Harnessing neo-domestication of wild pigmented rice for enhanced nutrition and sustainable agriculture

Advances in precision gene editing have enabled the rapid domestication of wild crop relatives, a process known as neo-domestication. During domestication, breeding rice for maximum productivity under optimal growth conditions reduced genetic diversity, eliminating variants for stress tolerance and grain nutrients. Wild rice varieties have rich genetic diversity, including variants for disease resistance, stress tolerance, and grain nutritional quality. For example, the grain of pigmented wild rice has abundant antioxidants (anthocyanins, proanthocyanidins, and flavonoids), but low yield, poor plant architecture, and long life cycle limit its cultivation. In this review, we address the neo-domestication of wild pigmented rice, focusing on recent progress, CRISPR-Cas editing toolboxes, selection of key candidate genes for domestication, identifying species with superior potential via generating genomic and multi-omics resources, efficient crop transformation methods and highlight strategies for the promotion and application pigmented rice. We also address critical outstanding questions and potential solutions to enable efficient neo-domestication of wild pigmented rice and thus enhance food security and nutrition.

Identification, characterization, and evolutionary analysis of aldehyde dehydrogenase (ALDH) genes superfamily in Medicago truncatula L

Aldehydes are reactive compounds that play crucial roles in various metabolic processes within plants. However, their accumulation can lead to toxic effects, Aldehyde dehydrogenases (ALDHs) represent a diverse family of enzymes that catalyze the oxidation of aldehydes to carboxylic acids. ALDHs help mitigate the toxic effects of these compounds and maintain cellular homeostasis in plants. In this study, a bioinformatics analysis of the Medicago truncatula genome identified 27 MtALDHs, which were classified into ten distinct groups based on their phylogenetic relationships. The distribution of these families across the chromosomes of M. truncatula is uneven, with segmental duplications being the primary factor contributing to the expansion of this gene family within the species. The gene structure and motif analysis within each ALDH family in M. truncatula, along with its orthologous genes in Arabidopsis, exhibits a high degree of conservation. The promoter region analysis of these genes reveals a rich abundance of cis-regulatory elements that respond to various environmental stresses and hormones. Furthermore, examination of the expression patterns of MtALDH genes using available microarray data indicated that several of these genes exhibit high expression levels throughout all developmental stages in M. truncatula. Additionally, some genes display tissue-specific expression and are induced in response to salt stress, suggesting a significant role for these genes in growth processes and stress responses within M. truncatula. The findings from this study provide essential insights and data necessary for the functional evaluation of each MtALDH gene during developmental stages and in response to environmental stresses.

ER-PM tether Syt1 limits cell-to-cell connectivity via plasmodesmata during innate immune responses in Arabidopsis

Upon perception of microbe-associated molecular patterns (MAMPs), plants close plasmodesmata (PD) as part of their innate immune responses. However, the signaling cascades and molecular mechanisms underlying MAMP-induced PD closure require further investigation. Here, we show that the endoplasmic reticulum (ER)-plasma membrane (PM) tether Synaptotagmin 1 (Syt1) modulates the response of PD to MAMPs. Following MAMP stimulation, Syt1 rapidly accumulates to PD and further recruits a putative calcium-permeable transporter, ANN4, to promote a localized, PD-associated Ca2+ elevation, leading to callose-dependent PD closure. Moreover, Syt1 can sense the increased level of PI(4,5)P2 at the PD-PM via its C2 domain. Disrupting the interaction between Syt1 and PM lipids by pharmaceutical approaches or site-directed mutagenesis leads to impaired PD response to MAMPs. Collectively, our findings reveal that Syt1 integrates phospholipid signaling from the PD-PM to regulate PD-localized Ca2+ elevation, thereby modulating intercellular communication for restricting the spread of bacterial infection.

BrCNGC12 and BrCNGC16 mediate Ca2+ absorption and transport to enhance resistance to tipburn in Chinese cabbage

Tipburn is a common physiological disorder in leafy vegetables, significantly impairing crop growth and commercial value. It is widely recognized that Ca2+ deficiency is a key factor triggering tipburn; however, the functions and regulatory mechanisms of genes conferring resistance remain largely unexplored. Through transcriptomic analysis of Chinese cabbage under normal (medium calcium, MCa) and Ca2+-deficient (low calcium, LCa) conditions, we observed that genes in the hormone and calcium signalling pathways exhibited significant responses to LCa stress. Among these, the cyclic nucleotide-gated ion channel (CNGC) genes BrCNGC12 and BrCNGC16, part of the calcium signalling pathway, were notably up-regulated and down-regulated, respectively, under LCa stress. Silencing BrCNGC12 in Chinese cabbage improves Ca2+ absorption and distribution, which strengthens tipburn resistance. Conversely, under LCa stress, heterologous expression of BrCNGC16 in Arabidopsis thaliana increases resistance to tipburn, whereas partial silencing of BrCNGC16 in Chinese cabbage diminishes resistance, with both outcomes linked to altered Ca2+ uptake and translocation. Additionally, overexpression of BrCNGC16 in Chinese cabbage promotes Ca2+ uptake and translocation, thereby enhancing resistance to tipburn and mitigating oxidative damage induced by Ca2+ deficiency. In conclusion, BrCNGC12 and BrCNGC16 play pivotal roles in tipburn resistance in Chinese cabbage, offering novel insights into the interplay between the calcium signalling pathway and tipburn resistance.

Here comes the sun: integration of light, temperature, and auxin during herbaceous plant grafting

MAIN CONCLUSION

Light and temperature can regulate auxin production which has been recently shown to be key during graft healing, suggesting that abiotic factors may be vital variables for future graft studies. Grafting is an important horticultural tool used to combine advantageous plant traits. Despite its broad usage, the mechanisms that underlie graft healing remain poorly understood. Recent work has highlighted the influence of high temperature-mediated auxin flow on graft success. Light and temperature sensing utilize partially overlapping mechanisms to regulate auxin biosynthesis, signaling, and transport. In this review, we explore the sensors and transcriptional regulators that modulate auxin response, specifically emphasizing how these components regulate graft success and vascular reconnection. We also discuss areas of graft biology regulated by auxin and underexplored areas of photobiology that may be key to a better understanding of graft mechanisms. This review underscores the importance of translating genetic findings from model systems into horticultural crops to expand our knowledge of economically valuable techniques like grafting.

Advances in bamboo genomics: Growth and development, stress tolerance, and genetic engineering

Bamboo is a fast-growing and ecologically significant plant with immense economic value due to its applications in construction, textiles, and bioenergy. However, research on bamboo has been hindered by its long vegetative period, unpredictable flowering cycles, and challenges in genetic transformation. Recent developments in advanced sequencing and genetic engineering technologies have provided new insights into bamboo's evolutionary history, developmental biology, and stress resilience, paving the way for improved conservation and sustainable utilization. This review synthesizes the latest findings on bamboo's genomics, biotechnology, and the molecular mechanisms governing its growth, development, and stress response. Key genes and regulatory pathways controlling its rapid growth, internode elongation, rhizome development, culm lignification, flowering, and abiotic stress responses have been identified through multi-omics and functional studies. Complex interactions among transcription factors, epigenetic regulators, and functionally important genes shape bamboo's unique growth characteristics. Moreover, progress in genetic engineering techniques, including clustered regularly interspaced short palindromic repeats-based genome editing, has opened new avenues for targeted genetic improvements. However, technical challenges, particularly the complexity of polyploid bamboo genomes and inefficient regeneration systems, remain significant barriers to functional studies and large-scale breeding efforts. By integrating recent genomic discoveries with advancements in biotechnology, this review proposes potential strategies to overcome existing technological limitations and to accelerate the development of improved bamboo varieties. Continued efforts in multi-omics research, gene-editing applications, and sustainable cultivation practices will be essential for harnessing bamboo as a resilient and renewable resource for the future. The review presented here not only deepens our understanding of bamboo's genetic architecture but also provides a foundation for future research aimed at optimizing its ecological and industrial potential.

Regulation of apocarotenoids for quality improvement and biofortification of horticultural crops

BACKGROUND

Agro-food production and consumption impact climate change and human health. Bioactive secondary metabolites in horticulture crops make them an indispensable part of environmentally sustainable and healthy diet. Among them, apocarotenoids from carotenoid degradation are promising in promoting a preference for plant-based foods over other metabolites.

AIM OF REVIEW

In horticulture crops, carotenoids are vital for photosynthesis and antioxidant defense, but their enzymatic or oxidative metabolites, apocarotenoids, offer greater structural diversity and biological functions. They serve as pigments, scents, signaling molecules, and growth regulators in crop growth and development and provide antioxidant, nutraceutical, and pharmaceutical benefits to human health. The carotenoids as bioactive compounds are well understood. By contrast, much less is explored and reviewed about apocarotenoids.

