Molecular Basis Of Disease Resistance Research Articles

The Analysis of Short-Term Differential Expression of Transcription Factor Family Genes in Diploid and Tetraploid Rice (Oryza sativa L.) Varieties during Blast Fungus Infection

The necessity to understand plant adaptations to environmental stressors is underscored by the role of polyploidy in species evolution. This study focuses on the superior stress resistance exhibited by autotetraploid rice, which arises from chromosome doubling, in comparison to its diploid donor. We provide a quantitative analysis that highlights the differing susceptibilities of diploid (GFD-2X) and autotetraploid (GFD-4X) rice to rice blast disease, with GFD-2X being significantly more susceptible. Our investigation centers on transcription factors (TFs), which are crucial in regulating biological stress responses, by analyzing their expression in the face of a pathogen attack. This study uncovers variations in the number and expression timing of differentially expressed TF genes, providing a quantitative view of GFD-4X’s resistance. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses confirm the role of specific pathways, including “response to stimulus” and the “MAPK signaling pathway,” in resistance mechanisms. An extensive analysis of protein–protein interaction networks further clarifies the complex role of TFs during stress responses. The rationale for our experimental approach is rooted in the imperative to decipher the molecular basis of disease resistance across different ploidies, which has implications for crop enhancement. The conclusion from our research is that autotetraploid rice has a unique and more effective defense response regulation system, facilitated by transcription factors, when faced with rice blast disease. This finding provides a foundation for future genetic strategies aimed at improving crop resistance.

Genetic composition and diversity of Arabica coffee in the crop's centre of origin and its impact on four major fungal diseases.

Conventional wisdom states that genetic variation reduces disease levels in plant populations. Nevertheless, crop species have been subject to a gradual loss of genetic variation through selection for specific traits during breeding, thereby increasing their vulnerability to biotic stresses such as pathogens. We explored how genetic variation in Arabica coffee sites in southwestern Ethiopia was related to the incidence of four major fungal diseases. Sixty sites were selected along a gradient of management intensity, ranging from nearly wild to intensively managed coffee stands. We used genotyping-by-sequencing of pooled leaf samples (pool-GBS) derived from 16 individual coffee shrubs in each of the 60sites to assess the variation in genetic composition (multivariate: reference allele frequency) and genetic diversity (univariate: mean expected heterozygosity) between sites. We found that genetic composition had a clear spatial pattern and that genetic diversity was higher in less managed sites. The incidence of the four fungal diseases was related to the genetic composition of the coffee stands, but in a specific way for each disease. In contrast, genetic diversity was only related to the within-site variation of coffee berry disease, but not to the mean incidence of any of the four diseases across sites. Given that fungal diseases are major challenges of Arabica coffee in its native range, our findings that genetic composition of coffee sites impacted the major fungal diseases may serve as baseline information to study the molecular basis of disease resistance in coffee. Overall, our study illustrates the need to consider both host genetic composition and genetic diversity when investigating the genetic basis for variation in disease levels.

A high-quality genome assembly of the eggplant provides insights into the molecular basis of disease resistance and chlorogenic acid synthesis.

The eggplant (Solanum melongena L.) is one of the most important Solanaceae crops, ranking third for total production and economic value in its genus. Herein, we report a high-quality, chromosome-scale eggplant reference genome sequence of 1155.8Mb, with an N50 of 93.9Mb, which was assembled by combining PacBio long reads and Hi-C sequencing data. Repetitive sequences occupied 70.1% of the assembly length, and 35,018 high-confidence protein-coding genes were annotated based on multiple sources. Comparative analysis revealed 646 species-specific families and 364 positive selection genes, conferring distinguishing traits on the eggplant. We performed genome-wide comparative identification of disease resistance genes and discovered an expanded gene family of bacterial spot resistance in eggplant and pepper, but not in tomato and potato. The genes involved in chlorogenic acid synthesis were comprehensively characterized. Highly similar chromosomal distribution patterns of polyphenol oxidase genes were observed in the eggplant, tomato, and potato genomes. The eggplant reference genome sequence will not only facilitate evolutionary studies of the Solanaceae but also facilitate their breeding and improvement.

