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Rice blast disease caused by Pyricularia oryzae is a major disease in Bangladesh. In the search of resistant source against P. oryzae, resistant gene (R-gene) was assessed by (i) host-pathogen interaction and (ii) PCR-based screening at the laboratory of Bangladesh Rice Research Institute. One hundred and forty four plant materials were classified into 10 cultivar groups (CG) based on their reaction patterns to four distinct blast isolates (SDBI; standard differential blast isolate) H-11-64, H-1-8, H-1-1 and H-11-67. The reaction patterns of plant materials to these four standard blast isolates indicated presence of Pish, Pi9, Pita2 and Pita genes and their combination in the genetic background of tested plant materials. Gene specific primer 195R-1/195F-1, Pita440 (YL153)/Pita440 (YL154), OSM89 and AOL45/AOL48 were used to identify and confirm the presence of Pi9, Pita, Pita2 and Pish genes in plant materials, respectively through PCR-based assay. Plant materials, H13, H23, H25, H35, H47, H49, H136, H138 harbored all three genes, Pita, Pita2 and Pish in their genetic background. The Pi9 gene together with Pita2 was detected in local rice cultivar H100 and H129, which were confirmed by DNA analysis in PCR assay. These materials could be used in gene pyramiding in promising high yielding cultivar for durable blast resistance.

Late blight, caused by the oomycete pathogen Phytophthora infestans, is the most devastating disease in potato. For sustainable management of this economically important disease, resistance breeding relies on the availability of resistance (R) genes. Such R genes against P. infestans have evolved in wild tuber-bearing Solanum species from North, Central and South America, upon co-evolution with cognate avirulence (Avr) genes. Here, we report how effectoromics screens with Avr2 of P. infestans revealed defense responses in diverse Solanum species that are native to Mexico and Peru. We found that the response to AVR2 in the Mexican Solanum species is mediated by R genes of the R2 family that resides on a major late blight locus on chromosome IV. In contrast, the response to AVR2 in Peruvian Solanum species is mediated by Rpi-mcq1, which resides on chromosome IX and does not belong to the R2 family. The data indicate that AVR2 recognition has evolved independently on two genetic loci in Mexican and Peruvian Solanum species, respectively. Detached leaf tests on potato cultivar ‘Désirée’ transformed with R genes from either the R2 or the Rpi-mcq1 locus revealed an overlapping, but distinct resistance profile to a panel of 18 diverse P. infestans isolates. The achieved insights in the molecular R – Avr gene interaction can lead to more educated exploitation of R genes and maximize the potential of generating more broad-spectrum, and potentially more durable control of the late blight disease in potato.

For over a century, breeders have worked to develop tomato (Solanum lycopersicum) cultivars with resistance to Fusarium wilt (Fol) caused by the soilborne fungus Fusarium oxysporum f. sp. lycopersici. Host resistance is the most effective strategy for the management of this disease. For each of the three Fol races, resistance has been introgressed from wild tomato species, predominately in the form of R genes. The I, I-2, I-3, and I-7 R genes have each been identified, as well as the corresponding Avr effectors in the fungus with the exception of Avr7. The mechanisms by which the R gene protein products recognize these effectors, however, has not been elucidated. Extensive genetic mapping, gene cloning, and genome sequencing efforts support the development of tightly-linked molecular markers, which greatly expedite tomato breeding and the development of elite, Fol resistant cultivars. These resources also provide important tools for pyramiding resistance genes and should support the durability of host resistance.

Recent progress in large-scale sequencing, genomics, and rapid gene isolation techniques has accelerated the identification of race-specific resistance (R) genes and their corresponding avirulence (Avr) genes in wheat, barley, rye, and their wild relatives. Here, we describe the growing repertoire of identified R and Avr genes with special emphasis on novel R gene architectures, revealing that there is a large diversity of proteins encoded by race-specific resistance genes that extends beyond the canonical nucleotide-binding domain leucine-rich repeat proteins. Immune receptors with unique domain architectures controlling race-specific resistance possibly reveal novel aspects on the biology of host–pathogen interactions. We conclude that the polyploid cereal genomes have a large evolutionary potential to generate diverse types of resistance genes.

