The phytohormone abscisic acid (ABA) regulates plant responses to environmental stresses, development, and immunity. Under unfavorable conditions, ABA forms a complex with its receptor proteins Pyrabactin Resistance 1 (PYR1)/PYR1-likes (PYLs)/Regulatory Component of ABA Receptors (RCARs), inhibiting Clade A Protein Phosphatases Type 2C (PP2Cs) and releasing Sucrose Non-Fermenting-1-Related Protein Kinase 2s (SnRK2s) from PP2C-mediated inhibition. Rapidly Accelerated Fibrosarcoma (RAF) kinases from the B1, B2, and B3 subgroups phosphorylate and reactivate SnRK2s, initiating ABA responses. While ABA does not significantly activate B-RAFs, their basal activity is essential for initiating ABA signaling. However, the mechanisms sustaining this basal B-RAF activity are not fully understood. In this study, we revealed that Clade A PP2Cs interact with and dephosphorylate a certain number of B3 subgroup RAFs at a conserved serine residue, corresponding to Ser619 in RAF3, within the phosphate-binding loop. A phosphomimicking mutation at this residue, RAF3^S619D, failed to bind ATP and exhibited diminished kinase activity in vitro and in vivo. Ser619 in RAF3 is an autophosphorylation site, phosphorylated by recombinant RAF3-KD but not by its substrate SnRK2.6. The RAF3^S619A mutant, abolishing Ser619 autophosphorylation, displayed increased kinase activity in vitro. The B-RAF high-order mutant OK¹⁰⁰-B3 carrying RAF3^S619A showed enhanced ABA sensitivity compared with those with wild-type RAF3. Thus, PP2C-mediated dephosphorylation and the autophosphorylation of this unique serine residue dynamically regulate ATP binding affinity and tightly control RAF3 activity during various ABA signaling phases. This intricate mechanism ensures rapid RAF–SnRK2 cascade activation during stress while promptly desensitizing RAFs once stress signaling commences.

Plants monitor daylength to synchronize their flowering time with their surroundings and thus maximize reproductive fitness. In Arabidopsis (Arabidopsis thaliana), CONSTANS (CO) activates the expression of FLOWERING LOCUS T (FT); this activation is a crucial aspect of the daylength-dependent regulation of flowering time. Here, we demonstrate that the basic leucine zipper 3 (bZIP3) transcription factor is important for CO-induced FT expression under long photoperiod conditions in Arabidopsis. We isolated bZIP3 as a CO-interacting protein by yeast two-hybrid screening and verified bZIP3–CO complex formation in Arabidopsis through co-immunoprecipitation assays. The temporal and spatial expression patterns of bZIP3 are very similar to those of CO, and bZIP3 protein levels fluctuate throughout the day, with high abundance in the late afternoon. The bzip3 mutant displayed delayed flowering under long photoperiods, whereas bZIP3 overexpression accelerated flowering regardless of daylength. bZIP3 directly binds to the FT promoter region containing CO-responsive elements in vivo. FT messenger RNA (mRNA) levels in the bzip3 mutant and bZIP3 overexpression lines correlated with their flowering times and changed only during the daytime. bZIP3 overexpression resulted in significantly lower FT transcript levels in the co mutant background than in the wild type. Furthermore, bZIP3 forms a complex with ASYMMETRIC LEAVES1 (AS1), a CO partner that helps CO induce FT expression. The bzip3 as1 double mutant flowered later than the two single mutants under longer daylengths, and FT mRNA levels were much lower in the double mutant than in the bzip3 single mutant. Collectively, our findings uncover a new layer of photoperiod-dependent FT regulation in which bZIP3 facilitates CO to activate FT transcription by forming a complex with AS1.

While many plant lineages display remarkable diversity in morphological form, our understanding of how phenotypic diversity, or disparity, arises in relation to genomic evolution over geologic scales remains poorly understood. Here, we investigated the relationship between phenotypic and genomic evolution in the Fagales, a lineage of woody plants that has been a dominant component of temperate and subtropical forests since the Late Cretaceous. We examine newly generated transcriptomic and trait datasets representing most extant genera and a rich diversity of Cretaceous fossil representatives. Our phylogenomic analyses identify recurrent hotspots of gene duplication and genomic conflict across the order. Our phenotypic analyses showed that the morphospace occupied by Fagales was largely filled by the early Cenozoic, and rates of evolution were highest during the early radiation of the Fagales crown and its major families. These results suggest that Fagales conforms to an “early-burst” model of disparification, with morphospace being filled early in the order's diversification history, and that elevated levels of phenotypic evolution also often correspond to hotspots of gene duplication. Species diversification appears decoupled from patterns of both phenotypic and genomic evolution, highlighting the multidimensional nature of the evolution of plant diversity across geological timescales.

