Overexpression of Arabidopsis Nucleotide-Binding and Leucine-Rich Repeat Genes RPS2 and RPM1(D505V) Confers Broad-Spectrum Disease Resistance in Rice

Genome-Wide Association Study for Identification of Marker-Trait Associations Conferring Resistance to Scald from Globally Collected Barley Germplasm

Scald is one of the major economically important foliar diseases in barley, causing up to 40% yield loss in susceptible varieties. The identification of quantitative trait loci and elite alleles that confer resistance to scald is imperative in reducing the threats to barley production. In this study, genome-wide association studies were conducted using a panel of 697 barley genotypes to identify quantitative trait loci for scald resistance. Field experiments were conducted over three consecutive years. Among different models used for genome-wide association studies analysis, FarmCPU was shown to be the best-suited model. Nineteen significant marker-trait associations related to scald resistance were identified across six different chromosomes. Eleven of these marker-trait associations correspond to previously reported scald resistance genes Rrs1, Rrs4, and Rrs2, respectively. Eight novel marker-trait associations were identified in this study, with the candidate genes encoding a diverse class of proteins, including region leucine-rich repeats, AP2/ERF transcription factor, homeodomain-leucine zipper, and protein kinase family proteins. The combination of identified superior alleles significantly reduces disease severity scores. The results will be valuable for marker-assisted breeding for developing scald-resistant varieties.

AraDQ: an automated digital phenotyping software for quantifying disease symptoms of flood-inoculated Arabidopsis seedlings

BACKGROUND

Plant scientists have largely relied on pathogen growth assays and/or transcript analysis of stress-responsive genes for quantification of disease severity and susceptibility. These methods are destructive to plants, labor-intensive, and time-consuming, thereby limiting their application in real-time, large-scale studies. Image-based plant phenotyping is an alternative approach that enables automated measurement of various symptoms. However, most of the currently available plant image analysis tools require specific hardware platform and vendor specific software packages, and thus, are not suited for researchers who are not primarily focused on plant phenotyping. In this study, we aimed to develop a digital phenotyping tool to enhance the speed, accuracy, and reliability of disease quantification in Arabidopsis.

RESULTS

Here, we present the Arabidopsis Disease Quantification (AraDQ) image analysis tool for examination of flood-inoculated Arabidopsis seedlings grown on plates containing plant growth media. It is a cross-platform application program with a user-friendly graphical interface that contains highly accurate deep neural networks for object detection and segmentation. The only prerequisite is that the input image should contain a fixed-sized 24-color balance card placed next to the objects of interest on a white background to ensure reliable and reproducible results, regardless of the image acquisition method. The image processing pipeline automatically calculates 10 different colors and morphological parameters for individual seedlings in the given image, and disease-associated phenotypic changes can be easily assessed by comparing plant images captured before and after infection. We conducted two case studies involving bacterial and plant mutants with reduced virulence and disease resistance capabilities, respectively, and thereby demonstrated that AraDQ can capture subtle changes in plant color and morphology with a high level of sensitivity.

CONCLUSIONS

AraDQ offers a simple, fast, and accurate approach for image-based quantification of plant disease symptoms using various parameters. Its fully automated pipeline neither requires prior image processing nor costly hardware setups, allowing easy implementation of the software by researchers interested in digital phenotyping of diseased plants.

Barley MLA3 recognizes the host-specificity effector Pwl2 from Magnaporthe oryzae

Plant nucleotide-binding leucine-rich repeat (NLRs) immune receptors directly or indirectly recognize pathogen-secreted effector molecules to initiate plant defense. Recognition of multiple pathogens by a single NLR is rare and usually occurs via monitoring for changes to host proteins; few characterized NLRs have been shown to recognize multiple effectors. The barley (Hordeum vulgare) NLR gene Mildew locus a (Mla) has undergone functional diversification, and the proteins encoded by different Mla alleles recognize host-adapted isolates of barley powdery mildew (Blumeria graminis f. sp. hordei [Bgh]). Here, we show that Mla3 also confers resistance to the rice blast fungus Magnaporthe oryzae in a dosage-dependent manner. Using a forward genetic screen, we discovered that the recognized effector from M. oryzae is Pathogenicity toward Weeping Lovegrass 2 (Pwl2), a host range determinant factor that prevents M. oryzae from infecting weeping lovegrass (Eragrostis curvula). Mla3 has therefore convergently evolved the capacity to recognize effectors from diverse pathogens.