The development of resistant varieties and hybrid combinations has been the most effective and economical strategy to control blast disease caused by Magnaporthe oryzae. However, the distribution of major R genes and blast resistance characterization in hybrid rice parents has not been well investigated, resulting in their limited use in hybrid rice blast-resistance breeding. In the present study, 88 elite indica hybrid rice parental lines were evaluated with 30 isolates of M. oryzae collected from the main planting area of indica hybrid rice in China and were characterized for the presence of 11 major resistance genes using molecular markers. The pathogenicity assays showed that four types of hybrid rice parent line showed some resistance to M. oryzae. However, the proportions of highly resistant lines and the mean resistance frequency (RF) varied among the four types, with resistance in decreasing order shown by three-line restorer lines, three-line maintainer lines, two-line sterile lines, and two-line restorer lines. All 88 hybrid rice parental lines carried more than one R gene, but none carried the R genes Pi1 and Pi2. Although Pid3 and Pi9 were present only in three-line restorer lines and Pigm only in three-line maintainer lines, the remaining six R genes (Pib, Pid2, Pi5, Pia, Pi54, and Pita) were present in the four types of hybrid rice parent with significantly different distribution frequencies. The correlation between R genes and resistance reactions was investigated. The results are expected to provide useful information for rational utilization of major R genes in hybrid rice breeding programs. Keywords: Hybrid rice parental lines, Magnaporthe oryzae, Pi genes, Resistance evaluation, Molecular markers

Phytophthora foot rot is a devastating disease in black pepper which is caused by P. capsici. Using host resistance is a major component in the integrated pest management of this disease. To explore the host resistance pattern, we studied the genotype specific differential expression of important pathogenesis related gene β 1, 3 glucanase and 5 R gene loci from resistant and susceptible varieties of black pepper. The relative expression of β 1, 3 glucanase was up regulated in resistant variety and down regulated in susceptible variety. R gene loci Pn CNBS 5, CNBS 3 and Pn CNBS 2 showed up regulation in susceptible variety in the early hours of infection while resistant genotype recorded its down regulation till 72 h suggesting that the selective down expression of these loci may be attributed to the resistance in the resistant variety. These R genes may be the susceptibility genes (S-genes) in black pepper for Phytophthora. The high relative expression of the R gene locus Pn CNBS 4 and Pn CNBS 1 in resistant genotype at early hours shows their involvement in resistance towards P. capsici. The differential expression of the R gene loci shows the genotype specific functional significance for Phytophthora resistance.

In Arabidopsis thaliana, RESISTANCE TO CMV(Y) (RCY1), which encodes a CC-NB-LRR class protein, confers the hypersensitive response (HR) to a yellow strain of cucumber mosaic virus [CMV(Y)]. A. thaliana ecotype Col-0 overexpressing RCY1 transgenes (Col::pRCY1-HA#13) shows extreme resistance (ER) to CMV(Y). To identify novel regulatory factors involved in high RCY1 expression and ER, suppressor of RCY1-mediated resistance to CMV(Y) (src) mutants were screened from Col::pRCY1-HA#13 mutagenized with ethyl methanesulfonate. The amounts of RCY1 transcript and RCY1 protein in five src mutant lines was significantly lower than in Col::pRCY1-HA#13. In src mutants, virus systemically spread without formation of necrotic local lesions in the inoculated leaves. Genetic analysis of progenies of crosses between the src mutant and Col::pRCY1-HA#13 suggested that paramutation might have occurred in these src mutants. Indeed, cytosines in the promoters but not in other genomic regions of the RCY1 transgenes are hypermethylated in these src mutant lines. Moreover, decreased RCY1 expression was correlated with increased methylation of the RCY1 promoter region. Treatment with 5-azacytidine decreased methylation in the promoter region and partially restored RCY1 expression. Taken together, SRC may be involved in RCY1-conferred resistance to CMV(Y) through the regulation of cytosine methylation of the RCY1 promoter.

In tomato, Verticillium resistance is determined by the Ve gene locus encoding two leucine-rich repeat-receptor-like proteins (Ve1, Ve2). The resistance function usually is attributed to Ve1 alone, with two known alleles: Ve1, encoding a resistance protein, and ve1, with a premature stop codon encoding a truncated product. We have examined further Ve-gene expression in resistant and susceptible near-isolines of Verticillium-infected Craigella tomatoes, using both quantitative RT-PCR and an alternative RFLP assay. Ve1 is induced differentially in resistant and susceptible plants, while Ve2 is constitutively expressed throughout disease development. Contrary to their putative role in Verticillium resistance, these profiles were observed even with compatible Verticillium interactions, some bacterial pathogens, and transgenic tomato plants expressing the fungal Ave1 effector. This suggests broader roles in disease and/or stress. To determine the contribution of plant hormones, abscisic acid, methyl jasmonate, naphthaleneacetic acid or salicylic acid were infused independently via the tomato root and effects on Ve1 induction were confirmed using biosynthesis mutants. While all the hormones modulated Ve1-gene induction, abscisic acid and salicylic acid were not required while jasmonic acid appears to play a more direct role.

