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Old trees are remarkable for their ability to endure for centuries or even millennia, acting as recordkeepers of historical climate and custodians of genetic diversity. The secret to their longevity has long been a subject of fascination. Despite the challenges associated with studying old trees, such as massive size, slow growth rate, long lifespan and often remote habitat, accumulating studies have investigated the mechanisms underlying tree aging and longevity over the past decade. The recent publication of high‐quality genomes of long‐lived tree species, coupled with research on stem cell function and secondary metabolites in longevity, has brought us closer to unlocking the secrets of arboreal longevity. This review provides an overview of the global distribution of old trees and examines the environmental and anthropogenic factors that shape their presence. We summarize the contributions of physiological characteristics, stem cell activity, and immune system responses to their extraordinary longevity. We also explore the genetic and epigenetic 'longevity code', which consists of resistance and defense genes, DNA repair genes and patterns of DNA methylation modification. Further, we highlight key areas for future research that could enhance our understanding of the mechanisms underlying tree longevity. Summary statement: The mechanism of tree longevity is highly complex, including modular growth and aging of the organism, maintenance of stem cell activity, expansion of resistance genes, accumulation of resistance substances, DNA repair and epigenetic modification. [ABSTRACT FROM AUTHOR]

Plant resistance (R) genes play a crucial role in the detection of effector proteins secreted by pathogens, either directly or indirectly, as well as in the subsequent activation of downstream defence mechanisms. However, little is known about how R genes regulate the defence responses of conifers, particularly Pinus massoniana, against the destructive pine wood nematode (PWN; Bursaphelenchus xylophilus). Here, we isolated and characterised PmHs1pro‐1, a nematode‐resistance gene of P. massoniana, using bioinformatics, molecular biology, histochemistry and transgenesis. Tissue‐specific expressional pattern and localisation of PmHs1pro‐1 suggested that it was a crucial positive regulator in response to PWN attack in resistant P. massoniana. Meanwhile, overexpression of PmHs1pro‐1 was found to activate reactive oxygen species (ROS) metabolism‐related enzymes and the expressional level of their key genes, including superoxide dismutase, peroxidase and catalase. In addition, we showed that PmHs1pro‐1 directly recognised the effector protein BxSCD1of PWN, and induced the ROS burst responding to PWN invasion in resistant P. massoniana. Our findings illustrated the molecular framework of R genes directly recognising the effector protein of pathology in pine, which offered a novel insight into the plant–pathogen arms race. Summary statement: We first identified and functionally characterised that PmHs1pro‐1 could directly recognise the effector protein BxSCD1, which consequently initiated the ROS burst to defend against pine wood nematode to prevent the withered appearance in the resistant Pinus massoniana. Our findings demonstrated the molecular framework of R genes directly recognising the effector protein of pathology in pines and offered a novel insight into the plant‐arm race of pathogens and plants. [ABSTRACT FROM AUTHOR]

Intracellular plant defense against pathogens is mediated by a class of disease resistance genes known as NB‐LRRs or NLRs (R genes). Many of the diseases these genes protect against are more prevalent in regions of higher rainfall, which provide better growth conditions for the pathogens. As such, we expect a higher selective pressure for the maintenance and proliferation of R genes in plants adapted to wetter conditions. In this study, we enriched libraries for R genes using RenSeq from baits primarily developed from the common sunflower (Helianthus annuus) reference genome. We sequenced the R gene libraries of Silphium integrifolium Michx, a perennial relative of sunflower, from 12 prairie remnants across a rainfall gradient in the Central Plains of the United States, with both Illumina short‐read (n = 99) and PacBio long‐read (n = 10) approaches. We found a positive relationship between the mean effective annual precipitation of a plant's source prairie remnant and the number of R genes in its genome, consistent with intensity of plant pathogen coevolution increasing with precipitation. We show that RenSeq can be applied to the study of ecological hypotheses in non‐model relatives of model organisms. [ABSTRACT FROM AUTHOR]

An effective tool for discovering differentially expressed genes (DEGs) related to late blight (LB) resistance is the transcriptome sequencing of potatoes. The aim of this study was to compare transcriptome expression analysis in incompatible and compatible interactions via high-throughput sequencing. Furthermore, we performed a bioinformatics analysis to screen a large number of specific transcription factors (TFs) and DEGs linked to Phytophthora infestans infection. Two locally cultivated potato varieties were chosen from evaluation assays conducted in two consecutive seasons and based on the disease severity (DS) values. These varieties were the highly resistant Jelly (HR) to P. infestans and the moderately susceptible Annabelle (MS). Ribonucleic acid-sequencing (RNA-seq) was achieved for the two varieties with their controls through the BGISEQ-500 sequencing platform. The RNA-seq analysis identified P. infestans-responsive genes and their expression in potatoes. The mechanism of the response of these cultivars to the P. infestans pathogen by TFs and DEG genes, which play an important role in defense response, was investigated. The Gene Ontology (GO) analysis classified 46,248 unigenes in the HR and 26,921 unigenes in MS into the following three categories: biological process, cellular component, and molecular functions. More genes were responsible for the cellular component category, biological process, and molecular functions in HR compared to MS. Moreover, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the significantly enriched DEGs were included in the plant–pathogen interaction, biosynthesis of secondary metabolites, and ribosome. In addition, 1874 transcription factor genes belonging to 85 families were indicated in the DEGs, of which MYB and AP2-EREBP genes were the most abundant. Besides, multiple genes related to LB resistance showed differential expression during infection. It also sheds light on the molecular mechanisms behind potato resistance to P. infestans infection. [ABSTRACT FROM AUTHOR]

Soybean (Glycine max) is an important oilseed, protein and biodiesel crop. It faces significant threats from bacterial, fungal and viral pathogens, which cause economic losses and jeopardises global food security. In this article, we explore the relationship between soybeans and these pathogens, focusing on the molecular responses that are crucial for soybeans defence mechanisms. Molecular responses involve small RNAs and specific genes, including resistance (R) genes that are pivotal in triggering immune responses. Functional genomics, which makes use of cutting-edge technologies, such as CRISPR Cas9 gene editing, allows us to identify genes that provide insights into the defence mechanisms of soybeans with the focus on using genomics to understand the mechanisms involved in host pathogen interactions and ultimately improve the resilience of soybeans. Genes like GmKR3 and GmVQ58 have demonstrated resistance against soybean mosaic virus and common cutworm, respectively. Genetic studies have identified quantitative trait loci (QTLs) including those linked with soybean cyst nematode, root-knot nematode and Phytophthora root and stem rot resistance. Additionally, resistance against Asian soybean rust and soybean cyst nematode involves specific genes and their variations in terms of different copy numbers. To address the challenges posed by evolving pathogens and meet the demands of a growing population, accelerated soybean breeding efforts leveraging functional genomics are imperative. Targeted breeding strategies based on a deeper understanding of soybean gene function and regulation will enhance disease resistance, ensuring sustainable agriculture and global food security. Collaborative research and continued technological advancements are crucial for securing a resilient and productive agricultural future. [ABSTRACT FROM AUTHOR]