Soybean (Glycine max) provides vegetable oils and proteins for human consumption. Its production depends on seeds and other production-related agronomic traits. How the seed traits are regulated in soybean remains largely unclear. In this study, we identified a miR172a-ERF416/413 module for the regulation of seed traits. The miR172a can cleave the targets ERF416 and ERF413 to affect the downstream gene expression for the reduction of soybean seed size and weight. Both the MIR172a-overexpressing transgenic soybean plants and the erf416/413 mutants produced smaller seeds than the control. Consistently, the ERF416-overexpressing transgenic soybean plants generated larger seeds. ERF416 and ERF413 were directly targeted to the promoter of GmKIX8-1 and GmSWEET10a to regulate their gene expression for seed size/weight control. Interestingly, the erf416/413 mutants showed higher seed yield per plant and higher total seed fatty acid (FA) content, whereas the MIR172a-transgenic soybean had lower total seed FA content compared with the control cultivar, suggesting that miR172a and ERF416/413 may function in FA accumulation through different pathways. Haplotypes of the ERF416 promoter region were further analyzed and Hap1 was correlated with higher gene expression and higher seed weight, while Hap3 was correlated with higher total seed lipid content. Our study revealed a new module for seed trait control. Manipulation of such alleles should facilitate breeding for high-oil and high-yield soybean cultivars.

Rates of protein evolution (d_N/d_S) vary widely across the tree of life. In plants, both life-history traits and GC-biased gene conversion (gBGC) are thought to contribute to this variation, although disentangling their individual contributions remains a challenge. Using information on variation in life-history traits and molecular data in 148 species from Poaceae subfamilies Bambusoideae (mostly woody) and Pooideae (exclusively herbaceous), we investigated the relative importance of modes of reproduction and the non-selective forces of gBGC on protein evolutionary rates between the two subfamilies. Elevated rates of protein evolution associated with relaxed purifying selection were more evident in woody bamboos than in Pooideae and were better explained by reproductive modes than by traits that are likely proxies of effective population size. Although gBGC slightly reduced protein evolutionary rates in both subfamilies, its contribution had only a limited effect on molecular divergence between the groups. Forward simulations generally supported our empirical results on the influence of reproductive mode on selection and gBGC. Our findings from two sister lineages of the grass family provide evidence for association between protein evolution and life-history traits governing reproductive mode and enhance understanding of molecular evolution in plants with contrasting reproductive strategies.

Bananas and plantains of the genus Musa constitute the most vital fruits and staple foods. Cultivated bananas may have originated from intraspecific and interspecific hybridizations of four wild species, namely Musa acuminata (A), M. balbisiana (B), M. schizocarpa (S), and the Australimusa species (T). Here, we appraise the advances made in banana genomics, genetics, and breeding over the past few decades. The sequencing of Musa genomes has been a major breakthrough in banana research programs, presenting unprecedented possibilities for gaining deeper insights into the evolution, domestication, breeding, and genetics of indispensable agronomic traits of bananas. Also, we delve into how these genetic facets, coupled with innovative genomic-assisted tools, including genomic selection and gene editing, propel advancements in banana breeding endeavors. Ultimately, we propose the forthcoming prospects within the domain of banana genetics and breeding.

The evolution of spermatophytes (seed plants) is relatively well known in their evolutionary relationships over temporal changes, but their spatial evolution is another critical yet often neglected lens, especially using a taxon-based approach. Here, by integrating geographic distributions and origin locations across 429 spermatophyte families worldwide with unsupervised machine learning approaches, we constructed a Spermatophyte Spatial Evolutionary System that classifies global spermatophytes into 18 distribution types and six distribution supertypes within three primary floristic elements: cosmopolitan, tropical, and temperate. We found that the three elements all primarily originated from Gondwana, with the cosmopolitan element being the youngest and the temperate element being the oldest in terms of origin. They primarily formed during the Tertiary, particularly between the Eocene and Miocene, driven mainly by climate, long-distance dispersal, and tectonic movement, while each exhibited distinct migration routes and formation models. Our results provide novel insights into the spatial evolution of global spermatophytes and highlight that similar distribution patterns of spermatophytes were driven by their comparable formation processes and mechanisms at the levels of floristic element, distribution supertype, and type.

