stem cell determinants in the root meristem and expand the understanding of gene regulation complexity in plant development.

Precision farming is an optimized management farming scheme that seeks to link the real-time needs of crops with the nutrients to be administered. Sensing platforms that can monitor the physiological status of crops in situ are key to enabling timely and localized interventions. However, the underdevelopment of plant sensing strategies limits the potential of precision farming. In this Review, we discuss the challenges and advancements in phyto-monitoring, focusing on strategies that are applicable to a wide range of plant species and suitable for field deployment. We explore species-agnostic sensors, including optical and electrochemical sensors, whose operation is based on principles that are widely applicable to all plant species. These platforms enable real-time monitoring of the physiological state of crops by assessing key biomarkers, such as plant hormones, and metabolites such as salicylic acid and reactive oxygen species. Evaluating these systems, we conclude that an integrative sensing approach is necessary to compensate for the limitations of the individual methods and can provide a holistic view of crop health. Cost-effective species-agnostic sensors are thus needed to provide information that can be used to minimize the resource footprint of farming and meet the growing global demand. Species-agnostic plant sensors can monitor the physiological health of a broad range of crops, which is vital for the implementation of precision farming. Here, we evaluate the different sensors in terms of their effectiveness and propose an integrated sensing approach.

Specific phytohormone combinations regulate plant growth and responses to environmental stimuli. Monitoring their distribution is key for understanding signaling cross-talk and detecting plant stress early. However, typical means of monitoring these chemicals are often laborious, destructive, or limited to model plants. In this study, we present an amperometric and minimally invasive sensing platform that can be attached to plant leaves for the simultaneous detection of two key phytohormones, auxin [indole-3-acetic acid (IAA)] and salicylic acid (SA). The platform incorporates magnetized microneedles coated with superparamagnetic Fe 3 O 4 intercalated into a scaffold of multiwalled carbon nanotubes (MWCNTs). It achieves detection limits of 1.41 μM (IAA) and 1.15 μM (SA) with a strong correlation ( R 2 ≥ 0.7) to ultrahigh-performance liquid chromatography–tandem mass spectrometry measurements. Furthermore, implementing cyclical amperometric cleaning extends the sensor lifespan by preventing electrode passivation. Last, the sensor’s capability to monitor the real-time plant responses to several stressors is validated, showcasing its potential for phytodiagnostics and precision farming.

Deserts are hostile environments to plant life due to exposure to abiotic stresses, including high temperature, heat, high light, low water availability, and poor soil quality. Desert plants have evolved to cope with these stresses, and for thousands of years humans have used these plants as sources of food, fiber, and medicine. Due to desertification, the amount of arable land is reduced every year; hence, the usage of these species as substitutes for some crops might become one of the solutions for food production and land remediation. Additionally, increasing our understanding of how these plants have adapted to their environment could aid in the generation of more resistant staple crops. In this review, we examine three desert plant species and discuss their developmental aspects, physiological adaptations, and genetic diversity and the related genomic resources available to date. We also address major environmental challenges and threats faced by these species as well as their potential use for improving food security through stimulating stress resistance in crops.

Plants employ sophisticated molecular machinery to fine-tune their responses to growth, developmental, and stress cues. Gene expression influences plant cellular responses through regulatory processes such as transcription and splicing. Pre-mRNA is alternatively spliced to increase the genome coding potential and further regulate expression. Serine/arginine-rich (SR) proteins, a family of pre-mRNA splicing factors, recognize splicing cis-elements and regulate both constitutive and alternative splicing. Several studies have reported SR protein genes in the rice genome, subdivided into six subfamilies based on their domain structures. Here, we identified a new splicing factor in rice with an RNA recognition motif (RRM) and SR-dipeptides, which is related to the SR proteins, subfamily SC. OsSCR106 regulates pre-mRNA splicing under abiotic stress conditions. It localizes to the nuclear speckles, a major site for pre-mRNA splicing in the cell. The loss-of-function scr106 mutant is hypersensitive to salt, abscisic acid, and low-temperature stress, and harbors a developmental abnormality indicated by the shorter length of the shoot and root. The hypersensitivity to stress phenotype was rescued by complementation using OsSCR106 fused behind its endogenous promoter. Global gene expression and genome-wide splicing analysis in wild-type and scr106 seedlings revealed that OsSCR106 regulates its targets, presumably through regulating the alternative 3'-splice site. Under salt stress conditions, we identified multiple splice isoforms regulated by OsSCR106. Collectively, our results suggest that OsSCR106 is an important splicing factor that plays a crucial role in accurate pre-mRNA splicing and regulates abiotic stress responses in plants.

Abstract In Arabidopsis thaliana, the nuclear protein DEK2 orchestrates diverse chromatin-related processes and exhibits phosphorylation in response to flagellin22 treatment, implicating its involvement in plant immunity against bacterial pathogens. Loss-of-function mutants of dek2 have their immunity compromised to both bacterial and fungal pathogens. Transcriptomic analysis of the dek2-1 mutant unveils AtDEK2 as a transcriptional repressor of defense-related genes, as well as genes associated with hormone synthesis and signaling. Chromatin immunoprecipitation sequencing (ChIP-Seq) analysis reveals that DEK2 binds to motifs of various transcription factor families, with a notable enrichment in class I TCP binding motif regions. Our findings indicate that DEK2 is recruited to specific chromatin regions by transcription factors and functions as a reader of the bivalent histone mark H3K4me3K27me3. Consequently, we propose a hypothetical working model wherein DEK2 acts as a transcriptional repressor targeting regions marked by H3K4me3K27me3, shedding light on its role in plant immunity.