The present study was performed to identify the tail rot disease causing bacterium in marine ornamental fish, Amphiprion sebae . Bacteria were isolated from the infected immune organs and tail region of A. sebae . Five different bacterial isolates (S1-S5) with different shape, size and colour were chosen for the infection study. The isolated strains were individually challenged with A. sebae at a constant dose of 1 × 10 7 CFU/fish. The virulent strain was found to be S-3, which showed maximum reproducing ability in A. sebae by causing typical tail rot disease and mortality. Furthermore, S-3 strain was identified as Vibrio parahaemolyticus by 16S rRNA gene sequencing (KF738005), biochemical analysis and amplification of tox R gene. Subsequently, extracellular products (ECPs) of V. parahaemolyticus were prepared by cellophane overlay method. The LD 50 value of V. parahaemolyticus and its ECP S were found to be 1 × 10 5 CFU and 5 μg/fish. The histology results revealed that V. parahaemolyticus and its ECP S are the major cause of tail rot disease in A. sebae .

Black spot disease, which is caused by the ascomycete Diplocarpon rosae, is the most severe disease in field-grown roses in temperate regions and has been distributed worldwide, probably together with commercial cultivars. Here, we present data indicating that muRdr1A is the active Rdr1 gene, a single-dominant TIR-NBS-LRR (Toll/interleukin-1 receptor-nucleotide binding site-leucine rich repeat) (TNL)-type resistance gene against black spot disease, which acts against a broad range of pathogenic isolates independent of the genetic background of the host genotype. Molecular analyses revealed that, compared with the original donor genotype, the multiple integrations that are found in the primary transgenic clone segregate into different integration patterns in its sexual progeny and do not show any sign of overexpression. Rdr1 provides resistance to 13 different single-spore isolates belonging to six different races and broad field mixtures of conidia; thus far, Rdr1 is only overcome by two races. The expression of muRdr1A, the active Rdr1 gene, leads to interaction patterns that are identical in the transgenic clones and the non-transgenic original donor genotype. This finding indicates that the interacting avirulence (Avr) factor on the pathogen side must be widespread among the pathogen populations and may have a central function in the rose-black spot interaction. Therefore, the Rdr1 gene, pyramided with only a few other R genes by sexual crosses, might be useful for breeding roses that are resistant to black spot because the spread of new pathogenic races of the fungus appears to be slow.

Autonomous hypersensitive responses (self-HRs) are caused by constitutively active R proteins. In this study, we identified an auto-activated form of the R gene Pvr9 (autoPvr9); the auto-activation results from an amino acid substitution between its NBS and LRR domains. Self-HR was strongly reduced or completely inhibited by fusion of an extra peptide to the autoPvr9 N-terminal or C-terminal, respectively. When an NIa recognition site was placed between autoPvr9 and the extra peptide, the fusion construct could trigger an NIa-dependent HR. Several C-terminal fusions were tested, but only those that maintained detectable protein expression were capable of an NIa-dependent HR. Our results suggest the potential for transforming malfunctioning and auto-activated R proteins into a new construct targeting potyviral NIa proteases.

Downy mildew, caused by Plasmopara viticola, can result in a substantial decrease in grapevine productivity. Vitis vinifera is a widely cultivated grapevine species, which is susceptible to this disease. Repeated pesticide applications are harmful for both the environment and human health. Thus, it is essential to develop varieties/cultivars that are resistant to downy mildew and other diseases. In our previous studies, we investigated the natural resistance of the Chinese wild grapevine V. quinquangularis accession 'PS' against P. viticola and obtained several candidate resistance (R) genes that may play important roles in plant disease resistance. In the present study, we isolated a CC-NBS-LRR-type R gene from 'PS' and designated it VqCN. Its open reading frame is 2676 bp which encodes a protein of 891 amino acids with a predicted molecular mass of 102.12 kDa and predicted isoelectric point of 6.53. Multiple alignments with other disease resistant (R) proteins revealed a conserved phosphate-binding loop (P-loop), resistance nucleotide binding site, a hydrophobic domain (GLPL) and methionine-histidine-aspartate (MHD) motifs, which are typical components of nucleotide-binding site leucine-rich repeat proteins, as well as a coiled-coil region in the N-terminus. Quantitative real-time polymerase chain reaction analysis showed that the transcript of VqCN was rapidly and highly induced after infection with P. viticola in 'PS'. Moreover, the leaves of susceptible 'Cabernet Sauvignon' transiently expressing VqCN manifested increased resistance to P. viticola. The results indicated that VqCN might play a positive role in protecting grapevine against infection with P. viticola. Cloning and functional analysis of a putative resistance gene provide a basis for disease-resistance breeding.