Deciphering the genetic architecture of resistance to Corynespora cassiicola in soybean (Glycine max L.) by integrating genome-wide association mapping and RNA-Seq analysis

Target spot caused by Corynespora cassiicola is a problematic disease in tropical and subtropical soybean (Glycine max) growing regions. Although resistant soybean genotypes have been identified, the genetic mechanisms underlying target spot resistance has not yet been studied. To address this knowledge gap, this is the first genome-wide association study (GWAS) conducted using the SoySNP50K array on a panel of 246 soybean accessions, aiming to unravel the genetic architecture of resistance. The results revealed significant associations of 14 and 33 loci with resistance to LIM01 and SSTA C. cassiicola isolates, respectively, with six loci demonstrating consistent associations across both isolates. To identify potential candidate genes within GWAS-identified loci, dynamic transcriptome profiling was conducted through RNA-Seq analysis. The analysis involved comparing gene expression patterns between resistant and susceptible genotypes, utilizing leaf tissue collected at different time points after inoculation. Integrating results of GWAS and RNA-Seq analyses identified 238 differentially expressed genes within a 200 kb region encompassing significant quantitative trait loci (QTLs) for disease severity ratings. These genes were involved in defense response to pathogen, innate immune response, chitinase activity, histone H3-K9 methylation, salicylic acid mediated signaling pathway, kinase activity, and biosynthesis of flavonoid, jasmonic acid, phenylpropanoid, and wax. In addition, when combining results from this study with previous GWAS research, 11 colocalized regions associated with disease resistance were identified for biotic and abiotic stress. This finding provides valuable insight into the genetic resources that can be harnessed for future breeding programs aiming to enhance soybean resistance against target spot and other diseases simultaneously.

Phased grapevine genome sequence of an Rpv12 carrier for biotechnological exploration of resistance to Plasmopara viticola

The downy mildew disease caused by the oomycete Plasmopara viticola is a serious threat for grapevine and can cause enormous yield losses in viticulture. The quantitative trait locus Rpv12, mediating resistance against P. viticola, was originally found in Asian Vitis amurensis. This locus and its genes were analyzed here in detail. A haplotype-separated genome sequence of the diploid Rpv12-carrier Gf.99-03 was created and annotated. The defense response against P. viticola was investigated in an infection time-course RNA-seq experiment, revealing approximately 600 upregulated Vitis genes during host-pathogen interaction. The Rpv12 regions of the resistance and the sensitivity encoding Gf.99-03 haplotype were structurally and functionally compared with each other. Two different clusters of resistance-related genes were identified within the Rpv12 locus. One cluster carries a set of four differentially expressed genes with three ACCELERATED CELL DEATH 6-like genes. The other cluster carries a set of six resistance gene analogs related to qualitative pathogen resistance. The Rpv12 locus and its candidate genes for P. viticola resistance provide a precious genetic resource for P. viticola resistance breeding. Newly developed co-segregating simple sequence repeat markers in close proximity to the R-genes enable its improved applicability in marker-assisted grapevine breeding.

Insights into the Molecular Basis of Huanglongbing Tolerance in Persian Lime (Citrus latifolia Tan.) through a Transcriptomic Approach

Huanglongbing (HLB) is a vascular disease of Citrus caused by three species of the α-proteobacteria "Candidatus Liberibacter", with "Candidatus Liberibacter asiaticus" (CLas) being the most widespread and the one causing significant economic losses in citrus-producing regions worldwide. However, Persian lime (Citrus latifolia Tanaka) has shown tolerance to the disease. To understand the molecular mechanisms of this tolerance, transcriptomic analysis of HLB was performed using asymptomatic and symptomatic leaves. RNA-Seq analysis revealed 652 differentially expressed genes (DEGs) in response to CLas infection, of which 457 were upregulated and 195 were downregulated. KEGG analysis revealed that after CLas infection, some DEGs were present in the plant-pathogen interaction and in the starch and sucrose metabolism pathways. DEGs present in the plant-pathogen interaction pathway suggests that tolerance against HLB in Persian lime could be mediated, at least partly, by the ClRSP2 and ClHSP90 genes. Previous reports documented that RSP2 and HSP90 showed low expression in susceptible citrus genotypes. Regarding the starch and sucrose metabolism pathways, some genes were identified as being related to the imbalance of starch accumulation. On the other hand, eight biotic stress-related genes were selected for further RT-qPCR analysis to validate our results. RT-qPCR results confirmed that symptomatic HLB leaves had high relative expression levels of the ClPR1, ClNFP, ClDR27, and ClSRK genes, whereas the ClHSL1, ClRPP13, ClPDR1, and ClNAC genes were expressed at lower levels than those from HLB asymptomatic leaves. Taken together, the present transcriptomic analysis contributes to the understanding of the CLas-Persian lime interaction in its natural environment and may set the basis for developing strategies for the integrated management of this important Citrus disease through the identification of blanks for genetic improvement.

