Nucleotide-binding Site Leucine-rich Repeat Research Articles

Genome- Wide Analysis of the Nucleotide Binding Site Leucine-Rich Repeat Genes of Four Orchids Revealed Extremely Low Numbers of Disease Resistance Genes.

Orchids are one of the most diverse flowering plant families, yet possibly maintain the smallest number of the nucleotide-binding site-leucine-rich repeat (NBS-LRR) type plant resistance (R) genes among the angiosperms. In this study, a genome-wide search in four orchid taxa identified 186 NBS-LRR genes. Furthermore, 214 NBS-LRR genes were identified from seven orchid transcriptomes. A phylogenetic analysis recovered 30 ancestral lineages (29 CNL and one RNL), far fewer than other angiosperm families. From the genetics aspect, the relatively low number of ancestral R genes is unlikely to explain the low number of R genes in orchids alone, as historical gene loss and scarce gene duplication has continuously occurred, which also contributes to the low number of R genes. Due to recent sharp expansions, Phalaenopsis equestris and Dendrobium catenatum having 52 and 115 genes, respectively, and exhibited an “early shrinking to recent expanding” evolutionary pattern, while Gastrodia elata and Apostasia shenzhenica both exhibit a “consistently shrinking” evolutionary pattern and have retained only five and 14 NBS-LRR genes, respectively. RNL genes remain in extremely low numbers with only one or two copies per genome. Notably, all of the orchid RNL genes belong to the ADR1 lineage. A separate lineage, NRG1, was entirely absent and was likely lost in the common ancestor of all monocots. All of the TNL genes were absent as well, coincident with the RNL NRG1 lineage, which supports the previously proposed notion that a potential functional association between the TNL and RNL NRG1 genes.

Genome-Wide Mining of Disease Resistance Gene Analogs Using Conserved Domains.

The production of legume crop species is severely affected by disease, imposing a significant yield loss annually worldwide. Plant resistance gene analogs (RGAs) play specific roles in plant resistance responses, and their identification and subsequent application in breeding programs help to reduce this yield loss. RGAs contain conserved domains and motifs, which can be used for their identification and classification. Nucleotide-binding site-leucine-rich repeat (NLR), receptor like kinase (RLK), and receptor like protein (RLP) genes are the main types of RGAs. Computational identification and characterization of RGAs has been performed successfully among different plant species. Here, we explain the computational workflow for genome-wide RGA identification in legumes.

Genome-wide association study identifies an NLR gene that confers partial resistance to Magnaporthe oryzae in rice.

SummaryBecause of the frequent breakdown of major resistance (R) genes, identification of new partial R genes against rice blast disease is an important goal of rice breeding. In this study, we used a core collection of the Rice Diversity Panel II (C‐RDP‐II), which contains 584 rice accessions and are genotyped with 700 000 single‐nucleotide polymorphism (SNP) markers. The C‐RDP‐II accessions were inoculated with three blast strains collected from different rice‐growing regions in China. Genome‐wide association study identified 27 loci associated with rice blast resistance (LABRs). Among them, 22 LABRs were not associated with any known blast R genes or QTLs. Interestingly, a nucleotide‐binding site leucine‐rich repeat (NLR) gene cluster exists in the LABR12 region on chromosome 4. One of the NLR genes is highly conserved in multiple partially resistant rice cultivars, and its expression is significantly up‐regulated at the early stages of rice blast infection. Knockout of this gene via CRISPR‐Cas9 in transgenic plants partially reduced blast resistance to four blast strains. The identification of this new non‐strain specific partial R gene, tentatively named rice blast Partial Resistance gene 1 (PiPR1), provides genetic material that will be useful for understanding the partial resistance mechanism and for breeding durably resistant cultivars against blast disease of rice.

