A truncated CC-NB-ARC gene TaRPP13L1-3D positively regulates powdery mildew resistance in wheat via the RanGAP-WPP complex-mediated nucleocytoplasmic shuttle

A translocation between chromosome 6 and 8 influences lncRNA_MYB114 and PpRPP13 expression and underpins red leaf trait and powdery mildew resistance in peach

Red leaf peach has important ornamental value owing to its characteristic leaf coloration. However, this species is highly susceptible to powdery mildew, and the mechanisms of red leaf formation, resistance to powdery mildew, and their relationship remain unclear. We performed population genetic analyses of red leaf peach, revealing that the translocation of chromosomes 6 and 8 is genetically linked to both the red leaf trait and powdery mildew resistance. Bulk segregant analysis-sequencing, genome resequencing, and expression analysis indicated that the PpMYB114 and the resistance gene PpRPP13 are responsible for the red leaf phenotype and powdery mildew resistance, respectively. The chromosomal translocation causes a promoter fragment of PpRPP13 on chromosome 8 to integrate into the antisense chain of PpMYB114 on chromosome 6, thereby enhancing the expression of PpMYB114 and inhibiting the expression of PpRPP13. Further, lncRNA-seq identified a new antisense lncRNA, lncRNA_MYB114, which is generated by the translocation and can activate PpMYB114 expression to synthesize anthocyanin. Moreover, the overexpression of PpRPP13 resulted in enhanced resistance to powdery mildew. In summary, these results revealed the molecular mechanism of a chromosomal translocation altering the expression of PpMYB114 and PpRPP13 to form the red leaf phenotype that is linked to powdery mildew susceptibility.

A Dual RNA-Seq Analysis Revealed Dynamic Arms Race during the Infestation of Wheat by the English Grain Aphid (Sitobion avenae)

Sitobion avenae is an important pest that threatens the safety of wheat production in China. However, the resistance mechanisms of wheat to S. avenae are not well understood at present. In this study, we investigated the mechanisms of interaction between wheat and S. avenae at four infestation time points (6, 24, 48, and 72 hpi) using a high-resolution time series dual transcriptomic analysis. The results showed that plant hormone signal transduction, phenylpropanoid biosynthesis, and flavonoid biosynthesis pathways were significantly activated in the wheat spike of Lunxuan144 during S. avenae infestation. Meanwhile, the functional analysis of the S. avenae transcriptome revealed that some secretory proteins participated in wheat-S. avenae interaction. This study sheds light on the arms race process between S. avenae and wheat, laying the foundation for the green prevention of S. avenae and providing a theoretical basis for mining the key functional genes in both wheat and S. avenae.

Genomic Signatures of Environmental Adaptation in Castanopsis hainanensis (Fagaceae)

As an endemic Castanopsis species on Hainan Island, Castanopsis hainanensis Merr. is uniquely adapted to tropical climatic conditions and occupies a relatively narrow habitat range. Given its long generation times, limited dispersal capacity, and ecological and economic importance, understanding the genomic processes shaping this dominant tree species is critical for conservation. Its adaptation to specialized habitats and distinct geographical distribution provide valuable insights into biodiversity challenges in island ecosystems. This study employs genome-wide single-nucleotide polymorphism (SNP) markers to investigate genetic structure, population dynamics, and adaptive variation. Analyses revealed weak genetic divergence among populations, suggesting high gene flow. Demographic reconstruction indicated a historical population bottleneck, consistent with MaxEnt modeling projections of future range contraction under climate change. Selective sweep and genotype-environment association (GEA) analyses identified SNPs strongly correlated with environmental variables, particularly moisture and temperature. Using these SNPs, we quantified the risk of non-adaptedness (RONA) across climate scenarios, pinpointing regions at heightened vulnerability. Gene Ontology (GO) enrichment highlighted the key genes involved in plant growth and stress adaptation. By integrating genomic and environmental data, this study establishes a framework for deciphering adaptive mechanisms of C. hainanensis and offers actionable insights for informed conservation strategies to mitigate climate-driven biodiversity loss.