Engineering effector-triggered immunity in rice: Obstacles and perspectives

Improving rice immunity is one of the most effective approaches to reduce yield loss by biotic factors, with the aim of increasing rice production by 2050 amidst limited natural resources. Triggering a fast and strong immune response to pathogens, effector-triggered immunity (ETI) has intrigued scientists to intensively study and utilize the mechanisms for engineering highly resistant plants. The conservation of ETI components and mechanisms across species enables the use of ETI components to generate broad-spectrum resistance in plants. Numerous efforts have been made to introduce new resistance (R) genes, widen the effector recognition spectrum and generate on-demand R genes. Although engineering ETI across plant species is still associated with multiple challenges, previous attempts have provided an enhanced understanding of ETI mechanisms. Here, we provide a survey of recent reports in the engineering of rice R genes. In addition, we suggest a framework for future studies of R gene-effector interactions, including genome-scale investigations in both rice and pathogens, followed by structural studies of R proteins and effectors, and potential strategies to use important ETI components to improve rice immunity.

Genetic mapping of the powdery mildew resistance gene Pm7 on oat chromosome 5D

Three independent experiments with different genetic backgrounds mapped the resistance gene Pm7 in the oat genome to the distal part of the long arm of chromosome 5D. Resistance of oat to Blumeria graminis DC. f. sp. avenae is an important breeding goal in Central and Western Europe. In this study, the position of the effective and widely used resistance gene Pm7 in the oat genome was determined based on three independent experiments with different genetic backgrounds: genome-wide association mapping in a diverse set of inbred oat lines and binary phenotype mapping in two bi-parental populations. Powdery mildew resistance was assessed in the field as well as by detached leaf tests in the laboratory. Genotyping-by-sequencing was conducted to establish comprehensive genetic fingerprints for subsequent genetic mapping experiments. All three mapping approaches located the gene to the distal part of the long arm of chromosome 5D in the hexaploid oat genome sequences of OT3098 and 'Sang.' Markers from this region were homologous to a region of chromosome 2Ce of the C-genome species, Avena eriantha, the donor of Pm7, which appears to be the ancestral source of a translocated region on the hexaploid chromosome 5D.

Transcriptome Dynamic Analysis Reveals New Candidate Genes Associated with Resistance to Fusarium Head Blight in Two Chinese Contrasting Wheat Genotypes