The island cotton NBS-LRR gene GbaNA1 confers resistance to the non-race 1 Verticillium dahliae isolate Vd991.

Wilt caused by Verticillium dahliae significantly reduces cotton yields, as host resistance in commercially cultivated Gossypium species is lacking. Understanding the molecular basis of disease resistance in non-commercial Gossypium species could galvanize the development of Verticillium wilt resistance in cultivated species. Nucleotide-binding site leucine-rich repeat (NBS-LRR) proteins play a central role in plant defence against pathogens. In this study, we focused on the relationship between a locus enriched with eight NBS-LRR genes and Verticillium wilt resistance in G. barbadense. Independent virus-induced gene silencing of each of the eight NBS-LRR genes in G. barbadense cultivar Hai 7124 revealed that silencing of GbaNA1 alone compromised the resistance of G. barbadense to V. dahliae isolate Vd991. In cultivar Hai 7124, GbaNA1 could be induced by V. dahliae isolate Vd991 and by ethylene, jasmonic acid and salicylic acid. Nuclear protein localization of GbaNA1 was demonstrated by transient expression. Sequencing of the GbaNA1 orthologue in nine G.hirsutum accessions revealed that all carried a non-functional allele, caused by a premature peptide truncation. In addition, all 10 G. barbadense and nine G. hirsutum accessions tested carried a full-length (∼1140 amino acids) homologue of the V. dahliae race 1 resistance gene Gbve1, although some sequence polymorphisms were observed. Verticillium dahliae Vd991 is a non-race 1 isolate that lacks the Ave1 gene. Thus, the resistance imparted by GbaNA1 appears to be mediated by a mechanism distinct from recognition of the fungal effector Ave1.

Comparative Transcriptome Analysis between Broccoli (Brassica oleracea var. italica) and Wild Cabbage (Brassica macrocarpa Guss.) in Response to Plasmodiophora brassicae during Different Infection Stages.

Clubroot, one of the most devastating diseases to the Brassicaceae family, is caused by the obligate biotrophic pathogen Plasmodiophora brassicae. However, studies of the molecular basis of disease resistance are still poor especially in quantitative resistance. In the present paper, two previously identified genotypes, a clubroot-resistant genotype (wild cabbage, B2013) and a clubroot-susceptible genotype (broccoli, 90196) were inoculated by P. brassicae for 0 (T0), 7 (T7), and 14 (T14) day after inoculation (DAI). Gene expression pattern analysis suggested that response changes in transcript level of two genotypes under P. brassicae infection were mainly activated at the primary stage (T7). Based on the results of DEGs functional enrichments from two infection stages, genes associated with cell wall biosynthesis, glucosinolate biosynthesis, and plant hormone signal transduction showed down-regulated at T14 compared to T7, indicating that defense responses to P. brassicae were induced earlier, and related pathways were repressed at T14. In addition, the genes related to NBS-LRR proteins, SA signal transduction, cell wall and phytoalexins biosynthesis, chitinase, Ca2+ signals and RBOH proteins were mainly up-regulated in B2013 by comparing those of 90196, indicating the pathways of response defense to clubroot were activated in the resistant genotype. This is the first report about comparative transcriptome analysis for broccoli and its wild relative during the different stages of P. brassicae infection and the results should be useful for molecular assisted screening and breeding of clubroot-resistant genotypes.

Molecular cloning, functional verification, and evolution of TmPm3, the powdery mildew resistance gene of Triticum monococcum L.