Colonisation of Oncidium orchid roots by the endophyte Piriformospora indica restricts Erwinia chrysanthemi infection, stimulates accumulation of NBS-LRR resistance gene transcripts and represses their targeting micro-RNAs in leaves

BackgroundErwinia chrysanthemi (Ec) is a destructive pathogen which causes soft-rot diseases in diverse plant species including orchids. We investigated whether colonization of Oncidium roots by the endophytic fungus Piriformospora indica (Pi) restricts Ec-induced disease development in leaves, and whether this might be related to the regulation of nucleotide binding site-leucine rich repeat (NBS-LRR) Resistance (R) genes.ResultsRoot colonization of Oncidium stackings by Pi restricts progression of Ec-induced disease development in the leaves. Since Pi does not inhibit Ec growth on agar plates, we tested whether NBS-LRR R gene transcripts and the levels of their potential target miRNAs in Oncidium leaves might be regulated by Pi. Using bioinformatic tools, we first identified NBS-LRR R gene sequences from Oncidium, which are predicted to be targets of miRNAs. Among them, the expression of two R genes was repressed and the accumulation of several regulatory miRNA stimulated by Ec in the leaves of Oncidium plants. This correlated with the progression of disease development, jasmonic and salicylic acid accumulation, ethylene synthesis and H2O2 production after Ec infection of Oncidium leaves. Interestingly, root colonization by Pi restricted disease development in the leaves, and this was accompanied by higher expression levels of several defense-related R genes and lower expression level of their target miRNA.ConclusionBased on these data we propose that Pi controls the levels of NBS-LRR R mRNAs and their target miRNAs in leaves. This regulatory circuit correlates with the protection of Oncidium plants against Ec infection, and molecular and biochemical investigations will demonstrate in the future whether, and if so, to what extent these two observations are related to each other.

Identification and Molecular Mapping of a Gummy Stem Blight Resistance Gene in Wild Watermelon (Citrullus amarus) Germplasm PI 189225.

Gummy stem blight (GSB), caused by Stagonosporopsis cucurbitacearum (syn. Didymella bryoniae), is a destructive foliar disease of watermelon in areas with hot and humid climates. The wild watermelon germplasm PI 189225 is a known source of resistance to GSB. The identification and use of molecular markers linked to resistance genes in the wild-type germplasm will speed up the introgression of GSB resistance into new watermelon varieties. An F2 segregating population was obtained from a cross between the resistant wild watermelon genotype PI 189225 and the susceptible genotype K3. The F2-derived F3 families were inoculated with a single isolate of S. cucurbitacearum (JS002) from Jiangsu Academy of Agricultural Sciences. The results of the genetic analysis demonstrated that GSB resistance in PI 189225 was controlled by a major quantitative trait locus (QTL), temporarily designated Qgsb8.1. Based on the results of bulk sergeant analysis and sequencing, one associated region spanning 5.7 Mb (10,358,659 to 16,101,517) on chromosome 8 was identified as responsible for the resistance to GSB using the Δ(single-nucleotide polymorphism [SNP]-index) method. The result of a QTL linkage analysis with Kompetitive allele-specific PCR (KASP) SNP markers further mapped the GSB resistance locus between the SNP markers KASP_JS9383 and KASP_JS9168 in a region of 571.27 kb on chromosome 8. According to the watermelon gene annotation database, the region contains approximately 19 annotated genes and, of these 19 genes, 2 are disease resistance gene analogs: Cla001017 (coiled-coil nucleotide-binding site leucine-rich repeat resistance protein) and Cla001019 (pathogenesis related). Reverse-transcription quantitative PCR demonstrated that the expression of the two genes changed following S. cucurbitacearum infection, suggesting that they play important roles in GSB resistance in watermelon. This result will facilitate fine mapping and cloning of the Qgsb8.1 locus, and the linked markers will further provide a useful tool for marker-assisted selection of this locus in watermelon breeding programs.

Characterization of disease resistance genes in the Brassica napus pangenome reveals significant structural variation.

SummaryMethods based on single nucleotide polymorphism (SNP), copy number variation (CNV) and presence/absence variation (PAV) discovery provide a valuable resource to study gene structure and evolution. However, as a result of these structural variations, a single reference genome is unable to cover the entire gene content of a species. Therefore, pangenomics analysis is needed to ensure that the genomic diversity within a species is fully represented. Brassica napus is one of the most important oilseed crops in the world and exhibits variability in its resistance genes across different cultivars. Here, we characterized resistance gene distribution across 50 B. napus lines. We identified a total of 1749 resistance gene analogs (RGAs), of which 996 are core and 753 are variable, 368 of which are not present in the reference genome (cv. Darmor‐bzh). In addition, a total of 15 318 SNPs were predicted within 1030 of the RGAs. The results showed that core R‐genes harbour more SNPs than variable genes. More nucleotide binding site‐leucine‐rich repeat (NBS‐LRR) genes were located in clusters than as singletons, with variable genes more likely to be found in clusters. We identified 106 RGA candidates linked to blackleg resistance quantitative trait locus (QTL). This study provides a better understanding of resistance genes to target for genomics‐based improvement and improved disease resistance.