In recent years, Fusarium head blight (FHB) has developed into a global disease that seriously affects the yield and quality of wheat. Effective measures to solve this problem include exploring disease-resistant genes and breeding disease-resistant varieties. In this study, we conducted a comparative transcriptome analysis to identify the important genes that are differentially expressed in FHB medium-resistant (Nankang 1) and FHB medium-susceptible (Shannong 102) wheat varieties for various periods after Fusarium graminearum infection using RNA-seq technology. In total, 96,628 differentially expressed genes (DEGs) were identified, 42,767 from Shannong 102 and 53,861 from Nankang 1 (FDR < 0.05 and |log2FC| > 1). Of these, 5754 and 6841 genes were found to be shared among the three time points in Shannong 102 and Nankang 1, respectively. After inoculation for 48 h, the number of upregulated genes in Nankang 1 was significantly lower than that of Shannong 102, but at 96 h, the number of DEGs in Nankang 1 was higher than that in Shannong 102. This indicated that Shannong 102 and Nankang 1 had different defensive responses to F. graminearum in the early stages of infection. By comparing the DEGs, there were 2282 genes shared at the three time points between the two strains. GO and KEGG analyses of these DEGs showed that the following pathways were associated with disease resistance genes: response to stimulus pathway in GO, glutathione metabolism, phenylpropanoid biosynthesis, plant hormone signal transduction, and plant-pathogen interaction in KEGG. Among them, 16 upregulated genes were identified in the plant-pathogen interaction pathway. There were five upregulated genes, TraesCS5A02G439700, TraesCS5B02G442900, TraesCS5B02G443300, TraesCS5B02G443400, and TraesCS5D02G446900, with significantly higher expression levels in Nankang 1 than in Shannong 102, and these genes may have an important role in regulating the resistance of Nankang 1 to F. graminearum infection. The PR proteins they encode are PR protein 1-9, PR protein 1-6, PR protein 1-7, PR protein 1-7, and PR protein 1-like. In addition, the number of DEGs in Nankang 1 was higher than that in Shannong 102 on almost all chromosomes, except chromosomes 1A and 3D, but especially on chromosomes 6B, 4B, 3B, and 5A. These results indicate that gene expression and the genetic background must be considered for FHB resistance in wheat breeding.

Engineering plant immune circuit: walking to the bright future with a novel toolbox

Plant pathogens destroy crops and cause severe yield losses, leading to an insufficient food supply to sustain the human population. Apart from relying on natural plant immune systems to combat biological agents or waiting for the appropriate evolutionary steps to occur over time, researchers are currently seeking new breakthrough methods to boost disease resistance in plants through genetic engineering. Here, we summarize the past two decades of research in disease resistance engineering against an assortment of pathogens through modifying the plant immune components (internal and external) with several biotechnological techniques. We also discuss potential strategies and provide perspectives on engineering plant immune systems for enhanced pathogen resistance and plant fitness.

Stress responsive OsHyPRP16 promoter driven early expression of resistance gene Pi54 potentiate the resistance against Magnaporthe oryzae in transgenic rice

The rice Hybrid Proline Rich Protein (HyPRP) encoding gene, OsHyPRP16 expression exhibit early upregulation in response to Magnaporthe oryzae inoculation. Here, we functionally characterized the OsHyPRP16 promoter through deletion analysis in transgenic Arabidopsis using GUS (β-glucuronidase) reporter assay. The promoter fragments, sequentially deleted from the 5' end could induce differential GUS activity in response to stresses induced by different hormones and abiotic stress conditions. In addition, a strong GUS induction was observed in M. oryzae inoculated transgenic Arabidopsis. Based on the insilico and stress-inducibility of D1 promoter fragment against various phytohormones and rice blast fungus, and with no basal activity under control conditions, we rationally selected D1 promoter fragment to drive the expression of a major rice blast resistance gene; Pi54 in the genetic background of blast susceptible TP309 rice line. The D1 promoter fragment was able to induce the expression of Pi54 at immediate-early stages of M. oryzae infection in transgenic rice. The transgenic plants with Pi54 under the control of D1 promoter fragment displayed complete resistance against M. oryzae infection as compared to control plants. The present study suggests that the D1 fragment of OsHyPRP16 promoter is a valuable tool for breeding and development of rice lines with early-inducible and pathogen-responsive enhanced disease resistance.

Rice transcriptome upon infection with Xanthomonas oryzae pv. oryzae relative to its avirulent T3SS-defective strain exposed modulation of many stress responsive genes

Xanthomonas oryzae pv. oryzae (Xoo) is a destructive pathogen that causes bacterial blight disease of rice worldwide. Xoo uses T3SS (type III secretion system) effectors to subvert rice innate immunity. However, the comprehensive knowledge of rice genes involved in T3SS effectors-mediated interaction remains unclear. In this study, the transcriptome profiles of rice infected with a virulent Xoo strain from North-eastern region of India relatives to its avirulent strain (that lacks functional T3SS) were analyzed at early (2-6 hpi) and late (16-24 hpi) hours of infection. Out of total 255 differentially expressed genes (DEGs), during early infection, 62 and 70 genes were upregulated and downregulated, respectively. At late infection, 70 and 53 genes were upregulated and downregulated, respectively. The transcriptomic data identified many differentially expressed resistant genes, transposons, transcription factors, serine/threonine protein kinase, cytochrome P450 and peroxidase genes that are involved in plant defense. Pathway analysis revealed that these DEGs are involved in hormone signaling, plant defense, cellular metabolism, growth and development processes. DEGs associated with plant defense were also validated through quantitative real-time PCR. Our study brings a comprehensive picture of the rice genes that are being differentially expressed during bacterial blight infection. Nevertheless, the DEG-associated pathways would provide sensible targets for developing resistance to bacterial blight.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03193-4.