KEY SCIENTIFIC CONCEPTS OF REVIEW

Recently identified metabolic pathways and components of apocarotenoids are reviewed. Their significance for quality formation in horticulture crops, including the regulation of pigmentation, aroma, flavor, architecture, nutrition value, and broader ecological interactions is discussed. Additionally, this review specifically highlights two representative apocarotenoids, retinal and abscisic acid (ABA), that exhibit conserved yet distinct regulatory functions across plant and animal kingdoms. Comprehensive dissection of apocarotenoid metabolism and their regulatory mechanisms will enhance apocarotenoid biofortification and subsequent biotechnological exploitation in horticultural commodities. We put forward the perspective that apocarotenoids could enhance horticultural crop quality and then promote sensory- and health-driven dietary choices which will in turn increase consumption and production of horticultural plants and promote both human and ecosystem health.

Rhizosphere bacteria degrade a key root exudate metabolite critical for pathogen germination and root infection

AIMS

Glutamine (Gln), present within potato root exudates, stimulates germination of resting spores and chemotactic attraction of zoospores of the plasmodiophorid pathogen, Spongospora subterranea. We hypothesized that rhizosphere bacteria could alter the rhizosphere metabolome by diminishing the occurrence of Gln with the eventual aim of reducing pathogen activation, attraction and infection. This study aimed to isolate and characterize bacteria capable of substantially degrading Gln within the potato rhizosphere.

METHODS AND RESULTS

Eleven bacteria were isolated from potato rhizosphere samples using Gln as a sole carbon source. Of these, Pantoea sp. (RR15) and Rhodococcus sp. (RR09) showed superior Gln degradation potential. Both isolates established within the potato rhizosphere and reduced Gln concentrations in situ. Further analysis of the rhizosphere metabolome showed significant treatment effects for a range of other organic compounds, including some known to stimulate or inhibit Spongospora subterranea germination and/or taxis.

CONCLUSIONS

We demonstrate that establishing selected bacteria in the rhizosphere of potatoes can successfully modify the root rhizosphere metabolome.

The tps5, tps10 and tps11 class II trehalose phosphate synthase mutants alter carbon allocation to starch and organic and amino acids at two different photoperiods in Arabidopsis

MAIN CONCLUSION

Altered C and N allocation in response to short- and long photoperiods in class II TPS mutants suggest that they negatively regulate the TPS1-Tre6P metabolic regulator system in A. thaliana. The biological function of class II TPS genes remains largely enigmatic, although there is evidence that they may play an important regulatory role in plant stress responses as well as in development and growth. Recent findings indicated that part of biological function of TPSII proteins may be related to their capacity to associate with the SnRK1 regulator of metabolism in order to inhibit its nuclear activity. The results of the present study show that insertional mutants of the TPS5, TPS10 and TPS11 class II TPS genes had a marked effect on the carbon allocation to non-structural carbohydrates, notably starch, and to organic and amino acids during both short- and long-day photoperiods. The results obtained in this study, which resembled those obtained previously in AhTPS1 overexpressing plants, suggest that these particular TPSII proteins may negatively regulate of C and N allocation to non-structural carbohydrates, organic and amino acids mediated by the TPS1-Tre6P central metabolic regulator system in A. thaliana plants. The effect observed was sometimes dependent on of the photoperiod employed and the mutant examined. The mechanism by means of which these TPS II proteins may specifically target TPSI activity and Tre6P levels in order to regulate C and N allocation in A. thaliana in response to short- and long-day photoperiods remains to be determined.

Interdependence of plasma membrane nanoscale dynamics of a kinase and its cognate substrate underlies Arabidopsis response to viral infection

Plant viruses represent a risk to agricultural production and as only a few treatments exist, it is urgent to identify resistance mechanisms and factors. In plant immunity, plasma membrane (PM)-localized proteins play an essential role in sensing the extracellular threat presented by bacteria, fungi, or herbivores. Viruses are intracellular pathogens and as such the role of the plant PM in detection and resistance against viruses is often overlooked. We investigated the role of the partially PM-bound Calcium-dependent protein kinase 3 (CPK3) in viral infection and we discovered that it displayed a specific ability to hamper viral propagation over CPK isoforms that are involved in immune response to extracellular pathogens. More and more evidence supports that the lateral organization of PM proteins and lipids underlies signal transduction in plants. We showed here that CPK3 diffusion in the PM is reduced upon activation as well as upon viral infection and that such immobilization depended on its substrate, Remorin (REM1.2), a scaffold protein. Furthermore, we discovered that the viral infection induced a CPK3-dependent increase of REM1.2 PM diffusion. Such interdependence was also observable regarding viral propagation. This study unveils a complex relationship between a kinase and its substrate that contrasts with the commonly described co-stabilisation upon activation while it proposes a PM-based mechanism involved in decreased sensitivity to viral infection in plants.

Genome-wide characterization and expression profiling of FIMBRIN gene family members in response to abiotic stress in Medicago sativa

BACKGROUND

Alfalfa is widely regarded as one of the most important forage crops globally. However, its growth and development are primarily constrained by various abiotic stresses. FIMBRINs are crucial actin-binding proteins involved in regulating cellular dynamics in plants under various stress conditions and during developmental processes. The Fimbrin (FIM) gene family has been reported only in Arabidopsis, while a comprehensive identification of the FIM gene family in alfalfa and the responses of its members to abiotic stresses remain unclear.

RESULTS

In this study, six MsFIM genes were identified in the alfalfa genome, distributed across three chromosomes. Phylogenetic analysis grouped these genes into four clades, all containing the conserved CH domain. Gene duplication events suggested that large fragment duplications contribute to gene amplification. Furthermore, cis-regulatory element analysis highlighted their pivotal roles in plant development and response to external abiotic stresses. RT-qPCR analyses revealed that the MsFIM genes exhibited differential expression across various tissues, with predominant expression in flowers, stems, and leaves. The MsFIM genes showed elevated expression under abiotic stresses (drought, cold, and salt) as well as hormone treatment (abscisic acid, ABA), suggesting that they served as positive regulators in alfalfa's resistance to abiotic stresses and its growth and development.

CONCLUSIONS

This study investigates the MsFIM genes in alfalfa, further analyzing their potential roles in plant development and response to abiotic stresses. These findings will provide novel insights into the molecular mechanisms of alfalfa's stress response.

Suppressing an auxin efflux transporter enhances rice adaptation to temperate habitats

Rice (Oryza sativa L.), a chilling-sensitive staple crop originating from tropical and subtropical Asia, can be cultivated in temperate regions through the introduction of chilling tolerance traits. However, the molecular mechanisms underlying this adaptation remain largely unknown. Herein, we show that HAN2, a quantitative trait locus, confers chilling tolerance in temperate japonica rice. HAN2 encodes an auxin efflux transporter (OsABCB5) and negatively regulates chilling tolerance, potentially via auxin-mediated signaling pathway. During rice domestication, HAN2 has undergone selective divergence between the indica and temperate japonica subspecies. In temperate japonica rice, the insertion of a Copia long terminal repeat retrotransposon downstream of HAN2 reduces its expression, thereby enhancing chilling tolerance and facilitating adaptation to temperate climates. Introgression of the temperate japonica HAN2 allele into indica rice significantly improves chilling tolerance at both seedling and booting stages. These findings advance our understanding of rice northward expansion and provide a valuable genetic resource for improving yield stability under chilling stress.

Joint linkage and association analysis identifies genomic regions and candidate genes for yield-related traits in wheat

KEY MESSAGE

Twenty-six QTLs associated with yield-related traits in wheat were identified through joint linkage and association analysis, with TraesCS5A03G0002500 being selected as a candidate gene for QGl.caas-5A.1. As a major staple crop worldwide, continuously increasing wheat yield is crucial for ensuring food security. Wheat yield is influenced by multiple traits, and elucidating the genetic basis of yield-related traits lays a foundation for future gene cloning and molecular mechanism studies. In this study, a recombinant inbred line (RIL) population derived from 292 lines of Hengguan 35/Zhoumai 18 was genotyped with the Affymetrix wheat 660 K SNP array. Combined with the phenotype of the RIL population in 13 environments, linkage analysis of six yield-related traits including plant height, grain number per spike, thousand-grain weight, grain length, grain width, and grain thickness was conducted. A total of 262 quantitative trait locus (QTLs) (logarithm of odds [LOD] > 3) were identified across 21 chromosomes, in which 50 QTLs were repeatedly detected in more than three environments. Numerous QTLs harbored cloned genes and overlapped with those reported in previous studies. Subsequently, joint analysis of genome-wide association study (GWAS) data from the advanced backcross-nested association mapping plus inter-crossed (AB-NAMIC) population and QTLs identified in the RIL population revealed 26 overlapping genomic regions. Notably, the QGl.caas-5A.1 associated with grain length on chromosome 5A was detected in both the RIL and AB-NAMIC populations, and TraesCS5A03G0002500 was selected as a candidate gene. A kompetitive allele-specific PCR (KASP) marker based on a variant [A/G] in TraesCS5A03G0002500 was developed and validated in a natural population containing 350 accessions. Taken together, these results provide valuable information for fine mapping and cloning of yield-related wheat genes in the future.