Transcriptome Profiles of Strawberry (Fragaria vesca) Fruit Interacting With Botrytis cinerea at Different Ripening Stages.

Gray mold caused by Botrytis cinerea is a major cause of economic losses in strawberry fruit production, limiting fruit shelf life and commercialization. When the fungus infects Fragaria × ananassa strawberry at flowering or unripe fruit stages, symptoms develop after an extended latent phase on ripe fruits before or after harvesting. To elucidate the growth kinetics of B. cinerea on flower/fruit and the molecular responses associated with low susceptibility of unripe fruit stages, woodland strawberry Fragaria vesca flowers and fruits, at unripe white and ripe red stages, were inoculated with B. cinerea. Quantification of fungal genomic DNA within 72 h postinoculation (hpi) showed limited fungal growth on open flower and white fruit, while on red fruit, the growth was exponential starting from 24 hpi and sporulation was observed within 48 hpi. RNA sequencing applied to white and red fruit at 24 hpi showed that a total of 2,141 genes (12.5% of the total expressed genes) were differentially expressed due to B. cinerea infection. A broad transcriptional reprogramming was observed in both unripe and ripe fruits, involving in particular receptor and signaling, secondary metabolites, and defense response pathways. Membrane-localized receptor-like kinases and nucleotide-binding site leucine-rich repeat genes were predominant in the surveillance system of the fruits, most of them being downregulated in white fruits and upregulated in red fruits. In general, unripe fruits exhibited a stronger defense response than red fruits. Genes encoding for pathogenesis-related proteins and flavonoid polyphenols as well as genes involved in cell-wall strengthening were upregulated, while cell-softening genes appeared to be switched off. As a result, B. cinerea remained quiescent in white fruits, while it was able to colonize ripe red fruits.

Large-scale identification and functional analysis of NLR genes in blast resistance in the Tetep rice genome sequence

Tetep is a rice cultivar known for broad-spectrum resistance to blast, a devastating fungal disease. The molecular basis for its broad-spectrum resistance is still poorly understood. Is it because Tetep has many more NLR genes than other cultivars? Or does Tetep possess multiple major NLR genes that can individually confer broad-spectrum resistance to blast? Moreover, are there many interacting NLR pairs in the Tetep genome? We sequenced its genome, obtained a high-quality assembly, and annotated 455 nucleotide-binding site leucine-rich repeat (NLR) genes. We cloned and tested 219 NLR genes as transgenes in 2 susceptible cultivars using 5 to 12 diversified pathogen strains; in many cases, fewer than 12 strains were successfully cultured for testing. Ninety cloned NLRs showed resistance to 1 or more pathogen strains and each strain was recognized by multiple NLRs. However, few NLRs showed resistance to >6 strains, so multiple NLRs are apparently required for Tetep's broad-spectrum resistance to blast. This was further supported by the pedigree analyses, which suggested a correlation between resistance and the number of Tetep-derived NLRs. In developing a method to identify NLR pairs each of which functions as a unit, we found that >20% of the NLRs in the Tetep and 3 other rice genomes are paired. Finally, we designed an extensive set of molecular markers for rapidly introducing clustered and paired NLRs in the Tetep genome for breeding new resistant cultivars. This study increased our understanding of the genetic basis of broad-spectrum blast resistance in rice.