Rice black-streaked dwarf virus (RBSDV) is a major viral pathogen threatening rice production worldwide. However, the molecular mechanisms underlying the arms race between RBSDV and its host remain largely elusive. Here, we demonstrate that RBSDV infection, or the expression of viral RNA-silencing suppressor protein P6, promotes the ubiquitination and degradation of rice small ubiquitin-like modifiers (SUMO) conjugating enzyme 1b (OsSCE1b). OsSCE1b catalyzes the SUMOylation of OsPelota, a protein involved in plant antiviral RNA decay. Furthermore, RBSDV P6 enhances the interaction between rice ubiquitin E3 ligases SINAT3/4/5 and OsSCE1b in the cytoplasm, leading to increased ubiquitination and degradation of OsSCE1b. Rice plants overexpressing OsSCE1b exhibited reduced susceptibility to RBSDV infection. Conversely, OsSCE1b knockdown and knockout lines, as well as OsPelota knockout lines, were more susceptible, indicating that both OsSCE1b and OsPelota negatively regulate RBSDV infection. Additionally, our findings show that OsSCE1b-catalyzed SUMOylated OsPelota interacts with the Hsp70 subfamily B suppressor OsHBS1, forming a complex that degrades RBSDV genomic RNAs containing one or more GA₆ motifs. Taken together, our data demonstrate that OsSCE1b negatively regulates RBSDV infection by promoting OsPelota SUMOylation and activating the antiviral RNA decay activity of the OsPelota–OsHBS1 complex. Conversely, RBSDV P6 promotes viral infection by enhancing OsSCE1b ubiquitination and degradation, thereby suppressing OsPelota SUMOylation and the rice antiviral RNA decay defense response.

Base editing technologies can improve crops, but their efficiency in maize remains suboptimal. This study attempts to overcome these limitations by examining optimized cytosine and adenine base editors (CBEs and ABEs), namely evoAPOBEC1, evoFERNY, evoCDA1, TadA8.20, and TadA8e, for precise genome editing in transient and stable expression maize cells. Employing a seed fluorescence reporter (SFR) system for rapid screening of BE transformants and transgene-free progenies, we enhanced editing efficiencies and heritability. Notably, TadA8.20 and evoCDA1 attained multiplexed editing efficiencies of up to 100.0% and 79.0% at the tested loci, respectively, with some homozygous and bi-allelic mutants exceeding 72.4% and 73.7%. Precise editing of ZmACC1/2 (acetyl-CoA carboxylase) improved herbicide resistance, with ZmACC2 mutants displaying improved performance. This study advances crop genetic engineering by facilitating robust, multi-locus modifications without altered agronomic performance, enhancing herbicide tolerance in maize. The successful utilization of these BE is a significant step forward in agricultural biotechnology and precision breeding.

Understanding plant adaptive strategies that determine species distributions and ecological optima is crucial for predicting responses to global change drivers. While functional traits provide mechanistic insights into distribution patterns, the specific trait syndromes that best predict elevational optima, particularly in less-studied regions such as the Himalayas, remain unclear. This study employs a novel hierarchical framework integrating morphological, anatomical, and physiological traits to explain elevational distributions among 310 plant species across a 3,500-m gradient (2,650–6,150 m). We analyzed 95,000 floristic records collected from 4,062 localities spanning 80,000 km² in Ladakh, NW Himalayas, India, to define elevational optima and link them with 17 functional traits from over 7,800 individuals. We assessed the roles of moisture and cold limitations on trait–optima relationships by comparing two contrasting habitats (dry steppe and wetter, colder alpine). The predictive power of functional traits was more pronounced in the alpine species facing more extreme abiotic stress than the steppe species. Our results indicate that conservative life history strategies strongly predict elevational optima in alpine areas, while drought avoidance and competitive dominance are key in steppe habitats. Trait syndromes combining short stature, compact growth forms, enhanced storage tissues, and features promoting water-use efficiency (δ¹³C), freezing resistance (fructan levels), and nutrient retention (high root nitrogen and leaf phosphorus) explained 61% of the variation in alpine species' optima. Conversely, lifespan and clonal propagation determined the optima of steppe species at lower elevations. The study emphasizes the importance of functional trait combinations in determining elevational optima, highlighting that alpine species prioritize resource conservation and stress tolerance, while steppe species focus on competitive growth strategies. This multi-trait approach contrasts with previous research focusing on single trait–elevation relationships, providing novel insights into the diverse mechanisms shaping elevational distributions and offering valuable predictive power for assessing vegetation responses to future climate change.

