Loss of function of a rice TPR-domain RNA-binding protein confers broad-spectrum disease resistance

The Magnaporthe oryzae effector MoBys1 suppresses rice immunity by targeting OsCAD2 to manipulate host jasmonate and lignin metabolism

Rice blast disease caused by Magnaporthe oryzae poses a severe threat to rice production. To counteract M. oryzae, plants synthesize jasmonate (JA) and lignin, two primary defense-related metabolites, to initiate defense programs. However, the mechanism through which M. oryzae modulates JA- and lignin-mediated plant immunity remains unclear. In this study, a novel M. oryzae effector, MoBys1, was identified as being involved in pathogenesis. Knockout of MoBys1 in M. oryzae significantly reduced its infection ability. Conversely, overexpression of MoBys1 in rice impaired the rice defense response. MoBys1 localizes to the plant cytoplasm and nucleus and interacts with rice cinnamyl alcohol dehydrogenase 2 (OsCAD2), an enzyme that catalyzes lignin biosynthesis. While OsCAD2 mutants exhibited weakened defenses, overexpression lines demonstrated enhanced resistance, highlighting the critical role of OsCAD2 in blast resistance. Furthermore, OsCAD2 functions as a transcription factor regulating a wide range of biological processes, including JA and lignin signaling pathways. The interaction between MoBys1 and OsCAD2 promotes OsCAD2 degradation, leading to reduced lignin and JA accumulation. These findings uncover a novel counter-defense mechanism by which M. oryzae employs the effector MoBys1 to degrade OsCAD2 and suppress host defense-related metabolite accumulation during infection.

Breeding D1-Type Hybrid Japonica Rice in Diverse Upland Rainfed Environments

'Dianheyou615' (DHY615) is an elite Dian (D1)-type hybrid japonica rice variety, renowned for its high yield, exceptional grain quality, and unique adaptability to both irrigated and rainfed conditions in the Yungui Plateau of southwestern China. However, the genetic mechanisms underlying the agronomic performance of the D1-type hybrid japonica rice remain unclear. In this study, a comprehensive analysis of 'DHY615''s agronomic performance, genetic genealogy, and molecular genetic foundation was conducted to dissect its desirable traits for upland rainfed cultivation across diverse ecological environments. The main findings indicate that 'DHY615' possesses 6432 heterozygous SNPs, with 57.48% and 14.43% located in the promoter and coding regions, respectively, potentially affecting key phenotypic traits. High-impact SNPs variants and numerous well-known functional genes were identified, such as OsAAP6, GS3, Sd1, Rf1, BADH2, BPh14, Rymv1, OsFRO1, NRT1.1B, SKC1, OsNCED2, and qUVR-10, which are likely linked to traits including plant architecture, grain yield, grain quality, and resistance to various biotic and abiotic stresses (e.g., disease, cold, drought, salt, high iron, and high UV radiation). Notably, 'Nan615' harbors a greater number of functional allele variants compared to 'H479A', which potentially explaining its superior grain yield and remarkable adaptability. This study offers novel and valuable insights into the molecular genetic foundation of the plateau D1-type hybrid japonica rice, underscoring its potential for sustainable rice production across diverse ecological zones, especially with its unparalleled high-altitude adaptability to rainfed upland planting.

Deciphering the regulatory network of lignocellulose biosynthesis in bread wheat through genome-wide association studies

KEY MESSAGE

This study identified 46 key QTL and 17 candidate genes and developed a KASP marker, providing valuable molecular tools for enhancing lignocellulose traits, lodging resistance, and bioenergy potential in wheat. Wheat lignocellulose, composed of lignin, cellulose, and hemicellulose, plays a crucial role in strengthening plant cell walls, enhancing lodging resistance, and contributing to bioenergy production. However, the genetic basis underlying the variation in lignocellulose content in wheat remains poorly understood. The stem lignin, cellulose, and hemicellulos contents in the second stem internode of a panel of 166 wheat accessions grown in three environments were measured, combined with the genotyping data with 660 K wheat SNP chip; a genome-wide association studies (GWAS) were conducted to identify loci associated with the lignocellulose content in wheat. Significant variations in lignin, cellulose, and hemicellulose contents were observed among the wheat accessions. GWAS identified 1146 significant SNPs associated with lignin, cellulose, and hemicellulose contents, distributed across the A, B, and D sub-genomes of wheat. Joint analysis of haplotype blocks refined these associations, identifying 46 significant quantitative trait loci (QTL) regions and 17 candidate genes, primarily linked to vascular development, hemicellulose synthesis, internode elongation regulation, and lignin biosynthesis. A KASP marker (NW_CC5951) for lignocellulose was developed. These findings provide valuable molecular markers for marker-assisted selection, supporting wheat breeding for improved stem quality and lodging resistance, and offer insights into balancing grain yield with lodging resistance and lignocellulosic energy production.

A WRKY transcription factor confers broad-spectrum resistance to biotic stresses and yield stability in rice

Plants are subject to attack by diverse pests and pathogens. Few genes conferring broad-spectrum resistance to both insects and pathogens have been identified. Because of the growth-defense tradeoff, it is often challenging to balance biotic stress resistance and yield for crops. Here, we report that OsWRKY36 suppresses the resistance to insects and pathogens via transcriptional repression of Phenylalanine Ammonia Lyases (PALs), a key enzyme in phenylpropanoid pathway in rice. Knocking out OsWRKY36 causes elevated lignin biosynthesis and increased sclerenchyma thickness of leaf sheath, leading to enhanced resistance to multiple pests and pathogens. Additionally, loss of OsWRKY36 also derepresses the transcription of Ideal Plant Architecture 1 (IPA1) and MONOCULM2 (MOC2), resulting in increased spikelet number per panicle and tiller number. These findings provide mechanistic insights into biotic stress tolerance in rice and offer a promising strategy to breed rice cultivars with broad-spectrum resistance to insects and pathogens while maintaining stable yield.

Ferroptosis in plant immunity

Plant cell death is mediated by calcium, iron, and reactive oxygen species (ROS) signaling in plant immunity. The reconstruction of a nucleotide-binding leucine-rich-repeat receptor (NLR) supramolecular structure, called the resistosome, is intimately involved in the hypersensitive response (HR), a type of cell death involved in effector-triggered immunity (ETI). Iron is a crucial redox catalyst in various cellular reactions. Ferroptosis is a regulated, non-apoptotic form of iron- and ROS-dependent cell death in plants. Pathogen infections trigger iron accumulation and ROS bursts in plant cells, leading to lipid peroxidation via the Fenton reaction and subsequent ferroptosis in plant cells similar to that in mammalian cells. The small-molecule inducer erastin triggers iron-dependent lipid ROS accumulation and glutathione depletion, leading to HR cell death in plant immunity. Calcium (Ca2+) is another major mediator of plant immunity. Cytoplasmic Ca2+ influx through calcium-permeable channels, the resistosomes, mediates iron- and ROS-dependent ferroptotic cell death under reduced glutathione reductase (GR) expression levels in the ETI response. Acibenzolar-S-methyl (ASM), a plant defense activator, enhances Ca2+ influx, ROS and iron accumulation, and lipid peroxidation to trigger ferroptotic cell death. These breakthroughs suggest a potential role for Ca2+ signaling in ferroptosis and its coordination with iron and ROS signaling in plant immunity. In this review, we highlight the essential roles of calcium, iron, and ROS signaling in ferroptosis during plant immunity and discuss advances in the understanding of how Ca2+-mediated ferroptotic cell death orchestrates effective plant immune responses against invading pathogens.