Powdery mildew (Pm) is one of the most harmful diseases in wheat. Three Pm-resistance genes, Pm3, Pm21, and Pm8, have been cloned but most Pm3/Pm8 alleles have lost their resistance to Pm in hexaploid wheat. In this study, a new Pm3 homolog gene (TmPm3) was isolated from Triticum monococcum L. using a homology-based cloning strategy, being the first report of a functional Pm3 homolog gene from a diploid wheat species. The transient expression of TmPm3 in leaf epidermal cells showed that over-expressed TmPm3 could significantly inhibit the penetration of Blumeria graminis f. sp tritici conidia spores and the formation of haustoria. Sequence analysis of Pm3 alleles shed new light on the evolution of Pm3 genes, providing a better understanding of the molecular basis of disease resistance. This study also suggested that homology-based cloning of resistance genes is a feasible method for the isolation of functional resistance genes from wheat germplasm.

Molecular breeding of rice for improved disease resistance, a review

Diseases are considered to be the major limiting factors in rice production around the globe. Considering rice as an important cereal crop, developing disease resistant cultivars is a prime objective of breeders. Compared to conventional breeding, molecular breeding especially using marker assisted selection appears to be more effective and precise. The best management of disease is to bring durable wide spectrum resistance in rice cultivars. This can be accomplished by accumulating both qualitative and quantitative resistance genes in to rice cultivars. Introducing these resistance genes from the wild relatives of rice in to commercial cultivars has greatly helped the breeders to accomplish this task. Marker assisted selection is extremely valuable in resolving the issues the breeders face with traditional breeding. A number of transgenic rice lines harboring the so called ‘foreign’ resistant genes have been produced. However such promising lines must be extensively replicated in fields to evaluate stable integration and continued expression of genes. None the less identification of disease resistance genes and quantitative trait loci (QTLs), use of marker assisted selection along with gene pyramiding and transgenic approaches all provide breeders a hope to build high yielding disease resistant cultivars. Based on such premises, we can truly envision broadening of our understanding the genetic and molecular basis of disease resistance in rice.

Partial resistance to clubroot in Arabidopsis is based on changes in the host primary metabolism and targeted cell division and expansion capacity.

To date, studies of the molecular basis of disease resistance mainly focused on qualitative resistance. However, deciphering mechanisms underlying quantitative resistance could lead to insights into the relationship between qualitative and quantitative resistance and guide the utilization of these two types of resistance to produce durably resistant cultivars. A functional genomics approach, using the CATMA whole-genome microarray, was used to detect changes in gene expression associated with partial quantitative resistance in the Arabidopsis thaliana–Plasmodiophora brassicae pathosystem. The time course of transcript abundance during partial clubroot resistance response was monitored at the whole plant level, and direct comparisons between partial resistance and susceptibility responses were made using the same host genotype. An increasingly complex host response was revealed, as was the differential influence of P. brassicae infection on the transcription of Arabidopsis genes according to the isolate used. We observed, at the transcriptomic level, that metabolic diversion by the pathogen was reduced or delayed, classical plant defense responses were induced earlier and/or more strongly, and cell enlargement and proliferation were actively inhibited in the partial quantitative resistance response compared to the susceptible one.Electronic supplementary materialThe online version of this article (doi:10.1007/s10142-013-0312-9) contains supplementary material, which is available to authorized users.

Involvement of hsr203J like gene homologue, protease and protease inhibitors in triggering differential defense response against Alternaria blight in Brassica

Transcript profiling of hsr203J, a known marker gene for Hypersensitive response (HR), was performed to delineate its role in differential defense against Alternaria brassicae in tolerant and susceptible genotypes of Brassica juncea. Reverse transcriptase (RT) PCR approach was utilized to investigate the correlation between expression of hsr203J like gene(s) and pathogenesis in stage dependent manner. It was revealed that the expression of hsr203J like gene increased as disease progressed from initial too late stage of infection in tolerant genotype. However, in susceptible genotype, its expression increased up to middle stage of infection with no expression in late stage of infection. In both genotypes, no expression of hsr203J like gene was observed in healthy leaves. It was observed that whereas three homologues of hsr203J like gene express at the late stage of infection in tolerant genotype, only single homologue of same expresses in susceptible genotype throughout all stages of infection. This indicates the role of hsr203J homologues in determining the differential defense response against Alternaria blight in Brassica. Determination of specific activity and in-gel assay revealed differential accumulation of protease and protease inhibitor in tolerant and susceptible genotypes at different stages of infection. Induction of differential protease and protease inhibitor activity appears to modulate the cell death during HR response to pathogen. Dissection of pathway leading to HR related cell death will enable us to know the molecular basis of disease resistance which will, in turn, help in engineering Brassica for resistance to Alternaria blight.