The CIN-TCP transcription factors regulate endocycle progression and pavement cell size by promoting cell wall pectin degradation

In plants, endoreplication, the process where nuclear DNA replicates in the absence of mitosis, and remodeling of the primary cell walls are both coupled with cell expansion. However, the mechanisms by which these two processes coordinate to determine cell size remain largely elusive. Here, employing the tcpΔ7 septuple mutant disabling seven of the eight CIN-TCP transcription factors in Arabidopsis, we find that hindered endoreplication progression in tcpΔ7 whereby ploidy increases from 8 C to beyond is correlated with an increase in cell wall pectin. CIN-TCPs transcriptionally activate POLYGALACTURONASE LIKE 1 (PGL1), which encodes a polygalacturonase downregulating both abundance and molecular mass of pectin polymers. Genetic analysis of PGL1 in both the wild type and tcpΔ7 backgrounds confirm that pectin reduction promotes endocycle progression and cell enlargement. Collectively, these findings reveal a critical role of pectin in regulating endoreplication, providing insights in the understanding of cell growth and organ development in plants.

Genome-wide identification of the regulatory network of mitogen-activated protein kinase signaling cascades gene families in Hevea Brasiliensis

BACKGROUND

The mitogen-activated protein kinase (MPK) cascade pathway represents a highly conserved signal transduction mechanism in plants, playing a crucial role in growth, development, and stress response. Nevertheless, systematic analysis on the MPK cascade genes in rubber trees remains unexplored.

RESULTS

We conducted a comprehensive identification of the MPK cascade gene family of Hevea brasiliensis, identifying a total of 20 HbMPKs, 13 HbMPKKs, and 167 HbMAPKKKs genes. Through phylogenetic analysis and compared to Arabidopsis MPK cascade genes, HbMPKs and HbMPKKs were categorized into categorized four subgroups with no significant expansion or contraction, while the notably expanded HbMAPKKKs were divided into three subgroups: Raf, ZIK, and MEKK. Conserved motifs, gene structure, and motif analysis further bolster the validity of phylogenetic classification. Furthermore, expression profiling analysis based on public transcriptomic data revealed that these genes were differentially expressed in various tissues and differentially regulated in response to different stresses. Among them, the genes highly expressed in latex or the upregulated genes after tapped including HbMPK8, HbMPK12, HbMPK19, HbMPKK6, HbMPKK9, HbMPKKK15, HbMPKKK21 might be related to latex development and natural rubber (NR) yield. Through yeast two-hybrid assays, we successfully pinpointed 34 pairs of HbMPKKK-HbMPKK-HbMPK interaction modules. Integrating the interaction network and gene expression patterns, 12 potential HbMPK cascade signaling modules including HbMPKKK6/41/79-HbMPKK1-HbMPK9/12/15 and HbMPKKK6/14/21/41/79-HbMPKK9-HbMPK9/15 might involve in NR production and stress responses.

CONCLUSIONS

Our study comprehensively unveils the multidimensional characteristics of the MPK cascade gene family in rubber trees and successfully identifies its core signaling cascade module, laying a crucial foundation for future in-depth exploration of the biological functions of the MPK cascade signaling module in rubber trees.

Enhanced Phytopathogen Biofilm Control in the Soybean Phyllosphere by the Phoresy of Bacteriophages Hitchhiking on Biocontrol Bacteria

Phage-based biocontrol has shown notable advantages in protecting plants against pathogenic bacteria in agricultural settings compared to chemical-based bactericides. However, the efficiency and scope of phage biocontrol of pathogenic bacteria are limited by the intrinsic properties of phages. Here, we investigated pathogen biofilm eradication in the phyllosphere using the phoresy system of hitchhiking phages onto carrier biocontrol bacteria. The phoresy system efficiently removed the pathogen biofilm in the soybean phyllosphere, reducing the total biomass by 58% and phytopathogens by 82% compared to the untreated control. Biofilm eradication tests demonstrated a significant combined beneficial effect (Bliss independence model, CI < 1) as phages improved carrier bacteria colonization by 1.2-fold and carrier bacteria facilitated phage infection by 1.4-fold. Transcriptomic analysis showed that phoresy significantly enhanced motility (e.g., fliC and pilD genes) and energy metabolism (e.g., pgm and pgk genes) of carrier bacteria and suppressed the defense system (e.g., MSH3 and FLS2 genes) and energy metabolism (e.g., petB and petC genes) of pathogens. Metabolomics analysis revealed that the phoresy system stimulated the secretion of beneficial metabolites (e.g., flavonoid and tropane alkaloid) that could enhance stress response and phyllosphere protection in soybeans. Overall, the phoresy of phages hitchhiking on biocontrol bacteria offers a novel and effective strategy for phyllosphere microbiome manipulation and bacterial disease control.

Black ink staining protocol: A cost-effective substitute in quantifying arbuscular mycorrhizal colonization in plant roots

Arbuscular mycorrhizal (AM) fungi, ubiquitously distributed across diverse terrestrial ecosystems, establish symbiotic associations with the majority of vascular plants, fulfilling essential physiological and ecological functions. Mycorrhizal development represents the initiation of host-fungus interactions and serves as a metric for assessing mutualistic efficacy. However, mycorrhizal detection underscores the urgent need to develop cost-effective, efficient, and environmentally benign dyestuff. Therefore, wild-collected and laboratory-grown roots of Medicago sativa were selected. Six reagents including black ink, red ink, acid fuchsin, trypan blue, Sudan IV, and aniline blue were evaluated in conjunction with computer vision techniques to identify optimal one. Concurrently, root characteristics were quantified, and interrelationships among root traits, image quality, and colonization indices were analyzed to unravel the mechanism of their interactions. The findings demonstrated that wild roots exhibited pronounced lignification, achieving a mycorrhizal colonization rate of 100 %, which was better than the two laboratory groups. And the fungal community displayed a markedly greater colonization intensity compared to the Claroideoglomus etunicatum. Evaluation of the six reagents revealed distinct staining efficacy, with significant variations in image clarity, gray-level co-occurrence matrix (GLCM) indices, and colonization parameters across treatments. Specifically, aniline blue proved ineffective, while Sudan IV showed selective binding. Notably, black ink in glacial acetic acid achieved optimal mycorrhizal detection efficacy. Moreover, correlation matrix identified microscopic image quality as critical determinant of quantification accuracy, influenced by both reagent types and root properties, and AvgDiam exerted the most substantial impact (|R| > 0.75).

Carbon metabolism and partitioning in citrus leaves is determined by hybrid, cultivar and leaf type

The partitioning and metabolism of carbohydrates and lignin in leaves are essential for numerous physiological functions, growth and development of plants. This study was aimed to characterize these processes in four leaf types (i.e., autumn-, summer-, spring- and current-year spring shoots) of two citrus hybrids (loose-skin mandarin cultivars OP (i.e., cultivars 'Orah' (OR) Citrus reticulata Blanco and 'Ponkan' (PO) Citrus reticulata Blanco and the sweet orange cultivars NT 'Newhall navel orange' (NO) Citrus sinensis (L.) Osbeck and 'Tarocco' (TA) Citrus sinensis (L.) Osbeck) differing in fruit maturation under field conditions. For this purpose, we analyzed the levels of foliar structural, non-structural carbohydrates and lignin and the expression of related genes. Our results showed that the contents of structural, non-structural carbohydrates and lignin measured in the two hybrids and its partitioning were mostly determined by differences in gene expression recorded in hybrids, cultivars and leaf type. Particularly, differences between leaf types were largely attributed to up- and down-regulation of the expression of genes of cellulose synthesis, lignin precursor synthesis, the Calvin cycle, glycolysis, the tricarbonic acid and starch synthesis and degradation pathways. These differences between leaf types required more complex transcriptional regulation than differences between hybrids and cultivars. The present results indicated that the two citrus hybrids studied differed in the expression of structural, non-structural carbohydrates and lignin-related genes. Future studies have to show if the differences observed in foliar partitioning and metabolism of carbohydrates and lignin are translated into partitioning and metabolism of carbohydrates and lignin in the roots.