Rice transcription factor bHLH25 confers resistance to multiple diseases by sensing H2O2

Hydrogen peroxide (H2O2) is a ubiquitous signal regulating many biological processes, including innate immunity, in all eukaryotes. However, it remains largely unknown that how transcription factors directly sense H2O2 in eukaryotes. Here, we report that rice basic/helix-loop-helix transcription factor bHLH25 directly senses H2O2 to confer resistance to multiple diseases caused by fungi or bacteria. Upon pathogen attack, rice plants increase the production of H2O2, which directly oxidizes bHLH25 at methionine 256 in the nucleus. Oxidized bHLH25 represses miR397b expression to activate lignin biosynthesis for plant cell wall reinforcement, preventing pathogens from penetrating plant cells. Lignin biosynthesis consumes H2O2 causing accumulation of non-oxidized bHLH25. Non-oxidized bHLH25 switches to promote the expression of Copalyl Diphosphate Synthase 2 (CPS2), which increases phytoalexin biosynthesis to inhibit expansion of pathogens that escape into plants. This oxidization/non-oxidation status change of bHLH25 allows plants to maintain H2O2, lignin and phytoalexin at optimized levels to effectively fight against pathogens and prevents these three molecules from over-accumulation that harms plants. Thus, our discovery reveals a novel mechanism by which a single protein promotes two independent defense pathways against pathogens. Importantly, the bHLH25 orthologues from available plant genomes all contain a conserved M256-like methionine suggesting the broad existence of this mechanism in the plant kingdom. Moreover, this Met-oxidation mechanism may also be employed by other eukaryotic transcription factors to sense H2O2 to change functions.

Genetic engineering, including genome editing, for enhancing broad-spectrum disease resistance in crops

Plant diseases, caused by a wide range of pathogens, severely reduce crop yield and quality, posing a significant threat to global food security. Developing broad-spectrum resistance (BSR) in crops is a key strategy for controlling crop diseases and ensuring sustainable crop production. Cloning disease-resistance (R) genes and understanding their underlying molecular mechanisms provide new genetic resources and strategies for crop breeding. Novel genetic engineering and genome editing tools have accelerated the study and engineering of BSR genes in crops, which is the primary focus of this review. We first summarize recent advances in understanding the plant immune system, followed by an examination of the molecular mechanisms underlying BSR in crops. Finally, we highlight diverse strategies employed to achieve BSR, including gene stacking to combine multiple R genes, multiplexed genome editing of susceptibility genes and promoter regions of executor R genes, editing cis-regulatory elements to fine-tune gene expression, RNA interference, saturation mutagenesis, and precise genomic insertions. The genetic studies and engineering of BSR are accelerating the breeding of disease-resistant cultivars, contributing to crop improvement and enhancing global food security.

LACCASE35 enhances lignification and resistance against Pseudomonas syringae pv. actinidiae infection in kiwifruit

Kiwifruit bacterial canker, a highly destructive disease caused by Pseudomonas syringae pv. actinidiae (Psa), seriously affects kiwifruit (Actinidia spp.) production. Lignin deposition in infected cells serves as a defense mechanism, effectively suppressing pathogen growth. However, the underlying process remains unclear. In this study, we determined that Psa infection leads to a significant increase in S-lignin accumulation in kiwifruit. The S/G ratio in lignin was higher in a Psa-resistant cultivar than in a Psa-sensitive cultivar. Furthermore, kiwifruit laccase 35 (AcLac35), encoding an enzyme in the lignin biosynthesis pathway with characteristic laccase activity, showed tissue-specific expression in plants and was upregulated following infection by Psa. Overexpressing AcLac35 in kiwifruit leaves resulted in greater lignin content than in wild-type leaves, leading to the formation of thicker cell walls, and also activated plant-pathogen interactions and MAPK pathways, thereby enhancing resistance against Psa infection. Yeast 1-hybrid assays, dual-LUC reporter assays, electrophoretic mobility shift assays, and transient injection experiments indicated that SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE 9 (AcSPL9) can bind to the AcLac35 promoter, thereby positively regulating its expression. Moreover, overexpression of AcSPL9 increased lignin accumulation in kiwifruit leaves, enhancing resistance to Psa, while virus-induced gene silencing of AcSPL9 expression reduced this resistance. Our findings reveal the function of AsSPL9-AcLac35 in kiwifruit, providing insight into enhancing resistance against Psa in kiwifruit.

Ubiquitination of OsCSN5 by OsPUB45 activates immunity by modulating the OsCUL3a-OsNPR1 module

The COP9 signalosome (CSN) is a highly conserved protein complex in eukaryotes, with CSN5 serving as its critical catalytic subunit. However, the role of CSN5 in plant immunity is largely unexplored. Here, we found that suppression of OsCSN5 in rice enhances resistance against the fungal pathogen Magnaporthe oryzae and the bacterial pathogen Xanthomonas oryzae pv. oryzae (Xoo) without affecting growth. OsCSN5 is ubiquitinated and degraded by the E3 ligase OsPUB45. Overexpression of OsPUB45 increased resistance against M. oryzae and Xoo, while dysfunction of OsPUB45 decreased resistance. In addition, OsCSN5 stabilized OsCUL3a to promote the degradation of a positive regulator OsNPR1. Overexpression of OsPUB45 compromised accumulation of OsCUL3a, leading to stabilization of OsNPR1, whereas mutations in OsPUB45 destabilized OsNPR1. These findings suggest that OsCSN5 stabilizes OsCUL3a to facilitate the degradation of OsNPR1, preventing its constitutive activation without infection. Conversely, OsPUB45 promotes the degradation of OsCSN5, contributing to immunity activation upon pathogen infection.

OsBRW1, a novel blast-resistant gene, coded a NBS-LRR protein to interact with OsSRFP1 to balance rice growth and resistance

It is urgent to mine novel blast-resistant genes in rice and develop new rice varieties with pyramiding blast-resistant genes. In this study, a new blast-resistant gene, OsBRW1, was screened from a set of rice near-isogenic lines (NILs) with different blast-resistant ability. Under the infection of Magnaporthe oryzae (M. oryzae), OsBRW1 in the resistant NIL Pi-4b was highly induced than that in the susceptible NIL Pi-1 and their parent line CO39, and the blast-resistant ability of OsBRW1 was further confirmed by using CRISPR/Cas9 knockout and over-expression methods. The protein encoded by OsBRW1 was a typical NBS-LRR with NB-ARC domain and localized in both cytoplasm and nucleus, and the transient expression of OsBRW1 was capable of triggering hypersensitive response in tobacco leaves. Protein interaction experiments showed that OsBRW1 protein directly interacted with OsSRFP1. At the early infection stage of M. oryzae, OsBRW1 gene induced OsSRFP1 to highly expression level and accumulated H2O2, up-regulated the defence responsive signalling transduction genes and the pathogenesis-related genes and increased JA and SA content in the resistant NIL Pi-4b. By contrary, lower content of endogenous JA and SA in osbrw1 mutants was found at the same stage. After that, OsSRFP1 was down-regulated to constitution abundance to balance the growth of the resistant NIL Pi-4b. In summary, OsBRW1 solicited OsSRFP1 to resist the infection of blast fungus in rice by inducing the synergism of induced systemic resistance (ISR) and system acquired resistance (SAR) and to balance the growth of rice plants.

Genome editing in Sub-Saharan Africa: a game-changing strategy for climate change mitigation and sustainable agriculture

Sub-Saharan Africa's agricultural sector faces a multifaceted challenge due to climate change consisting of high temperatures, changing precipitation trends, alongside intensified pest and disease outbreaks. Conventional plant breeding methods have historically contributed to yield gains in Africa, and the intensifying demand for food security outpaces these improvements due to a confluence of factors, including rising urbanization, improved living standards, and population growth. To address escalating food demands amidst urbanization, rising living standards, and population growth, a paradigm shift toward more sustainable and innovative crop improvement strategies is imperative. Genome editing technologies offer a promising avenue for achieving sustained yield increases while bolstering resilience against escalating biotic and abiotic stresses associated with climate change. Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein (CRISPR/Cas) is unique due to its ubiquity, efficacy, alongside precision, making it a pivotal tool for Sub-Saharan African crop improvement. This review highlights the challenges and explores the prospect of gene editing to secure the region's future foods.

Development of an infiltration-based RNA preservation method for cryogen-free storage of leaves for gene expression analyses in field-grown plants

BACKGROUND

Gene expression is a fundamental process for plants to express their phenotype, and its analysis is the basis of molecular studies. However, the instability of RNA often poses an obstacle to analyzing plants grown in fields or remote locations where the availability of liquid nitrogen or dry ice is limited. To deepen our understanding of plant phenotypes and tolerance to field-specific stresses, it is crucial to develop methodologies to maintain plant RNA intact and safely transfer it for downstream analyses such as qPCR and RNA-seq.