The Avr avirulence gene of Phytophthora infestans and R gene of the potato are the genetic components of the gene-for-gene interaction resulting in host plant resistance. This effector-triggered immunity has been recently exploited to generate extreme resistance to late blight in potato by genetic engineering. The choice of the R genes, their number forming a R gene stack, and the pathogen Avr gene diversity will likely determine how long this extreme resistance will last. Here, we report on a comparative study on the Rpi-vnt1.1 gene which originated from Solanum venturii, and was introduced in the potato variety ‘Desiree’ by genetic transformation, and the Avr-vnt1 gene from two isolates of the EC-1 lineage of P. infestans. EC-1 was reported previously as not expressing the Avr-vnt1 gene and, therefore, being virulent on Rpi-vnt1.1 transgenic plants. Unexpectedly, whole-plant resistance assays identified 5 out of 52 transgenic events as resistant to two isolates of P. infestans, POX067 and POX109, belonging to the EC-1 lineage. We demonstrated that in both isolates, the Avr-vnt1.1 gene was expressed at a low level. Expression of the Rpi-vnt1.1 gene was shown to be rapidly increased by two-fold and subsequently to have steady state expression for at least 5 days after the inoculation. The Rpi-vnt1.1 gene in addition to other R genes as a stack in farmers’ preferred varieties will confer extreme resistance to late blight disease and rotations of plants with different R-gene-stack in time is likely to last longer than plants with single R gene.

MicroRNAs (miRNAs) are universal regulators that repress target gene expression in eukaryotes and play essential roles in plant immune responses. miRNAs were recently found to be involved in soybean and Phytophthora sojae interactions. Here, we screened miR1510, which was repressed in soybean during infection with P. sojae, indicating that it might be involved in soybean response to pathogens. To further uncover the roles of miRNAs in soybean, gma-miR1510a/b was overexpressed in the hairy roots of soybean using an Arabidopsis miR319a precursor as the backbone. The gma-miR1510a/b-overexpressing hairy roots showed enhanced susceptibility to P. sojae, and the results showed that miR1510 guides the cleavage of the Glyma.16G135500 gene, which encodes a classic type of plant disease resistance-associated gene that harbors the Toll-interleukin-like receptor (TIR) domain and nucleotide-binding site-leucine-rich repeat (NB-LRR) domain. Noticeably, several biotic stresses and hormone-responsive cis-regulatory elements were found to be present in the promoters of gma-MIR1510a and the target gene. Collectively, the results obtained in the current study reveal that gma-miR1510 regulates the target NB-LRR immune receptor gene Glyma.16G135500 and thus plays a crucial role in regulating the resistance of soybean to P. sojae.