DNAs from the cytoplasmic genomes often communicate with the nuclear genome during regulation, development, and evolution. However, the dynamics of cytonuclear interaction during crop domestication have still been rarely investigated. Here, we examine cytonuclear interactions during grapevine domestication using pan-mitogenome, pan-plastome, and haplotype-resolved nuclear genomes, all assembled from long-read sequences across 33 wild and domesticated grapevine accessions. Structural variation shaped the mitogenomic variation in gene contents, leading to duplications of three specific genes during grapevine domestication (one cox and two rpl genes). Extensive genomic signals of cytonuclear interactions were detected, including a total of 212–431 nuclear–mitochondrial segments (NUMTs) and 95–205 nuclear–plastid segments (NUPTs). These results showed that NUMTs were under strong selection and were more abundant in cultivated grapes, whereas NUPTs dominated in wild grapes, indicating the evolutionary trajectories of cytonuclear interactions during grape domestication. Through Genome-Wide Association Study (GWAS), we identified 84 candidate genes associated with mitochondrial–nuclear genome interactions. Among these, the PFD1 gene acts as a signaling regulator, modulating specific signaling pathways regulated by the mitochondria. Interestingly, there are significantly more cytonuclear interaction genes near NUMTs than in other genomic regions, suggesting NUMT-mediated interactions between the nuclear and mitochondrial genomes. Overall, our study provides evidence that NUMTs promote cytonuclear interaction during grapevine domestication, offering new insight into the impact of cytonuclear interactions on plant evolution, genetics, and breeding.

Bananas (Musa ssp.) are globally important staple crops increasingly constrained by biotic stressors, climatic instability, and the high labor demands of cultivation. The genetic improvement of dwarf phenotypes offers a strategic pathway to enhance mechanization and reduce production costs. In this study, we have carried out whole-genome resequencing of 300 Musa accessions to analyze genome-wide allelic diversity and identify loci associated with shoot architecture. Our analysis uncovered extensive genetic variation within the A subgenome, pivotal for environmental adaptability, and detected introgression from Musa itinerans (subgroup A) into cultivated varieties (subgroup F), suggesting a broadened genetic base amenable to breeding. A genome-wide association study (GWAS) pinpointed MabHLH30 as a crucial gene associated plant stature. Functional validation confirmed MabHLH30 as a critical regulator of plant stature and leaf morphology. Leveraging this finding, we developed molecular markers for MabHLH30, enabling marker-assisted selection (MAS) to accelerate the breeding of compact, high-yielding cultivars. Collectively, these results provide a genomic framework for the targeted improvement of banana architecture and represent a valuable resource for cultivar development under diverse agroecological conditions.

Root nodules are specialized organs formed by the symbiotic relationship between legumes and soil-borne rhizobia, facilitating an exchange of energy and nutrients essential for both organisms. This process is accompanied by dynamic changes in genomic organization and gene expression. While the three-dimensional (3D) architecture of the genome is known to influence gene regulation, its role in nodulation and symbiotic nitrogen fixation remains largely unexplored. In this study, we present the first high-resolution (40 kb) 3D genomic map of peanut roots and root nodules, generated using a high-throughput/resolution chromosome conformation capture strategy. Compared to roots, ∼2.0% of chromosomal regions in nodules transition from a repressive (B) to an active (A) compartment and exhibit significant alterations in topologically associated domains (TADs). Peanut nodules also show more extensive cis-interactions, with 100s of differentially expressed genes enriched in symbiotic pathways and nitrate metabolism. Additionally, assay for transposase-accessible chromatin with high-throughput sequencing identifies 25,863 and 14,703 open chromatin regions (OCRs) in roots and nodules, respectively. By integrating OCR mapping with epigenomic modifications, we reveal dynamic local OCRs (LoOCRs) and histone modifications associated with nodulation-related genes. Notably, novel TADs and long-range chromatin loops are detected in peanut nodules, including an H3K27me3 modification-mediated loop that may regulate the expression of Nodule Inception. Another altered chromatin loop highlights the nodule highly expressed AhMsrA gene, which positively influences nodulation. Together, these findings shed new light on how chromatin architecture shapes gene expression during legume nodulation and nitrogen fixation.