RESULTS

In this study, the author developed a novel tissue preservation method that involved the infiltration of RNA preservation solution into the leaf apoplast using a syringe and subsequent storage at 4 °C. RNA-seq using samples stored for 5 d and principal component analyses showed that rice leaves treated with the infiltration method maintained the original transcriptome pattern better than those treated with the traditional method when the leaves were simply immersed in the solution. Additionally, it was also found that extracted RNA can be transported with minimum risk of degradation when it is bound to the membrane of RNA extraction kits. The developed infiltration method was applied to rice plants grown in a local farmer's field in northern Madagascar to analyze the expression of nutrient-responsive genes, suggesting nutrient imbalances in some of the fields examined.

CONCLUSIONS

This study showed that the developed infiltration method was effective in preserving the transcriptome status of rice and sorghum leaves when liquid nitrogen or a deep freezer is not available. The developed method was useful for diagnosing plants in the field based on the expression of nutrient-responsive marker genes. Moreover, the method used to protect RNA samples from degradation during transportation offers the possibility to use them for RNA-seq. This novel technique could pave the way for revealing the molecular basis of plant phenotypes by accelerating gene expression analyses using plant samples that are unique in the field.

Lr34/Yr18/Sr57/Pm38 confers broad-spectrum resistance to fungal diseases via sinapyl alcohol transport for cell wall lignification in wheat

The widely recognized pleiotropic adult plant resistance gene Lr34 encodes an ATP-binding cassette transporter and plays an important role in breeding wheat for enhanced resistance to multiple fungal diseases. Despite its significance, the mechanisms underlying Lr34-mediated pathogen defense remain largely unknown. Our study demonstrates that wheat lines carrying the Lr34res allele exhibit thicker cell walls and enhanced resistance to fungal penetration compared to those without Lr34res. Transcriptome and metabolite profiling revealed that the lignin biosynthetic pathway is suppressed in lr34 mutants, indicating a disruption in cell wall lignification. Additionally, we discovered that lr34 mutant lines are hypersensitive to sinapyl alcohol, a major monolignol crucial for cell wall lignification. Yeast accumulation and efflux assays confirmed that the LR34 protein functions as a sinapyl alcohol transporter. Both genetic and virus-induced gene silencing experiments demonstrated that the disease resistance conferred by Lr34 can be enhanced by incorporating the TaCOMT-3B gene, which is responsible for the biosynthesis of sinapyl alcohol. Collectively, our findings provide novel insights into the role of Lr34 in disease resistance through mediating sinapyl alcohol transport and cell wall deposition, and highlight the synergistic effect of TaCOMT-3B and Lr34 against multiple fungal pathogens by mediating cell wall lignification in adult wheat plants.

Rice E3 ubiquitin ligases: From key modulators of host immunity to potential breeding applications

To combat pathogen attacks, plants have developed a highly advanced immune system, which requires tight regulation to initiate robust defense responses while simultaneously preventing autoimmunity. The ubiquitin-proteasome system (UPS), which is responsible for degrading excess or misfolded proteins, has vital roles in ensuring strong and effective immune responses. E3 ligases, as key UPS components, play extensively documented roles in rice immunity by modulating the ubiquitination and degradation of downstream substrates involved in various immune signaling pathways. Here, we summarize the crucial roles of rice E3 ligases in both pathogen/microbe/damage-associated molecular pattern-triggered immunity and effector-triggered immunity, highlight the molecular mechanisms by which E3 ligases function in rice immune signaling, and emphasize the functions of E3 ligases as targets of pathogen effectors for pathogenesis. We also discuss potential strategies for application of immunity-associated E3 ligases in breeding of disease-resistant rice varieties without growth penalty. This review provides a comprehensive and updated understanding of the sophisticated and interconnected regulatory functions of E3 ligases in rice immunity and in balancing immunity with growth and development.

Engineering a conserved immune coreceptor into a primed state enhances fungal resistance in crops without growth penalty

Plants must tactically balance immunity and growth when combating lethal pathogens like fungi. CHITIN ELICITOR RECEPTOR KINASE 1 (CERK1), a conserved cell-surface co-receptor for the fungal elicitor chitin, enables plants to induce chitin-triggered immunity to counteract fungal invasion. Previously, we reported that bacterial infection can prime CERK1 through juxtamembrane (JM) phosphorylation to enhance fungal resistance, which only occurs in Arabidopsis (Arabidopsis thaliana) and its close relatives in Brassicaceae. Here, we aim to transfer the priming mechanism of Arabidopsis CERK1 (AtCERK1) to crop CERK1 via JM substitution. We revealed in protoplasts that the entire AtCERK1 JM variable region (AtJM) is essential for imparting the bacterial elicitor flg22-induced primed state to the Nicotiana benthamiana CERK1 (NbCERK1). The NbCERK1 chimera containing AtJM (NbCERK1AtJM) and similarly constructed rice (Oryza sativa) OsCERK1AtJM could undergo flg22-induced JM phosphorylation and confer enhanced antifungal immunity upon bacterial coinfection. Moreover, the NbCERK1AtJM+3D derivative with AtJM phosphomimetic mutations to mimic a constant primed state and similarly constructed OsCERK1AtJM+3D were sufficient to mediate strengthened chitin responses and fungal resistance in transgenic plants independent of bacterial infection. Importantly, no growth and reproduction defects were observed in these plants. Taken together, this study demonstrates that manipulating the primed state of a cell-surface immune receptor offers an effective approach to improve disease resistance in crops without compromising growth and yield and showcases how fundamental insights in plant biology can be translated into crop breeding applications.

Maize stigmas react differently to self- and cross-pollination and fungal invasion

During sexual reproduction in flowering plants, tip-growing pollen tubes travel from the stigma inside the maternal tissues of the pistil toward ovules. In maize (Zea mays L.), the stigma is highly elongated, forming thread-like strands known as silks. Only compatible pollen tubes successfully penetrate and grow through the transmitting tract of the silk to reach the ovules. Like pollen, fungal spores germinate at the surface of silks and generate tube-like structures (hyphae) penetrating silk tissue. To elucidate commonalities and differences between silk responses to these distinctive invading cells, we compared growth behavior of the various invaders as well as the silk transcriptome after self-pollination, cross-pollination, and infection using 2 different fungi. We report that self-pollination triggers mainly senescence genes, whereas incompatible pollen from Tripsacum dactyloides leads to downregulation of rehydration, microtubule, and cell wall-related genes, explaining the slower pollen tube growth and arrest. Invasion by the ascomycete Fusarium graminearum triggers numerous defense responses including the activation of monolignol biosynthesis and NAC as well as WRKY transcription factor genes, whereas responses to the basidiomycete Ustilago maydis are generally much weaker. We present evidence that incompatible pollination and fungal infection trigger transcriptional reprograming of maize silks cell wall. Pathogen invasion also activates the phytoalexin biosynthesis pathway.

A novel Pik allele confers extended resistance to rice blast

In the ongoing arms race between rice and Magnaporthe oryzae, the pathogen employs effectors to evade the immune response, while the host develops resistance genes to recognise these effectors and confer resistance. In this study, we identified a novel Pik allele, Pik-W25, from wild rice WR25 through bulked-segregant analysis, creating the Pik-W25 NIL (Near-isogenic Lines) named G9. Pik-W25 conferred resistance to isolates expressing AvrPik-C/D/E alleles. CRISPR-Cas9 editing was used to generate transgenic lines with a loss of function in Pik-W25-1 and Pik-W25-2, resulting in loss of resistance in G9 to isolates expressing the three alleles, confirming that Pik-W25-induced immunity required both Pik-W25-1 and Pik-W25-2. Yeast two-hybrid (Y2H) and split luciferase complementation assays showed interactions between Pik-W25-1 and the three alleles, while Pik-W25-2 could not interact with AvrPik-C, -D, and -E alleles with Y2H assay, indicating Pik-W25-1 acts as an adaptor and Pik-W25-2 transduces the signal to trigger resistance. The Pik-W25 NIL exhibited enhanced field resistance to leaf and panicle blast without significant changes in morphology or development compared to the parent variety CO39, suggesting its potential for resistance breeding. These findings advance our knowledge of rice blast resistance mechanisms and offer valuable resources for effective and sustainable control strategies.