Pathogen recognition receptors encoded by R genes play a key role in plant protection. Nowadays, R genes are a basis for breeding many crops, including potato. Many potato R genes have been discovered and found suitable for breeding thanks to the studies of a wide variety of wild potato species. The use of primitive cultivated potato species (PCPS) as representatives of the primary gene pool can also be promising in this respect. PCPS are the closest to the early domesticated forms of potato; therefore, their investigation could help understand the evolution of R genes. The present study was aimed at identifying and analyzing R genes in PCPS listed in the open database of NCBI and Solomics DB. In total, the study involved 27 accessions belonging to three species: Solanum phureja Juz. & Bukasov, S. stenotomum Juz. & Bukasov and S. goniocalyx Juz. & Bukasov Materials for the analysis were the sequencing data for the said three species from the PRJNA394943 and PRJCA006011 projects. An in silico search was carried out for sequences homologous to 26 R genes identified in potato species differing in phylogenetic distance from PCPS, namely nightshade (S. americanum), North- (S. bulbocastanum, S. demissum) and South-American (S. venturii, S. berthaultii) wild potato species, as well as the cultivated potato species S. tuberosum and S. andigenum. Homologs of all investigated protein-coding sequences were discovered in PCPS with a relatively high degree of similarity (85–100 %). Homologs of the Rpi-R3b, Rpi-amr3 and Rpi-ber1 genes have been identified in PCPS for the first time. An analysis of polymorphism of nucleotide and amino acid sequences has been carried out for 15 R genes. The differences in frequencies of substitutions in PCPS have been demonstrated by analysis of R genes, the reference sequences of which have been identified in different species. For all the studied NBS-LRR genes, the proportion of substituted amino acids in the LRR domain exceeds this figure for the NBS domain. The potential prospects of using PCPS as sources of resistance to Verticillium wilt have been shown.

Three potato cultivars, Payette Russet, Dark Red Norland, and Chieftain were challenged with four strains of potato virus Y (PVY), PVYO, PVYEu−N, PVYN−Wi, and PVYNTN. Cultivars Dark Red Norland and Chieftain exhibited strain-specific, hypersensitive resistance to PVYO and PVYNTN strains.. These same two cultivars, Dark Red Norland and Chieftain, appeared to have an additional resistance source in their genomes providing partial resistance against PVYN−Wi but were found fully susceptible to the non-recombinant PVYEu−N strain. Payette Russet was found immune to the same four strains of PVY; PVYO, PVYEu−N, PVYN−Wi, and PVYNTN, and was additionally challenged with the total of 18 isolates of PVY representing 12 genetic variants of the virus from potato and non-potato solanaceous hosts. None of the 18 isolates of the virus was found able to replicate in the inoculated or upper non-inoculated leaves of Payette Russet, confirming the broad specificity of the Rysto gene present in the Payette Russet genome. [ABSTRACT FROM AUTHOR]

Northern corn leaf blight, caused by Exserohilum turcicum, is mainly controlled by the use of resistant cultivars. Maize lines carrying individual resistance genes B37Ht1, B37Ht2, B37Ht3, and B37Htn1 express different defense symptoms having an impact on the photosynthetic activity, the accumulation of reactive oxygen species, and epidemiological parameters. Plants were inoculated with a race 0 isolate of E. turcicum conferring a compatible interaction with B37 and incompatible interactions with plants carrying resistance genes. Five days postinoculation (dpi), the resistant lines displayed a reduction in leaf CO2 assimilation of 30 to 80% compared with healthy plants. At 14 dpi, inoculated plants of B37Ht1 showed a significant decrease in leaf CO2 assimilation, similar to B37 (up to 94%). The instantaneous carboxylation efficiency was significantly reduced on inoculated plants of the lines B37Ht2, B37Ht3, and B37Htn1 (54 to 81%) at 5 dpi. Curiously, the reduction in carboxylation efficiency for B37 and B37Ht1 (up to 95%) was higher at 14 dpi than at 5 dpi (up to 81%). At 6 dpi, low levels of H2O2 were detected in B37Ht1, in contrast to B37Htn1, where a high H2O2 level and peroxidase activity were observed. The sporulation rate on B37Ht1, B37Ht3, and B37Htn1 decreased by 92% compared with the susceptible control, whereas strong sporulation occurred in lesions on line B37Ht2. The resistance in maize to E. turcicum conferred by Ht resistance genes is associated with photosynthetic costs and may have quite contrasting effects on host physiology and major epidemiological parameters, such as sporulation, which contributes inoculum for secondary infections. [ABSTRACT FROM AUTHOR]

Resistance (R) genes in the Triticeae tribe include not only genes encoding the canonical intracellular nucleotide-binding leucine-rich-repeat proteins (NLRs) but also genes encoding kinase fusion proteins (KFPs). Exploring these unconventional KFPs may expand the scope of effector-triggered immunity (ETI) and will have significant implications for crop improvement. [ABSTRACT FROM AUTHOR]

Biotic stress factors cause massive damage to crops and account for major economic losses globally. With the global temperature on the rise, a great threat looms on the global economy and food security as sustainable agriculture is expected to be devastated by larger outbreaks of diseases worldwide. Plants have developed versatile counter-strategies to overcome these stressors. These strategies rely on preformed defense or induced defense responses which, in turn, entail a complex crosstalk among different signaling pathways. Once the presence of a pathogen is detected, the plant host switches on its defense response. Very specific recognition of the invading pathogen is mediated via the detection of their Avr effector proteins by the cognate elements in the plant host, i.e., the R proteins, encoded by R genes. Successful recognition of Avr by the cognate host R proteins sets distinct signaling cascade(s) into motion to activate defense responses. The nucleotide-binding leucine-rich repeat proteins (NB-LRRs or NLRs) represent the major class of R proteins and insights gained regarding their structural complexity and underlying signal transduction has enabled researchers to exploit them for competent introgression of disease resistance in plants against a single or a broad range of pathogens. In addition to conventional breeding, more recent biotechnological interventions have also been employed to develop plants with improved disease resistance with the use of R genes. The domain of R gene-mediated disease resistance has gained much attention from plant breeders and through experimental interventions, many promising opportunities for conferring resistance for effective management of diseases have come forth. This review attempts to summarize the progress made hitherto and focuses on how the knowledge base so created has been used to find out solutions to the major biotic problems occurring throughout the world. [ABSTRACT FROM AUTHOR]

Summary: Soybean rust (SBR), caused by the obligate biotrophic fungus Phakopsora pachyrhizi, is a devastating foliar disease threatening soybean production. To date, no commercial cultivars conferring durable resistance to SBR are available. The development of long‐lasting SBR resistance has been hindered by the lack of understanding of this complex pathosystem, encompassing challenges posed by intricate genetic structures in both the host and pathogen, leading to a gap in the knowledge of gene‐for‐gene interactions between soybean and P. pachyrhizi. In this review, we focus on recent advancements and emerging technologies that can be used to improve our understanding of the P. pachyrhizi‐soybean molecular interactions. We further explore approaches used to combat SBR, including conventional breeding, transgenic approaches and RNA interference, and how advances in our understanding of plant immune networks, the availability of new molecular tools, and the recent sequencing of the P. pachyrhizi genome could be used to aid in the development of better genetic resistance against SBR. Lastly, we discuss the research gaps of this pathosystem and how new technologies can be used to shed light on these questions and to develop durable next‐generation SBR‐resistant soybean plants. [ABSTRACT FROM AUTHOR]