Host–pathogen co-evolution shapes resistance (R) proteins and their recognition of pathogen avirulence factors. However, little attention has been paid to naturally occurring genetic diversity in R genes. In this study, 12 Solanum bulbocastanum accessions from the Commonwealth Potato Collection were screened for resistance to Phytophthora infestans, identifying 11 resistant and one susceptible accession. Targeted enrichment sequencing of nucleotide-binding leucine-rich repeat (NLR) genes using RenSeq, followed by diagnostic RenSeq (dRenSeq) analysis, revealed that all accessions except 7650 contained Rpi-blb1/RB variants. Variants in accessions 7641 and 7648 were non-functional, while three novel functional variants were identified. Cloning and functional analysis of Rpi-blb1/RB variants assessed their recognition of the avirulence factor IPI-O1. Three variants were functional, conferring resistance to P. infestans. Variants in accessions 7644 and 7647 also recognized IPI-O4, confirmed in transgenic potatoes. Analysis of a non-functional variant in S. bulbocastanum accession 7648 identified amino acid Ser347 in the nucleotide-binding (NB-ARC) domain as critical for cell-death initiation following IPI-O1 recognition. Predictions from the FunFOLD2 protein–ligand interaction model suggested that Ser347 is essential for ATP binding, suggesting potential inhibition on pentameric resistosome assembly. Western blot analysis revealed that the mutation of Ser347 to Asn markedly compromises the Rpi-blb1/RB protein stability, and co-immunoprecipitation assay further confirmed that this mutation severely disrupts the self-association of CCNB, thereby preventing Rpi-blb1/RB activation. Consistently, substituting Asn347 with serine restored function, underscoring its key role in Rpi-blb1/RB activity. Cell biology experiments demonstrated that Rpi-blb1/RB relocalize to the plasma membrane in response to IPI-O1. This relocalization depends on Ser347, further supporting the idea that its mutation affects resistosome formation, impairing resistance. This study provides an in-depth functional analysis of natural Rpi-blb1/RB diversity, offering insights into NLR protein evolution and resistance mechanisms in potatoes.

Plants exhibit remarkable abilities to learn, communicate, memorize, and develop stimulus-dependent decision-making circuits. Unlike animals, plant memory is uniquely rooted in cellular, molecular, and biochemical networks, lacking specialized organs for these functions. Consequently, plants can effectively learn and respond to diverse challenges, becoming used to recurring signals. Artificial intelligence (AI) and machine learning (ML) represent the new frontiers of biological sciences, offering the potential to predict crop behavior under environmental stresses associated with climate change. Epigenetic mechanisms, serving as the foundational blueprints of plant memory, are crucial in regulating plant adaptation to environmental stimuli. They achieve this adaptation by modulating chromatin structure and accessibility, which contribute to gene expression regulation and allow plants to adapt dynamically to changing environmental conditions. In this review, we describe novel methods and approaches in AI and ML to elucidate how plant memory occurs in response to environmental stimuli and priming mechanisms. Furthermore, we explore innovative strategies exploiting transgenerational memory for plant breeding to develop crops resilient to multiple stresses. In this context, AI and ML can aid in integrating and analyzing epigenetic data of plant stress responses to optimize the training of the parental plants.

INOSITOL-REQUIRING ENZYME 1 (IRE1) is conserved in plants and mammals to regulate stress responses. Here, we found that TaIRE1 is involved in the unconventional splicing of cell membrane-localized TabZIP60 messenger RNA (mRNA), which results in a nucleus resident protein form (TabZIP60s), and enhanced heat stress tolerance. Transcriptome analysis together with binding element prediction revealed 121 high-confidence targets of TabZIP60s responsive to heat stress in wheat (Triticum aestivum), including heat shock protein genes. Interestingly, we found that an asparagine to glutamic acid substitution, located next to DNA-binding domain of TabZIP60s, results in reduced binding affinity and transcriptional activity to downstream targets, and this heat stress tolerance inferior allele was positively selected during modern wheat breeding programs in China, possibly due to their negative effects on yield potential. Finally, we showed that TaIRE1 is also responsible for the mis-cleavage of miR172 precursors, and consequently contribute to heat stress tolerance. To the best of our knowledge, this represents the first report showing that, like in mammals, IRE1 also regulates miRNA cleavage in response to heat stress in plants. Together, this coordinate control of two signaling pathways provides new insights into heat stress tolerance regulation in wheat.