Diversity and structural-functional insights of alpha-solenoid proteins

Alpha-solenoids are a significant and diverse subset of structured tandem repeat proteins (STRPs) that are important in various domains of life. This review examines their structural and functional diversity and highlights their role in critical cellular processes such as signaling, apoptosis, and transcriptional regulation. Alpha-solenoids can be classified into three geometric folds: low curvature, high curvature, and corkscrew, as well as eight subfolds: ankyrin repeats; Huntingtin, elongation factor 3, protein phosphatase 2A, and target of rapamycin; armadillo repeats; tetratricopeptide repeats; pentatricopeptide repeats; Pumilio repeats; transcription activator-like; and Sel-1 and Sel-1-like repeats. These subfolds represent distinct protein families with unique structural properties and functions, highlighting the versatility of alpha-solenoids. The review also discusses their association with disease, highlighting their potential as therapeutic targets and their role in protein design. Advances in state-of-the-art structure prediction methods provide new opportunities and challenges in the functional characterization and classification of this kind of fold, emphasizing the need for continued development of methods for their identification and proper data curation and deposition in the main databases.

Regulation of maize growth and immunity by ZmSKI3-mediated RNA decay and post-transcriptional gene silencing

Disease resistance is often associated with compromised plant growth and yield due to defense-growth tradeoffs. However, key components and mechanisms underlying the defense-growth tradeoffs are rarely explored in maize. In this study, we find that ZmSKI3, a putative subunit of the SUPERKILLER (SKI) complex that mediates the 3'-5' degradation of RNA, regulates both plant development and disease resistance in maize. The Zmski3 mutants showed retarded plant growth and constitutively activated defense responses, while the ZmSKI3 overexpression lines are more susceptible to Curvularia lunata and Bipolaris maydis. Consistently, the expression of defense-related genes was generally up-regulated, while expressions of growth-related genes were mostly down-regulated in leaves of the Zmski3-1 mutant compared to that of wild type. In addition, 223 differentially expressed genes that are up-regulated in Zmski3-1 mutant but down-regulated in the ZmSKI3 overexpression line are identified as potential target genes of ZmSKI3. Moreover, small interfering RNAs targeting the transcripts of the defense- and growth-related genes are differentially accumulated, likely to combat the increase of defense-related transcripts but decrease of growth-related transcripts in Zmski3-1 mutant. Taken together, our study indicates that plant growth and immunity could be regulated by both ZmSKI3-mediated RNA decay and post-transcriptional gene silencing in maize.

Exploring the molecular mechanisms of rice blast resistance and advances in breeding for disease tolerance

Rice blast, caused by the fungus Magnaporthe oryzae (syn. Pyricularia oryzae), is a major problem in rice cultivation and ranks among the most severe fungal diseases. Cloning and identifying resistance genes in rice, coupled with a comprehensive examination of the interaction between M. oryzae and rice, may provide insights into the mechanisms of rice disease resistance and facilitate the creation of new rice varieties with improved germplasm. These efforts are essential for protecting food security. This review examines the discovery of genes that confer resistance or susceptiblity to M. oryzae in rice over the last decade. It also discusses how knowledge of molecular mechanisms has been used in rice breeding and outlines key strategies for creating rice varieties resistant to this disease. The strategies discussed include gene pyramiding, molecular design breeding, editing susceptibility genes, and increasing expression of resistance genes through pathogen challenge. We address the prospects and challenges in breeding for rice blast resistance, emphasizing the need to fully exploit germplasm resources, employ cutting-edge methods to identify new resistance genes, and develop innovative breeding cultivars. Additionally, we underscore the importance of understanding the molecular basis of rice blast resistance and developing novel cultivars with broad-spectrum disease resistance.

Dynamics of epitranscriptomes uncover translational reprogramming directed by ac4C in rice during pathogen infection

Messenger RNA modifications play pivotal roles in RNA biology, but comprehensive landscape changes of epitranscriptomes remain largely unknown in plant immune response. Here we report translational reprogramming directed by ac4C mRNA modification upon pathogen challenge. We first investigate the dynamics of translatomes and epitranscriptomes and uncover that the change in ac4C at single-base resolution promotes translational reprogramming upon Magnaporthe oryzae infection. Then by characterizing the specific distributions of m1A, 2'O-Nm, ac4C, m5C, m6A and m7G, we find that ac4Cs, unlike other modifications, are enriched at the 3rd position of codons, which stabilizes the Watson-Crick base pairing. Importantly, we demonstrate that upon pathogen infection, the increased expression of the ac4C writer OsNAT10/OsACYR (N-ACETYLTRANSFERASE FOR CYTIDINE IN RNA) promotes translation to facilitate rapid activation of immune responses, including the enhancement of jasmonic acid biosynthesis. Our study provides an atlas of mRNA modifications and insights into ac4C function in plant immunity.

Trans-crop applications of atypical R genes for multipathogen resistance

Genetic resistance to plant diseases is essential for global food security. Significant progress has been achieved for plant disease-resistance (R) genes comprising nucleotide-binding domain, leucine-rich repeat-containing receptors (NLRs), and membrane-localized receptor-like kinases or proteins (RLKs/RLPs), which we refer to as typical R genes. However, there is a knowledge gap in how non-receptor-type or atypical R genes contribute to plant immunity. Here, we summarize resources and technologies facilitating the study of atypical R genes, examine diverse atypical R proteins for broad-spectrum resistance, and outline potential approaches for trans-crop applications of atypical R genes. Studies of atypical R genes are important for a holistic understanding of plant immunity and the development of novel strategies in disease control and crop improvement.

The potato RNA metabolism machinery is targeted by the cyst nematode effector RHA1B for successful parasitism

The potato (Solanum tuberosum) cyst nematode Globodera pallida induces a multinucleate feeding site (syncytium) in potato roots as its sole source of nutrition. Here, we demonstrate that the G. pallida effector RING-H2 finger A1b (RHA1B), which is a functional ubiquitin ligase, interferes with the carbon catabolite repression 4 (CCR4)-negative on TATA-less (NOT) deadenylase-based RNA metabolism machinery that regulates syncytium development in G. pallida-infected potato. Specifically, RHA1B targets the CCR4-associated factor 1 (CAF1) and StNOT10 subunits of the CCR4-NOT complex for proteasome-mediated degradation, leading to upregulation of the cyclin gene StCycA2 involved in syncytium formation. The StCAF1 subunit of CCR4-NOT recruits the RNA binding protein StPUM5 to deadenylate StCycA2 mRNA, resulting in shortened poly-A tails of StCycA2 mRNA and subsequently reduced transcript levels. Knockdown of either subunit (StCAF1 or StNOT10) of the CCR4-NOT complex or StPUM5 in transgenic potato plants resulted in enlarged syncytia and enhanced susceptibility to G. pallida infection, which resembles the phenotypes of StCycA2 overexpression transgenic potato plants. Genetic analyses indicate that transgenic potato plants overexpressing RHA1B exhibit similar phenotypes as transgenic potato plants with knockdown of StNOT10, StCAF1, or StPUM5. Thus, our data suggest that G. pallida utilizes the RHA1B effector to manipulate RNA metabolism in host plants, thereby promoting syncytium development for parasitic success.

Genome editing for improvement of biotic and abiotic stress tolerance in cereals

Global agricultural production must quadruple by 2050 to fulfil the needs of a growing global population, but climate change exacerbates the difficulty. Cereals are a very important source of food for the world population. Improved cultivars are needed, with better resistance to abiotic stresses like drought, salt, and increasing temperatures, and resilience to biotic stressors like bacterial and fungal infections, and pest infestation. A popular, versatile, and helpful method for functional genomics and crop improvement is genome editing. Rapidly developing genome editing techniques including clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein (Cas) are very important. This review focuses on how CRISPR/Cas9 genome editing might enhance cereals' agronomic qualities in the face of climate change, providing important insights for future applications. Genome editing efforts should focus on improving characteristics that confer tolerance to conditions exacerbated by climate change (e.g. drought, salt, rising temperatures). Improved water usage efficiency, salt tolerance, and heat stress resilience are all desirable characteristics. Cultivars that are more resilient to insect infestations and a wide range of biotic stressors, such as bacterial and fungal diseases, should be created. Genome editing can precisely target genes linked to disease resistance pathways to strengthen cereals' natural defensive systems.