Powdery mildew, caused by Podosphaera macularis, is one of the most important diseases of hop in the Pacific Northwest of the United States. Resistant cultivars exist; however, recently, the pathogen has overcome two sources of resistance in popular cultivars. Breeding for new, emerging races of the pathogen is thus a continuing priority. We used RNA-seq to understand gene expression trends in a resistant (cv. USDA Nugget) and a susceptible (cv. Symphony) hop cultivar along a time series following inoculation. We found stronger transcriptional reprogramming in the resistant cultivar than the susceptible cultivar. Transcripts that increased in expression within 12 h post-inoculation in the resistant cultivar included genes in the jasmonic acid biosynthesis pathway, as well as phenylpropanoid biosynthesis. Transcripts that had a positive correlation with time post-inoculation in the resistant cultivar included genes involved in phosphorylation, cell-surface signaling pathways, and response to jasmonic acid. We used untargeted HPLC–HR-MS/MS analysis and confirmed an increase in jasmonic acid and several phenolic compounds. We hypothesize that resistance to powdery mildew in cv. Nugget may be at least partially due to perception of the pathogen outside of the cell, and transcriptional and metabolic reprogramming is mediated by jasmonic acid signaling. At least part of that transcriptional and metabolic reprogramming involves changes to lignin production, which might reinforce the cell wall. The multi-omics approach to describe the contrasting responses of a resistant and a susceptible hop cultivar following inoculation with this important pathogen may indicate new strategies for developing resistant germplasm and control methods. [Figure: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Rice blast disease caused by the fungus Pyricularia oryzae is one of the most devastating diseases of rice (Oryza sativa L.). Therefore, the use of resistant rice varieties would be the most effective way to control this disease. Based on disease evaluation, upland rice varieties were classified into two groups: resistant (35%) and moderately resistant (65%). Forty upland rice varieties and two lowland rice varieties were genotyped for seven major rice blast resistance genes Pi37, Pid2, Pi9, Pi36(t), Pi5, Pik-m, and Pi54. The gene frequencies of the seven major R genes ranged from 2.38% to 100%. The 42 varieties contained one to five R genes. Two varieties had five blast resistance genes, whereas 21 varieties contained four R genes, 15 varieties contained three R genes, 3 varieties contained two R genes, and only one variety contained one R gene. Furthermore, the relationship between the presence of different R genes and disease reactions was investigated using a multiple stepwise regression model. Three markers, Pi5, Pi54MAS, and Ckm2, for three R genes (Pi5, Pi54, and Pik-m) were moderately correlated with blast disease with partial correlation coefficients of 0.35 to 0.47. These results provide new sources of resistance genes for designing future breeding program to develop leaf blast-resistant rice varieties. [ABSTRACT FROM AUTHOR]

Abstract Background Bacterial leaf blight (BLB) is a highly destructive disease, causing significant yield losses in rice (Oryza sativa). Genetic variation is contemplated as the most effective measure for inducing resistance in plants. The mutant line T1247 derived from R3550 (BLB susceptible) was highly resistant to BLB. Therefore, by utilizing this valuable source, we employed bulk segregant analysis (BSA) and transcriptome profiling to identify the genetic basis of BLB resistance in T1247. Results The differential subtraction method in BSA identified a quantitative trait locus (QTL) on chromosome 11 spanning a 27-27.45 Mb region with 33 genes and 4 differentially expressed genes (DEGs). Four DEGs (P

Plants use different receptors to detect potential pathogens: membrane-anchored pattern recognition receptors (PRRs) activated upon perception of pathogen-associated molecular patterns (PAMPs) that elicit pattern-triggered immunity (PTI); and intracellular nucleotide-binding leucine-rich repeat proteins (NLRs) activated by detection of pathogen-derived effectors, activating effector-triggered immunity (ETI). The interconnections between PTI and ETI responses have been increasingly reported. Elevated NLR levels may cause autoimmunity, with symptoms ranging from fitness cost to developmental arrest, sometimes combined with run-away cell death, making accurate control of NLR dosage key for plant survival. Small RNA-mediated gene regulation has emerged as a major mechanism of control of NLR dosage. Twenty-two nucleotide miRNAs with the unique ability to trigger secondary siRNA production from target transcripts are particularly prevalent in NLR regulation. They enhance repression of the primary NLR target, but also bring about repression of NLRs only complementary to secondary siRNAs. We summarize current knowledge on miRNAs and siRNAs in the regulation of NLR expression with an emphasis on 22 nt miRNAs and propose that miRNA and siRNA regulation of NLR levels provides additional links between PTI and NLR defense pathways to increase plant responsiveness against a broad spectrum of pathogens and control an efficient deployment of defenses. [ABSTRACT FROM AUTHOR]

Glomerella leaf spot (GLS), caused by the fungal pathogen Colletotrichum fructicola, significantly threatens apple production. Some resistances to plant disease are mediated by the accumulation of nucleotide‐binding site and leucine‐rich repeat (NBS‐LRR) proteins that are encoded by a major class of plant disease resistance genes (R genes). However, the R genes that confer resistance to GLS in apple remain largely unclear. Malus hupehensis YT521‐B homology domain‐containing protein 2 (MhYTP2) was identified as an N6‐methyladenosine RNA methylation (m6A) modified RNA reader in our previous study. However, whether MhYTP2 binds to mRNAs without m6A RNA modifications remains unknown. In this study, we discovered that MhYTP2 exerts both m6A‐dependent and ‐independent functions by analysing previously obtained RNA immunoprecipitation sequencing results. The overexpression of MhYTP2 significantly reduced the resistance of apple to GLS and down‐regulated the transcript levels of some R genes whose transcripts do not contain m6A modifications. Further analysis indicated that MhYTP2 binds to and reduces the stability of MdRGA2L mRNA. MdRGA2L positively regulates resistance to GLS by activating salicylic acid signalling. Our findings revealed that MhYTP2 plays an essential role in the regulation of resistance to GLS and identified a promising R gene, MdRGA2L, for use in developing apple cultivars with GLS resistance. [ABSTRACT FROM AUTHOR]