Effect of salt stress on K+/Na+ homeostasis, osmotic adjustment, and expression profiles of high-affinity potassium transporter (HKT) genes

Salt stress is one of the major threats affecting crop yield. We assessed the behaviour of three barley genotypes, Ardhaoui, Manel, and Testour under 200 mM NaCl with the aim of evaluating the physiological and molecular mechanisms involved in barley salinity tolerance. Results revealed that salinity stress significantly decreases plant growth and water-holding capacity, particularly in the salt-sensitive genotype Testour. Tissue ionic content assessment demonstrated significantly distinct salinity-induced responses. The salt-tolerant genotype Ardhaoui accumulated more K+ and less Na+ content in both leaves and roots compared with the two other genotypes, leading to an increased K+/Na+ ratio. Furthermore, the genotype Ardhaoui exhibited a stronger selectivity transport capacity of K+ over Na+ from root to leaf compared to both Manel and Testour. This effect was due to enhanced K⁺ retention and Na⁺ exclusion, regulated by HvHKT expression. Indeed, higher HvHKT2;1 gene transcript abundance was detected in both leaves and roots of the Ardhaoui genotype, as well as an upregulation of HvHKT1;1 and HvHKT1, mainly in Ardhaoui roots. In view of the severe impact of salinity on plant development, these findings could be applied to the genetic improvement of plant salinity tolerance.

Transcriptomic profiling reveals bud dormancy stage dynamics in Japanese cedar (Cryptomeria japonica) throughout the nongrowing period

This study aimed to characterize the vegetative bud status of Japanese cedar (Cryptomeria japonica [L.f.] D. Don) throughout the nongrowing period (October-March). Based on the results of twig experiments and transcriptome analysis, we divided the nongrowing period into four stages. Buds were estimated to form between October and November (stage 1), with bud hardening continuing until December (stage 2). Endodormancy was released and transitioned into ecodormancy in mid-to-late December, with the timing varying by genotype. Buds endured harsh winter conditions during January and February (stage 3) and prepared for subsequent growth in March (stage 4). The number of days to bud burst (DBB) under forcing conditions gradually decreased after the transition to ecodormancy, culminating in bud burst in the field in late April. Transcriptome analysis identified key genes presumed to regulate these stages, such as CONSTANS-like and core clock genes. Furthermore, analysis of three genotypes with differing dormancy characteristics revealed DBB-associated genes, indicating the potential involvement of phytohormone cytokinins in regulating bud burst. Additionally, the PEBP- and SVP-like genes, known for their roles in dormancy regulation in other tree species, exhibited distinct expression patterns in Japanese cedar, highlighting variations in dormancy control mechanisms. This study is the first to categorize bud dormancy stages in conifers during the nongrowing period based on molecular data, and the results provide foundational insights for future investigations into conifer dormancy.

Comparative analysis of synteny and functional divergence of APX genes in Fragaria vesca and Fragaria×ananassa

BACKGROUND

Ascorbate peroxidase (APX) is a key enzyme that removes reactive oxygen species (ROS) in the ascorbic acid-glutathione cycle. Although APX genes have been reported in many species, comparative analysis of genome-wide, promoters, and gene functions between F. vesca (Fragaria vesca L.) and F. × ananassa (Fragaria×ananassa Duch.) have not been comprehensively explored.

RESULTS

In this study, seven FvAPX and twenty FaAPX genes were divided into five subgroups. By comparative analysis of the 5 motifs between F. vesca and F. × ananassa, it was found that some fragments were gained/lost. These amino acid fragments might be closely related to the function of the APX genes. Synteny analysis of F. vesca and F. × ananassa showed that there were more collinearity genes with grapes. Compared with F. × ananassa, the FvAPX2, FvAPX3, FvAPX4, and FvAPX6 proteins were more likely to use Val and Leu in F. vesca. The RT‒qPCR results confirmed that FaAPX5 and FvAPX7 were obviously upregulated under the NaCl, PEG, and H2O2 treatments. The GUS assay showed that FvAPX7 had stronger promoter activity than FaAPX5. Additionally, the overexpression of FvAPX7 and FaAPX5 in 'Benihoppe' leaves and Arabidopsis (Arabidopsis thaliana) improved activities of POD, SOD, CAT, and APX, and decreased the relative electrical conductivity and H2O2 content under NaCl, H2O2, and drought stresses.

CONCLUSIONS

Collectively, our study provides comprehensive insight regarding the evolutionary relationship between F. vesca and F. × ananassa and offers substantial opportunities for further research on the functions of APX genes.

Natural allelic variation of NAC transcription factor 22 regulates starch biosynthesis and properties in sweetpotato

Sweetpotato (Ipomoea batatas) starch is in high demand globally as a food and industrial product. However, the regulatory mechanisms governing starch biosynthesis and starch properties in this important crop remain largely unknown. Here we identified a natural allelic variant in the promoter of IbNAC22, encoding a NAC (NAM, ATAF1/2, and CUC2) transcription factor, which is closely linked to starch content in sweetpotato. In high-starch sweetpotato varieties, the T/C haplotype and a 13-bp deletion in the IbNAC22 promoter resulted in higher transcriptional activity. The high-starch IbNAC22 haplotype is more prevalent in regions of China where the sweetpotato starch industry is well developed, indicating that this advantageous allele type has been utilized in breeding starchy sweetpotato varieties in China. IbNAC22 is highly expressed in storage roots and starch-rich sweetpotato accessions. Overexpression of IbNAC22 significantly improved starch and amylose contents, as well as granule size and gelatinization temperature, and decreased starch crystallinity, whereas IbNAC22 knockdown had the opposite effects. IbNAC22 directly activates the expression of IbGBSSI, a key gene for amylose biosynthesis, but suppresses the expression of IbSBEI, a key gene for amylopectin biosynthesis. IbNAC22 directly interacts with IbNF-YA10. Overexpressing of IbNF-YA10 significantly improved starch and amylose contents, and starch gelatinization temperature, but decreased granule size, crystallinity, and amylopectin chain length distribution. IbNF-YA10 directly activates IbAGPL and IbGBSSI, which are key genes involved in starch and amylose biosynthesis. IbNAC22-IbNF-YA10 heterodimers further enhance the IbNF-YA10-induced activation of IbAGPL and IbGBSSI. These findings increase our understanding of starch biosynthesis and starch properties and provide strategies and candidate genes for the improvement of starchy root and tuber crops.

Simultaneous Cd immobilization and oxidative stress alleviation in Brassica chinensis by a novel phosphate-solubilizing strain Sutcliffiella horikoshii P1

Microbial remediation of cadmium (Cd) pollution offers economically green and operationally simple advantages, particularly in environments with mild contamination. The acquisition of efficient strains and coupling between bacterial response and plant fitness are current research emphases in the remediation process. In this study, a novel phosphate-solubilizing strain with outstanding Cd-resistance, Sutcliffiella (S.) horikoshii P1 was isolated. Cd removal efficiency reached 98.85 % by the strain within 24 h at an initial concentration of 5 mg/L. Distribution analysis revealed that the dominant mechanism of Cd removal by the strain varies with Cd concentrations. Notably, the seed soaking of Brassica chinensis with S. horikoshii P1 could improve seed germination rate and growth potential regardless of the presence of Cd stress. Morphological and biochemical trait analysis revealed that the inoculated strain also increased fresh weight and reduced the Cd phytoavailability of Brassica chinensis by producing active substances and alleviating plant oxidative stress. Pot experiment demonstrated that the transport factor (TF) and bioconcentration factor (BCF) decreased by 22.76 % and 33.59 %, respectively, and Cd content in edible parts met food safety standards. Whole-genome sequencing analysis demonstrated that functional genes related to heavy metal resistance and transport (cadC, czcD, znuA, etc.), and gene clusters involved in siderophore secretion may regulate Cd immobilization and the plant growth-promoting effect of S. horikoshii P1. The results underscored the feasibility and effectiveness of Sutcliffiella horikoshii in addressing Cd contamination and promoting plant growth, providing a basis for the future application in agricultural safe production.

Glucosinolates can act as signals to modulate intercellular trafficking via plasmodesmata

Plasmodesmata (PD) allow direct communication across the cellulosic plant cell wall, facilitating the intercellular movement of metabolites and signaling molecules within the symplast. In Arabidopsis thaliana embryos with reduced levels of the chloroplast RNA helicase ISE2, intercellular trafficking and the number of branched PD were increased. We therefore investigated the relationship between altered ISE2 expression and intercellular trafficking. Gene expression analyses in Arabidopsis tissues where ISE2 expression was increased or decreased identified genes associated with the metabolism of glucosinolates (GLSs) as highly affected. Concomitant with changes in the expression of GLS-related genes, plants with abnormal ISE2 expression contained altered GLS metabolic profiles compared with wild-type (WT) counterparts. Indeed, changes in the expression of GLS-associated genes led to altered intercellular trafficking in Arabidopsis leaves. Exogenous application of GLSs but not their breakdown products also resulted in altered intercellular trafficking. These changes in trafficking may be mediated by callose levels at PD as exogenous GLS treatment was sufficient to modulate plasmodesmal callose in WT plants. Furthermore, auxin metabolism was perturbed in plants with increased indole-type GLS levels. These findings suggest that GLSs, which are themselves transported between cells via PD, can act on PD to regulate plasmodesmal trafficking capacity.