A dual transcriptome analysis reveals accession-specific resistance responses in Lathyrus sativus against Erysiphe pisi

Lathyrus sativus (grass pea) is a valuable crop for sustainable agriculture, offering dietary benefits and desirable agronomic traits. However, its yield stability is limited by diseases such as powdery mildew caused by Erysiphe pisi. Increasing fungal resistance to pesticides and environmental concerns demand the development of resistant crop varieties. To identify key defense mechanisms and effector genes involved in the Lathyrus sativus-Erysiphe pisi interaction we analyzed four L. sativus accessions exhibiting varying resistance to E. pisi (resistant, partially resistant, partially susceptible, and susceptible) using a dual RNA-Seq experiment across different time points. We observed a host biphasic response, characterized by an initial burst of gene expression, followed by a quiescent phase, and a subsequent wave of intense gene expression. Common L. sativus defense mechanisms included antifungal protein expression, cell wall reinforcement, and reactive oxygen species-mediated defense. These defenses involved respectively Bowman-Birk type proteinase inhibitors, peptidyl-prolyl cis-trans isomerases and mannitol dehydrogenases. The resistant accession specifically activated early reinforcement of structural barriers associated with lignin biosynthesis and the phenylpropanoid pathway, along with sustained chemical defenses (e.g. eugenol synthase 1), epigenetic regulation, and oxidative stress responses thorough peroxidases and heat shock proteins. The partial resistant accession exhibited a front-loaded defense response at early infection stages. Contrastingly, the partially susceptible accession exhibited a weaker baseline defense, with a slower and less robust response targeting pathogen infection. We identified potential E. pisi effectors, including genes involved in cell wall hydrolysis (e.g. mannosidase DCW1), nutrient acquisition (e.g. secreted alpha-glucosidase), and virulence (e.g. SnodProt1), with a higher diversity of effectors identified in the susceptible accession. In conclusion, this study identifies novel targets such as NLRs and effectors, antifungal proteins and genes related to cell wall reinforcement, within the complex Lathyrus sativus-Erysiphe pisi interaction to support future breeding programs aimed at enhancing resistance to E. pisi in L. sativus and related species.

TaANK-TPR1 enhances wheat resistance against stripe rust via controlling gene expression and protein activity of NLR protein TaRPP13L1

Nucleotide-binding site, leucine-rich repeat (NLR) proteins activate a robust immune response on recognition of pathogen invasion. However, the function and regulatory mechanisms of NLRs during Puccinia striiformis f. sp. tritici (Pst) infection in wheat remain elusive. Here, we identify an ankyrin (ANK) repeat and tetratricopeptide repeat (TPR)-containing protein, TaANK-TPR1, which plays a positive role in the regulation of wheat resistance against Pst and the immune response of NLR. TaANK-TPR1 targets the NLR protein TaRPP13L1 (Recognition of PeronosporaParasitica 13-like 1) to facilitate its homodimerization and cell death to enhance the resistance of wheat against Pst. Meanwhile, TaANK-TPR1 binds to the TGACGT motif (methyl jasmonate-responsive element) of the TaRPP13L1 promoter and activates TaRPP13L1 transcription. Both TaANK-TPR1 and TaRPP13L1 respond to jasmonic acid (JA) signaling via the TGACGT element. Importantly, overexpressing TaRPP13L1 confers robust rust resistance without impacting important agronomic traits in the field. These findings identify a regulatory mechanism of NLR protein and provide targets for improving crop disease resistance.