Two infectious clones of turnip mosaic virus (TuMV), pKBC-1 and pKBC-8, with differential infectivity in Chinese cabbage (Brassica rapa subsp. pekinensis), were obtained. Both infected Nicotiana benthamiana systemically, inducing similar symptoms, whereas only virus KBC-8 infected Chinese cabbage systemically. To identify the determinants affecting infectivity on Chinese cabbage, chimeric clones were constructed by restriction fragment exchange between the parental clones and tested on several Chinese cabbage cultivars. Chimeric clones plN8C and p8NlC demonstrated that the C-terminal portion of the polyprotein determines systemic infection of Chinese cabbage despite only three amino acid differences in this region, in the cylindrical inclusion (CI), viral protein genome-linked (VPg), and coat protein (CP). A second pair of hybrid constructs, pHindIII-lN8C and pHindIII-8NlC, failed to infect cultivars CR Victory and Jinseonnorang systemically, yet pHindlII-lN8C caused hypersensitive response-like lesions on inoculated leaves of these cultivars, and could systemically infect cultivars CR Chusarang and Jeongsang; this suggests that R genes effective against TuMV may exist in the first two cultivars but not the latter two. Constructs with single amino acid changes in both VPg (K2045E) and CP (Y3095H) failed to infect Chinese cabbage, implying that at least one of these two amino acid substitutions is essential for successful infection on Chinese cabbage. Successful infection by mutant KBC-8-CP-H and delayed infection with mutant HJYl-VPg-E following mutation or reversion suggested that VPg (2045 K) is the residue required for infection of Chinese cabbage and involved in the interaction between VPg and eukaryotic initiation factor eIF(iso)4E, confirmed by yeast two-hybrid assay. [ABSTRACT FROM AUTHOR]

Induction of R-gene-mediated antiviral resistance results in phenotypically different responses depending on host R gene—virus combinations. The responses include a hypersensitive response (HR), in which virus infection is stopped within the initially infected tissues to form necrotic local lesions (NLLs) by induction of programmed-cell death (PCD), as well as an extreme resistance (ER), in which virus replication is suppressed at the cellular level without PCD induction. A response that causes only tiny NLLs is called a micro-HR, and a response that causes systemic death of the plant by systemic PCD induction is called a systemic HR (SHR). In this study, we used our RCY1—cucumber mosaic virus (CMV) coat protein (CP) system as a model system for R gene—virus recognition and resistance induction, and showed that artificial deletion/alanine substitutions in an arginine-rich motif in CMV CP changed the induced response from an HR to an ER and to intermediate responses between an ER and a micro-HR, where different numbers of tiny NLLs were formed. Using a micro-HR inducing variant, we showed that viral MOI (multiplicity of infection) reduced by 51.5% upon a micro-HR induction, which was much greater than the reduction observed upon an HR induction, providing the first quantitative evidence that a micro-HR is a result of enhanced resistance. Based on the obtained results, we discuss a possible molecular mechanism for the induction of enhanced resistance and the mechanisms for the induction of phenotypically different responses. [ABSTRACT FROM AUTHOR]

Bacterial leaf blight (BLB) disease of rice caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the significant constraints for rice production. A study was carried out to analyze the virulence, genetic diversity, and population structure of Xoo isolates collected from different rice ecosystems of Karnataka, India. The taxonomic identity of all 54 isolates was confirmed using a Xoo-specific PCR assay. The virulence assay on a set of twenty-eight near-isogenic differentials identified nine pathotype groups (KPthX-1 to KPthX-9). Among them, KPthX-6 was highly virulent, whereas KPthx-2 was less virulent. Differentials with four and five resistance (R) genes (Xa4+xa5+xa13+Xa21, Xa4+Xa7+xa13+Xa21, and Xa4+xa5+Xa7+xa13+Xa21) were effective against all the pathotypes. Further, genetic diversity was deduced using a universal marker set, JEL-1, and JEL-2, complementary to a conserved repetitive sequence IS1112. The amplicon size and numbers varied from 100 bp to 3 Kb and 1 to 25. Based on the amplicon counts, Jaccard's co-efficient and phylogenetic analyses were carried out and categorized the 54 isolates into three clusters (I to III). Cluster-II contains the maximum number of isolates (27), followed by cluster-I (23 isolates) and cluster-III (one isolate). The structure analysis categorized the isolates into five subgroups, viz. SG1, SG2, SG3, SG4, and SG5 indicate the existence of five subpopulations. The present study has identified the genetic and virulence diversity of the Xoo population and reported the effective R gene/s for different rice ecosystems, which can be used in the breeding program for the eco-specific management of BLB of rice.

Background: Bacterial leaf blight (BLB) is a highly destructive disease, causing significant yield losses in rice (Oryza sativa). Genetic variation is contemplated as the most effective measure for inducing resistance in plants. The mutant line T1247 derived from R3550 (BLB susceptible) was highly resistant to BLB. Therefore, by utilizing this valuable source, we employed bulk segregant analysis (BSA) and transcriptome profiling to identify the genetic basis of BLB resistance in T1247. Results: The differential subtraction method in BSA identified a quantitative trait locus (QTL) on chromosome 11 spanning a 27-27.45 Mb region with 33 genes and 4 differentially expressed genes (DEGs). Four DEGs (P < 0.01) with three putative candidate genes, OsR498G1120557200, OsR498G1120555700, and OsR498G1120563600,0.01 in the QTL region were identified with specific regulation as a response to BLB inoculation. Moreover, transcriptome profiling identified 37 resistance analogs genes displaying differential regulation. Conclusions: Our study provides a substantial addition to the available information regarding QTLs associated with BLB, and further functional verification of identified candidate genes can broaden the scope of understanding the BLB resistance mechanism in rice. [ABSTRACT FROM AUTHOR]

Rice blast, caused by the Magnaporthe oryzae fungus, is one of the most devastating rice diseases worldwide. Developing resistant varieties by pyramiding different blast resistance (R) genes is an effective approach to control the disease. However, due to complex interactions among R genes and crop genetic backgrounds, different R-gene combinations may have varying effects on resistance. Here, we report the identification of two core R-gene combinations that will benefit the improvement of Geng (Japonica) rice blast resistance. We first evaluated 68 Geng rice cultivars at seedling stage by challenging with 58 M. oryzae isolates. To evaluate panicle blast resistance, we inoculated 190 Geng rice cultivars at boosting stage with five groups of mixed conidial suspensions (MCSs), with each containing 5–6 isolates. More than 60% cultivars displayed moderate or lower levels of susceptibility to panicle blast against the five MCSs. Most cultivars contained two to six R genes detected by the functional markers corresponding to 18 known R genes. Through multinomial logistics regression analysis, we found that Pi-zt, Pita, Pi3/5/I, and Pikh loci contributed significantly to seedling blast resistance, and Pita, Pi3/5/i, Pia, and Pit contributed significantly to panicle blast resistance. For gene combinations, Pita+Pi3/5/i and Pita+Pia yielded more stable pyramiding effects on panicle blast resistance against all five MCSs and were designated as core R-gene combinations. Up to 51.6% Geng cultivars in the Jiangsu area contained Pita, but less than 30% harbored either Pia or Pi3/5/i, leading to less cultivars containing Pita+Pia (15.8%) or Pita+Pi3/5/i (5.8%). Only a few varieties simultaneously contained Pia and Pi3/5/i, implying the opportunity to use hybrid breeding procedures to efficiently generate varieties with either Pita+Pia or Pita+Pi3/5/i. This study provides valuable information for breeders to develop Geng rice cultivars with high resistance to blast, especially panicle blast. [ABSTRACT FROM AUTHOR]