RcSRR1 interferes with the RcCSN5B-mediated deneddylation of RcCRL4 to modulate RcCO proteolysis and prevent rose flowering under red light

Light is essential for rose (Rosa spp.) growth and development. Different light qualities play differing roles in the rose floral transition, but the molecular mechanisms underlying their effects are not fully understood. Here, we observed that red light suppresses rose flowering and increases the expression of sensitivity to red light reduced 1 (RcSRR1) compared with white light. Virus-induced gene silencing (VIGS) of RcSRR1 led to early flowering under white light and especially under red light, suggesting that this gene is a flowering repressor with a predominant function under red light. We determined that RcSRR1 interacts with the COP9 signalosome subunit 5B (RcCSN5B), while RcCSN5B, RcCOP1, and RcCO physically interact with each other. Furthermore, the RcCSN5B-induced deneddylation of Cullin4-RING E3 ubiquitin ligase (RcCRL4) in rose was reduced by the addition of RcSRR1, suggesting that the interaction between RcSRR1 and RcCSN5B relieves the deneddylation of the RcCRL4-COP1/SPA complex to enhance RcCO proteolysis, which subsequently suppresses the transcriptional activation of RcFT and ultimately flowering. Far-red light-related sequence like 1 (RcFRSL3) was shown to specifically bind to the G-box motif of the RcSRR1 promoter to repress its transcription, removing its inhibition of RcFT expression and inducing flowering. Red light inhibited RcFRSL3 expression, thereby promoting the expression of RcSRR1 to inhibit flowering. Taken together, these results provide a previously uncharacterized mechanism by which the RcFRSL3-RcSRR1-RcCSN5B module targets RcCO stability to regulate flowering under different light conditions in rose plants.

Positive regulation of BBX11 by NAC053 confers stomatal and apoplastic immunity against bacterial infection in Arabidopsis

Stomatal immunity and apoplastic immunity are critical for preventing microbial phytopathogenesis. However, the specific regulatory mechanisms of these resistances remain unclear. In this study, a BBX11 transcription factor (TF) was identified in Arabidopsis and was found to participate in stomatal and apoplast immunity. Phenotypic, biochemical, and genetic analyses revealed that NAC053 contributed to Arabidopsis resistance against Pseudomonas syringae pv tomato DC3000 (Pst DC3000) by positively regulating BBX11. BBX11 TF that was expressed constitutively in guard cells acts as a positive regulator of plant defense against Pst DC3000 through the suppression of coronatine (COR)-induced stomatal reopening, mitigating the virulence of COR and alleviating COR-triggered systemic susceptibility in the apoplast. BBX11 was found to be involved in PTI responses induced by flg22, such as stomatal closure, reactive oxygen species accumulation, MAPK activation, and callose deposition, thereby enhancing disease resistance. Yeast one-hybrid screening identified NAC053 as a potential TF that interacted with the promoter of BBX11. NAC053 also positively regulated resistance to Pst DC3000. These findings underscore the significance of transcriptional activation of BBX11 by NAC053 in stomatal and apoplastic immunity against Pst DC3000, enhancing understanding of plant regulatory mechanisms in response to bacterial pathogens.

Compartmentation of multiple metabolic enzymes and their preparation in vitro and in cellulo

Compartmentalization of multiple enzymes in cellulo and in vitro is a means of controlling the cascade reaction of metabolic enzymes. The compartmentation of enzymes through liquid-liquid phase separation may facilitate the reversible control of biocatalytic cascade reactions, thereby reducing the transcriptional and translational burden. This has attracted attention as a potential application in bioproduction. Recent research has demonstrated the existence and regulatory mechanisms of various enzyme compartments within cells. Mounting evidence suggests that enzyme compartmentation allows in vitro and in vivo regulation of cellular metabolism. However, the comprehensive regulatory mechanisms of enzyme condensates in cells and ideal organization of cellular systems remain unknown. This review provides an overview of the recent progress in multiple enzyme compartmentation in cells and summarizes strategies to reconstruct multiple enzyme assemblies in vitro and in cellulo. By examining parallel examples, we have evaluated the consensus and future perspectives of enzyme condensation.

An overview of cytoplasmic male sterility in Brassica napus

Rapeseed (Brassica napus ) is one of the world's most important oilseed crops, supplying humans with oil products, nutritious feed for livestock, and natural resources for industrial applications. Due to immense population pressure, more seed production is needed for human consumption due to its high quality of food products. As a vital genetic resource, male sterility provides ease in hybrid seed production and heterosis breeding. Better utilization of male sterility requires understanding its mechanisms, mode of action, and genes involved to be characterized in detail. Cytoplasmic male sterility (CMS) has been reported in many plant species and is a maternally inherited trait that restricts viable pollen development and production. The mitochondrial genome is involved in the induction of male sterility, while the nuclear genome plays its role in the restoration. Presently, rapeseed has more than 10 CMS systems. Pol-CMS and Shaan2A are autoplasmic resources that arose via natural mutation, while Nap-CMS and Nsa-CMS are alloplasmic and were created by intergeneric hybridisation. In this review, we discuss the types of male sterility systems in rapeseed and provide comprehensive information on CMS in rapeseed with a particular focus and emphasis the types of CMS in rapeseed.

PhWRKY30 activates salicylic acid biosynthesis to positively regulate antiviral defense response in petunia

Petunia (Petunia hybrida) plants are highly threatened by a diversity of viruses, causing substantial damage to ornamental quality and seed yield. However, the regulatory mechanism of virus resistance in petunia is largely unknown. Here, we revealed that a member of petunia WRKY transcription factors, PhWRKY30, was dramatically up-regulated following Tobacco rattle virus (TRV) infection. Down-regulation of PhWRKY30 through TRV-based virus-induced gene silencing increased green fluorescent protein (GFP)-marked TRV RNA accumulation and exacerbated the symptomatic severity. In comparison with wild-type (WT) plants, PhWRKY30-RNAi transgenic petunia plants exhibited a compromised resistance to TRV infection, whereas an enhanced resistance was observed in PhWRKY30-overexpressing (OE) transgenic plants. PhWRKY30 affected salicylic acid (SA) production and expression of arogenate dehydratase 1 (PhADT1), phenylalanine ammonia-lyase 1 (PhPAL1), PhPAL2b, nonexpressor of pathogenesis-related proteins 1 (PhNPR1), and PhPR1 in SA biosynthesis and signaling pathway. SA treatment restored the reduced TRV resistance to WT levels in PhWRKY30-RNAi plants, and application of SA biosynthesis inhibitor 2-aminoindan-2-phosphonic acid inhibited promoted resistance in PhWRKY30-OE plants. The protein-DNA binding assays showed that PhWRKY30 specifically bound to the promoter of PhPAL2b. RNAi silencing and overexpression of PhPAL2b led to decreased and increased TRV resistance, respectively. The transcription of a number of reactive oxygen species- and RNA silencing-associated genes was changed in PhWRKY30 and PhPAL2b transgenic lines. PhWRKY30 and PhPAL2b were further characterized to be involved in the resistance to Tobacco mosaic virus (TMV) invasion. Our findings demonstrate that PhWRKY30 positively regulates antiviral defense against TRV and TMV infections by modulating SA content.

Changes in leaf economic trait relationships across a precipitation gradient are related to differential gene expression in a C4 perennial grass

The leaf economics spectrum (LES) describes a suite of functional traits that consistently covary at large spatial and taxonomic scales. Despite its importance at these larger scales, few studies have examined the major drivers of intraspecific variation in the LES - phenotypic plasticity and standing genetic variation. Using experimental precipitation manipulations, we examined whether covariation among leaf economics traits and selection on leaf economics traits and trait combinations change as diverse genotypes of the widespread perennial grass Panicum virgatum are exposed to differences in precipitation. We also used RNA-Seq to examine whether groups of co-expressed genes that align with leaf economics traits function in processes hypothesized to underlie the LES. Water availability impacted leaf economics trait covariation in important ways - covariation between leaf economics traits and selection on covariation between traits (i.e. correlational selection) tended to be strongest when water availability was high. Additionally, many genes associated with leaf economics traits functioned in processes that may explain how the LES originates, such as chloroplasts, cell walls, and nitrogen metabolism. Water availability is likely an important modulator of selection and evolution of the LES in P. virgatum that can be better understood by examining gene expression.

Regulation of seed germination: ROS, epigenetic, and hormonal aspects

BACKGROUND

The whole life of a plant is regulated by complex environmental or hormonal signaling networks that control genomic stability, environmental signal transduction, and gene expression affecting plant development and viability. Seed germination, responsible for the transformation from seed to seedling, is a key initiation step in plant growth and is controlled by unique physiological and biochemical processes. It is continuously modulated by various factors including epigenetic modifications, hormone transport, ROS signaling, and interaction among them. ROS showed versatile crucial functions in seed germination including various physiological oxidations to nucleic acid, protein, lipid, or chromatin in the cytoplasm, cell wall, and nucleus.