Late blight pathogen Phytophthora infestans secretes numerous effectors to suppress plant immunity. However, little is known about their underlying biochemical mechanisms. Here we report that, in the host Nicotiana benthamiana, P. infestans core RXLR effector Pi17063 suppresses plant immunity by targeting the host plasma membrane and NbRab-G3 proteins, small GTPases of the Ras-related brain (Rab) family. Pi17063 functions as their specific GTPase-activating protein (GAP), driving them to the cytoplasm-localized guanosine diphosphate (GDP)-bound inactive state. Mutant analysis of the conserved Pi17063 arginine residues showed the essential role of its GAP activity for virulence contribution. All four NbRab-G3 subfamily members are positive immune regulators, and NbRab-G3c mutants lost the ability to switch between active and inactive states and showed compromised immune function. Consistent with this, both silencing and overexpression of an endogenous GAP, NbGYP, inhibited NbRab-G3c-mediated plant immunity. Our results revealed positive immune roles of host NbRab-G3 GTPases, the importance of their state balance, and the biochemical mechanism by which their functions are suppressed by a P. infestans effector, providing insights into understanding eukaryotic effector-mediated plant susceptibility.

Hidden hunger, caused by chronic micronutrient deficiencies, affects billions of people worldwide and remains a critical public health issue despite progress in food production. Biofortification offers a promising solution by enhancing nutrient levels within plant tissues through traditional breeding or advanced biotechnologies. Recent advancements in plant synthetic biology have significantly improved biofortification strategies, enabling precise and targeted nutrient enrichment. This mini-review outlines five core strategies in synthetic biology-based biofortification: overexpression of endogenous biosynthetic genes, introduction of heterologous biosynthetic pathways, expression of nutrient-specific transporters, optimization of transcriptional regulation, and protein (directed) evolution. Vitamin B₁ biofortification serves as a primary illustrative example due to its historical importance and ongoing relevance. Recent breakthroughs, particularly from Chinese research teams, are also highlighted. Together, these strategies offer transformative potential for addressing global nutritional challenges through precise, sustainable and innovative plant-based approaches.

Transcription factors (TFs) function as master regulators in multiple signaling pathways and govern diverse developmental and adaptive processes in plants. Some TFs identified in crop plants play critical roles in regulating yield through changes in plant architecture, including roots, stems, leaves, flowers, fruits, and grains. Although altering crop architecture can increase yields, the extent of yield enhancement is frequently hampered by diseases. Developing new crop varieties with improved yields and enhanced disease resistance remains challenging because immune system activation often impairs plant growth. Recently, approaches using TF engineering have made substantial progress in elevating both growth performance and disease resistance. However, most of these techniques rely on traditional transgenic methods. This review highlights discoveries in the last decade demonstrating improvements in growth performance, yield and immunity through TF engineering. We focus mainly on changes in plant architecture related to improved yield and disease resistance. We conclude with perspectives on the potential application of these discoveries for generating desirable crop traits by merging the most noteworthy biotechnology approaches, such as clustered regularly interspaced small palindromic repeats (CRISPR)/CRISPR-associated protein 9-mediated genome editing, with canonical molecular biology.

The SDS-sedimentation volume (SSV) is a critical indicator for assessing wheat gluten quality and is widely used when evaluating wheat processing quality. However, the molecular mechanisms regulating SSV remain poorly understood. In this study, we performed an analysis of quantitative trait loci (QTLs) for SSV using a recombinant inbred line (RIL) population derived from a cross between TAA10 and XX329, and identified four environmentally stable QTLs located on chromosomes 1D, 2D, 4D, and 6D. Among them, the effects of Qssv.cau-1D and Qssv.cau-6D were likely to be explained by genome variations at the Glu-D1 and Gli-D2 loci. We fine mapped Qssv.cau-2D to the candidate causal gene TaSED, encoding a nucleolar protein. Gene-edited TaSED knockout mutants (tased) had a lower SSV, while TaSED overexpression lines showed a higher SSV. We demonstrated that TaSED interacted with the transcription factor TaSPA to enhance its transcriptional activation activity of glutenin and gliadin, whose expression was downregulated in tased and upregulated in TaSED-OE plants, with corresponding differences in glutenin and gliadin content compared with the wild-type. A molecular marker sedTX was further developed based on a nonsynonymous mutation of the parents in TaSED that could be used to identify haplotypes with high SSV effectively. Our findings elucidate a molecular mechanism governing SSV and reveal valuable variants with promising applications for improving wheat quality.