A review of approaches to control bacterial leaf blight in rice

The Gram-negative bacteria Xanthomonas oryzae pv. oryzae, the causative agent of bacterial leaf blight (BLB), received attention for being an economically damaging pathogen of rice worldwide. This damage prompted efforts to better understand the molecular mechanisms governing BLB disease progression. This research revealed numerous virulence factors that are employed by this vascular pathogen to invade the host, outcompete host defence mechanisms, and cause disease. In this review, we emphasize the virulence factors and molecular mechanisms that X. oryzae pv. oryzae uses to impair host defences, recent insights into the cellular and molecular mechanisms underlying host-pathogen interactions and components of pathogenicity, methods for developing X. oryzae pv. oryzae-resistant rice cultivars, strategies to mitigate disease outbreaks, and newly discovered genes and tools for disease management. We conclude that the implementation and application of cutting-edge technologies and tools are crucial to avoid yield losses from BLB and ensure food security.

A high-density linkage map of finger millet provides QTL for blast resistance and other agronomic traits

Finger millet [Eleusine coracana (L.) Gaertn.] is a critical subsistence crop in eastern Africa and southern Asia but has few genomic resources and modern breeding programs. To aid in the understanding of finger millet genomic organization and genes underlying disease resistance and agronomically important traits, we generated a F_2:3 population from a cross between E. coracana (L.) Gaertn. subsp. coracana accession ACC 100007 and E. coracana (L.) Gaertn. subsp. africana , accession GBK 030647. Phenotypic data on morphology, yield, and blast (Magnaporthe oryzae) resistance traits were taken on a subset of the F_2:3 population in a Kenyan field trial. The F_2:3 population was genotyped via genotyping-by-sequencing (GBS) and the UGbS-Flex pipeline was used for sequence alignment, nucleotide polymorphism calling, and genetic map construction. An 18-linkage-group genetic map consisting of 5,422 markers was generated that enabled comparative genomic analyses with rice (Oryza sativa L.), foxtail millet [Setaria italica (L.) P. Beauv.], and sorghum [Sorghum bicolor (L.) Moench]. Notably, we identified conserved acrocentric homoeologous chromosomes (4A and 4B in finger millet) across all species. Significant quantitative trait loci (QTL) were discovered for flowering date, plant height, panicle number, and blast incidence and severity. Sixteen putative candidate genes that may underlie trait variation were identified. Seven LEUCINE-RICH REPEAT-CONTAINING PROTEIN genes, with homology to nucleotide-binding site leucine-rich repeat (NBS-LRR) disease resistance proteins, were found on three chromosomes under blast resistance QTL. This high-marker-density genetic map provides an important tool for plant breeding programs and identifies genomic regions and genes of critical interest for agronomic traits and blast resistance.

Closer vein spacing by ectopic expression of nucleotide-binding and leucine-rich repeat proteins in rice leaves

Elevated expression of nucleotide-binding and leucine-rich repeat proteins led to closer vein spacing and higher vein density in rice leaves. To feed the growing global population and mitigate the negative effects of climate change, there is a need to improve the photosynthetic capacity and efficiency of major crops such as rice to enhance grain yield potential. Alterations in internal leaf morphology and cellular architecture are needed to underpin some of these improvements. One of the targets is to generate a "Kranz-like" anatomy in leaves that includes decreased interveinal spacing close to that in C₄ plant species. As C₄ photosynthesis has evolved from C₃ photosynthesis independently in multiple lineages, the genes required to facilitate C₄ may already be present in the rice genome. The Taiwan Rice Insertional Mutants (TRIM) population offers the advantage of gain-of-function phenotype trapping, which accelerates the identification of rice gene function. In the present study, we screened the TRIM population to determine the extent to which genetic plasticity can alter vein density (VD) in rice. Close vein spacing mutant 1 (CVS1), identified from a VD screening of approximately 17,000 TRIM lines, conferred heritable high leaf VD. Increased vein number in CVS1 was confirmed to be associated with activated expression of two nucleotide-binding and leucine-rich repeat (NB-LRR) proteins. Overexpression of the two NB-LRR genes individually in rice recapitulates the high VD phenotype, due mainly to reduced interveinal mesophyll cell (M cell) number, length, bulliform cell size and thus interveinal distance. Our studies demonstrate that the trait of high VD in rice can be achieved by elevated expression of NB-LRR proteins limited to no yield penalty.