The MdVQ37-MdWRKY100 complex regulates salicylic acid content and MdRPM1 expression to modulate resistance to Glomerella leaf spot in apples

Glomerella leaf spot (GLS), caused by the fungus Colletotrichum fructicola, is considered one of the most destructive diseases affecting apples. The VQ-WRKY complex plays a crucial role in the response of plants to biotic stresses. However, our understanding of the defensive role of the VQ-WRKY complex on woody plants, particularly apples, under biotic stress, remains limited. In this study, we elucidated the molecular mechanisms underlying the defensive role of the apple MdVQ37-MdWRKY100 module in response to GLS infection. The overexpression of MdWRKY100 enhanced resistance to C. fructicola, whereas MdWRKY100 RNA interference in apple plants reduced resistance to C. fructicola by affecting salicylic acid (SA) content and the expression level of the CC-NBS-LRR resistance gene MdRPM1. DAP-seq, Y1H, EMSA, and RT-qPCR assays indicated that MdWRKY100 inhibited the expression of MdWRKY17, a positive regulatory factor gene of SA degradation, upregulated the expression of MdPAL1, a key enzyme gene of SA biosynthesis, and promoted MdRPM1 expression by directly binding to their promotors. Transient overexpression and silencing experiments showed that MdPAL1 and MdRPM1 positively regulated GLS resistance in apples. Furthermore, the overexpression of MdVQ37 increased the susceptibility to C. fructicola by reducing the SA content and expression level of MdRPM1. Additionally, MdVQ37 interacted with MdWRKY100, which repressed the transcriptional activity of MdWRKY100. In summary, these results revealed the molecular mechanism through which the apple MdVQ37-MdWRKY100 module responds to GLS infection by regulating SA content and MdRPM1 expression, providing novel insights into the involvement of the VQ-WRKY complex in plant pathogen defence responses.

A genome-wide association study of panicle blast resistance to Magnaporthe oryzae in rice

Rice blast, caused by Magnaporthe oryzae (M. oryzae), is one of the most serious diseases worldwide. Developing blast-resistant rice varieties is an effective strategy to control the spread of rice blast and reduce the reliance on chemical pesticides. In this study, 477 sequenced rice germplasms from 48 countries were inoculated and assessed at the booting stage. We found that 23 germplasms exhibited high panicle blast resistance against M. oryzae. Genome-wide association analysis (GWAS) identified 43 quantitative trait loci (QTLs) significantly associated (P < 1.0 × 10-4) with resistance to rice panicle blast. These QTL intervals encompass four genes (OsAKT1, OsRACK1A, Bsr-k1 and Pi25/Pid3) previously reported to contribute to rice blast resistance. We selected QTLs with -Log10 (P-value) greater than 6.0 or those detected in two-year replicates, amounting to 12 QTLs, for further candidate gene analysis. Three blast resistance candidate genes (Os06g0316800, Os06g0320000, Pi25/Pid3) were identified based on significant single nucleotide polymorphisms (SNP) distributions within annotated gene sequences across these 12 QTLs and the differential expression levels among blast-resistant varieties after 72 h of inoculation. Os06g0316800 encodes a glycine-rich protein, OsGrp6, an important component of plant cell walls involved in cellular stress responses and signaling. Os06g0320000 encodes a protein with unknown function (DUF953), part of the thioredoxin-like family, which is crucial for maintaining reactive oxygen species (ROS) homeostasis in vivo, named as OsTrxl1. Lastly, Pi25/Pid3 encodes a disease resistance protein, underscoring its potential importance in plant biology. By analyzing the haplotypes of these three genes, we identified favorable haplotypes for blast resistance, providing valuable genetic resources for future rice blast resistance breeding programs.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-024-01486-5.

In-silico study of protein-protein interactions in wheat blast using docking and molecular dynamics simulation approach

Despite advancements in agricultural research and the introduction of modern biotechnological and farming techniques, food security remains a significant issue. Although the efforts of farmers to meet the demands of a growing population, many plant diseases caused by pathogens, through their effects on cell division and tissue growth, lead to the annual loss of countless food crops. The recently emerged wheat blast fungus Magnaporthe oryzae pathotype Triticum (MoT) poses a significant danger to worldwide wheat cultivation. The fungus is a highly varied lineage of the M. oryzae, responsible for causing rice blast disease. In spite of being a significant challenge to successful wheat production in South America since 1985, the underlying biology of the wheat blast pathogen is still not fully understood. The initial outbreak of the wheat blast in South Asia had a severe impact on wheat production, resulting in a complete loss of yield in affected fields. For the purpose of enhancing disease management, it's vital to acquire a comprehensive comprehension of the infection biology of the fungus and its interaction with wheat plants on molecular levels. Host-pathogen protein interactions (HPIs) have the potential to reveal the pathogens' mechanism for overcoming the host organism. The current study delves into the interactions between the host plant wheat and MoT through protein-protein interactions, molecular docking, and 100 ns molecular dynamic simulations. This research uncovers the structural and functional basis of these proteins, leading to improved plant health and production.Communicated by Ramaswamy H. Sarma.

The potential of genome editing to create novel alleles of resistance genes in rice

Rice, a staple food for a significant portion of the global population, faces persistent threats from various pathogens and pests, necessitating the development of resilient crop varieties. Deployment of resistance genes in rice is the best practice to manage diseases and reduce environmental damage by reducing the application of agro-chemicals. Genome editing technologies, such as CRISPR-Cas, have revolutionized the field of molecular biology, offering precise and efficient tools for targeted modifications within the rice genome. This study delves into the application of these tools to engineer novel alleles of resistance genes in rice, aiming to enhance the plant's innate ability to combat evolving threats. By harnessing the power of genome editing, researchers can introduce tailored genetic modifications that bolster the plant's defense mechanisms without compromising its essential characteristics. In this study, we synthesize recent advancements in genome editing methodologies applicable to rice and discuss the ethical considerations and regulatory frameworks surrounding the creation of genetically modified crops. Additionally, it explores potential challenges and future prospects for deploying edited rice varieties in agricultural landscapes. In summary, this study highlights the promise of genome editing in reshaping the genetic landscape of rice to confront emerging challenges, contributing to global food security and sustainable agriculture practices.

C-terminal frameshift mutations generate viable knockout mutants with developmental defects for three essential protein kinases

Loss-of-function mutants are fundamental resources for gene function studies. However, it is difficult to generate viable and heritable knockout mutants for essential genes. Here, we show that targeted editing of the C-terminal sequence of the embryo lethal gene MITOGEN-ACTIVATED PROTEIN KINASES 1 (OsMPK1) results in weak mutants. This C-terminal-edited osmpk1 mutants displayed severe developmental defects and altered disease resistance but generated tens of viable seeds that inherited the mutations. Using the same C-terminal editing approach, we also obtained viable mutants for a wall-associated protein kinase (Os07g0493200) and a leucine-rich repeat receptor-like protein kinase (Os01g0239700), while the null mutations of these genes were lethal. These data suggest that protein kinase activity could be reduced by introducing frameshift mutations adjacent to the C-terminus, which could generate valuable resources for gene function studies and tune protein kinase activity for signaling pathway engineering.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42994-024-00165-5.

Revisiting growth-defence trade-offs and breeding strategies in crops

Plants have evolved a multi-layered immune system to fight off pathogens. However, immune activation is costly and is often associated with growth and development penalty. In crops, yield is the main breeding target and is usually affected by high disease resistance. Therefore, proper balance between growth and defence is critical for achieving efficient crop improvement. This review highlights recent advances in attempts designed to alleviate the trade-offs between growth and disease resistance in crops mediated by resistance (R) genes, susceptibility (S) genes and pleiotropic genes. We also provide an update on strategies for optimizing the growth-defence trade-offs to breed future crops with desirable disease resistance and high yield.