R genes with colossal contributions to disease resistance possess conserved domains with confounded roles. Based on the conserved domains, R genes encoded proteins are classified. The members of nucleotide-binding site, NBS-Leucine rich repeats, LRR class of R genes are significant candidates involved in plant disease-resistance pathways. In this study, the genetic elements contributing to stem and crown rot disease resistance were explored through transcriptome probing based on conserved NBS domain under disease stress in berseem clover. Expression analysis of identified gene sequences revealed their upregulation during stem and crown rot disease. The in silico characterization imparted strong support towards the predictive role of identified RGAs in disease resistance. [ABSTRACT FROM AUTHOR]

Radish (Raphanus sativus L.) is an important root vegetable crop that is easily infected by various pathogens that result in decreased yield and quality. Nucleotide-binding site and leucine-rich repeat (NBS-LRR) genes play vital roles in resisting pathogen infection in plants. However, the genome-wide characterization and functional roles of NBS-LRR genes remain largely unexplored in radish. Here, a total of 187 RsNBS-LRR genes were identified at the whole-genome level in radish, among which 80 RsNBS-LRR genes were unevenly distributed on nine radish chromosomes. Interestingly, 15 clusters containing 36 RsNBS-LRR genes occurred in eight chromosomes. RNA-Seq data showed that several RsNBS-LRR genes exhibited significant differential expression profiles in different radish tissues. Moreover, a range of cis-acting regulatory elements associated with ABA, MeJA, or SA were identified in the promoter region of some RsNBS-LRR genes. RT-qPCR analysis showed that the expression of a few RsNBS-LRR genes (e.g., RsNBS021 and RsNBS163) was significantly induced under Peronospora parasitica infection and/or ABA treatment, indicating that they might play critical roles in ABA-dependent defense resistance processes. These results could enhance our understanding of the evolutionary relationship of RsNBS-LRR genes and facilitate the genetic manipulation of disease resistance in radish breeding programs. [ABSTRACT FROM AUTHOR]

Banana is one of the major food crops and its production is subject to many pests and diseases. Banana breeding exploits wild relatives and progenitor species for the introgression of resistant genes (R) into cultivated varieties to overcome these hurdles. With advances in sequencing technologies, whole-genome sequences are available for many Musa spp. and many of them are potential donors of disease resistance genes. Considering their potential role, R genes from these species were explored to develop an user-friendly open-access database that will be useful for studying and implementing disease resistance in bananas. MusaRgene database is complemented with complete details of 3598 R genes identified from eight Musa spp. and rice, Arabidopsis, sorghum along with its classification and separate modules on its expression under various stresses in resistant and susceptible cultivars and corresponding SSRs are also provided. This database can be regarded as the primary resource of information on R genes from bananas and their relatives. R genes from other allele mining studies are also incorporated which will enable the identification of its homolog in related Musa spp. MusaRgene database will aid in the identification of genes and markers associated, cloning of full-length R genes, and genetic transformation or gene editing of the R genes in susceptible cultivars. Multiple R genes can also be identified for pyramiding the genes to increase the level of resistance and durability. Overall, this database will facilitate the understanding of defense mechanisms in bananas against biotic or abiotic stresses leading to the development of promising disease-resistant varieties. [ABSTRACT FROM AUTHOR]

Plants, like animals, are constantly exposed to abiotic and biotic stresses, which often inhibit plant growth and development, and cause tissue damage, disease, and even plant death. Efficient and timely response to stress requires appropriate co‐ and posttranscriptional reprogramming of gene expression. Alternative pre‐mRNA splicing provides an important layer of this regulation by controlling the level of factors involved in stress response and generating additional protein isoforms with specific features. Recent high‐throughput studies have revealed that several defence genes undergo alternative splicing that is often affected by pathogen infection. Despite extensive work, the exact mechanisms underlying these relationships are still unclear, but the contribution of alternative protein isoforms to the defence response and the role of regulatory factors, including components of the splicing machinery, have been established. Modulation of gene expression in response to stress includes alternative splicing, chromatin remodelling, histone modifications, and nucleosome occupancy. How these processes affect plant immunity is mostly unknown, but these facets open new regulatory possibilities. Here we provide an overview of the current state of knowledge and recent findings regarding the growing importance of alternative splicing in plant response to biotic stress. [ABSTRACT FROM AUTHOR]

Abstract Background Pi-ta is a major blast resistant gene, introgressed from indica rice varieties. In this study, diversity of the Pi-ta gene of 47 Sri Lankan rice accessions was studied by bioinformatics, and the results were validated with molecular and disease reaction assays. Sequences of rice accessions at the locus Os12g0281300 were retrieved from Rice SNP-Seek Database, and the coding sequence of reference Pi-ta gene of cultivar Tetep (accession no. GQ918486.1) was obtained from GenBank. Comparisons were made at nucleotide, amino acid, and protein structure level, and the 3D models predicted using Phyre2 software were superimposed using TM-align software. Results In silico analysis revealed that 10 accessions possessed resistant allele of the Pi-ta gene. The remaining accessions recorded high polymorphism in the leucine-rich domain resulting in 9 allele types, leading to single–amino acid substitutions at 27 different positions including a functional mutation of alanine to serine at the 918th amino acid position. None of the genotypes led to truncations in the amino acid sequence. The in silico analysis results were validated on 23 accessions comprising resistant and susceptible genotypes and another 25 cultivars from Northern Sri Lanka, by molecular assay using YL183/YL87 and YL155/YL87 resistant and susceptible allele-specific markers. Resistance of Pi-ta gene for the causal fungus, Magnaporthe oryzae, was further validated through pathogenicity assay. Conclusion The Pi-ta gene, especially the LRD region, revealed significant variations within Sri Lankan rice cultivars leading to high levels of resistance against blast. This information would be highly useful in breeding programmes for resistance against rice blast.

Brassica crop diseases caused by various pathogens, including viruses, bacteria, fungi and oomycetes, have devastating effects on the plants, leading to significant yield loss. This effect is worsened by the impact of climate change and the pressure to increase cultivation worldwide to feed the burgeoning population. As such, managing Brassica diseases has become a challenge demanding a rapid solution. In this review, we provide a detailed introduction of the plant immune system, discuss the evolutionary pattern of both dominant and recessive disease resistance (R) genes in Brassica and discuss the role of epigenetics in R gene evolution. Reviewing the current findings of how R genes evolve in Brassica spp. provides further insight for the development of creative ideas for crop improvement in relation to breeding sustainable, high quality, disease-resistant Brassica crops. [ABSTRACT FROM AUTHOR]