Development and application of marker-assisted selection (MAS) tools for breeding of western white pine (Pinus monticola Douglas ex D. Don) resistance to blister rust (Cronartium ribicola J.C. Fisch.) in British Columbia

Cronartium ribicola causes white pine blister rust (WPBR) on five-needle pines worldwide. After accidental introduction into North America about 100 years ago, this invasive fungus has caused heavy mortality in western white pine (Pinus monticola) and other related five-needle pines across North America. Breeding by selection of rare resistant trees is time-consuming; therefore, genomics-based tools are highly desirable to speed up the breeding process. Our laboratory previously constructed genetic maps for the P. monticola Cr2 locus that confers major gene resistance (MGR) to WPBR and identified several nucleotide-binding site leucine-rich repeat (NBS-LRR) genes as Cr2 positional candidates. In the present study, single nucleotide polymorphism (SNP) loci within Cr2 candidate genes (contig58688 and contig41490) were selected to develop qPCR-based genotyping assays using two SNP genotyping technologies (TaqMan and Kompetitive Allele Specific PCR-KASP). To evaluate the utility and efficiency of these marker-assisted selection (MAS) tools in British Columbia’s (BC’s) breeding program, we analyzed 46 open-pollinated bulk seedlots that were randomly selected across BC’s landscape. SNP genotyping results were highly consistent, with matching rates of over 99% between TaqMan and KASP assays for each specific SNP locus. The Cr2-linked alleles were absent in all genotyped samples for the snp58688-82Y locus and about 86% of all genotyped samples for the snp41490-1778M locus. These results demonstrate that both the TaqMan and KASP SNP genotyping assays are powerful MAS tools with accuracy up to 100% for prediction of Cr2-resistance in wild parental trees, as well as for resistance selection among their progeny following cross-pollination with MGR trees across BC’s landscape.

Genome wide identification of nucleotide-binding site leucine-rich repeat (NBS-LRR) gene encoding regions in Solanum lycopersicum resistant to environmental pathogens by computational methods

Genome wide identification of nucleotide-binding site leucine-rich repeat (NBS-LRR) gene encoding regions in Solanum lycopersicum resistant to environmental pathogens by computational methods

A maize polygalacturonase functions as a suppressor of programmed cell death in plants

BackgroundThe hypersensitive defense response (HR) in plants is a fast, localized necrotic response around the point of pathogen ingress. HR is usually triggered by a pathogen recognition event mediated by a nucleotide-binding site, leucine-rich repeat (NLR) protein. The autoactive maize NLR gene Rp1-D21 confers a spontaneous HR response in the absence of pathogen recognition. Previous work identified a set of loci associated with variation in the strength of Rp1-D21-induced HR. A polygalacturonase gene homolog, here termed ZmPGH1, was identified as a possible causal gene at one of these loci on chromosome 7.ResultsExpression of ZmPGH1 inhibited the HR-inducing activity of both Rp1-D21 and that of another autoactive NLR, RPM1(D505V), in a Nicotiana benthamiana transient expression assay system. Overexpression of ZmPGH1 in a transposon insertion line of maize was associated with suppression of chemically-induced programmed cell death and with suppression of HR induced by Rp1-D21 in maize plants grown in the field.ConclusionsZmPGH1 functions as a suppressor of programmed cell death induced by at least two autoactive NLR proteins and by two chemical inducers. These findings deepen our understanding of the control of the HR in plants.

Identifying candidate genes for Phytophthora capsici resistance in pepper (Capsicum annuum) via genotyping-by-sequencing-based QTL mapping and genome-wide association study

Phytophthora capsici (Leon.) is a globally prevalent, devastating oomycete pathogen that causes root rot in pepper (Capsicum annuum). Several studies have identified quantitative trait loci (QTL) underlying resistance to P. capsici root rot (PcRR). However, breeding for pepper cultivars resistant to PcRR remains challenging due to the complexity of PcRR resistance. Here, we combined traditional QTL mapping with GWAS to broaden our understanding of PcRR resistance in pepper. Three major-effect loci (5.1, 5.2, and 5.3) conferring broad-spectrum resistance to three isolates of P. capsici were mapped to pepper chromosome P5. In addition, QTLs with epistatic interactions and minor effects specific to isolate and environment were detected on other chromosomes. GWAS detected 117 significant SNPs across the genome associated with PcRR resistance, including SNPs on chromosomes P5, P7, and P11 that colocalized with the QTLs identified here and in previous studies. Clusters of candidate nucleotide-binding site-leucine-rich repeat (NBS-LRR) and receptor-like kinase (RLK) genes were predicted within the QTL and GWAS regions; such genes often function in disease resistance. These candidate genes lay the foundation for the molecular dissection of PcRR resistance. SNP markers associated with QTLs for PcRR resistance will be useful for marker-assisted breeding and genomic selection in pepper breeding.