Identification and Fine-Mapping of a New Bacterial Blight Resistance Gene, Xa47(t), in G252, an Introgression Line of Yuanjiang Common Wild Rice (Oryza rufipogon)

Bacterial blight (BB) disease caused by Xanthomonas oryzae pv. oryzae is a common, widespread, and highly devastating disease that affects rice yield. Breeding resistant cultivars is considered the most effective measure for controlling this disease. The introgression line G252 derived from Yuanjiang common wild rice (Oryza rufipogon) was highly resistant to all tested strains, including C5, C9, PXO99, PB, T7147Y8, Hzhj19, YM1, YM187, YJdp-2, and YJws-2. To identify the BB resistance gene(s) of G252, we developed an F₂ population from the cross between G252 and 02428. A linkage analysis was performed for the phenotype and genotype of the population. A segregation ratio of 3:1 was observed between the resistant and susceptible individuals in the F₂ progeny, indicating a dominant resistance gene, Xa47(t), in G252. The resistance gene was mapped within an approximately 26.24-kb physical region on chromosome 11 between two InDel markers, R13I14 and 13rbq-71. Moreover, one InDel marker, Hxjy-1, co-segregated with Xa47(t). Three genes were predicted within the target region, including a promising candidate gene encoding a nucleotide-binding domain and leucine-rich repeat (NLR) protein (LOC_Os11g46200) by combining the structure and expression analysis. Physical mapping data suggested that Xa47(t) is a new broad-spectrum BB resistance gene without identified allelic genes.

Recent Progress in Rice Broad-Spectrum Disease Resistance

Rice is one of the most important food crops in the world. However, stable rice production is constrained by various diseases, in particular rice blast, sheath blight, bacterial blight, and virus diseases. Breeding and cultivation of resistant rice varieties is the most effective method to control the infection of pathogens. Exploitation and utilization of the genetic determinants of broad-spectrum resistance represent a desired way to improve the resistance of susceptible rice varieties. Recently, researchers have focused on the identification of rice broad-spectrum disease resistance genes, which include R genes, defense-regulator genes, and quantitative trait loci (QTL) against two or more pathogen species or many isolates of the same pathogen species. The cloning of broad-spectrum disease resistance genes and understanding their underlying mechanisms not only provide new genetic resources for breeding broad-spectrum rice varieties, but also promote the development of new disease resistance breeding strategies, such as editing susceptibility and executor R genes. In this review, the most recent advances in the identification of broad-spectrum disease resistance genes in rice and their application in crop improvement through biotechnology approaches during the past 10 years are summarized.

Molecular and functional analysis of a brown planthopper resistance protein with two nucleotide-binding site domains

The brown planthopper (Nilaparvata lugens Stål, BPH) resistance gene BPH9 encodes an unusual coiled-coil (CC) nucleotide-binding leucine-rich repeat (LRR) protein with two nucleotide-binding site (NBS) domains. To understand how this CC-NBS-NBS-LRR (CNNL) protein regulates defense signaling and BPH resistance, we dissected each domain's functions. The CC domain of BPH9 self-associated and was sufficient to induce cell death. The region of 97-115 residues in the CC domain is crucial for self-association and activation. NBS2, which contains a complete set of NBS function motifs and inhibits CC domain activation, rather than NBS1, acts as a molecular switch to regulate the activity of BPH9. We demonstrated that the CC domain, the NBS domain, and the LRR domain of BPH9 associate with each other and themselves in planta. Further domain swapping experiments revealed that the CC domains of BPH9 and susceptible alleles were similarly competent to induce resistance and the hypersensitive response, while the LRR domain of BPH9 confers resistance specificity to BPH. These findings provide new insights into the regulatory mechanisms governing the activity of CNNL proteins.