NBS-LRR genes are the largest gene family in plants conferring resistance to pathogens. At present, studies on the evolution of NBS-LRR genes in angiosperms mainly focused on monocots and eudicots, while studies on NBS-LRR genes in the basal angiosperms are limited. Euryale ferox represents an early-diverging angiosperm order, Nymphaeales, and confronts various pathogens during its lifetime, which can cause serious economic losses in terms of yield and quality. In this study, we performed a genome-wide identification and analysis of NBS-LRR genes in E. ferox. All 131 identified NBS-LRR genes could be divided into three subclasses according to different domain combinations, including 18 RNLs , 40 CNLs , and 73 TNLs. The E. ferox NBS-LRR genes are unevenly distributed on 29 chromosomes; 87 genes are clustered at 18 multigene loci, and 44 genes are singletons. Gene duplication analysis revealed that segmental duplications acted as a major mechanism for NBS-LRR gene expansions but not for RNL genes, because 18 RNL genes were scattered over 11 chromosomes without synteny loci, indicating that the expansion of RNL genes could have been caused by ectopic duplications. Ancestral gene reconciliation based on phylogenetic analysis revealed that there were at least 122 ancestral NBS-LRR lineages in the common ancestor of the three Nymphaeaceae species, suggesting that NBS-LRR genes expanded slightly during speciation in E. ferox. Transcriptome analysis showed that the majority of NBS-LRR genes were at a low level of expression without pathogen stimulation. Overall, this study characterized the profile of NBS-LRR genes in E. ferox and should serve as a valuable resource for disease resistance breeding in E. ferox. [ABSTRACT FROM AUTHOR]

The genome of an organism is regulated in concert with the organized action of various genetic regulators at different hierarchical levels. Small non-coding RNAs are one of these regulators, among which microRNAs (miRNAs), a distinguished sRNA group with decisive functions in the development, growth and stress-responsive activities of both plants as well as animals, are keenly explored over a good number of years. Recent studies in plants revealed that apart from the silencing activity exhibited by miRNAs on their targets, miRNAs of specific size and structural features can direct the phasing pattern of their target loci to form phased secondary small interfering RNAs (phasiRNAs). These trigger-miRNAs were identified to target both coding and long non-coding RNAs that act as potent phasiRNA precursors or PHAS loci. The phasiRNAs produced thereby exhibit a role in enhancing further downstream regulation either on their own precursors or on those transcripts that are distinct from their genetic source of origin. Hence, these tiny regulators can stimulate an elaborative cascade of interacting RNA networks via cis and trans-regulatory mechanisms. Our review focuses on the comprehensive understanding of phasiRNAs and their trigger miRNAs, by giving much emphasis on their role in the regulation of plant defense responses, together with a summary of the computational tools available for the prediction of the same. [ABSTRACT FROM AUTHOR]

NBS-LRR genes are the largest gene family in plants conferring resistance to pathogens. At present, studies on the evolution of NBS-LRR genes in angiosperms mainly focused on monocots and eudicots, while studies on NBS-LRR genes in the basal angiosperms are limited. Euryale ferox represents an early-diverging angiosperm order, Nymphaeales, and confronts various pathogens during its lifetime, which can cause serious economic losses in terms of yield and quality. In this study, we performed a genome-wide identification and analysis of NBS-LRR genes in E. ferox. All 131 identified NBS-LRR genes could be divided into three subclasses according to different domain combinations, including 18 RNLs, 40 CNLs, and 73 TNLs. The E. ferox NBS-LRR genes are unevenly distributed on 29 chromosomes; 87 genes are clustered at 18 multigene loci, and 44 genes are singletons. Gene duplication analysis revealed that segmental duplications acted as a major mechanism for NBS-LRR gene expansions but not for RNL genes, because 18 RNL genes were scattered over 11 chromosomes without synteny loci, indicating that the expansion of RNL genes could have been caused by ectopic duplications. Ancestral gene reconciliation based on phylogenetic analysis revealed that there were at least 122 ancestral NBS-LRR lineages in the common ancestor of the three Nymphaeaceae species, suggesting that NBS-LRR genes expanded slightly during speciation in E. ferox. Transcriptome analysis showed that the majority of NBS-LRR genes were at a low level of expression without pathogen stimulation. Overall, this study characterized the profile of NBS-LRR genes in E. ferox and should serve as a valuable resource for disease resistance breeding in E. ferox.

Rice false smut (RFS), an emerging major fungal disease worldwide caused by Ustilaginoidea virens, affects rice grain quality and yield. RFS cause 2.8–49% global yield loss depending upon disease severity and cultivars. In India, the yield loss due to RFS ranged from 2 to 75%. Identification of the genes or quantitative trait loci (QTLs) governing disease resistance would be of utmost importance towards mitigating the economic losses incurred due to RFS. Here, we report mapping of RFS resistance QTLs from a resistant breeding line RYT2668. The mapping population was evaluated for RFS resistance under the field condition in three cropping seasons 2013, 2015, and 2016. A positive correlation among infected panicle/plant, total smut ball/panicle, and disease score was observed in the years 2013, 2015, and the mean data. A total of seven QTLs were mapped on rice chromosomes 2, 4, 5, 7, and 9 using 2326 single nucleotide polymorphism markers. Of these, two QTLs, qRFSr5.3 and qRFSr7.1a, were associated with the infected panicle per plant, one QTL qRFsr9.1 with total smut ball per panicle, and four QTLs qRFSr2.2, qRFSr4.3, qRFSr5.4, and qRFSr7.1b with disease score. Among them, a novel QTL qRFSr9.1 on chromosome 9 exhibits the largest phenotypic effect. The prediction of putative candidate genes within the qRFSr9.1 revealed four nucleotide-binding sites–leucine-rich repeat (NBS-LRR) domain-containing disease resistance proteins. In summary, our findings mark the hotspot region of rice chromosomes carrying genes/QTLs for resistance to the RFS disease. [ABSTRACT FROM AUTHOR]

Abstract Background As rice (Oryza sativa) is the staple food of more than half the world’s population, rice production contributes greatly to global food security. Rice blast caused by the fungus Magnaporthe oryzae (M. oryzae) is a devastating disease that affects rice yields and grain quality, resulting in substantial economic losses annually. Because the fungus evolves rapidly, the resistance conferred by most the single blast-resistance genes is broken after a few years of intensive agricultural use. Therefore, effective resistance breeding in rice requires continual enrichment of the reservoir of resistance genes, alleles, or QTLs. Seed banks represent a rich source of genetic diversity; however, they have not been extensively used to identify novel genes and alleles. Results We carried out a large-scale screen for novel blast-resistance alleles in 1883 rice varieties from major rice-producing areas across China. Of these, 361 varieties showed at least moderate resistance to natural infection by rice blast at rice blast nurseries in Enshi and Yichang, Hubei Province. We used sequence-based allele mining to amplify and sequence the allelic variants of the major rice blast-resistance genes at the Pi2/Pi9 locus of chromosome 6 from the 361 blast-resistant varieties, and the full-length coding region of this gene could be amplified from 107 varieties. Thirteen novel Pi9 alleles (named Pi9-Type1 to Pi9-Type13) were identified in these 107 varieties based on comparison to the Pi9 referenced sequence. Based on the sequencing results, the Pi2/Pi9 locus of the 107 varieties was divided into 15 genotypes (including three different genotypes of Pi9-Type5). Fifteen varieties, each representing one genotype, were evaluated for resistance to 34 M. oryzae isolates. The alleles from seven varieties with the highest resistance and widest resistance spectra were selected for transformation into the susceptible variety J23B to construct near-isogenic lines (NILs). These NILs showed resistance in a field test in Enshi and Yichang, indicating that the seven novel rice blast-resistance tandem-repeat regions at the Pi2/Pi9 locus of chromosome 6 could potentially serve as a genetic resource for molecular breeding of resistance to rice blast. Conclusions The thirteen novel Pi9 alleles identified in this study expand the list of available of blast-resistance alleles. Seven tandem-repeat regions of the Pi2/Pi9 locus from different donors were characterized as broad-spectrum rice blast-resistance fragments; these donors enrich the genetic resources available for rice blast-resistance breeding programs.