Fine mapping and identification of the rice blast-resistance locus Pi-kf2(t) as a new member of the Pi2/Pi9 multigene family

The identification and utilization of broad-spectrum resistance genes is the most effective and economical strategy of controlling rice blast disease. Kangfeng B (KFB), an elite Chinese rice cultivar, has been shown to exhibit broad-spectrum resistance to 53 isolates of Magnaporthe oryzae, the rice blast causative agent, from different regions of China. In this study, we identified a dominant blast-resistance gene at the Pi2/Pi9 locus from cultivar KFB, through genetic analysis and physical mapping. Allele-specific marker-based assessment revealed that Pi2, Pi9, and Piz-t are not the blast-resistance genes in KFB. By combining bulked segregation analysis (BSA) and recessive class analysis (RCA), the blast-resistance gene was fine-mapped to an approximately 249-kb interval between markers InDel-22 and Rm7213 on chromosome 6. Three bacterial artificial chromosome (BAC) clones spanning the region were identified. This region contains 19 predicted genes, including 7 nucleotide binding site–leucine-rich repeat (NBS-LRR) genes at the Pi2/Pi9 locus in japonica cv. Nipponbare genome. Further sequence comparison of the four functional NBS-LRR genes revealed that NBS-LRR2 and NBS-LRR4, as evidenced by their allelic/orthologous to Pi9 or Pi2, had significant differences of 9 to 43 and 14 to 48 amino acids in KFB, respectively, unlike the other known Pi2/Pi9 alleles, suggesting that KFB carries a hitherto undocumented member of the Pi2/Pi9 multigene family. It was tentatively designated as Pi-kf2(t). Our results provide essential information for the isolation of the Pi-kf2(t) gene and will facilitate both map-based cloning and marker-assisted selection of this gene for rice blast-resistance breeding.

Characterization of blast resistance related protein domains in wheat for molecular marker development

Wheat blast is a devastating disease which is baffling scientists from its inception. This study characterized the blast resistance related protein domains with a view to develop molecular markers to identify resistant wheat genotypes against Blast fungus Magnaporthe oryzae. A genome browse analysis detected that the candidate resistance gene against blast could be located in several different chromosomes. An in silico analysis was collected with fifty nucleotide-binding site leucine-rich repeat (NBS-LRR), leucine-rich repeat (LRR), pathogenesis and resistance protein-encoding accessions on the basis of the previous resistance report. The phylogenetic tree of those putative resistance accessions, bearing resistance related protein-encoding domains, showed that an NBS-LRR accession JP957107.1 has 67% similarity with the disease resistance protein domain encoding accession of Brazilian resistant cultivar Thatcher. By contrast, the rice blast resistance Pita gene has 72% similarity with 18 pathogenesis protein domain encoding accessions. Among putative protein domains, disease resistance protein of Thatcher has 78% similarity with two NBS-LRR protein domains AAZ99757.1 and AAZ99757.1. Eighteen microsatellite markers were designed from eighteen putative NBS-LRR protein encoding accessions along with Piz3 marker. The 19 markers were unable to separate resistant and susceptible genotypes. Diffused versus conspicuous bands indicated either presence of insertion/deletion (InDel) or single nucleotide polymorphism (SNP) among wheat genotypes. Detection of InDel or SNP markers is a subject of further investigation. Additional markers are needed to be designed using new NBS-LRR, pathogenesis, coiled-coil (CC), translocated intimin receptor (TIR) resistance protein encoding accessions to find out markers specific for blast resistance.
 J. Bangladesh Agril. Univ. 17(2): 161–171, June 2019