Transcription activator-like effectors (TALEs) mimic eukaryotic transcriptional activators and translocate into host plant cells via the bacterial type III secretion system (T3SS) during pathogenic interactions. They play a crucial role in disease development by regulating host genes. Despite this, the regulatory mechanisms by which TALEs control OsWRKY transcription factors (TFs) remain poorly understood. In this study, we show that two TALEs from Xanthomonas oryzae pv. oryzae (Xoo) individually modulate two OsWRKY TFs, resulting in increased susceptibility and reduced host defense. Specifically, Xoo1219 and Xoo2145 activate the expression of OsWRKY104 and OsWRKY55, respectively, through direct interactions. OsWRKY104 increases the susceptibility to Xoo by activating OsSWEET11 and OsSWEET14, while OsWRKY55 suppresses host defense against Xoo by directly regulating OsWRKY62. These findings suggest that TALEs hijack the host's OsWRKY TFs to create a favorable environment for bacterial survival.

In recent decades, research on model organisms has significantly increased our understanding of core biological processes in plant science. However, this focus has created a substantial knowledge bottleneck due to the limited phylogenetic and ecological spectrum covered. Gymnosperms, especially conifers, represent a molecular and ecological diversity hotspot among seed plants. Despite their importance, research on these species is notably underrepresented, primarily due to a slower pace of investigation resulting from a lack of community-based resources and databases. To fill this gap, we developed the P(inus)ra(diata)-G(ene)E(xpression) (Pra-GE)-ATLAS, which consists of several tools and two main modules: transcriptomics and proteomics, presented in this work for the forestry commercial and stress-sensitive species Pinus radiata. We have summarized and centralized all the available information to provide a comprehensive view of the gene expression landscape. To illustrate how applications of the database lead to new biological insights, we have integrated multiple regulatory layers across tissues and stressors. While stress favors the retention of small introns, harmonized alternative splicing analyses reveal that genes with conifers' iconic large introns tend to be under constitutive regulation. Furthermore, the degree of convergence between stressors differed between regulatory layers, with proteomic responses remaining highly distinctive even through intergenerational memory tolerance. Overall, the Pra-GE-ATLAS aims to narrow the distance between angiosperms and gymnosperms resources, deepening our understanding of how characteristic pine features have evolved. Pra-GE-ATLAS DB is available at: http://pra-ge-atlas.valmei.es.

Phosphatidylinositol 4,5-bisphosphate (PI(4,5)P₂) is known to be an instrumental anionic phospholipid in governing pollen germination and pollen tube growth. However, the precise functions and regulatory mechanisms of PI(4,5)P₂ in pollen polarity establishment and germination remain poorly understood. Our previous studies demonstrated the pivotal involvement of Arabidopsis formin homology 5 (AtFH5)-dependent vesicle trafficking in polarity establishment of pollen. Here, we observed that PI(4,5)P₂ accumulated and oscillated at the prospective germination site, a process closely associated with the rotational movement of AtFH5-labeled vesicles. Disruption of the mobility of AtFH5-labeled vesicles, either through AtFH5 mutation or pharmacological treatment, significantly perturbed the accumulation of PI(4,5)P₂ at the plasma membrane. Subcellular localization and genetic analysis revealed that two phosphatidylinositol 4-phosphate 5-kinases, AtPIP5K1 and AtPIP5K4, are essential for PI(4,5)P₂ oscillation at the germination site prior to pollen germination. Furthermore, we found that the dynamics of AtPIP5K4 depended on the mobility of AtFH5-labeled vesicles and reduced PI(4,5)P₂ in turn disturbed the attachment of AtFH5-labeled secretory vesicles to the plasma membrane. In conclusion, these findings collectively highlight the reciprocal regulation of AtFH5-labeled secretory vesicles and PI(4,5)P₂ oscillations at the plasma membrane, providing critical insights into the molecular mechanism underlying polarity establishment during pollen germination.