A double-stranded RNA binding protein enhances drought resistance via protein phase separation in rice

Drought stress significantly impacts global rice production, highlighting the critical need to understand the genetic basis of drought resistance in rice. Here, through a genome-wide association study, we reveal that natural variations in DROUGHT RESISTANCE GENE 9 (DRG9), encoding a double-stranded RNA (dsRNA) binding protein, contribute to drought resistance. Under drought stress, DRG9 condenses into stress granules (SGs) through liquid-liquid phase separation via a crucial α-helix. DRG9 recruits the mRNAs of OsNCED4, a key gene for the biosynthesis of abscisic acid, into SGs and protects them from degradation. In drought-resistant DRG9 allele, natural variations in the coding region, causing an amino acid substitution (G267F) within the zinc finger domain, increase DRG9's binding ability to OsNCED4 mRNA and enhance drought resistance. Introgression of the drought-resistant DRG9 allele into the elite rice Huanghuazhan significantly improves its drought resistance. Thus, our study underscores the role of a dsRNA-binding protein in drought resistance and its promising value in breeding drought-resistant rice.

Lignin Biosynthesis and Its Diversified Roles in Disease Resistance

Lignin is complex, three-dimensional biopolymer existing in plant cell wall. Lignin biosynthesis is increasingly highlighted because it is closely related to the wide applications in agriculture and industry productions, including in pulping process, forage digestibility, bio-fuel, and carbon sequestration. The functions of lignin in planta have also attracted more attentions recently, particularly in plant defense response against different pathogens. In this brief review, the progress in lignin biosynthesis is discussed, and the lignin's roles in disease resistance are thoroughly elucidated. This issue will help in developing broad-spectrum resistant crops in agriculture.

Grass lignin: biosynthesis, biological roles, and industrial applications

Lignin is a phenolic heteropolymer found in most terrestrial plants that contributes an essential role in plant growth, abiotic stress tolerance, and biotic stress resistance. Recent research in grass lignin biosynthesis has found differences compared to dicots such as Arabidopsis thaliana. For example, the prolific incorporation of hydroxycinnamic acids into grass secondary cell walls improve the structural integrity of vascular and structural elements via covalent crosslinking. Conversely, fundamental monolignol chemistry conserves the mechanisms of monolignol translocation and polymerization across the plant phylum. Emerging evidence suggests grass lignin compositions contribute to abiotic stress tolerance, and periods of biotic stress often alter cereal lignin compositions to hinder pathogenesis. This same recalcitrance also inhibits industrial valorization of plant biomass, making lignin alterations and reductions a prolific field of research. This review presents an update of grass lignin biosynthesis, translocation, and polymerization, highlights how lignified grass cell walls contribute to plant development and stress responses, and briefly addresses genetic engineering strategies that may benefit industrial applications.

DGW1, encoding an hnRNP-like RNA binding protein, positively regulates grain size and weight by interacting with GW6 mRNA

Grain size and weight determine rice yield. Although numerous genes and pathways involved in regulating grain size have been identified, our knowledge of post-transcriptional control of grain size remains elusive. In this study, we characterize a rice mutant, decreased grain width and weight 1 (dgw1), which produces small grains. We show that DGW1 encodes a member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family protein and preferentially expresses in developing panicles, positively regulating grain size by promoting cell expansion in spikelet hulls. Overexpression of DGW1 increases grain weight and grain numbers, leading to a significant rise in rice grain yield. We further demonstrate that DGW1 functions in grain size regulation by directly binding to the mRNA of Grain Width 6 (GW6), a critical grain size regulator in rice. Overexpression of GW6 restored the grain size phenotype of DGW1-knockout plants. DGW1 interacts with two oligouridylate binding proteins (OsUBP1a and OsUBP1b), which also bind the GW6 mRNA. In addition, the second RRM domain of DGW1 is indispensable for its mediated protein-RNA and protein-protein interactions. In summary, our findings identify a new regulatory module of DGW1-GW6 that regulates rice grain size and weight, providing important insights into the function of hnRNP-like proteins in the regulation of grain size.

Multi-Omics Approach Reveals OsPIL1 as a Regulator Promotes Rice Growth, Grain Development, and Blast Resistance

Rice (Oryza sativa) is a crucial crop, achieving high yield concurrent pathogen resistance remains a challenge. Transcription factors play roles in growth and abiotic tolerance. However, rice phytochrome-interacting factor-like 1 (OsPIL1) in pathogen resistance and agronomic traits remains unexplored. We generated OsPIL1 overexpressing (OsPIL1 OE) rice lines and evaluated their impact on growth, grain development, and resistance to Magnaporthe oryzae. Multiomics analysis (RNA-seq, metabolomics, and CUT&Tag) and RT-qPCR validated OsPIL1 target genes and key metabolites. In the results, OsPIL1 OE rice lines exhibited robust growth, longer grains, and enhanced resistance to M. oryzae without compromising growth. Integrative multiomics analysis revealed a coordinated regulatory network centered on OsPIL1, explaining these desirable traits. OsPIL1 likely acts as a positive regulator, targeting transcriptional elements or specific genes with direct functions in several biological programs. In particular, a range of key signaling genes (phosphatases, kinases, plant hormone genes, transcription factors), and metabolites (linolenic acid, vitamin E, trigonelline, d-glucose, serotonin, choline, genistein, riboflavin) contributed to enhanced rice growth, grain size, pathogen resistance, or a combination of these traits. These findings highlight OsPIL1's regulatory role in promoting important traits and provide insights into potential strategies for rice breeding.

Genome-Wide Association Study Identifies Rice Panicle Blast-Resistant Gene Pb4 Encoding a Wall-Associated Kinase

Rice blast is one of the most devastating diseases, causing a significant reduction in global rice production. Developing and utilizing resistant varieties has proven to be the most efficient and cost-effective approach to control blasts. However, due to environmental pressure and intense pathogenic selection, resistance has rapidly broken down, and more durable resistance genes are being discovered. In this paper, a novel wall-associated kinase (WAK) gene, Pb4, which confers resistance to rice blast, was identified through a genome-wide association study (GWAS) utilizing 249 rice accessions. Pb4 comprises an N-terminal signal peptide, extracellular GUB domain, EGF domain, EGF-Ca2+ domain, and intracellular Ser/Thr protein kinase domain. The extracellular domain (GUB domain, EGF domain, and EGF-Ca2+ domain) of Pb4 can interact with the extracellular domain of CEBiP. Additionally, its expression is induced by chitin and polygalacturonic acid. Furthermore, transgenic plants overexpressing Pb4 enhance resistance to rice blast. In summary, this study identified a novel rice blast-resistant gene, Pb4, and provides a theoretical basis for understanding the role of WAKs in mediating rice resistance against rice blast disease.

The phenylalanine ammonia-lyase inhibitor AIP induces rice defence against the root-knot nematode Meloidogyne graminicola

The phenylalanine ammonia-lyase (PAL) enzyme catalyses the conversion of l-phenylalanine to trans-cinnamic acid. This conversion is the first step in phenylpropanoid biosynthesis in plants. The phenylpropanoid pathway produces diverse plant metabolites that play essential roles in various processes, including structural support and defence. Previous studies have shown that mutation of the PAL genes enhances disease susceptibility. Here, we investigated the functions of the rice PAL genes using 2-aminoindan-2-phosphonic acid (AIP), a strong competitive inhibitor of PAL enzymes. We show that the application of AIP can significantly reduce the PAL activity of rice crude protein extracts in vitro. However, when AIP was applied to intact rice plants, it reduced infection of the root-knot nematode Meloidogyne graminicola. RNA-seq showed that AIP treatment resulted in a rapid but transient upregulation of defence-related genes in roots. Moreover, targeted metabolomics demonstrated higher levels of jasmonates and antimicrobial flavonoids and diterpenoids accumulating after AIP treatment. Furthermore, chemical inhibition of the jasmonate pathway abolished the effect of AIP on nematode infection. Our results show that disturbance of the phenylpropanoid pathway by the PAL inhibitor AIP induces defence in rice against M. graminicola by activating jasmonate-mediated defence.