The arms race between tomato and Fusarium oxysporum

The interaction between tomato and Fusarium oxysporum f. sp. lycopersici has become a model system for the study of the molecular basis of disease resistance and susceptibility. Gene-for-gene interactions in this system have provided the basis for the development of tomato cultivars resistant to Fusarium wilt disease. Over the last 6 years, new insights into the molecular basis of these gene-for-gene interactions have been obtained. Highlights are the identification of three avirulence genes in F. oxysporum f. sp. lycopersici and the development of a molecular switch model for I-2, a nucleotide-binding and leucine-rich repeat-type resistance protein which mediates the recognition of the Avr2 protein. We summarize these findings here and present possible scenarios for the ongoing molecular arms race between tomato and F. oxysporum f. sp. lycopersici in both nature and agriculture.

Accumulation of Defence Response‐related and Unique Expressed Sequence Tags during the Incompatible Interaction in theOryza sativa–Magnaporthe oryzaePathosystem

AbstractResistance gene‐dependent accumulation of expressed sequence tags (ESTs) was studied in a blast resistant, Oryzasativassp.indicacv. Tetep after challenge inoculation with an incompatible race ofMagnaporthe oryzae. The nucleotide sequence of 287 randomly selected cDNA clones from the rice cDNA library constructed from the RNA isolated after challenge inoculation of the host was obtained and submitted in NCBI Genbank (Accession Nos.DN475717–DN475431). Of these, 184 (63%) ESTs were highly representative of the rice transcriptomes. A set of 178 unique transcripts was identified after assembly of 287 ESTs into unigenes. These unigenes were categorized into 17 functional groups. Analysis of this EST library illustrated a broad functional representation. Twenty‐one unigenes were identified as putative homologues of the genes that were up regulated during host–pathogen interaction. Similarity search of 178 unigenes with NCBI database of 14 plants unigenes showed similarity ranging from 29–100%. The unigenes obtained in this study were physically located on the pseudomolecules of rice genome. This information can be used for determining the arrays of genes being expressed duringOryza sativa–M. oryzaeinteractions, which will be helpful in understanding the molecular basis of disease resistance.

Molecular Basis of Disease Resistance Acquired through Cold Acclimation in Overwintering Plants

Plants require substantial resistance against freezing and pathogens for overwintering. These two traits are acquired through cold acclimation. In contrast to freezing tolerance, molecular basis of disease resistance acquired through cold acclimation is poorly understood. Recent studies have suggested that pathogenesis-related (PR) proteins that are secreted into the apoplast during cold acclimation are responsible for the disease resistance. Interestingly, some of the cold-induced PR proteins display both antifungal and antifreeze activities, suggesting a dual function in protecting plants from overwintering stresses. The signaling pathway for cold-induced disease resistance is currently unknown but can be independent of pathogen-induced defense mechanisms.

Identification of quantitative trait loci controlling partial clubroot resistance in new mapping populations of Arabidopsis thaliana

To date, mechanisms of partial quantitative resistance, under polygenic control, remain poorly understood, studies of the molecular basis of disease resistance have mainly focused on qualitative variation under oligogenic control. However, oligogenic conferred resistance is rapidly overcome by the pathogen and knowledge of the relationship between qualitative and quantitative resistance is necessary to develop durably resistant cultivars. In this study, we exploited the Arabidopsis thaliana-Plasmodiophora brassicae pathosystem to decipher the genetic architecture determining partial resistance. This soil-borne pathogen causes clubroot, one of the economically most important diseases of Brassica crops in the world. A quantitative trait locus (QTL) approach was carried out using two segregating populations (F(2) and recombinant inbred lines) from crosses between the partially resistant accession Burren and the susceptible accession Columbia. Four additive QTLs (one moderate and three minor) controlling partial resistance to clubroot were identified, all the resistance alleles being derived from the partially resistant parent. In addition, four epistatic regions, which have no additive effect on resistance, were also found to be involved in partial resistance. An examination of candidate genes suggested that a potentially diverse array of mechanisms is related to the different QTLs. By fine-mapping and cloning these regions, the mechanisms involved in partial resistance will be identified.