Plants have evolved a sophisticated chemical defense network to counteract pathogens, with phenolamides and salicylic acid (SA) playing pivotal roles in the immune response. However, the synergistic regulatory mechanisms of their biosynthesis remain to be explored. Here, we identified a biosynthetic gene cluster on chromosome 2 (BGC2) associated with the biosynthesis of phenolamide and SA, wherein the key component SlEPS1 exhibits dual catalytic functions for the synthesis of phenolamides and SA. Overexpression of the key component SlEPS1 of BGC2 in tomato enhanced resistance to the bacterial pathogen Pst DC3000, whereas knockout plants were more susceptible. Exogenous applications of SA and phenolamides revealed that these two compounds act synergistically to enhance plant resistance. Notably, during tomato domestication, a disease-resistant allele of SlEPS1, SlEPS1^HapB, was subject to negative selection, leading to a reduction in phenolamide and SA levels and compromised disease resistance in modern varieties. Moreover, the SlMYB78 directly regulates the BGC2 gene cluster to enhance phenolamide and SA biosynthesis, modulating resistance to Pst DC3000. Our study employed multi-omics approaches to describe the synergistic regulation of phenolamide and SA biosynthesis, offering new insights into the complexity of plant immune-related metabolism.

Deep learning-based genomic prediction (DL-based GP) has shown promising performance compared to traditional GP methods in plant breeding, particularly in handling large, complex multi-omics data sets. However, the effective development and widespread adoption of DL-based GP still face substantial challenges, including the need for large, high-quality data sets, inconsistencies in performance benchmarking, and the integration of environmental factors. Here, we summarize the key obstacles impeding the development of DL-based GP models and propose future developing directions, such as modular approaches, data augmentation, and advanced attention mechanisms.

Pollen hydration, germination, and tube growth are vital processes for the successful fertilization of flowering plants. These processes involve complex signaling pathways. Reactive oxygen species (ROS) generated in apoplast involves signaling for the cell wall expansion during tube growth, however molecular regulators are less known. We identified pollen-specific receptor-like kinase (OsPRK) family genes from rice (Oryza sativa), which have conserved leucine-rich repeat (LRR) and kinase domains. To understand the function of these genes, we produced single and triple mutations for OsPRK1, OsPRK2, and OsPRK3 using the clustered regularly interspaced palindromic repeats (CRISPR/Cas9) system. Among these mutants, triple knockout (KO) lines (osprk1/2/3) exhibited the male-sterile phenotype with normal vegetative growth and floret formation. Through cytological analysis, we confirmed that the reduced seed fertility was due to defects in pollen hydration and germination with low ROS accumulation. This defect of pollen germination was partially recovered by treatment with exogenous H₂O₂. We also confirmed that OsPRKs could interact with the LRR extension protein. Our results suggest that rice PRKs redundantly play a role in ROS signaling for pollen hydration and germination, and fertility can be controlled by exogenous application.

Silicon (Si) plays a crucial role in plant growth, development, and stress tolerance. However, in some consumable plant products, such as fruits, Si deposition leads to the formation of a white powdery layer known as bloom, which diminishes glossiness and consumer appeal. Despite its significance, the genetic basis of bloom formation remains largely unexplored. Here, we identified a unique cucumber backbone parent line exhibiting bloomless fruit, which was designated bloomless cucumber 1 (bec1). Map-based cloning of the bec1 locus revealed that BEC1, harboring a natural C-to-T variation at the 754th base of its coding region, is a strong candidate gene for the bloomless trait. Functional validation through gene-editing mutants and BEC1::BEC1-GFP transgenic lines confirmed that BEC1, encoding a Si efflux transporter, is responsible for bloom formation. Mutation of BEC1 impaired Si uptake, thereby preventing the deposition of Si on the surface of glandular trichomes and resulting in bloomless fruits. Additionally, Si deficiency in BEC1 mutants compromised resistance to Corynespora cassiicola and chilling stress. Interestingly, grafting bec1 scions onto bloom rootstocks restored the Si accumulation and stress resistance, while maintaining bloomless phenotype. Overall, our findings elucidate the role of BEC1 in bloom formation and provide a valuable genetic target for breeding bloomless cucumber with enhanced stress resilience.