Phytophthora infestans RXLR effector Pi23014 targets host RNA-binding protein NbRBP3a to suppress plant immunity

Phytophthora infestans is a destructive oomycete that causes the late blight of potato and tomato worldwide. It secretes numerous small proteins called effectors in order to manipulate host cell components and suppress plant immunity. Identifying the targets of these effectors is crucial for understanding P. infestans pathogenesis and host plant immunity. In this study, we show that the virulence RXLR effector Pi23014 of P. infestans targets the host nucleus and chloroplasts. By using a liquid chromatogrpahy-tandem mass spectrometry assay and co-immunoprecipitation assasys, we show that it interacts with NbRBP3a, a putative glycine-rich RNA-binding protein. We confirmed the co-localization of Pi23014 and NbRBP3a within the nucleus, by using bimolecular fluorescence complementation. Reverse transcription-quantitative PCR assays showed that the expression of NbRBP3a was induced in Nicotiana benthamiana during P. infestans infection and the expression of marker genes for multiple defence pathways were significantly down-regulated in NbRBP3-silenced plants compared with GFP-silenced plants. Agrobacterium tumefaciens-mediated transient overexpression of NbRBP3a significantly enhanced plant resistance to P. infestans. Mutations in the N-terminus RNA recognition motif (RRM) of NbRBP3a abolished its interaction with Pi23014 and eliminated its capability to enhance plant resistance to leaf colonization by P. infestans. We further showed that silencing NbRBP3 reduced photosystem II activity, reduced host photosynthetic efficiency, attenuated Pi23014-mediated suppression of cell death triggered by P. infestans pathogen-associated molecular pattern elicitor INF1, and suppressed plant immunity.

Characterization of caffeoyl shikimate esterase gene family identifies CsCSE5 as a positive regulator of Podosphaera xanthii and Corynespora cassiicola pathogen resistance in cucumber

KEY MESSAGE

CsCSE genes might be involved in the tolerance of cucumber to pathogens. Silencing of the CsCSE5 gene resulted in attenuated resistance of cucumber to Podosphaera xanthii and Corynespora cassiicola. Caffeoyl shikimate esterase (CSE), a key enzyme in the lignin biosynthetic pathway, has recently been characterized to play a key role in defense against pathogenic infection in plants. However, a systematic analysis of the CSE gene family in cucumber (Cucumis sativus) has not yet been conducted. Here, we identified eight CsCSE genes from the cucumber genome via bioinformatic analyses, and these genes were unevenly distributed on chromosomes 1, 3, 4, and 5. Results from multiple sequence alignment indicated that the CsCSE proteins had domains required for CSE activity. Phylogenetic analysis of gene structure and protein motifs revealed the conservation and diversity of the CsCSE gene family. Collinearity analysis showed that CsCSE genes had high homology with CSE genes in wax gourd (Benincasa hispida). Cis-acting element analysis of the promoters suggested that CsCSE genes might play important roles in growth, development, and stress tolerance. Expression pattern analysis indicated that CsCSE5 might be involved in regulating the resistance of cucumber to pathogens. Functional verification data confirmed that CsCSE5 positively regulates the resistance of cucumber to powdery mildew pathogen Podosphaera xanthii and target leaf spot pathogen Corynespora cassiicola. The results of our study provide information that will aid the genetic improvement of resistant cucumber varieties.

Gibberellin signaling regulates lignin biosynthesis to modulate rice seed shattering

The elimination of seed shattering was a key step in rice (Oryza sativa) domestication. In this paper, we show that increasing the gibberellic acid (GA) content or response in the abscission region enhanced seed shattering in rice. We demonstrate that SLENDER RICE1 (SLR1), the key repressor of GA signaling, could physically interact with the rice seed shattering-related transcription factors quantitative trait locus of seed shattering on chromosome 1 (qSH1), O. sativa HOMEOBOX 15 (OSH15), and SUPERNUMERARY BRACT (SNB). Importantly, these physical interactions interfered with the direct binding of these three regulators to the lignin biosynthesis gene 4-COUMARATE: COENZYME A LIGASE 3 (4CL3), thereby derepressing its expression. Derepression of 4CL3 led to increased lignin deposition in the abscission region, causing reduced rice seed shattering. Importantly, we also show that modulating GA content could alter the degree of seed shattering to increase harvest efficiency. Our results reveal that the "Green Revolution" phytohormone GA is important for regulating rice seed shattering, and we provide an applicable breeding strategy for high-efficiency rice harvesting.

Biotechnological and Biocontrol Approaches for Mitigating Postharvest Diseases Caused by Fungal Pathogens and Their Mycotoxins in Fruits: A Review

Postharvest diseases caused by fungal pathogens are significant contributors to the postharvest losses of fruits. Moreover, some fungal pathogens produce mycotoxins, which further compromise the safety and quality of fruits. In this review, the potential of biotechnological and biocontrol approaches for mitigating postharvest diseases and mycotoxins in fruits is explored. The review begins by discussing the impact of postharvest diseases on fruit quality and postharvest losses. Next, it provides an overview of major postharvest diseases caused by fungal pathogens. Subsequently, it delves into the role of biotechnological approaches in controlling these diseases. The review also explored the application of biocontrol agents, such as antagonistic yeasts, bacteria, and fungi, which can suppress pathogen growth. Furthermore, future trends and challenges in these two approaches are discussed in detail. Overall, this review can provide insights into promising biotechnological and biocontrol strategies for managing postharvest diseases and mycotoxins in fruits.

Crop adaptation to climate change: An evolutionary perspective

The disciplines of evolutionary biology and plant and animal breeding have been intertwined throughout their development, with responses to artificial selection yielding insights into the action of natural selection and evolutionary biology providing statistical and conceptual guidance for modern breeding. Here we offer an evolutionary perspective on a grand challenge of the 21st century: feeding humanity in the face of climate change. We first highlight promising strategies currently under way to adapt crops to current and future climate change. These include methods to match crop varieties with current and predicted environments and to optimize breeding goals, management practices, and crop microbiomes to enhance yield and sustainable production. We also describe the promise of crop wild relatives and recent technological innovations such as speed breeding, genomic selection, and genome editing for improving environmental resilience of existing crop varieties or for developing new crops. Next, we discuss how methods and theory from evolutionary biology can enhance these existing strategies and suggest novel approaches. We focus initially on methods for reconstructing the evolutionary history of crops and their pests and symbionts, because such historical information provides an overall framework for crop-improvement efforts. We then describe how evolutionary approaches can be used to detect and mitigate the accumulation of deleterious mutations in crop genomes, identify alleles and mutations that underlie adaptation (and maladaptation) to agricultural environments, mitigate evolutionary trade-offs, and improve critical proteins. Continuing feedback between the evolution and crop biology communities will ensure optimal design of strategies for adapting crops to climate change.

Utilizing differences in bTH tolerance between the parents of two-line hybrid rice to improve the purity of hybrid rice seed

Introduction

Two-line hybrid rice based on Photoperiod/thermo-sensitive genic male sterile (P/TGMS) lines has been developed and applied widely in agriculture due to the freedom in making hybrid combinations, less difficulty in breeding sterile lines, and simpler procedures for breeding and producing hybrid seed. However, there are certain risks associated with hybrid seed production; if the temperature during the P/TGMS fertility-sensitive period is lower than the critical temperature, seed production will fail due to self-pollination. In a previous study, we found that the issue of insufficient purity of two-line hybrid rice seed could be initially addressed by using the difference in tolerance to β-triketone herbicides (bTHs) between the female parent and the hybrid seeds.

Methods

In this study, we further investigated the types of applicable herbicides, application methods, application time, and the effects on physiological and biochemical indexes and yield in rice.