Bacterial blight of rice, caused by Xanthomonas oryzae pv. oryzae, is one of the most destructive bacterial diseases throughout the major rice-growing regions in the world. The rice disease resistance (R) gene Xa10 confers race-specific disease resistance to X. oryzae pv. oryzae strains that deliver the corresponding transcription activator-like (TAL) effector AvrXa10. Upon bacterial infection, AvrXa10 binds specifically to the effector binding element in the promoter of the R gene and activates its expression. Xa10 encodes an executor R protein that triggers hypersensitive response and activates disease resistance. ‘Nipponbare’ rice carries two Xa10-like genes in its genome, of which one is the susceptible allele of the Xa23 gene, a Xa10-like TAL effector-dependent executor R gene isolated recently from ‘CBB23’ rice. However, the function of the two Xa10-like genes in disease resistance to X. oryzae pv. oryzae strains has not been investigated. Here, we designated the two Xa10-like genes as Xa10-Ni and Xa23-Ni and characterized their function for disease resistance to rice bacterial blight. Both Xa10-Ni and Xa23-Ni provided disease resistance to X. oryzae pv. oryzae strains that deliver the matching artificially designed TAL effectors (dTALE). Transgenic rice plants containing Xa10-Ni and Xa23-Ni under the Xa10 promoter provided specific disease resistance to X. oryzae pv. oryzae strains that deliver AvrXa10. Xa10-Ni and Xa23-Ni knock-out mutants abolished dTALE-dependent disease resistance to X. oryzae pv. oryzae. Heterologous expression of Xa10-Ni and Xa23-Ni in Nicotiana benthamiana triggered cell death. The 19-amino-acid residues at the N-terminal regions of XA10 or XA10-Ni are dispensable for their function in inducing cell death in N. benthamiana and the C-terminal regions of XA10, XA10-Ni, and XA23-Ni are interchangeable among each other without affecting their function. Like XA10, both XA10-Ni and XA23-Ni locate to the endoplasmic reticulum (ER) membrane, show self-interaction, and induce ER Ca2+ depletion in leaf cells of N. benthamiana. The results indicate that Xa10-Ni and Xa23-Ni in Nipponbare encode functional executor R proteins, which induce cell death in both monocotyledonous and dicotyledonous plants and have the potential of being engineered to provide broad-spectrum disease resistance to plant-pathogenic Xanthomonas spp.

In the changing climatic scenario, in addition to leaf blast, neck blast caused by Magnaporthae oryzae has become more prominent in all rice growing ecosystems. Cultivars having field resistance often shows durable resistance to two phases of the blast. In this work, we found that Akhanaphou, an unique rice landrace of North-East India, having a high level of field resistance to both leaf and neck blast. We identified two novel QTLs (Quantitative trait loci) i . e . qLNBL -5 and qLNBL-7 using two consecutive years phenotypic data generated from two different environments. Both of these QTLs confer resistance toward leaf as well as neck blast by contributing 26% and 25% phenotypic variance toward the resistance. We also identified stable recombinant inbred lines (RILs) having these two QTLs. The identified unique landrace and its derived RILs can be served as valuable genetic resources; these can be readily used in rice resistance breeding programs.

This study describes late blight resistance of potato breeding lines resulting from crosses between cultivar ‘Sárpo Mira’ and Rpi-phu1 gene donors. The progeny is investigated for the presence of Rpi-Smira1 and Rpi-phu1 resistance (R) genes. Interestingly, in detached-leaflet tests, plants with both R genes withstood the infection of the Phytophthora infestans isolate virulent to each gene separately, due to either interaction of these genes or the presence of additional resistance loci. The interaction was studied further in three chosen breeding lines on the transcriptional level. The Rpi-phu1 expression, measured over 5 days, revealed different patterns depending on the outcome of the interaction with P. infestans: it increased in infected plants whereas it remained low and stable when infection was unsuccessful. The expression patterns of P. infestans effectors Avr-vnt1, AvrSmira1, and Avr8, recognized by the Rpi-phu1, Rpi-Smira1, and Rpi-Smira2 genes, respectively, were evaluated in the same experimental setup. This is the first report that the Avr-vnt1 effector expression is not switched off permanently in virulent isolates to avoid recognition by an R protein but can reappear in a postbiotrophic phase and is present constantly when infecting plants without the corresponding R gene. Both a plant and a pathogen can react to the other interacting side by changing the transcript accumulation of R genes or effectors.

Transient gene expression in protoplasts has been applied to the analysis of gene expression, promoter activity, subcellular localization of proteins, and genome editing. Its advantages have been realized in recent years in various physiological, biochemical, genetic, and molecular biological studies. The omics and systems biology studies of plant development and their interactions with the environment have revitalized this approach. Early plant-pathogen interaction represents one of the most unique signalling research areas. Here, we try to discuss some developments and current applications of the protoplast system. It is for sure that the system will significantly bridge the gap between high throughput approaches and functional analysis in the study of plant-pathogen interactions in the omics era.