Identification and functional characterization of the RPP13 gene family in potato (Solanum tuberosum L.) for disease resistance

Potato (Solanum tuberosum L.), as the world's fourth largest food crop, plays a crucial role in ensuring food security through its disease resistance. The RPP13 gene family is known to play a pivotal role in plant disease resistance responses; however, its specific functions in potato remain unclear. In this study, we conducted the first comprehensive identification and analysis of 28 RPP13 gene family members in potato, examining their gene structures, chromosomal locations, expression patterns, and functional characteristics. Gene structure analysis revealed that most members contain the typical CC-NBS-LRR domains, with exon numbers ranging from 1 to 6. Phylogenetic analysis grouped these genes into four evolutionary clades, indicating a high level of conservation. Cis-regulatory element analysis identified that the promoter region of StRPP13-26 is enriched with pathogen-responsive elements such as the WUN-motif and MYC, suggesting its potential role in disease defense. Expression pattern analysis showed that StRPP13-8, StRPP13-10, and StRPP13-23 are highly expressed in various tissues, indicating their involvement in basic physiological functions, whereas StRPP13-6 and StRPP13-25 are mainly induced under specific pathogen infection conditions. Transcriptome and qRT-PCR analyses further revealed functional divergence of the RPP13 gene family in response to potato scab disease. Notably, StRPP13-11 was significantly downregulated in both resistant and susceptible cultivars, suggesting its crucial role in the early stages of pathogen recognition. Subcellular localization experiments showed that the StRPP13-11 protein is localized in the chloroplast. Combined with transcriptome-based functional enrichment analysis, this finding implies that StRPP13-11 may participate in disease defense by regulating photosynthesis-related genes and the dynamic balance of reactive oxygen species within the chloroplast. This study provides new insights into the potential functions of the RPP13 gene family in potato disease resistance mechanisms, offering valuable genetic resources and theoretical support for future disease-resistant breeding programs.

TaNAC1 boosts powdery mildew resistance by phosphorylation-dependent regulation of TaSec1a and TaCAMTA4 via PP2Ac/CDPK20

The integrity of wheat (Triticum aestivum) production is increasingly jeopardized by the fungal pathogen Blumeria graminis f. sp. tritici (Bgt), particularly amid the vicissitudes of climate change. Here, we delineated the role of a wheat transcription factor, TaNAC1, which precipitates cellular apoptosis and fortifies resistance against Bgt. Utilizing BiFC, co-immunoprecipitation, protein quantification, luciferase report assays, we determined that cytoplasmic TaNAC1-7A undergoes phosphorylation at the S184/S258 sites by TaCDPK20, facilitating its nuclear translocation. This migration appears to prime further phosphorylation by TaMPK1, thereby enhancing transcriptional regulatory activity. Notably, the apoptotic activity of phosphorylated TaNAC1-7A is negatively modulated by the nuclear protein phosphatase PP2Ac. Furthermore, activation of TaNAC1 phosphorylation initiates transcription of downstream genes TaSec1a and TaCAMTA4, through binding to the C[T/G]T[N7]A[A/C]G nucleic acid motif. Suppression of TaNAC1, TaCDPK20, and TaMPK1 in wheat compromises its resistance to Bgt strain E09, whereas overexpression of TaNAC1 and silencing of PP2Ac markedly elevate resistance levels. Our results reveal the pivotal role of TaNAC1 in basal resistance which is mediated by its effects on homotypic fusion, vacuolar protein sorting, and the expression of defense-related genes. The findings highlight the potential through targeting TaNAC1 and its regulators as a strategy for improving wheat's resistance to fungal pathogens.

Identification of nuclear membrane SUN proteins and components associated with wheat fungal stress responses