Diversity, structure and function of the coiled-coil domains of plant NLR immune receptors

Plant nucleotide-binding, leucine-rich repeat receptors (NLRs) perceive pathogen avirulence effectors and activate defense responses. Nucleotide-binding, leucine-rich repeat receptors are classified into coiled-coil (CC)-containing and Toll/interleukin-1 receptor (TIR)-containing NLRs. Recent advances suggest that NLR CC domains often function in signaling activation, especially for induction of cell death. In this review, we outline our current understanding of NLR CC domains, including their diversity/classification and structure, their roles in cell death induction, disease resistance, and interaction with other proteins. Furthermore, we provide possible directions for future work.

Metabolic and Transcriptomic Profiling of Lilium Leaves Infected With Botrytis elliptica Reveals Different Stages of Plant Defense Mechanisms

Botrytis elliptica, the causal agent of gray mold disease, poses a major threat to commercial Lilium production, limiting its ornamental value and yield. The molecular and metabolic regulation mechanisms of Lilium's defense response to B. elliptica infection have not been completely elucidated. Here, we performed transcriptomic and metabolomic analyses of B. elliptica resistant Lilium oriental hybrid "Sorbonne" to understand the molecular basis of gray mold disease resistance in gray mold disease. A total of 115 differentially accumulated metabolites (DAMs) were detected by comparing the different temporal stages of pathogen infection. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed the differentially expressed genes (DEGs) and DAMs were enriched in the phenylpropanoid and flavonoid pathways at all stages of infection, demonstrating the prominence of these pathways in the defense response of "Sorbonne" to B. elliptica. Network analysis revealed high interconnectivity of the induced defense response. Furthermore, time-course analysis of the transcriptome and a weighted gene coexpression network analysis (WGCNA) led to the identification of a number of hub genes at different stages, revealing that jasmonic acid (JA), salicylic acid (SA), brassinolide (BR), and calcium ions (Ca²⁺) play a crucial role in the response of "Sorbonne" to fungal infection. Our work provides a comprehensive perspective on the defense response of Lilium to B. elliptica infection, along with a potential transcriptional regulatory network underlying the defense response, thereby offering gene candidates for resistance breeding and metabolic engineering of Lilium.

RIN13-mediated disease resistance depends on the SNC1-EDS1/PAD4 signaling pathway in Arabidopsis

Plants have evolved an innate immune system to protect themselves from pathogen invasion with the help of intracellular nucleotide-binding leucine-rich repeat (NLR) receptors, though the mechanisms remain largely undefined. RIN13 (RPM1-interacting protein 13) was previously reported to enhance disease resistance, and suppress RPM1 (a CNL-type NLR)-mediated hypersensitive response in Arabidopsis via an as yet unknown mechanism. Here, we show that RIN13 is a nuclear-localized protein, and functions therein. Overexpression of RIN13 leads to autoimmunity with high accumulation of salicylic acid (SA), constitutive expression of pathogenesis-related genes, enhanced resistance to a virulent pathogen, and dwarfism. In addition, genetic and transcriptome analyses show that SA-dependent and SA-independent pathways are both required for RIN13-mediated disease resistance, with the EDS1/PAD4 complex as an integration point. RIN13-induced dwarfism was rescued completely by either the pad4-1 or the eds1-2 mutant but partially by snc1-r1, a mutant of the TNL gene SNC1, suggesting the involvement of EDS1/PAD4 and SNC1 in RIN13 functioning. Furthermore, transient expression assays indicated that RIN13 promotes the nuclear accumulation of PAD4. Collectively, our study uncovered a signaling pathway whereby SNC1 and EDS1/PAD4 act together to modulate RIN13-triggered plant defense responses.