Plant microRNAs are crucial for post-transcriptional regulation of gene expression, with some of them particularly involved in regulating several disease resistance (R) genes. This study is a computational screening for microRNAs potentially involved in the regulation of disease resistance in bread wheat Triticum aestivum, through the genome and transcriptome of this crop species. We used plant miRNAs of the superfamily miR-482/2118 to find complementarities with the expressed sequence tags (ESTs) coding NBS-LRR proteins of the bread wheat. This analysis revealed a vast recognition potential, highlighting highly variable miRNA-mRNA hybridization schemes. Precursors of miR-2118/482 sequences that showed a potential for recognizing wheat NBS-LRR ESTs were used as input for similarity search in the T. aestivum transcriptome shotgun assemblies (TSA) database, enabling the identification of a couple of wheat TSA sequences (JV952948.1 and JV851699.1) that were predicted to adopt a stable miRNA/miRNA* duplex structure. The genomic regions corresponding to both predicted tae-miR-2118 genes were determined on wheat chromosomes 2DL and 5AS. The findings of the present study will contribute to a better understanding of R gene expression regulation in wheat.

Western white pine (Pinus monticola Dougl.) is an important forest tree species, which is intensively plagued by the fungus Cronartium ribicola. Resistance gene analogs (RGAs) are the most highly abundant class of potential resistance (R) genes sharing greatly conserved domains and structures. Hence RGAs are crucial components for disease resistance breeding programs on P. monticola serving as useful functional markers. A total of 33 P. monticola RGAs gene homologues were mined from GenBank, encoding for R gene members of the TIR-NBS-LRR subfamily. The existence of positive selection acting upon RGAs was determined using a series of maximum likelihood analyses. Robust evidence of positive selection was showed to be acting widely in three clades across RGA gene phylogeny, both on terminal and ancestral lineages. Furthermore, our analysis revealed that the majority of positively selected residues sites are localized widely across these RGAs sequences, putatively affecting the structures of their ligand-binding domains and offering novel specificities. These results may find immediate application in ongoing disease resistance breeding programs.

Radish is an important root vegetable crop worldwide. However, it is susceptible to a variety of diseases leading to decline in yield and quality. The plant nucleotide-binding site (NBS)-leucine-rich repeat (LRR) gene superfamily is effective against a big range of pathogens. Therefore, the isolation and identification of such R gene analogue (RGA) is a critical foundation for improving disease resistance in plants. So far, however, no comprehensive isolation of NBS-LRR RGAs has been reported in radish. In this study, a total of 36,613 unigenes representing 81,481 unique transcripts with an average length of 1253.22 nt were obtained from radish leaf transcriptome. In total, 38 NBS-encoding sequences were successfully identified via bioinformatics analysis. Multiple sequence alignment analysis classified these sequences into toll and interleukin-1 receptor (TIR)-NBS-LRR and non-TIR-NBS-LRR subclasses based on the presence of a TIR domain at the N-terminus. Phylogenetic tree analysis of the deduced amino acid sequences grouped these sequences into six classes. Non-synonymous to synonymous substitution ratio suggested that NBS-encoding sequences of RGAs in radish were subject to purification or negative selection. Additionally, RT-qPCR analysis revealed that several RsRGAs expressed differentially under three tested abiotic stimuli (SA, MeJA and ABA), suggesting that they might be involved in defense responses by activating signaling pathways. These results could provide valuable information for further identification of plant RGAs and accelerate genetic improvement of disease resistances in radish breeding programs.

In tropical forests, rarer species show increased sensitivity to species-specific soil pathogens and more negative effects of conspecific density on seedling survival (NDD). These patterns suggest a connection between ecology and immunity, perhaps because small population size disproportionately reduces genetic diversity of hyperdiverse loci such as immunity genes. In an experiment examining seedling roots from six species in one tropical tree community, we found that smaller populations have reduced amino acid diversity in pathogen resistance (R) genes but not the transcriptome in general. Normalized R gene amino acid diversity varied with local abundance and prior measures of differences in sensitivity to conspecific soil and NDD. After exposure to live soil, species with lower R gene diversity had reduced defence gene induction, more cosusceptibility of maternal cohorts to colonization by potentially pathogenic fungi, reduced root growth arrest (an R gene-mediated response) and their root-associated fungi showed lower induction of self-defence (antioxidants). Local abundance was not related to the ability to induce immune responses when pathogen recognition was bypassed by application of salicylic acid, a phytohormone that activates defence responses downstream of R gene signalling. These initial results support the hypothesis that smaller local tree populations have reduced R gene diversity and recognition-dependent immune responses, along with greater cosusceptibility to species-specific pathogens that may facilitate disease transmission and NDD. Locally rare species may be less able to increase their equilibrium abundance without genetic boosts to defence via immigration of novel R gene alleles from a larger and more diverse regional population.