AIM

of review: This review intends to provide novel insights into underlying mechanisms of seed germination especially associated with the ROS, and considers how these versatile regulatory mechanisms can be developed as useful tools for crop improvement.

KEY SCIENTIFIC CONCEPTS OF REVIEW

We have summarized the generation and elimination of ROS during seed germination, with a specific focus on uncovering and understanding the mechanisms of seed germination at the level of phytohormones, ROS, and epigenetic switches, as well as the close connections between them. The findings exhibit that ROS plays multiple roles in regulating the ethylene, ABA, and GA homeostasis as well as the Ca2+ signaling, NO signaling, and MAPK cascade in seed germination via either the signal trigger or the oxidative modifier agent. Further, ROS shows the potential in the nuclear genome remodeling and some epigenetic modifiers function, although the detailed mechanisms are unclear in seed germination. We propose that ROS functions as a hub in the complex network regulating seed germination.

Biosynthesis and functions of triterpenoids in cereals

BACKGROUND

Triterpenoids are versatile secondary metabolites with a diverse array of physiological activities, possessing valuable pharmacological effects and influencing the growth and development of plants. As more triterpenoids in cereals are unearthed and characterized, their biological roles in plant growth and development are gaining recognition.

AIM OF THE REVIEW

This review provides an overview of the structures, biosynthetic pathways, and diverse biological functions of triterpenoids identified in cereals. Our goal is to establish a basis for further exploration of triterpenoids with novel structures and functional activities in cereals, and to facilitate the potential application of triterpenoids in grain breeding, thus accelerating the development of superior grain varieties.

KEY SCIENTIFIC CONCEPTS OF THE REVIEW

This review consolidates information on various triterpenoid skeletons and derivatives found in cereals, and summarizes the pivotal enzyme genes involved, including oxidosqualene cyclase (OSC) and other triterpenoid modifying enzymes like cytochrome P450, glycosyltransferase, and acyltransferase. Triterpenoid-modifying enzymes exhibit specificity towards catalytic sites within triterpenoid skeletons, generating a diverse array of functional triterpenoid derivatives. Furthermore, triterpenoids have been shown to significantly impact the nutritional value, yield, disease resistance, and stress response of cereals.

A Genome-Wide Association Screen for Genes Affecting Leaf Trichome Development and Epidermal Metal Accumulation in Arabidopsis

To identify novel genes engaged in plant epidermal development, we characterized the phenotypic variability of rosette leaf epidermis of 310 sequenced Arabidopsis thaliana accessions, focusing on trichome shape and distribution, compositional characteristics of the trichome cell wall, and histologically detectable metal ion distribution. Some of these traits correlated with cLimate parameters of our accession's locations of origin, suggesting environmental selection. A novel metal deposition pattern in stomatal guard cells was observed in some accessions. Subsequent GWAS analysis identified 1546 loci with protein sequence-altering SNPs associated with one or more traits, including 5 genes with previously reported relevant mutant phenotypes and 80 additional genes with known or predicted roles in relevant developmental and cellular processes. Some candidates, including GFS9/TT9, exhibited environmentally correlated allele distribution. Several large gene famiLies, namely DUF674, DUF784, DUF1262, DUF1985, DUF3741, cytochrome P450, receptor-Like kinases, Cys/His-rich C1 domain proteins and formins were overrepresented among the candidates for various traits, suggesting epidermal development-related functions. A possible participation of formins in guard cell metal deposition was supported by observations in available loss of function mutants. Screening of candidate gene lists against the STRING interactome database uncovered several predominantly nuclear protein interaction networks with possible novel roles in epidermal development.

Ferritin From Striped Stem Borer (Chilo suppressalis) Oral Secretion Acts as an Effector Helping to Maintain Iron Homoeostasis and Impair Defenses in Rice

The striped stem borer (Chilo suppressalis, SSB) is a highly destructive insect pest in rice (Oryza sativa). SSB oral secretions (OSs) can induce plant defense responses in rice. However, the specific effectors in SSB OSs that mediate these interactions with rice remain poorly understood. In this study, hallmarks of ferroptosis-like plant defense response, such as the reprogramming of ferroptosis-related genes, reduced glutathione levels, accumulation of ferric ion, and enhanced lipid peroxidation by reactive oxygen species (ROS), were detected in rice subjected to SSB infestation and SSB OSs treatment. Furthermore, we identified and characterized a protein from SSB OSs, the ferritin CsFer1, which plays a critical role in the regulation of plant iron homoeostasis. CsFer1 was shown to possess Fe2+ binding capacity and ferroxidase activity. Through recombinant CsFer1 protein treatment, overexpression of CsFer1 in rice and SSB larvae with silencing CsFer1 feeding in rice, we found that CsFer1 helped maintain iron homoeostasis under SSB infestation, suppressing H2O2 and JA accumulation, ultimately compromising rice resistance to herbivorous pests. Moreover, such a phenomenon about the regulation of iron homoeostasis and suppression of insect resistance was observed in the CsFer1 overexpressed tobacco. Collectively, these findings suggest that CsFer1 functions as an effector involved in the regulation of iron homoeostasis- and lipid peroxidation-related plant defense during plant-insect interaction.

Early signalling events induced by glycine application in protoplasts of Mimosa pudica motor cells

Some amino acids have been shown to be signalling molecules in various developmental and stress processes, besides their roles in plant nutrition. Glycine is absorbed by pulvinar motor cells of Mimosa pudica according to an H+-Gly cotransport mechanism and under the control of calcium availability. Noteworthy, glycine triggers early plasma membrane depolarization and H+ migration. The unicellular model of protoplasts isolated from pulvini absorbed glycine with characteristics similar to those determined on multicellular motor tissues, considering metabolism regulation, plasma membrane functionality and calcium control. This model allows to observe that a rapid increase of glycine uptake rate occurs in the first 3 min following 10 mM glycine application. Additionally, we monitored a rapid transient increase (within 5-11 s) of the cytoplasmic free calcium ([Ca2+]c) measured by cytofluorimetric determination using Indo-1-loaded protoplasts. The low [Ca2+]c increase seen in nominally Ca2+-free medium and the inhibition of [Ca2+]c increase after treatment with channel inhibitors (LaCl3, nifedipine) argue for a Ca2+ mobilization from external stores. This observation emphasized the signalling role of glycine at the plasma membrane site.

Ethylene response factor AeABR1 regulates chlorophyll degradation in post-harvest okras

Chlorophyll degradation, marked by the loss of green color, is a prominent feature of okra storage after harvest, posing challenges for its storage, transportation, and marketability. In order to investigate the regulatory mechanisms of chlorophyll degradation in okras, we isolated and characterized AeABR1, a repressor of abscisic acid (ABA) that belongs to the ethylene-responsive element-binding factor (ERF/AP2) superfamily of ERF transcription factors. The transcriptional levels of AeABR1 during storage were closely linked to the degreening of okra fruit (R-values ranging from -0.714 to -0.516, P < 0.05) and the production of ethylene (R = -0.362, P < 0.05). Subcellular localization analysis revealed that AeABR1 was mostly located in the nucleus. Functional studies demonstrated that the transient expression of AeABR1 induced rapid chlorophyll degradation in the leaves of okra and N. benthamiana. Similar results were observed in transgenic Arabidopsis seedlings expressing AeABR1, which exhibited yellowing growth phenotypes, reduced chlorophyll content, and elevated chlorophyll catabolic genes (CCGs) expression levels. AeABR1 substantially induced the activities of AeCLH1 promoters. These findings indicated that AeABR1 may act as an activator of AeCLH1 genes and an accelerator of chlorophyll degradation in post-harvest okras.

Unraveling the evolution of the ATB2 subgroup basic leucine zipper transcription factors in plants and decoding the positive effects of BdibZIP44 and BdibZIP53 on heat stress in Brachypodium distachyon

In plants, basic region/leucine zipper motif (bZIP) transcription factors (TFs) stand as pivotal regulators in a broad spectrum of developmental mechanisms and adaptive strategies against environmental pressures. However, the ancestral origins and the evolutionary progression of their functional diversity across plant species have yet to be thoroughly illuminated. This study delved into the ATB2 subgroup bZIP homologs, tracing them back to the ancestral charophyte lineage predating land plant emergence, and categorized them into four distinct phylogenetic clusters (Clades A to D). Of particular note, our findings highlighted bZIP44_GBF6 and bZIP53 orthologs as angiosperm-specific innovations, distinguished by the acquisition of novel protein motifs and an intensified regime of purifying selection, reflecting their specialized evolutionary trajectories. Through synteny analysis, we uncovered that whole-genome duplication (WGD) events, post-monocot/dicot split, have played independent yet pivotal roles in shaping the bZIP44_GBF6 and bZIP53 lineages. Furthermore, an assessment of codon usage patterns disclosed a conspicuous bias in monocots favoring G3s, C3s, Gc3s, and GC content, while demonstrating a relative avoidance of T3s, A3s, and Nc usage frequencies. Functionally, we demonstrated that BdibZIP44 and BdibZIP53, localized to the nucleus, possessed the capability to dimerize, both homotypically and heterotypically. These proteins exhibited inducible expression under heat stress conditions in Brachypodium distachyon, implicating them in thermotolerance mechanisms. Overexpression studies reinforced their positive regulatory influence on heat stress resilience by augmenting the enzymatic activity of antioxidants, including catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD), which collectively enhance the clearance of deleterious reactive oxygen species (ROS). Taken together, this research significantly advanced our understanding of the origins and the adaptive evolutionary journey of ATB2 subgroup bZIP homologs in the plant kingdom. Moreover, it elucidated the vital roles of BdibZIP44 and BdibZIP53 in orchestrating a robust defense against high-temperature stress, thereby contributing to the broader discourse on plant adaptation and survival strategies under changing climatic conditions.