In eukaryotes, the nuclear membrane that encapsulates genomic DNA is composed of an inner nuclear membrane (INM), an outer nuclear membrane (ONM), and a perinuclear space. SUN proteins located in the INM and KASH proteins in the ONM form the SUN-KASH NM-bridge, which functions as the junction of the nucleocytoplasmic complex junction. Proteins containing the SUN domain showed the highest correlation with differentially accumulated proteins (DAPs) in the wheat response to fungal stress. To understand the characteristics of SUN and its associated proteins in wheat responding to pathogen stress, here we investigated and comprehensive analyzed SUN- and KASH-related proteins among the DAPs under fungi infection based on their conserved motifs. In total, four SUN proteins, one WPP domain-interacting protein (WIP), four WPP domain-interacting tail-anchored proteins (WIT), two WPP proteins and one Ran GTPase activating protein (RanGAP) were identified. Following transient expression of Nicotiana benthamiana, TaSUN2, TaRanGAP2, TaWIT1 and TaWIP1 were identified as nuclear membrane proteins, while TaWPP1 and TaWPP2 were expressed in both the nucleus and cell membrane. RT-qPCR analysis demonstrated that the transcription of TaSUN2, TaRanGAP2 and TaWPP1 were strongly upregulated in response to fungal infection. Furthermore, using the bimolecular fluorescence complementation, the luciferase complementation and a nuclear and split-ubiquitin-based membrane yeast two-hybrid systems, we substantiated the interaction between TaSUN2 and TaWIP1, as well as TaWIP1/WIT1 and TaWPP1/WPP2. Silencing of TaSUN2, TaRanGAP2 and TaWPP1 in wheat leaves promoted powdery mildew infection and hyphal growth, and reduced the expression of TaBRI1, TaBAK1 and Ta14-3-3, indicating that these NM proteins play a positive role in resistance to fungal stress. Our study reveals the characteristics of NM proteins and propose the preliminary construction of SUN-WIP-WPP-RanGAP complex in wheat, which represents a foundation for detail elucidating their functions in wheat in future.

Integrative transcriptomic analysis unveils lncRNA-miRNA-mRNA interplay in tomato plants responding to Ralstonia solanacearum

Ralstonia solanacearum, a bacterial plant pathogen, poses a significant threat to tomato (Solanum lycopersicum) production through destructive wilt disease. While noncoding RNA has emerged as a crucial regulator in plant disease, its specific involvement in tomato bacterial wilt remains limited. Here, we conducted a comprehensive analysis of the transcriptional landscape, encompassing both mRNAs and noncoding RNAs, in a tomato resistant line ('ZRS_7') and a susceptible line ('HTY_9') upon R. solanacearum inoculation using high-throughput RNA sequencing. Differential expression (DE) analysis revealed significant alterations in 7506 mRNAs, 997 lncRNAs, and 69 miRNAs between 'ZRS_7' and 'HTY_9' after pathogen exposure. Notably, 4548 mRNAs, 367 lncRNAs, and 26 miRNAs exhibited genotype-specific responses to R. solanacearum inoculation. GO and KEGG pathway analyses unveiled the potential involvement of noncoding RNAs in the response to bacterial wilt disease, targeting receptor-like kinases, cell wall-related genes, glutamate decarboxylases, and other key pathways. Furthermore, we constructed a comprehensive competing endogenous RNA (ceRNA) network incorporating 13 DE-miRNAs, 30 DE-lncRNAs, and 127 DEGs, providing insights into their potential contributions to the response against bacterial inoculation. Importantly, the characterization of possible endogenous target mimics (eTMs) of Sly-miR482e-3p via VIGS technology demonstrated the significant impact of eTM482e-3p-1 silencing on tomato's sensitivity to R. solanacearum. These findings support the existence of an eTM482e-3p-1-Sly-miR482e-3p-NBS-LRRs network in regulating tomato's response to the pathogen. Collectively, our findings shed light on the intricate interactions among lncRNAs, miRNAs, and mRNAs as underlying factors in conferring resistance to R. solanacearum in tomato.

Fighting wheat powdery mildew: from genes to fields

KEY MESSAGE

Host resistance conferred by Pm genes provides an effective strategy to control powdery mildew. The study of Pm genes helps modern breeding develop toward more intelligent and customized. Powdery mildew of wheat is one of the most destructive diseases seriously threatening the crop yield and quality worldwide. The genetic research on powdery mildew (Pm) resistance has entered a new era. Many Pm genes from wheat and its wild and domesticated relatives have been mined and cloned. Meanwhile, modern breeding strategies based on high-throughput sequencing and genome editing are emerging and developing toward more intelligent and customized. This review highlights mining and cloning of Pm genes, molecular mechanism studies on the resistance and avirulence genes, and prospects for genomic-assisted breeding for powdery mildew resistance in wheat.