Salinity is a significant threat that causes considerable yield losses in date palm. The root endophytic fungus Piriformospora indica has proven effective in providing salt stress tolerance to host plants. However, the underlying molecular mechanism facilitating the date palm’s response to P. indica inoculation, and its involvement in the salt stress tolerance, remains unknown. In this study, the colonization of P. indica on date palm seedlings exposed to saline conditions was observed through confocal microscopy, and its impact on gene expressions was evaluated using the transcriptomic analysis. Our findings show that P. indica colonization reinforced the cortical cells, prevented them from plasmolysis and cell death under salinity. The RNAseq analysis produced clean reads ranging from 62,040,451 to 3,652,095 across the treatment groups, successfully assembling into 30,600 annotated genes. Out of them, the number of differentially expressed genes (DEGs) varied across the treatments: i.e., 2523, 2031, and 1936 DEGs were upregulated, while 2323, 959, and 3546 were downregulated in Salt, Fungi, and Fungi+Salt groups, respectively. Furthermore, principal component analysis based on transcriptome profiles revealed discrete clustering of samples from different treatment groups. KEGG and GO pathways enrichment analysis highlighted variation in the number and types of enriched pathways among the treatments. Our study indicated variations in gene expression related to plant hormone biosynthesis and signal transduction (auxin, abscisic acid, gibberellin, and ethylene), ABC transporters, sodium/hydrogen exchanger, cation HKT transporter, transcription factors such as WRKY and MYBs, and the plant immune system (lipoxygenase and jasmonate) of the date palm seedlings. By characterizing the transcriptome of date palm roots under salt stress and with colonization of P. indica, the present findings provide valuable perspectives on the molecular mechanisms responsible for inducing salinity stress tolerance in plants.

AbstractBy providing adaptive advantages to plants, desert microorganisms are emerging as promising solutions to mitigate the negative and abrupt effects of climate change in agriculture. Among these, pseudomonads, commonly found in soil and in association with plants' root system, have been shown to enhance plant tolerance to salinity and drought, primarily affecting root system architecture in various hosts. However, a comprehensive understanding of how these bacteria affect plant responses at the cellular, physiological and molecular levels is still lacking. In this study, we investigated the effects of two Pseudomonas spp. strains, E102 and E141, which were previously isolated from date palm roots and have demonstrated efficacy in promoting drought tolerance in their hosts. These strains colonize plant roots, influencing root architecture by inhibiting primary root growth while promoting root hair elongation and lateral root formation. Strains E102 and E141 increased auxin levels in Arabidopsis, whereas this effect was diminished in IAA‐defective mutant strains, which exhibited reduced IAA production. In all cases, the effectiveness of the bacteria relies on the functioning of the plant auxin response and transport machinery. Notably, such physiological and morphological changes provide an adaptive advantage to the plant, specifically under stress conditions such as salinity. Collectively, this study demonstrates that by leveraging the host's auxin signalling machinery, strains E102 and E141 significantly improve plant resilience to abiotic stresses, positioning them as potential biopromoters/bioprotectors for crop production and ecosystem restoration in alignment with Nature‐based Solution approaches.

Real-time monitoring of phytohormones in horticultural plants is difficult due to the lack of biosensors for these systems. Phytohormones that are associated with biotic stress responses, such as salicylic acid (SA), indole-3-acetic acid (IAA), abscisic acid (ABA), and auxin, can be detected using chromatography and fluorescent sensors, but these techniques are not suitable for field deployment. The electrochemically active nature of phytohormones can be exploited to detect these molecules in living plant tissue. Incorporating phytohormone-selective minimally invasive electrodes allows for continuous monitoring applications. This strategy can also be applied to electrochemically inactive phytohormones by utilizing impedimetric measurements.

Jasmine (Jasminum sambac Aiton) is a well-known cultivated plant species for its fragrant flowers used in the perfume industry and cosmetics. However, the genetic basis of its floral scent is largely unknown. In this study, using PacBio, Illumina, 10× Genomics and high-throughput chromosome conformation capture (Hi-C) sequencing technologies, a high-quality chromosome-level reference genome for J. sambac was obtained, exploiting a double-petal phenotype cultivar ‘Shuangbanmoli’ (JSSB). The results showed that the final assembled genome of JSSB is 580.33 Mb in size (contig N50 = 1.05 Mb; scaffold N50 = 45.07 Mb) with a total of 39 618 predicted protein-coding genes. Our analyses revealed that the JSSB genome has undergone an ancient whole-genome duplication (WGD) event at 91.68 million years ago (Mya). It was estimated that J. sambac diverged from the lineage leading to Olea europaea and Osmanthus fragrans about 28.8 Mya. On the basis of a combination of genomic, transcriptomic and metabolomic analyses, a range of floral scent volatiles and genes were identified involved in the benzenoid/phenylpropanoid and terpenoid biosynthesis pathways. The results provide new insights into the molecular mechanism of its fragrance biosynthesis in jasmine.

The rising global occurrence of plant pathogens highlights the need for a thorough reassessment of current disease detection and management schemes. To that end, we review the utility and limitations of the available sensing platforms deployed for phytodiagnostics in the field. We also discuss recent advances in the use of broad-spectrum biomarkers such as phytohormones and volatile organic compounds (VOCs), and assess the feasibility of deploying these platforms on a large scale. Because these platforms are often complementary, we propose a compressed sensing approach that combines several sensing platforms to manage plant pathogens while minimizing additional costs. Finally, we provide an outlook for the potential benefits of integrating new sensing technologies into farming for timely interventions.