Sugarcane (Saccharum spp.), main sugar crop worldwide, is affected by multiple pathogens. One of the most important viral diseases in this crop is mosaic, caused by Sugarcane mosaic virus (SCMV). This research was conducted with the objective of demonstrating the ability of two bioproducts to induce defenses response against this virus. The first based on the encapsulation of the endopolygalacturonase enzyme of the yeast Kluyveromyces marxianus CCEBI 2011 and another whose active principle is constituted by phenolic compounds produced by sugarcane in temporary immersion bioreactors. SP70-1284 cultivars susceptible to SCMV and resistant C323-68 were treated with the bioproducts and inoculated with SCMV. The severity of the infection, the accumulation of superoxide radicals and the expression of 10 defense-related genes were evaluated. The resistant cultivar did not show symptoms of infection during the development of the experiment, while in the susceptible the application of both bioproducts decreased the severity of the infection between 38.9 and 44.4% with respect to the control. The presence of superoxide radicals was observed in the first hours of sugarcane-SCMV interaction, while at 28 days’ post inoculation, a differentiated expression of three genes related to antiviral defense was observed. The ability of both bioproducts to induce defensive responses in sugarcane against SCMV was demonstrated.

Globodera pallida is a white potato cyst nematode present in the Andes, which causes huge losses to Peruvian farmers. An RNA-seq analysis allowed the identification of candidate genes that could mediate resistance against this pathogen. Two varieties, “María Huanca” (Solanum andigena) clone resistant (CIP 279142.12) and “Chimbina Colorada” (Solanum chaucha) (CIP 701013) clone susceptible to G. pallida, were used to identify differentially expressed genes. Total RNA from roots was extracted 72 hours post inoculation with second stage juveniles. Sequencing was done using the Illumina Hiseq 2500 platform. Reads were screened for quality issues and then mapped to the reference potato genome (clone DM1-3516 R44 v4.03). Here, we report 27717 and 27750 genes expressed in the resistant and susceptible variety respectively. The comparative analysis of expression identified 100 candidate genes. 91 genes were associated with resistance to G. pallida with Fold Change ≥ 2 (p

Radish (Raphanus sativus L.) is an important root vegetable crop that is easily infected by various pathogens that result in decreased yield and quality. Nucleotide-binding site and leucine-rich repeat (NBS-LRR) genes play vital roles in resisting pathogen infection in plants. However, the genome-wide characterization and functional roles of NBS-LRR genes remain largely unexplored in radish. Here, a total of 187 RsNBS-LRR genes were identified at the whole-genome level in radish, among which 80 RsNBS-LRR genes were unevenly distributed on nine radish chromosomes. Interestingly, 15 clusters containing 36 RsNBS-LRR genes occurred in eight chromosomes. RNA-Seq data showed that several RsNBS-LRR genes exhibited significant differential expression profiles in different radish tissues. Moreover, a range of cis-acting regulatory elements associated with ABA, MeJA, or SA were identified in the promoter region of some RsNBS-LRR genes. RT-qPCR analysis showed that the expression of a few RsNBS-LRR genes (e.g., RsNBS021 and RsNBS163) was significantly induced under Peronospora parasitica infection and/or ABA treatment, indicating that they might play critical roles in ABA-dependent defense resistance processes. These results could enhance our understanding of the evolutionary relationship of RsNBS-LRR genes and facilitate the genetic manipulation of disease resistance in radish breeding programs.

MicroRNAs are 20–24 nucleotide non-coding RNAs and play important roles in plant-environment interactions. In recent years, many microRNAs (miRNAs) have been found to regulate rice immunity against rice blast fungus. However, there are limited studies about miRNAs that directly target resistance (R) genes to regulate rice immunity. In this study, by deep sequencing, small RNA libraries were constructed from four-leaf stage seedlings of the resistant variety Ziyu44 and susceptible variety Jiangnanxiangnuo (JNXN) upon Magnaporthe oryzae infection, we found that much more miRNAs were significantly differentially expressed in Ziyu44 than in JNXN. Among these miRNAs, we focused on miR9664, a newly identified rice miRNA in our sequencing, which was upregulated lightly in Ziyu44 and drastically in JNXN at 24–48 h post-inoculation (hpi). The transgenic plants overexpressing miR9664 (miR9664-oe) displayed reduced defense responses to M. oryzae, while those knocking down miR9664 (miR9664-m) displayed enhanced defense responses to M. oryzae. Most of the detected miR9664 predicted target genes were reduced in the miR9664-oe lines while increased in the miR9664-m lines. The cleavage site of LOC_Os08g07774 was confirmed by RLM-RACE. Meanwhile, after being inoculated with M. oryzae, the genes were expressed differently between Ziyu44 and JNXN. The results suggest that miR9664-mediated R gene turnover contributes to Ziyu44 broad-spectrum resistance to rice blast fungus. Taken together, our research identified a new rice miRNA that directly targets R genes to regulate rice immunity against rice blast fungus, adding significant information to the study of rice–M. oryzae interaction.

Background: Pi-ta is a major blast resistant gene, introgressed from indica rice varieties. In this study, diversity of the Pi-ta gene of 47 Sri Lankan rice accessions was studied by bioinformatics, and the results were validated with molecular and disease reaction assays. Sequences of rice accessions at the locus Os12g0281300 were retrieved from Rice SNP-Seek Database, and the coding sequence of reference Pi-ta gene of cultivar Tetep (accession no. GQ918486.1) was obtained from GenBank. Comparisons were made at nucleotide, amino acid, and protein structure level, and the 3D models predicted using Phyre2 software were superimposed using TM-align software. Results: In silico analysis revealed that 10 accessions possessed resistant allele of the Pi-ta gene. The remaining accessions recorded high polymorphism in the leucine-rich domain resulting in 9 allele types, leading to single–amino acid substitutions at 27 different positions including a functional mutation of alanine to serine at the 918th amino acid position. None of the genotypes led to truncations in the amino acid sequence. The in silico analysis results were validated on 23 accessions comprising resistant and susceptible genotypes and another 25 cultivars from Northern Sri Lanka, by molecular assay using YL183/YL87 and YL155/YL87 resistant and susceptible allele-specific markers. Resistance of Pi-ta gene for the causal fungus, Magnaporthe oryzae, was further validated through pathogenicity assay. Conclusion: The Pi-ta gene, especially the LRD region, revealed significant variations within Sri Lankan rice cultivars leading to high levels of resistance against blast. This information would be highly useful in breeding programmes for resistance against rice blast. [ABSTRACT FROM AUTHOR]