A necessary considering factor for breeding: growth-defense tradeoff in plants

Crop diseases cause enormous yield losses and threaten global food security. Deployment of resistant cultivars can effectively control the disease and to minimize crop losses. However, high level of genetic immunity to disease was often accompanied by an undesired reduction in crop growth and yield. Recently, literatures have been rapidly emerged in understanding the mechanism of disease resistance and development genes in crop plants. To determine how and why the costs and the likely benefit of resistance genes caused in crop varieties, we re-summarized the present knowledge about the crosstalk between plant development and disease resistance caused by those genes that function as plasma membrane residents, MAPK cassette, nuclear envelope (NE) channels components and pleiotropic regulators. Considering the growth-defense tradeoffs on the basis of current advances, finally, we try to understand and suggest that a reasonable balancing strategies based on the interplay between immunity with growth should be considered to enhance immunity capacity without yield penalty in future crop breeding.

Genome-wide identification and characterization of lipoxygenase genes related to the English grain aphid infestation response in wheat

44 wheat LOX genes were identified by silico genome-wide search method. TaLOX5, 7, 10, 24, 29, 33 were specifically expressed post aphid infestation, indicating their participation in wheat-aphid interaction. In plants, LOX genes play important roles in various biological progresses including seed germination, tuber development, plant vegetative growth and most crucially in plant signal transduction, stress response and plant defense against plant diseases and insects. Although LOX genes have been characterized in many species, the importance of the LOX family in wheat has still not been well understood, hampering further improvement of wheat under stress conditions. Here, we identified 44 LOX genes (TaLOXs) in the whole wheat genome and classified into three subfamilies (9-LOXs, Type I 13-LOXs and Type II 13-LOXs) according to phylogenetic relationships. The TaLOXs belonging to the same subgroup shared similar gene structures and motif organizations. Synteny analysis demonstrated that segmental duplication events mainly contributed to the expansion of the LOX gene family in wheat. The results of protein-protein interaction network (PPI) and miRNA-TaLOXs predictions revealed that three TaLOXs (TaLOX20, 22 and 37) interacted mostly with proteins related to methyl jasmonate (MeJA) signaling pathway. The expression patterns of TaLOXs in different tissues (root, stem, leaf, spike and grain) under diverse abiotic stresses (heat, cold, drought, drought and heat combined treatment, and salt) as well as under diverse biotic stresses (powdery mildew pathogen, Fusarium graminearum and stripe rust pathogen) were systematically analyzed using RNA-seq data. We obtained aphid-responsive candidate genes by RNA-seq data of wheat after the English grain aphid infestation. Aphid-responsive candidate genes, including TaLOX5, 7, 10, 24, 29 and 33, were up-regulated in the wheat aphid-resistant genotype (Lunxuan144), while they were little expressed in the susceptible genotype (Jimai22) during late response (48 h and 72 h) to the English grain aphid infestation. Meanwhile, qRT-PCR analysis was used to validate these aphid-responsive candidate genes. The genetic divergence and diversity of all the TaLOXs in bread wheat and its relative species were investigated by available resequencing data. Finally, the 3D structure of the TaLOX proteins was predicted based on the homology modeling method. This study not only systematically investigated the characteristics and evolutionary relationships of TaLOXs, but also provided potential candidate genes in response to the English grain aphid infestation and laid the foundation to further study the regulatory roles in the English grain aphid infestation of LOX family in wheat and beyond.