Transcriptome analysis provides insights into the mechanisms underlying wheat cultivar Shumai126 responding to stripe rust

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a destructive fungal disease of wheat globally. Breeding resistance cultivars is one of the most cost-effective methods to control Pst. Shumai126 (SM126), a high-yielding commercial wheat cultivar, showed strong stripe rust resistance for more than ten years. However, the molecular mechanisms and the responsive genes underlying the SM126 resistance to Pst have not been explored yet. In the present study, RNA-seq was used to analyze changes in the transcriptome at different time points of Pst infection in seedling leaves of SM126. In total, 520, 148 and 1439 differentially expressed genes (DEGs) were found to be up- or down-regulated after Pst infection at 1, 3, and 7 days post inoculation, respectively. The majority of DEGs exhibited transient expression patterns during Pst infection at different time points. GO and KEGG enrichment analysis revealed that many biological processes, such as photosynthesis, flavonoid biosynthesis, oxidative phosphorylation, MAPK signaling pathway, and phenylalanine metabolism are involved in SM126 response to Pst. Expression of genes involved in the plant-pathogen interaction pathway was detected and some key genes showed differential expression. DEGs encoded R proteins and transcription factors were also identified. Our study suggests the gene resources in SM126 related to stripe rust response could be valuable for understanding the mechanisms involved in stripe rust resistance and improvement of wheat resistance to Pst.

Whole genome re-sequencing of sweet cherry (Prunus avium L.) yields insights into genomic diversity of a fruit species

Sweet cherries, Prunus avium L. (Rosaceae), are gaining importance due to their perenniallity and nutritional attributes beneficial for human health. Interestingly, sweet cherry cultivars exhibit a wide range of phenotypic diversity in important agronomic traits, such as flowering time and defense reactions against pathogens. In this study, whole-genome resequencing (WGRS) was employed to characterize genetic variation, population structure and allelic variants in a panel of 20 sweet cherry and one wild cherry genotypes, embodying the majority of cultivated Greek germplasm and a representative of a local wild cherry elite phenotype. The 21 genotypes were sequenced in an average depth of coverage of 33.91×. and effective mapping depth, to the genomic reference sequence of 'Satonishiki' cultivar, between 22.21× to 36.62×. Discriminant analysis of principal components (DAPC) with SNPs revealed two clusters of genotypes. There was a rapid linkage disequilibrium decay, as the majority of SNP pairs with r2 in near complete disequilibrium (>0.8) were found at physical distances less than 10 kb. Functional analysis of the variants showed that the genomic ratio of non-synonymous/synonymous (dN/dS) changes was 1.78. The higher dN frequency in the Greek cohort of sweet cherry could be the result of artificial selection pressure imposed by breeding, in combination with the vegetative propagation of domesticated cultivars through grafting. The majority of SNPs with high impact (e.g., stop codon gaining, frameshift), were identified in genes involved in flowering time, dormancy and defense reactions against pathogens, providing promising resources for future breeding programs. Our study has established the foundation for further large scale characterization of sweet cherry germplasm, enabling breeders to incorporate diverse germplasm and allelic variants to fine tune flowering and maturity time and disease resistance in sweet cherry cultivars.

The barley stripe mosaic virus expression system reveals the wheat C2H2 zinc finger protein TaZFP1B as a key regulator of drought tolerance

BACKGROUND

Drought stress is one of the major factors limiting wheat production globally. Improving drought tolerance is important for agriculture sustainability. Although various morphological, physiological and biochemical responses associated with drought tolerance have been documented, the molecular mechanisms and regulatory genes that are needed to improve drought tolerance in crops require further investigation. We have used a novel 4-component version (for overexpression) and a 3-component version (for underexpression) of a barley stripe mosaic virus-based (BSMV) system for functional characterization of the C2H2-type zinc finger protein TaZFP1B in wheat. These expression systems avoid the need to produce transgenic plant lines and greatly speed up functional gene characterization.

RESULTS

We show that overexpression of TaZFP1B stimulates plant growth and up-regulates different oxidative stress-responsive genes under well-watered conditions. Plants that overexpress TaZFP1B are more drought tolerant at critical periods of the plant's life cycle. Furthermore, RNA-Seq analysis revealed that plants overexpressing TaZFP1B reprogram their transcriptome, resulting in physiological and physical modifications that help wheat to grow and survive under drought stress. In contrast, plants transformed to underexpress TaZFP1B are significantly less tolerant to drought and growth is negatively affected.

CONCLUSIONS

This study clearly shows that the two versions of the BSMV system can be used for fast and efficient functional characterization of genes in crops. The extent of transcriptome reprogramming in plants that overexpress TaZFP1B indicates that the encoded transcription factor is a key regulator of drought tolerance in wheat.