Results

The results showed that this method could be used for hybrid purification by soaking seeds and spraying plants with the bTH benzobicylon (BBC) at safe concentrations in the range of 37.5-112.5 mg/L, and the seeds could be soaked in BBC at a treatment rate of 75.0 mg/L for 36-55 h without significant negative effects. The safe concentration for spraying in the field is 50.0-400.0 mg/L BBC at the three-leaf stage. Unlike BBC, Mesotrione (MST) can only be sprayed to achieve hybrid purification at concentrations between 10.0 and 70.0 mg/L without affecting yield. The three methods of hybrid seed purification can reach 100% efficiency without compromising the nutritional growth and yield of hybrid rice. Moreover, transcriptome sequencing revealed that 299 up-regulated significant differentially expressed genes (DEGs) in the resistant material (Huazhan) poisoned by BBC, were mainly enriched in phenylalanine metabolism and phenylpropanoid biosynthesis pathway, it may eliminate the toxic effects of herbicides through this way.

Discussion

Our study establishes a foundation for the application of the bTH seed purification strategy and the three methods provide an effective mechanism for improving the purity of two-line hybrid rice seeds.

Genome-wide association mapping of rust resistance in Aegilops longissima

The rust diseases, including leaf rust caused by Puccinia triticina (Pt), stem rust caused by P. graminis f. sp. tritici (Pgt), and stripe rust caused by P. striiformis f. sp. tritici (Pst), are major limiting factors in wheat production worldwide. Identification of novel sources of rust resistance genes is key to developing cultivars resistant to rapidly evolving pathogen populations. Aegilops longissima is a diploid wild grass native to the Levant and closely related to the modern bread wheat D subgenome. To explore resistance genes in the species, we evaluated a large panel of Ae. longissima for resistance to several races of Pt, Pgt, and Pst, and conducted a genome-wide association study (GWAS) to map rust resistance loci in the species. A panel of 404 Ae. longissima accessions, mostly collected from Israel, were screened for seedling-stage resistance to four races of Pt, four races of Pgt, and three races of Pst. Out of the 404 accessions screened, two were found that were resistant to all 11 races of the three rust pathogens screened. The percentage of all accessions screened that were resistant to a given rust pathogen race ranged from 18.5% to 99.7%. Genotyping-by-sequencing (GBS) was performed on 381 accessions of the Ae. longissima panel, wherein 125,343 single nucleotide polymorphisms (SNPs) were obtained after alignment to the Ae. longissima reference genome assembly and quality control filtering. Genetic diversity analysis revealed the presence of two distinct subpopulations, which followed a geographic pattern of a northern and a southern subpopulation. Association mapping was performed in the genotyped portion of the collection (n = 381) and in each subpopulation (n = 204 and 174) independently via a single-locus mixed-linear model, and two multi-locus models, FarmCPU, and BLINK. A large number (195) of markers were significantly associated with resistance to at least one of 10 rust pathogen races evaluated, nine of which are key candidate markers for further investigation due to their detection via multiple models and/or their association with resistance to more than one pathogen race. The novel resistance loci identified will provide additional diversity available for use in wheat breeding.

Multi-generation study of heavy ion beam-induced mutations and agronomic trait variations to accelerate rice breeding

Heavy ion beam (HIB) is an effective physical mutagen that has been widely used in plant mutational breeding. Systemic knowledge of the effects caused by different HIB doses at developmental and genomic levels will facilitate efficient breeding for crops. Here we examined the effects of HIB systematically. Kitaake rice seeds were irradiated by ten doses of carbon ion beams (CIB, 25 - 300 Gy), which is the most widely used HIB. We initially examined the growth, development and photosynthetic parameters of the M₁ population and found that doses exceeding 125 Gy caused significant physiological damages to rice. Subsequently, we analyzed the genomic variations in 179 M₂ individuals from six treatments (25 - 150 Gy) via whole-genome sequencing (WGS). The mutation rate peaks at 100 Gy (2.66×10^-7/bp). Importantly, we found that mutations shared among different panicles of the same M₁ individual are at low ratios, validating the hypothesis that different panicles may be derived from different progenitor cells. Furthermore, we isolated 129 mutants with distinct phenotypic variations, including changes in agronomic traits, from 11,720 M₂ plants, accounting for a 1.1% mutation rate. Among them, about 50% possess stable inheritance in M₃. WGS data of 11 stable M₄ mutants, including three lines with higher yields, reveal their genomic mutational profiles and candidate genes. Our results demonstrate that HIB is an effective tool that facilitates breeding, that the optimal dose range for rice is 67 - 90% median lethal dose (LD₅₀), and that the mutants isolated here can be further used for functional genomic research, genetic analysis, and breeding.

Genome editing of a rice CDP-DAG synthase confers multipathogen resistance

The discovery and application of genome editing introduced a new era of plant breeding by giving researchers efficient tools for the precise engineering of crop genomes1. Here we demonstrate the power of genome editing for engineering broad-spectrum disease resistance in rice (Oryza sativa). We first isolated a lesion mimic mutant (LMM) from a mutagenized rice population. We then demonstrated that a 29-base-pair deletion in a gene we named RESISTANCE TO BLAST1 (RBL1) caused broad-spectrum disease resistance and showed that this mutation caused an approximately 20-fold reduction in yield. RBL1 encodes a cytidine diphosphate diacylglycerol synthase that is required for phospholipid biosynthesis2. Mutation of RBL1 results in reduced levels of phosphatidylinositol and its derivative phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2). In rice, PtdIns(4,5)P2 is enriched in cellular structures that are specifically associated with effector secretion and fungal infection, suggesting that it has a role as a disease-susceptibility factor3. By using targeted genome editing, we obtained an allele of RBL1, named RBL1Δ12, which confers broad-spectrum disease resistance but does not decrease yield in a model rice variety, as assessed in small-scale field trials. Our study has demonstrated the benefits of editing an LMM gene, a strategy relevant to diverse LMM genes and crops.

Overexpression of a beta-1,6-glucanase gene GluM in transgenic rice confers high resistance to rice blast, sheath blight and false smut

BACKGROUND

Frequent fungal diseases tend to lead to severe losses in rice production. As a main component of the fungal cell wall, glucan plays an important role in the growth and development of fungi. Glucanase can inhibit the growth of fungi by breaking glycosidic bonds, and may be a promising target for developing rice varieties with broad-spectrum disease resistance.

RESULTS

We transferred a codon-optimized β-1,6-glucanase gene (GluM) from myxobacteria into the japonica rice variety Zhonghua11 (ZH11), and obtained a large number of individual transgenic plants with GluM overexpression. Based on molecular analysis, three single-copy homozygous lines with GluM overexpression were selected for assessment of fungal disease resistance at the T₃ generation. Compared with that of the recipient cultivar ZH11, the area of rice blast lesion in transgenic rice was reduced by 82.71%; that of sheath blight lesion was decreased by 35.76%-43.67%; the sheath blight resistance in the field was enhanced by an average of 0.75 grade over 3 years; and the incidence of diseased panicles due to rice false smut was decreased by 65.79%. More importantly, there was no obvious loss of yield (without a significant effect on agronomic traits). Furthermore, plants overexpressing a β-1,6-glucanase gene showed higher disease resistance than rice plants overexpressing a β-1,3-glucanase gene derived from tobacco.

CONCLUSION

The β-1,6-glucanase gene GluM can confer broad-spectrum disease resistance to rice, providing an environmentally friendly alternative way to effectively manage fungal pathogens in rice production. © 2023 Society of Chemical Industry.

Recent Trends and Advancements in CRISPR-Based Tools for Enhancing Resistance against Plant Pathogens

Targeted genome editing technologies are becoming the most important and widely used genetic tools in studies of phytopathology. The "clustered regularly interspaced short palindromic repeats (CRISPR)" and its accompanying proteins (Cas) have been first identified as a natural system associated with the adaptive immunity of prokaryotes that have been successfully used in various genome-editing techniques because of its flexibility, simplicity, and high efficiency in recent years. In this review, we have provided a general idea about different CRISPR/Cas systems and their uses in phytopathology. This review focuses on the benefits of knock-down technologies for targeting important genes involved in the susceptibility and gaining resistance against viral, bacterial, and fungal pathogens by targeting the negative regulators of defense pathways of hosts in crop plants via different CRISPR/Cas systems. Moreover, the possible strategies to employ CRISPR/Cas system for improving pathogen resistance in plants and studying plant-pathogen interactions have been discussed.