To elucidate R-gene evolution, we compared the genomic compositions and structures of chromosome regions carrying R-gene clusters among cultivated and wild rice species. Map-based sequencing and gene annotation of orthologous genomic regions (1.2 to 1.9 Mb) close to the terminal end of the long arm of rice chromosome 11 revealed R-gene clusters within six cultivated and ancestral wild rice accessions. NBS-LRR R-genes were much more abundant in Asian cultivated rice (O. sativa L.) than in its ancestors, indicating that homologs of functional genes involved in the same pathway likely increase in number because of tandem duplication of chromosomal segments and were selected during cultivation. Phylogenetic analysis using amino acid sequences indicated that homologs of paired Pikm1–Pikm2 (NBS-LRR) genes conferring rice-blast resistance were likely conserved among all cultivated and wild rice species we examined, and the homolog of Xa3/Xa26 (LRR-RLK) conferring bacterial blight resistance was lacking only in Kasalath.

White rust, causal agent oomycete Albugo candida, is a significant disease of the cultivated Brassica species. The Indian gene pool lines of oilseed mustard, Brassica juncea, are highly susceptible to the pathogen. Resistance to A. candida has been reported in the east European gene pool lines of mustard and mapped to LG A4 in line Heera and LG A5 in line Donskaja-IV. A new resistance-conferring locus to A. candida isolate AcB1 has been mapped to LG A6 of B. juncea line Tumida-a Chinese vegetable type mustard using an F1DH mapping population that has been developed from a Tumida × Varuna (susceptible Indian gene pool line) cross. A molecular map containing 8,303 genic and GBS markers was used to map the resistance trait to an interval of 63.0 cM-70.8 cM on LG A6. Genome assemblies of Tumida and Varuna were used to find the genes present within the flanking markers discerned by genetic mapping. The most likely candidate gene in the mapped interval is BjuA046215, a CC-NBS-LRR (CNL) type R gene that encodes a protein with all the specific subdomains of the proteins encoded by such genes. Alleles of BjuA046215 in Varuna and other lines of the Indian and the east European gene pools encode proteins that have truncated LRR domains. Analysis of the syntenic regions in some of the Brassicaceae genomes and phylogenetic analysis of CNL type R genes showed BjuA046215 to be closely related to a recently described white rust resistance-conferring R gene BjuWRR1 in B. juncea Donskaja-IV, both belonging to the CNL-D group of R genes. Related R genes in Arabidopsis thaliana confer resistance to another oomycete, Peronospora parasitica.

The development of pathogen resistant crops is increasingly important in the face of the global climate changes and of the new agriculture requirements. In the past decades, an enormous amount of genomic information has been released. Plant breeders can take advantage of information provided by bioinformatic supports to increase the likelihood of obtaining resistant genotypes. Basic information on resistance genes (R-genes) and resistant genotypes can be recovered in database developed for facilitating scientific literature and genetic resources search. Bioinformatic tools that enable the analysis of the R-gene organization in individual genomes, the detection of genetic diversity in different individuals, the assessment of relationships between genomes and the localization of individual R-genes are also available. Cross investigations of plant expression pattern during pathogen challenge promote several biological observations and discoveries. The accessibility of genetic and genomic resources could be improved by the development of platforms to link and integrate databases and tools. Advanced efforts to build up an integrated crop improvement information network are depicted.

Wild potato species continue to be a rich source of genes for resistance to late blight in potato breeding. Whilst many dominant resistance genes from such sources have been characterised and used in breeding, quantitative resistance also offers potential for breeding when the loci underlying the resistance can be identified and tagged using molecular markers. In this study, F1 populations were created from crosses between blight susceptible parents and lines exhibiting strong partial resistance to late blight derived from the South American wild species Solanum microdontum and Solanum pampasense. Both populations exhibited continuous variation for resistance to late blight over multiple field-testing seasons. High density genetic maps were created using single nucleotide polymorphism (SNP) markers, enabling mapping of quantitative trait loci (QTLs) for late blight resistance that were consistently expressed over multiple years in both populations. In the population created with the S. microdontum source, QTLs for resistance consistently expressed over three years and explaining a large portion (21&ndash, 47%) of the phenotypic variation were found on chromosomes 5 and 6, and a further resistance QTL on chromosome 10, apparently related to foliar development, was discovered in 2016 only. In the population created with the S. pampasense source, QTLs for resistance were found in over two years on chromosomes 11 and 12. For all loci detected consistently across years, the QTLs span known R gene clusters and so they likely represent novel late blight resistance genes. Simple genetic models following the effect of the presence or absence of SNPs associated with consistently effective loci in both populations demonstrated that marker assisted selection (MAS) strategies to introgress and pyramid these loci have potential in resistance breeding strategies.