Development of InDel marker for rice blast resistance gene Pi9

Pi9 is one of the major blast resistance genes which encodes a nucleotide-binding site-leucine-rich repeat (NBS-LRR) domain-containing protein. This gene was observed to show resistance against many pathotypes of the blast pathogen in Malaysia. Resistance allele Pi9 from rice variety 75-1-127 had previously been cloned using map-based cloning strategy. The gene sequence was used to design specific primers to amplify susceptible Pi9 allele from MR219 rice variety prior to cloning. The resistance and susceptible allele of Pi9 were 8.587kb and 8.785kb in length respectively. Allele mining was carried out by comparing between the susceptible and resistance allele of Pi9. One potential InDels polymorphism at position 590bp and 920bp was identified. Primer named as Pi9_InDel was designed targeting this region in such a way that the resistance and susceptible genotypes yielded 327 bp and 438 bp amplicon respectively.

Current status on mapping of genes for resistance to leaf- and neck-blast disease in rice.

Blast disease caused by fungal pathogen Pyricularia oryzae is a major threat to rice productivity worldwide. The rice-blast pathogen can infect both leaves and panicle neck nodes. Nearly, 118 genes for resistance to leaf blast have been identified and 25 of these have been molecularly characterized. A great majority of these genes encode nucleotide-binding site-leucine-rich repeat (NBS-LRR) proteins and are organized into clusters as allelic or tightly linked genes. Compared to ever expanding list of leaf-blast-resistance genes, a few major genes mediating protection to neck blast have been identified. A great majority of the genetic studies conducted with the genotypes differing in the degree of susceptibility/resistance to neck blast have suggested quantitative inheritance for the trait. Several reports on co-localization of gene/QTLs for leaf- and neck-blast resistance in rice genome have suggested the existence of common genes for resistance to both phases of the disease albeit inconsistencies in the genomic positions leaf- and neck-blast-resistance genes in some instances have presented the contrasting scenario. There is a strong evidence to suggest that developmentally regulated expression of many blast-resistance genes is a key determinant deciding their effectiveness against leaf or neck blast. Testing of currently characterized leaf-blast-resistance genes for their reaction to neck blast is required to expand the existing repertoire resistance genes against neck blast. Current developments in the understanding of molecular basis of host-pathogen interactions in rice-blast pathosystem offer novel possibilities for achieving durable resistance to blast through exploitation of natural or genetically engineered loss-of-function alleles of host susceptibility genes.

Identification and expression profiling analysis of NBS-LRR genes involved in Fusarium oxysporum f.sp. conglutinans resistance in cabbage.

As one of the most important resistance (R) gene families in plants, the NBS-LRR genes, encoding proteins with nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domains, play significant roles in resisting pathogens. The published genomic data for cabbage (Brassica oleracea L.) provide valuable data to identify and characterize the genomic organization of cabbage NBS-LRR genes. Ultimately, we identified 105 TIR (N-terminal Toll/interleukin-1 receptor)-NBS-LRR (TNL) genes and 33 CC (coiled-coil)-NBS-LRR (CNL) genes. Further research indicated that 50.7% of the 138 NBS-LRR genes exist in 27 clusters and there are large differences among the gene structures and protein characteristics. Conserved motif and phylogenetic analysis showed that the structures of TNLs and CNLs were similar, with some differences. These NBS-LRRs are evolved under negative selection and mostly arose from whole-genome duplication events during evolution. Tissue-expression profiling of NBS-LRR genes revealed that 37.1% of the TNL genes are highly or specifically expressed in roots, especially the genes on chromosome 7 (76.5%). Digital gene expression and reverse transcription PCR analyses revealed the expression patterns of the NBS-LRR genes upon challenge by Fusarium oxysporum f.sp. conglutinans: nine genes were upregulated, and five were downregulated. The major resistance gene Foc1 probably works together with the other four genes in the same cluster to resist F. oxysporum infection.

Importance of OsRac1 and RAI1 in signalling of nucleotide-binding site leucine-rich repeat protein-mediated resistance to rice blast disease.