Plastidial metabolites and retrograde signaling: A case study of MEP pathway intermediate MEcPP that orchestrates plant growth and stress responses

Plants are frequently exposed to environmental stresses. In a plant cell, chloroplast acts as machinery that rapidly senses changing environmental conditions and coordinates with the nucleus and other subcellular organelles by exchanging plastidial metabolites, proteins/peptides, or lipid derivatives, some of which may act as retrograde signals. These specific plastidial metabolites include carotenoid derivatives, isoprenes, phosphoadenosines, tetrapyrroles, phytohormone (like salicylic acid), and reactive electrophile species (RES), which mediate retrograde communications to sustain stress conditions. The methylerythritol phosphate (MEP) pathway is an essential and evolutionarily conserved isoprenoid biosynthetic pathway operating in bacteria and plastids, synthesizing metabolites such as terpenoids, gibberellins, abscisic acid, phytol chain of chlorophyll, carotenoids, tocopherols, and glycosides. The MEP pathway is susceptible to oxidative stress, which results in the overaccumulation of its intermediates, such as methylerythritol cyclodiphosphate (MEcPP). Recent studies revealed that under stress conditions, leading to its accumulation, MEcPP mediates retrograde signaling that alters the nuclear gene expression, leading to growth inhibition and acclimation. This review covers aspects of its generation, signaling, mechanism of action, and interplay with other factors to acquire adaptive responses during stress conditions. The review highlights the importance of plastids as sensors of stress and plastidial metabolites as retrograde signals communicating with nucleus and other sub-cellular organelles to regulate plants' response to different stress conditions.

Multiple layers of regulators emerge in the network controlling lateral root organogenesis

Lateral root (LR) formation is a postembryonic organogenesis process that is crucial for plant root system development and adaptation to heterogenous soil environments. Since the early 1990s, a wealth of experimental data on arabidopsis (Arabidopsis thaliana) has helped reveal the LR formation regulatory network, in which dynamic auxin distribution and transcriptional cascades direct root cells through their organogenesis pathway. Some parts of this network appear conserved across diverse plant species or distinct developmental contexts. Recently, our knowledge of this process dramatically expanded thanks to technical advances, from single cell profiling to whole-root system phenotyping. Interestingly, new players are now emerging in this network, such as fatty acids and reactive oxygen species (ROS), transforming our knowledge of this hidden half of plant biology.

Genome-Wide Association Studies Reveal the Genetic Architecture of Ionomic Variation in Grains of Tartary Buckwheat

Tartary buckwheat (Fagopyrum tataricum) is esteemed as a medicinal crop due to its high nutritional and health value. However, the genetic basis for the variations in Tartary buckwheat grain ionome remains inadequately understood. Through genome-wide association studies (GWAS) on grain ionome, 52 genetic loci are identified associated with 10 elements undergoing selection. Molecular experiments have shown that the variation in FtACA13's promoter (an auto-inhibited Ca2+-ATPase) is accountable for grain sodium concentration and salt tolerance, which underwent selection during domestication. FtYPQ1 (a vacuolar amino acid transporter) exhibits zinc transport activity, enhancing tolerance to excessive zinc stress and raising zinc accumulation. Additionally, FtNHX2 (a Na+/H+ exchanger) positively regulates arsenic content. Further genomic comparative analysis of "20A1" (wild accession) and "Pinku" (cultivated accession) unveiled structural variants in key genes involved in ion uptake and transport that may result in considerable changes in their functions. This research establishes the initial comprehensive grain ionome atlas in Tartary buckwheat, which will significantly aid in genetic improvement for nutrient biofortification.

Functional analysis of the epsilon glutathione S-transferases in the adaptation of Spodoptera litura to xanthotoxin

Through long-term coevolution with host plants, insects have evolved sophisticated detoxification systems to counteract plant secondary metabolites (PSMs). However, the precise mechanisms underlying these adaptations remain incompletely characterized. Our previous research identified epsilon glutathione S-transferases (GSTes) as critical mediators of xanthotoxin adaptation in Spodoptera litura, a model linear furanocoumarin. This study reveals that heterologous overexpression of five xanthotoxin-responsive GSTes in Escherichia coli significantly enhances bacterial tolerance to this PSM. Disk diffusion assays and metabolic studies demonstrated that both GSTe1 and GSTe16 mediate xanthotoxin adaptation via dual mechanisms involving antioxidant activity and catalytic metabolism. Fluorescent competitive binding experiments indicated that all five GSTes exhibit non-catalytic xanthotoxin sequestration capabilities. These in vitro observations were complemented by in vivo genetic manipulation of GSTe16, which exhibited the most potent defense activity against xanthotoxin. CRISPR/Cas9-mediated GSTe16 knockout in S. litura significantly increased larval susceptibility to xanthotoxin, while transgenic Drosophila melanogaster overexpressing GSTe16 showed enhanced tolerance to xanthotoxin. Furthermore, the endogenous biosynthesis of 20-hydroxyecdysone (20E) was provoked upon exposure to xanthotoxin, and 20E application enhanced the larval tolerance to xanthotoxin as well as the expression levels of GSTe16. Dual-luciferase reporter assays identified two functional cis-regulatory elements in the GSTe16 promoter that facilitate transcriptional activation by the ecdysone receptor (EcR)/ultraspiracle (USP) heterodimer. Overall, this study elucidates the biochemical defense characteristics and transcriptional responses of GSTes to xanthotoxin in S. litura, providing novel insights into the counter-defense mechanisms of herbivorous insects against host plants.

The dual-action evolutionarily conserved NatB catalytic subunit NAA20 regulates poplar root development in response to salt and osmotic stresses

In Populus simonii, the N-terminal acetyltransferase subunit gene PsiNAA20 was induced by salt stress and osmotic stress and regulates root development. The spatiotemporal specificity of PsiNAA20-interacting gene expression and translation efficiency suggested dual functions in poplar root development under salt stress and osmotic stress.

Gretchen Hagen 3.6-like promotes anthocyanin accumulation by negatively regulating the expression of basic helix-loop-helix transcription factor 106 in grapevine

Anthocyanins are mainly synthesized from flavonoid precursors in plants. Although there have been numerous studies on the biosynthesis of anthocyanins, few have sought to explore how Gretchen Hagen 3 (GH3) genes regulate the production of anthocyanins. In this study, a VaGH3.6-like gene was identified, and its overexpression in grapevine callus tissues and berry skins promoted significant accumulation of anthocyanins and reduced endogenous IAA content under light conditions, whereas callus tissues transformed with a mutant VaGH3.6-like showed the opposite results. The overexpression of VaGH3.6-like was observed to directly promote the accumulation of flavonoids under dark conditions, whereas the accumulation was significantly reduced in mutants. In addition, the VabHLH106 transcription factor, a negative regulator of VaGH3.6-like, was screened via RNA-seq. Subsequent analyses using Y2H, Y1H, DLR™, and EMSA analyses revealed that VabHLH106 represses VaGH3.6-like expression by directly binding to two E-box elements in its promoter region. Interestingly, VaGH3.6-like overexpression regulates VabHLH106 expression via a negative feedback mechanism, attenuating the repressive effect of VabHLH106 on the downstream genes VvLDOX, VvCYP75B2, and VvCYP73A3, thus leading to an increasing in the synthesis of anthocyanins in grapes. These findings provide a new theoretical basis for further understanding the molecular mechanisms underlying accumulation of anthocyanins in grapes.