MicroRNAs are 20–24 nucleotide non-coding RNAs and play important roles in plant-environment interactions. In recent years, many microRNAs (miRNAs) have been found to regulate rice immunity against rice blast fungus. However, there are limited studies about miRNAs that directly target resistance (R) genes to regulate rice immunity. In this study, by deep sequencing, small RNA libraries were constructed from four-leaf stage seedlings of the resistant variety Ziyu44 and susceptible variety Jiangnanxiangnuo (JNXN) upon Magnaporthe oryzae infection, we found that much more miRNAs were significantly differentially expressed in Ziyu44 than in JNXN. Among these miRNAs, we focused on miR9664, a newly identified rice miRNA in our sequencing, which was upregulated lightly in Ziyu44 and drastically in JNXN at 24–48 h post-inoculation (hpi). The transgenic plants overexpressing miR9664 (miR9664-oe) displayed reduced defense responses to M. oryzae , while those knocking down miR9664 (miR9664-m) displayed enhanced defense responses to M. oryzae. Most of the detected miR9664 predicted target genes were reduced in the miR9664-oe lines while increased in the miR9664-m lines. The cleavage site of LOC_Os08g07774 was confirmed by RLM-RACE. Meanwhile, after being inoculated with M. oryzae , the genes were expressed differently between Ziyu44 and JNXN. The results suggest that miR9664-mediated R gene turnover contributes to Ziyu44 broad-spectrum resistance to rice blast fungus. Taken together, our research identified a new rice miRNA that directly targets R genes to regulate rice immunity against rice blast fungus, adding significant information to the study of rice– M. oryzae interaction. [ABSTRACT FROM AUTHOR]

Cucumber mosaic virus (CMV) severely reduces crop productivity and is considered as a major global plant virus affecting important agricultural and ornamental crops. On infected crops, it causes severe disease symptoms such as mosaic, mosaic mottling, stunting and stem necrosis. Controlling disease propagation has become a serious challenge due to the advent of new strains of CMV, vector biotypes and an expanding host range. The use of resistant cultivars, on the other hand, is the greatest way to tackle this difficulty. In this regard, an attempt was undertaken to explore the previously available chilli-CMV transcriptome data for the presence of resistance (R) genes. Seven R genes were chosen and their physico-chemical characteristics were evaluated. Further, R genes were also extracted from CMV infected hosts using BLAST sequence similarity search tool. The diversity study of R gene proteins revealed that Capsicum annuum R gene proteins clustered closely with Solanum lycopersicum and Nicotiana tabacum R gene proteins and had the highest per cent of amino acid similarity with good query coverage. A venn graph was drawn based on similarity to the proteins database of Oryza sativa, Arabidopsis thaliana, Zea mays and Vitis vinifera to determine the distribution of R gene proteins across diverse crops. Four R gene proteins shared homology with proteins from all of the crops mentioned above. One among the three R gene proteins was found in all crops except Z. mays. The other two R gene proteins were identified in Z. mays, O. sativa and A. thaliana and Vitis vinifera species, respectively. These mined R genes can be used to produce CMV resistance varities. Furthermore, the R proteins can be utilized to study protein-protein interactions. [ABSTRACT FROM AUTHOR]

Resistance (R) genes usually compete in a coevolutionary arms race with reciprocal effectors to confer strain‐specific resistance to pathogens or herbivorous insects. Here, we investigate the specificity of SLI1, a recently identified R gene in Arabidopsis that encodes a small heat shock‐like protein involved in resistance to Myzus persicae aphids. In a panel with several aphid and whitefly species, SLI1 compromised reproductive rates of three species: the tobacco aphid M. persicae nicotianae, the cabbage aphid Brevicoryne brassicae and the cabbage whitefly Aleyrodes proletella. Electrical penetration graph recording of aphid behaviour, revealed shorter salivations and a 3‐to‐5‐fold increase in phloem feeding on sli1 loss‐of‐function plants. The mustard aphid Lipaphis erysimi and Bemisia tabaci whitefly were not affected by SLI1. Unlike the other two aphid species, L. erysimi exhibited repetitive salivations preceding successful phloem feeding, indicating a role of salivary effectors in overcoming SLI1‐mediated resistance. Microscopic characterization showed that SLI1 proteins localize in the sieve tubes of virtually all above‐ and below‐ground tissues and co‐localize with the aphid stylet tip after penetration of the sieve element plasma membrane. These observations reveal an unconventional R gene that escapes the paradigm of strain specificity and confers broad‐spectrum quantitative resistance to phloem‐feeding insects. We found that the Arabidopsis R gene SLI1 is not strain specific, but affects a wide range of phloem‐feeding insects, including two aphid and a whitefly species, via a phloem‐located mechanism that co‐localizes with the insect stylet tip. [ABSTRACT FROM AUTHOR]

The nucleotide-binding sites (NBS) domain is the highly conserved domain of nucleotide-binding sitesleucine rich repeats (NBS-LRR) class encoded by resistance genes (R genes), and it is used to identify disease resistancerelated genes. This study was based on the genome-wide identification of NBS-LRR encoding genes in Trifolium pratense to recover resistance gene analogs (RGAs) in Trifolium alexandrinum. In T. pratense, 251 protein sequences were identified to have the NBS domain. Of these, 16 NBS proteins were predicted to be localized to the mitochondria, 9 to the chloroplasts, 44 to the secretory pathways, and 182 to subcellular locations other than chloroplasts or mitochondria. The structure pattern of predicted NBS genes of the NBS-LRR group was displayed as single gene architecture having an untranslated region (UTRs) with four CD regions. The conserved sequences of the NBS-LRR group were used for primer designing to recover RGAs from T. alexandrinum. A maximum likelihood method based phylogram was constructed for exploring the phylogenetic relationship amongst NBS genes encoding protein sequences of T. pratense and R genes of Medicago truncatula and Medicago sativa encoding protein sequences having NBS-LRR domain that showed the highly close phylogenetic relationship among them, which supported the highly conserved nature of NBS-LRR class. Hence, we used the conserved NBS-LRR genetic regions to recover the RGAs from the T. alexandrinum genome. Therefore, the DNA of a cultivar of T. alexandrinum was subjected to polymerase chain reaction (PCR) analysis using the primer designed from these regions; and all primers, except RNL3-F/R, RNL5-F/R, and RNL7-F/R, gave the amplification. [ABSTRACT FROM AUTHOR]

Abstract Rice (Oryza sativa L.) is a staple food crop, feeding more than 50% of the world’s population. Diseases caused by bacterial, fungal, and viral pathogens constantly threaten the rice production and lead to enormous yield losses. Bacterial blight (BB) and bacterial leaf streak (BLS), caused respectively by gram-negative bacteria Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas oryzae pv. oryzicola (Xoc), are two important diseases affecting rice production worldwide. Due to the economic importance, extensive genetic and genomic studies have been conducted to elucidate the molecular mechanism of rice response to Xoo and Xoc in the last two decades. A series of resistance (R) genes and their cognate avirulence and virulence effector genes have been characterized. Here, we summarize the recent advances in studies on interactions between rice and the two pathogens through these R genes or their products and effectors. Breeding strategies to develop varieties with durable and broad-spectrum resistance to Xanthomonas oryzae based on the published studies are also discussed.