Almost 48 years after the gene-for-gene interaction model was proposed by Flor, NBS-LRR resistance (R) genes are still the focus of intense research interest. Also called NB-LRR, NB-ARC, NLR (Nucleotide Binding Domain and Leucine-rich Repeat), this group regards the largest R gene class, accounting for more than half of the plant R genes, with an impressing number and structural diversity, especially in angiosperms. With the omics advent, especially genomics and transcriptomics, an emergence of the so-called NLRomics came out, allowing the annotation and comparative analysis of NBS-LRR members at functional and structural level on a previously unfeasible scale. The present chapter provides a retrospective of studies involving NBS-LRR genes and proteins, including information on mechanisms of action, regulation, patterns of expression, subcellular localization, origin, diversification, and evolution in plants. Aspects of plant-pathogen coevolution are discussed, as well as resistance-breaking mechanisms reported in the literature. Main databases compiling NBS-LRR genes are discussed, and a routine for their annotation and structural analysis is presented. Practical implications of NBS-LRR molecules are considered, together with aspects about existing limitations and their potential biotechnological applications.

SolariX is a compendium of DNA sequence tags from the nucleotide binding site (NBS) domain of disease resistance genes of the common potato, Solanum tuberosum Group Tuberosum. The sequences, which we call NBS tags, for nearly all NBS domains from 91 genomes—representing a wide range of historical and contemporary potato cultivars, 24 breeding programs and 200 years—were generated using just 16 amplification primers and high-throughput sequencing. The NBS tags were mapped to 587 NBS domains on the draft potato genome DM, where we detected an average, over all the samples, of 26 nucleotide polymorphisms on each locus. The total number of NBS domains observed, differed between potato cultivars. However, both modern and old cultivars possessed comparable levels of variability, and neither the individual breeder or country nor the generation or time appeared to correlate with the NBS domain frequencies. Our attempts to detect haplotypes (i.e., sets of linked nucleotide polymorphisms) frequently yielded more than the possible 4 alleles per domain indicating potential locus intermixing during the mapping of NBS tags to the DM reference genome. Mapping inaccuracies were likely a consequence of the differences of each cultivar to the reference genome used, coupled with high levels of NBS domain sequence similarity. We illustrate that the SolariX database is useful to search for polymorphism linked with NBS-LRR R gene alleles conferring specific disease resistance and to develop molecular markers for selection.

The discovery and deployment of new broad-spectrum resistance (R) genes from cultivated rice and its wild relatives is a strategy to broaden the genetic basis of modern rice cultivars to combat rice blast disease. Oryza glaberrima possessing many valuable traits for tolerance to biotic and abiotic stresses, is an elite gene pool for improvement of Asian cultivated rice. An introgression line IL106 derived from O. glaberrima (Acc. IRGC100137) confers complete resistance to Magnaporthe oryzae in blast nursery. Genetic analysis using 2185 BC6F2 progenies derived from a cross between IL106 and the recurrent parent Dianjingyou 1 showed that IL106 harbors a single dominant resistance gene against M. oryzae strain 09BSH-10-5A. This gene was preliminarily mapped on the long arm of chromosome 6 of rice in a region of ca. 0.9 cM delimited by two SSR markers (RM20650 and RM20701). In order to finely map this gene, 17,100 additional progenies were further analyzed. As a result, this gene was further narrowed down to a region flanked by two molecular markers STS69-15 and STS69-7, and co-segregated with 3 molecular markers, RM20676, STS69-21 and STS69-22 on the long arm of chromosome 6. Based on reference genome sequences, this R gene was mapped in silico in 76.1-Kb and 67.7-Kb physical intervals, and containing 4 and 3 NBS-LRR candidate genes in O. sativa cultivar Nipponbare and O. glaberrima cultivar CG14, respectively. Because no blast resistance gene was finely mapped in this physical interval before, this R gene was considered as not described yet and designated as Pi69(t), which is the first identified and finely mapped blast R gene from O. glaberrima, as far as we know. Evaluation of IL106 with 151 blast strains collected from 6 countries in Asia showed that 148 strains are avirulent on IL106, suggesting that Pi69(t) is a broad-spectrum blast R gene, and a promising resistant resource for improvement of Asian cultivated rice.