Arabidopsis perceives caterpillar oral secretion to increase resistance by reactive oxygen species-enhanced glucosinolate hydrolysis

In Arabidopsis, the outbreaks of reactive oxygen species (ROS) occur upon pathogen recognition by pattern- and effector-triggered immunity (PTI and ETI, respectively), which plays a significant role in disease resistance. Here, we found that Arabidopsis also experiences two outbreaks of ROS (oral secretion (OS)-induced ROS (ROSOS)) upon the perception of OS from cotton bollworm (Helicoverpa armigera) and other lepidopterans. Oral secretion-induced ROS burst requires the PTI machinery, including BRI1-ASSOCIATED RECEPTOR KINASE1 (BAK1) and BOTRYTIS-INDUCED KINASE1 (BIK1). Oral secretion-induced ROS are primarily produced by respiratory burst oxidase homologue D (RBOHD) in the apoplast, and the double mutant, rbohdf, exhibits reduced resistance to lepidopterans. Insect biting rather than wounding induces the gene expressions of plant defense-associated respiratory burst and toxin catabolic processes, facilitating the breakdown of leaf glucosinolates into bioactive intermediates, like sulforaphane, thereby impeding insect herbivory. Our investigation demonstrates that Arabidopsis perceives insect OS in a BAK1-BIK1-dependent manner and employs RBOHD to produce ROS in the apoplast, thereby enhancing its insect resistance by accelerating glucosinolate hydrolysis.

Major facilitator family transporters specifically enhance caffeyl alcohol uptake during C-lignin biosynthesis

The mode of transport of lignin monomers to the sites of polymerization in the apoplast remains controversial. C-Lignin is a recently discovered form of lignin found in some seed coats that is composed exclusively of units derived from caffeyl alcohol. RNA-seq and proteome analyses identified a number of transporters co-expressed with C-lignin deposition in the seed coat of Cleome hassleriana. Cloning and influx/efflux analysis assays in yeast identified two low-affinity transporters, ChPLT3 and ChSUC1, that were active with caffeyl alcohol but not with the classical monolignols p-coumaryl, coniferyl, and sinapyl alcohols, consistent with molecular modeling and docking studies. Expression of ChPLT3 in Arabidopsis seedlings enhanced root growth in the presence of caffeyl alcohol, and expression of ChPLT3 and ChSUC1 correlated with lignin C-unit content in hairy roots of Medicago truncatula. We present a model, consistent with phylogenetic and evolutionary considerations, whereby passive caffeyl alcohol transport may be supplemented by hitchhiking on secondary active transporters to ensure the synthesis of C-lignin, and inhibition of synthesis of G-lignin, in the apoplast.

GLR3.6T807I Mutation of Casuarina equisetifolia Is Associated With a Decreased JA Response to Insect Feeding by Lymantria xylina

Lymantria xylina is the most important defoliator, damaging the effective coastal windbreak tree species Casuarina equisetifolia. However, the underlying genetic mechanisms through which C. equisetifolia responds to L. xylina attacks remain unknown. Here, we compared the transcriptional, phytohormone and metabolic differences between susceptible (S) and resistant (R) C. equisetifolia cultivars in response to L. xylina feeding. The main L. xylina-induced resistance in C. equisetifolia was a jasmonate (JA) response and JA synthesis was highly induced by L. xylina feeding at both the transcriptional and metabolic levels, thus promoting flavonoid accumulation. The JA response was highly activated by L. xylina feeding on the R but not in the S cultivar, although the JA signalling pathway was intact in both cultivars. We found a single amino acid mutation in the homologues of glutamate receptor-like protein 3.6 (CeGLR3.6T807I) in the S cultivar. Compared with the GLR3.6 homologues in the R cultivar, phosphorylation of CeGLR3.6T807I was not induced by insect feeding, leading to a decreased JA response in the S cultivar. Collectively, this study provides new insights into the function of CeGLR3.6 in regulating the JA response of C. equisetifolia to L. xylina feeding.

Development and application of a sex-linked marker for Herpetospermum pedunculosum based on whole-genome resequencing

Sex-specific DNA markers are effective tools for sex identification and sex-controlled breeding of dioecious organisms. The seeds of the dioecious Herpetospermum pedunculosum are utilized in traditional Chinese medicine, and the development of sex-linked markers for seedlings is crucial for enhancing the number of female plants. In this study, we screened sex-specific markers based on whole-genome resequencing of 20 male and 24 female H. pedunculosum individuals, and validated a male-specific DNA fragment of 505 bp among 80 individuals from four populations using simple PCR. The findings provide a reliable male-specific marker for the sex identification of H. pedunculosum seedlings.

Circadian regulation of key physiological processes by the RITMO1 clock protein in the marine diatom Phaeodactylum tricornutum

Phasing biological and physiological processes to periodic light-dark cycles is crucial for the life of most organisms. Marine diatoms, as many phytoplanktonic species, exhibit biological rhythms, yet their molecular timekeepers remain largely uncharacterized. Recently, the bHLH-PAS protein RITMO1 has been proposed to act as a regulator of diatom circadian rhythms. In this study, we first determined the physiological conditions to monitor circadian clock activity and its perturbation in the diatom model species Phaeodactylum tricornutum by using cell fluorescence as a circadian output. Employing ectopic overexpression, targeted gene mutagenesis, and functional complementation, we then investigated the role of RITMO1 in various circadian processes. Our data reveal that RITMO1 significantly influences the P. tricornutum circadian rhythms not only of cellular fluorescence, but also of photosynthesis and of the expression of clock-controlled genes, including transcription factors and putative clock input/output components. RITMO1 effects on rhythmicity are unambiguously detectable under free-running conditions. By uncovering the complex regulation of biological rhythms in P. tricornutum, these findings advance our understanding of the endogenous factors controlling diatom physiological responses to environmental changes. They also offer initial insights into the mechanistic principles of oscillator functions in a major group of phytoplankton, which remain largely unexplored in chronobiology.

Integration of single-nuclei transcriptome and bulk RNA-seq to unravel the role of AhWRKY70 in regulating stem cell development in Arachis hypogaea L

Peanut stem is a vital organ to provide mechanical support and energy for aerial tissue development. However, the transcriptional regulatory mechanisms underlying stem development at a single-cell resolution remain unclear. Herein, single-nuclei isolation coupled with fluorescent-activated cell sorting was employed to construct a cell atlas of peanut seedling stems using microdroplets-based single-nuclei RNA-sequencing. This approach yielded 29 308 cells with 53 349 expressed genes underlying the identification of five cell types characterized by known marker genes. Additionally, 2053 differentially expressed genes (DEGs) were identified across different cell types. Furthermore, 3306 core-DEGs involved in cell development trajectories were used to construct a transcription factor (TF) interaction network, providing insights into specific biological pathways and transcriptional regulation dynamics underlying cell-type differentiation. Additionally, 1446 DEGs associated with different cell-cycle profile were identified, revealing that peanut stem elongation and cell expansion are closely linked to auxin-responsive pathway. This was supported by the examination of endogenous phytohormones and the identification of 10 hormone-responsive DEGs. Moreover, AhWRKY70 was localized in the nucleus and is highly enriched in stem cortex and xylem cells and exhibits a tissue-specific expression pattern that regulates stem growth. Overexpression of AhWRKY70 in Arabidopsis led to accelerated stem growth by modulating the phytohormone signalling pathway, influencing the expression of sixteen auxin and ethylene-responsive genes as demonstrated by transcriptome sequencing. In conclusion, the single-cell atlas provides a foundational dataset for understanding gene expression heterogeneity in peanut seedling stems. The elucidation of AhWRKY70 function expands our understanding of the roles of WRKY family members in peanut.

Mitochondrial gene editing and allotopic expression unveil the role of orf125 in the induction of male fertility in some Solanum spp. hybrids and in the evolution of the common potato

Genic-cytoplasmic male sterility (CMS) due to interactions between nuclear and cytoplasmic genomes is a well-known phenomenon in some Solanum spp. hybrids, but genes involved are not known. In this study, the chondriomes of two isonuclear male-fertile and sterile somatic hybrids (SH9A and SH9B, respectively) between the common potato (S. tuberosum Group Tuberosum, tbr) and the wild species S. commersonii were sequenced and compared to those of parental species to identify mitochondrial genes involved in the expression of male sterility. A putative novel gene (orf125) was found only in tbr and in male-sterile hybrids. Physical or functional deletion of orf125 by mtDNA editing in SH9B and its allotopic expression in SH9A clearly demonstrated that orf125 affects male fertility. Besides knockout mutants induced by mitoTALEN and DddA-derived cytosine base editing, specific orf125 missense mutations generated by the latter approach also induced reversion to male fertility in edited SH9B plants, prompting further studies on ORF125 structure-function relationship. The organization of the mitochondrial genome region implicated in CMS was found to be conserved across all common potato accessions, while an identical copy of tbr orf125 was detected in accessions belonging to the S. berthaultii species complex (ber). Such findings corroborate the hypothesis that ber accessions with T/β cytoplasm outcrossed as female with Andean potato, giving rise to the differentiation of the Chilean potato, and highlight the origin of mitochondrial factors contributing to genic-cytoplasmic male sterility in some tuber-bearing Solanum hybrids. Our results contribute to the development of innovative breeding approaches in potato.