The genetic basis of quantitative variation in susceptibility of Arabidopsis thaliana to Pseudomonas syringae (Pst DC3000): evidence for a new genetic factor of large effect

* Pathogens represent an important threat to plant communities and agriculture, and can shape many aspects of plant evolution. Natural variation in plant disease susceptibility is typically quantitative, yet studies on the molecular basis of disease resistance have focused mainly on qualitative variation. * Here we investigated the genetic architecture of quantitative susceptibility to the bacterium Pseudomonas syringae by performing a quantitative trait locus (QTL) analysis on the F2 progeny of two natural accessions of Arabidopsis thaliana under two nutrient treatments. * We found that a single QTL explains most of the variation (77%) in susceptibility between accessions Columbia (Col-0) and San Feliu-2 (Sf-2), and its effect is independent of nutrients. The Sf-2 allele at this QTL is dominant and can reduce the bacterial population size by 31-fold, much like a classical resistance (R) gene. However, minor QTLs, whose effects are altered by nutrient treatment, were also detected. * Surprisingly, we found that none of the QTLs for susceptibility had any effect on fruit production, suggesting that the use of resistance genes for crop improvement and evolutionary analysis of plant-pathogen interactions requires caution.

Local inflammation as a possible mechanism of resistance to gastrointestinal nematodes in Angus heifers

Understanding mechanisms of resistance to gastrointestinal nematodes is important in developing effective and sustainable control programs. A resource population of Angus cattle consisting of approximately 600 animals with complete pedigree records has been developed. The majority of these animals were completely characterized for their resistance to natural challenge by gastrointestinal nematodes. As the first step towards understanding the molecular basis of disease resistance, we investigated expression profiles of 17 cytokines, cytokine receptors, and chemokines using real-time RT-PCR in animals demonstrating resistance or susceptibility to pasture challenge. The animals exposed to natural infection for approximately 6 months were treated to remove existing parasites and then experimentally challenged with both Ostertagia ostertagi and Cooperia oncophora. The mRNA expression profiles of these genes in abomasal and mesenteric lymph nodes (ALN, MLN), fundic and pyloric abomasa (FA, PA), and small intestine (SI) were compared between resistant and susceptible animals. Resistant heifers exhibited elevated expression of inflammatory cytokines such as TNFα, IL-1β, and MIP-1α in fundic and pyloric abomasa 7 days post infection. Expression levels of IL-10, polymeric immunoglobullin receptor gene (PIGR), and WSX-1 were also 2.7–19.9-folds higher in resistant than susceptible heifers in these tissues. No difference in expression of CXCL6, CXCL10, IFN-γ, IL-2, IL-4, IL-6, IL-8, IL-12 p40, IL-13, IL-15 and IL-18 was observed between the two groups. The expression of MIP-1α, IL-6, and IL-10 was also elevated in small intestines in resistant animals. In contrast, little difference in expression of these genes was detected between resistant and susceptible groups in the draining lymph nodes. These data indicate that resistant animals can better maintain inflammatory responses at the site of infection, suggesting a possible novel mechanism of resistance.

Molecular genetics of disease resistance in cereals.