Plants depend on Resistance (R) genes, most of which encode nucleotide-binding site leucine-rich repeat (NLR) proteins, for pathogen race-specific disease resistance. However, only a few immediate downstream targets of R proteins have been characterized, and the signalling pathways for R-protein-induced immunity are largely unknown. In rice (Oryza sativa), NLR proteins serve as important immune receptors in the response to rice blast disease caused by the fungus Magnaporthe oryzae. We used site-directed mutagenesis to create an autoactive form of the NLR protein PID3 that confers blast resistance and used transgenic rice to test the resulting immunity and gene expression changes. We identified OsRac1, a known GTPase, as a signalling molecule in PID3-mediated blast resistance, implicating OsRac1 as a possible common factor downstream of rice NLR proteins. We also identified RAI1, a transcriptional activator, as a PID3 interactor required for PID3-mediated blast resistance and showed that RAI1 expression is induced by PID3 via a process mediated by OsRac1. This study describes a new signalling pathway for NLR protein-mediated blast resistance and shows that OsRac1 and RAI1 act together to play a critical role in this process.

RRM Transcription Factors Interact with NLRs and Regulate Broad-Spectrum Blast Resistance in Rice.

Nucleotide-binding site leucine-rich repeat (NLR) receptors perceive pathogen effectors and trigger plant immunity. However, the mechanisms underlying NLR-triggered defense responses remain obscure. The recently discovered Pigm locus in rice encodes a cluster of NLRs, including PigmR, which confers broad-spectrum resistance to blast fungus. Here, we identify PIBP1 (PigmR-INTERACTING and BLAST RESISTANCE PROTEIN 1), an RRM (RNA-recognition motif) protein that specifically interacts with PigmR and other similar NLRs to trigger blast resistance. PigmR-promoted nuclear accumulation of PIBP1 ensures full blast resistance. We find that PIBP1 and a homolog, Os06 g02240, bind DNA and function as unconventional transcription factors at the promoters of the defense genes OsWAK14 and OsPAL1, activating their expression. Knockout of PIBP1 and Os06 g02240 greatly attenuated blast resistance. Collectively, our study discovers previously unappreciated RRM transcription factors that directly interact with NLRs to activate plant defense, establishing a direct link between transcriptional activation of immune responses with NLR-mediated pathogen perception.

Fine mapping of a panicle blast resistance gene Pb-bd1 in Japonica landrace Bodao and its application in rice breeding

BackgroundRice blast caused by Magnaporthe oryzae is the most devastating disease in rice production. Compared with seedling blast, panicle blast is considered to be more destructive, which can occur without being preceded by severe seedling blast. However, panicle blast resistance research is rarely reported.ResultsBodao, a japonica landrace from Taihu Lake region, showed a high level of panicle blast resistance. In this study, a mapping population of 212 recombination inbreeding lines (RILs) was developed from a cross of Bodao and the susceptible cultivar Suyunuo, and the RILs were evaluated for panicle blast resistance in three trials. Two quantitative trait loci (QTLs) qPb11–1 and qPb6–1 for panicle-blast resistance were identified, including a major QTL qPb11–1 (Pb-bd1) on chromosome 11 of Bodao explaining from 55.31% to 71.68% of the phenotype variance, and a minor QTL qPb6–1 on chromosome 6 of Suyunuo explaining from 3.54% to 6.98% of the phenotype variance. With the various segregation populations, Pb-bd1 was fine mapped in a 40.6 Kb region flanked by markers BS83 and BS98, and six candidate genes were identified within this region, including one gene encoding NAC domain-containing protein, one gene encoding unknown expression proteins, two genes encoding nucleotide binding site-leucine rich repeat (NBS-LRR) type disease resistance proteins, and two genes encoding von Willebrand factor type A (VWA) domain containing proteins. For application in rice breeding, three introgression lines of Pb-bd1with significantly enhanced panicle blast resistance were developed by using molecular assisted method (MAS) from the commercial variety Nanjing46 (NJ46).ConclusionTwo QTLs, qPb11–1(Pb-bd1) and qPb6–1 conferring panicle blast resistance, were identified from japonica landrace Bodao and Suyunuo.qPb11–1(Pb-bd1) was fine mapped in a 40.6 Kb region flanked by marker BS83 and BS98. Three introgression lines of Pb-bd1with significantly enhanced panicle blast resistance were developed by MAS method from the commercial variety NJ46. It indicated that Pb-bd1 would be useful gene source in panicle blast resistance breeding.