TaSYP137 and TaVAMP723, the SNAREs Proteins from Wheat, Reduce Resistance to Blumeria graminis f. sp. tritici

SNARE protein is an essential factor driving vesicle fusion in eukaryotes. Several SNAREs have been shown to play a crucial role in protecting against powdery mildew and other pathogens. In our previous study, we identified SNARE family members and analyzed their expression pattern in response to powdery mildew infection. Based on quantitative expression and RNA-seq results, we focused on TaSYP137/TaVAMP723 and hypothesized that they play an important role in the interaction between wheat and Blumeria graminis f. sp. Tritici (Bgt). In this study, we measured the expression patterns of TaSYP132/TaVAMP723 genes in wheat post-infection with Bgt and found that the expression pattern of TaSYP137/TaVAMP723 was opposite in resistant and susceptible wheat samples infected by Bgt. The overexpression of TaSYP137/TaVAMP723 disrupted wheat's defense against Bgt infection, while silencing these genes enhanced its resistance to Bgt. Subcellular localization studies revealed that TaSYP137/TaVAMP723 are present in both the plasma membrane and nucleus. The interaction between TaSYP137 and TaVAMP723 was confirmed using the yeast two-hybrid (Y2H) system. This study offers novel insights into the involvement of SNARE proteins in the resistance of wheat against Bgt, thereby enhancing our comprehension of the role of the SNARE family in the pathways related to plant disease resistance.

Combating powdery mildew: Advances in molecular interactions between Blumeria graminis f. sp. tritici and wheat

Wheat powdery mildew caused by a biotrophic fungus Blumeria graminis f. sp. tritici (Bgt), is a widespread airborne disease which continues to threaten global wheat production. One of the most chemical-free and cost-effective approaches for the management of wheat powdery mildew is the exploitation of resistant cultivars. Accumulating evidence has reported that more than 100 powdery mildew resistance genes or alleles mapping to 63 different loci (Pm1-Pm68) have been identified from common wheat and its wild relatives, and only a few of them have been cloned so far. However, continuous emergence of new pathogen races with novel degrees of virulence renders wheat resistance genes ineffective. An essential breeding strategy for achieving more durable resistance is the pyramiding of resistance genes into a single genotype. The genetics of host-pathogen interactions integrated with temperature conditions and the interaction between resistance genes and their corresponding pathogen a virulence genes or other resistance genes within the wheat genome determine the expression of resistance genes. Considerable progress has been made in revealing Bgt pathogenesis mechanisms, identification of resistance genes and breeding of wheat powdery mildew resistant cultivars. A detailed understanding of the molecular interactions between wheat and Bgt will facilitate the development of novel and effective approaches for controlling powdery mildew. This review gives a succinct overview of the molecular basis of interactions between wheat and Bgt, and wheat defense mechanisms against Bgt infection. It will also unleash the unsung roles of epigenetic processes, autophagy and silicon in wheat resistance to Bgt.

Grapevine VaRPP13 protein enhances oomycetes resistance by activating SA signal pathway

Expression of the VaRPP13 in Arabidopsis and tobacco enhanced resistance to oomycete pathogens, and this enhancement is closely related to the activation of salicylic acid (SA) signaling pathway. Resistance (R) genes, which usually contain a nucleotide-binding site and a leucine-rich repeat (NBS-LRR) domain, play crucial roles in disease resistance. In this study, we cloned a CC-NBS-LRR gene VaRPP13 from Vitis amurensis 'Shuang Hong' grapevine, and investigated its function on disease resistance. VaRPP13 expression was induced by Plasmopara viticola, an oomycetes pathogen causing downy mildew disease in grapevine. Heterologous expression VaRPP13 could also enhance resistance to Hyaloperonospora arabidopsidis in Arabidopsis thaliana and Phytophthora capsici in Nicotiana benthamiana, both oomycete pathogens. Further study indicated that VaRPP13 could enhance the expression of genes in SA signal pathway, while exogenous SA could also induce the expression of VaRPP13. In conclusion, our studies demonstrated that VaRPP13 contributes to a broad-spectrum resistance to oomycetes via activating SA signaling pathway.