This Botanical Briefing attempts to summarize what is currently known about the molecular bases of disease resistance in cereal species and suggests future research directions. An increasing number of resistance (R) genes have been isolated from rice, maize, wheat and barley that encode both structurally related and unique proteins. This R protein diversity may be attributable to the different modus operandi employed by pathogen species in some cases, but it is also a consequence of multiple defence strategies being employed against phytopathogens. Mutational analysis of barley has identified additional genes required for activation of an R gene-mediated defence response upon pathogen infection. In some instances very closely related barley R proteins require different proteins for defence activation, demonstrating that, within a single plant species, multiple resistance signalling pathways and different resistance strategies have evolved to confer protection against a single pathogen species. Despite the apparent diversity of cereal resistance mechanisms, some of the additional molecules required for R protein function are conserved amongst cereal and dicotyledonous species and even other eukaryotic species. Thus the derivation of functional homologues and interacting partner proteins from other species is contributing to the understanding of resistance signalling in cereals. The potential and limit of utilizing the rice genome sequence for further R gene isolation from cereal species is also considered, as are the new biotechnological possibilities for disease control arising from R gene isolation. Molecular analyses in cereals have further highlighted the complexity of plant-pathogen co-evolution and have shown that numerous active and passive defence strategies are employed by plants against phytopathogens. Many advances in understanding the molecular basis of disease resistance in cereals have focused on monogenic resistance traits. Future research targets are likely to include less experimentally tractable, durable polygenic resistances and nonhost resistance mechanisms.

The molecular basis of disease resistance in rice.

The rice gene Xa21 conferring resistance to Xanthomonas oryzae pv. oryzae (Xoo), was isolated using a map-based cloning strategy. Compared with previously cloned genes, the structure of Xa21 represents a novel class of plant disease R genes encoding a putative receptor kinase (RK). This article proposes a model for the mode of action of Xa21 and summarizes our current knowledge of the modular basis of resistance in rice to bacterial leaf blight and blast.

The Pto kinase mediates a signaling pathway leading to the oxidative burst in tomato.

The Pto gene encodes a serine/threonine kinase that confers resistance in tomato to Pseudomonas syringae pv. tomato strains that express the avirulence gene avrPto. Partial characterization of the Pto signal transduction pathway and the availability of transgenic tomato lines (+/- Pto) make this an ideal system for exploring the molecular basis of disease resistance. In this paper, we test two transgenic tomato cell suspension cultures (+/-Pto) for production of H2O2 following independent challenge with two strains of P. syringae pv. tomato (+/-avrPto). Only when Pto and avrPto are present in the corresponding organisms are two distinct phases of the oxidative burst seen, a rapid first burst followed by a slower and more prolonged second burst. In the remaining three plant-pathogen interactions, we observe either no burst or only a first burst, indicating that the second burst is correlated with disease resistance. Further support for this observation comes from the finding that both resistant and susceptible tomato lines produce the critical second oxidative burst when challenged with P. syringae pv. tabaci, a nonhost pathogen that elicits a hypersensitive response on both tomato lines. The Pto kinase is not required, however, for the oxidative burst initiated by non-specific elicitors such as oligogalacturonides or osmotic stress. A model describing a possible role for the Pto kinase in the overall scheme of oxidative burst signaling is proposed.

Gene expression in susceptible and disease resistant interactions of peas induced with Fusarium solani pathogens and chitosan

A first step for establishing the molecular basis of disease resistance in plants may be to identify genes whose expression closely follows the events occurring during infection. Nine pea clones were available from a prior screening of a cDNA library, developed from a single population of pea mRNA induced 8 h following inoculation with Fusarium solani f. sp. phaseoli. Transcription and accumulation of RNA homologous to these clones were compared over a 48 h infection course following the treatment of pea pods with either compatible or incompatible forms of F. solani or chitosan, a minor component of the fungal cell wall which is known to induce disease resistance. The incompatible reaction of the pea tissue is clearly distinguished from the compatible reaction on the basis of gene expression. Three of the cloned genes, designated Group I clones, show a large induction of their RNAs in disease resisting tissue which temporally correlates with the resistance observed cytologically. In the compatible reaction activation of Group I genes is commonly weaker or delayed, and is suppressed 12–24 h after inoculation, compared with the incompatible reaction. Genes homologous with Group II clones showed only a partial fit to the activity expected for resistance genes. We propose that selecting cloned genes whose time course of induction matches the response of plant issue to infection is a useful preliminary screening technique towards obtaining gene candidates for cross-species transformation experiments.