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The Solanaceae family occupies a significant position, and the study of resistance genes within this family is extremely valuable. Therefore, our goal is to examine disease resistance genes based on the high-quality representative genomes of Solanaceae crops, and to develop corresponding Simple Sequence Repeat (SSR) molecular markers. Among nine representative Solanaceae species, we identified 819 NBS-LRR genes, which were further divided into 583 CC-NBS-LRR (CNL), 54 RPW8-NBS-LRR (RNL), and 182 TIR-NBS-LRR (TNL) genes. Whole genome duplication (WGD) has played a very important role in the expansion of NBS-LRR genes in Solanaceae crops. Gene structure analysis showed the striking similarity in the conserved motifs of NBS-LRR genes, which suggests a common ancestral origin, followed by evolutionary differentiation and amplification. Gene clustering and events like rearrangement within the NBS-LRR family contribute to their scattered chromosomal distribution. Our findings reveal that the majority of NBS-LRR family genes across all examined species predominantly localize to chromosomal termini. The analysis indicates the significant impact of the most recent whole genome triplication (WGT) on the NBS-LRR family genes. Moreover, we constructed Protein–Protein Interaction (PPI) networks for all 819 NBS-LRR genes, identifying 3820 potential PPI pairs. Notably, 97 genes displayed clear interactive relationships, highlighting their potential role in disease resistance processes. A total of 22,226 SSRs were detected from all genes of nine Solanaceae species. Among these SSRs, we screened 43 NBS-LRR-associated SSRs. Our study lays the foundation for further exploration into SSR development and genetic mapping related to disease resistance in Solanaceae species. [ABSTRACT FROM AUTHOR]

Abstract Background Nitric oxide (NO) is pivotal in regulating the activity of NBS-LRR specific R genes, crucial components of the plant’s immune system. It is noteworthy that previous research has not included a genome-wide analysis of NO-responsive NBS-LRR genes in plants. Results The current study examined 29 NO-induced NBS-LRR genes from Arabidopsis thaliana, along with two monocots (rice and maize) and two dicots (soybean and tomato) using genome-wide analysis tools. These NBS-LRR genes were subjected to comprehensive characterization, including analysis of their physio-chemical properties, phylogenetic relationships, domain and motif identification, exon/intron structures, cis-elements, protein-protein interactions, prediction of S-Nitrosylation sites, and comparison of transcriptomic and qRT-PCR data. Results showed the diverse distribution of NBS-LRR genes across chromosomes, and variations in amino acid number, exons/introns, molecular weight, and theoretical isoelectric point, and they were found in various cellular locations like the plasma membrane, cytoplasm, and nucleus. These genes predominantly harbor the NB-ARC superfamily, LRR, LRR_8, and TIR domains, as also confirmed by motif analysis. Additionally, they feature species-specific PLN00113 superfamily and RX-CC_like domain in dicots and monocots, respectively, both responsive to defense against pathogen attacks. The NO-induced NBS-LRR genes of Arabidopsis reveal the presence of cis-elements responsive to phytohormones, light, stress, and growth, suggesting a wide range of responses mediated by NO. Protein-protein interactions, coupled with the prediction of S-Nitrosylation sites, offer valuable insights into the regulatory role of NO at the protein level within each respective species. Conclusion These above findings aimed to provide a thorough understanding of the impact of NO on NBS-LRR genes and their relationships with key plant species.

Abstract Background The presence of potato cyst nematodes (PCN) causes a significant risk to potato crops globally, leading to reduced yields and economic losses. While the plant Solanum sisymbriifolium is known for its resistance to PCN and can be used as a trap crop, the molecular mechanisms behind this resistance remain poorly understood. In this study, genes differentially expressed were identified in control and infected plants during the early stages of the S. sisymbriifolium - G. pallida interaction. Results Gene expression profiles were characterized for two S. sisymbriifolium cultivars, Melody and Sis6001, uninfected and infected by G. pallida. The comparative transcriptome analysis revealed a total of 4,087 and 2,043 differentially expressed genes (DEGs) in response to nematode infection in the cultivars Melody and Sis6001, respectively. Gene ontology (GO) enrichment analysis provided insights into the response of the plant to nematode infection, indicating an activation of the plant metabolism, oxidative stress leading to defence mechanism activation, and modification of the plant cell wall. Genes associated with the jasmonic and salicylic acid pathways were also found to be differentially expressed, suggesting their involvement in the plant’s defence response. In addition, the analysis of NBS-LRR domain-containing transcripts that play an important role in hypersensitive response and programmed cell death led to the identification of ten transcripts that had no annotations from the databases, with emphasis on TRINITY_DN52667_C1_G1, found to be upregulated in both cultivars. Conclusions These findings represent an important step towards understanding the molecular basis underlying plant resistance to nematodes and facilitating the development of more effective control strategies against PCN.

Bracts are leaf‐like structures in flowering plants. They serve multiple functions such as attracting pollinators, aiding tolerance of abiotic stressors, and conducting photosynthesis. While previous studies extensively examine bract function, the molecular mechanisms underlying bract growth remain unknown. Here, the map‐based isolation and characterization of a crucial factor responsible for cotton bract development, identified from a mutant known as frego bract (fg), discovered by Frego in 1945 are presented. This gene, named Ghfg, encodes a CC‐NB‐ARC‐LRR (CNL) family protein. Through analysis of bract form in plants with virus‐induced gene silencing (VIGS) and transgenic plants, this gene is confirmed to be the causal gene under the fg locus. Furthermore, high‐resolution single‐cell transcriptomic landscape of cotton bracts is generated, which reveals differences related to auxin in proliferating cells from TM‐1 and T582; differences in auxin distribution and ROS accumulation are experimentally verified. These findings suggest that GhFG is in a self‐activated state in the fg mutant, and its activity leads to ROS accumulation that impacts auxin distribution and transport. Finally, an island cotton variety with the frego bract trait is developed, demonstrating a novel solution for reducing the high impurity rate caused by bract remnants. [ABSTRACT FROM AUTHOR]

Background: The presence of potato cyst nematodes (PCN) causes a significant risk to potato crops globally, leading to reduced yields and economic losses. While the plant Solanum sisymbriifolium is known for its resistance to PCN and can be used as a trap crop, the molecular mechanisms behind this resistance remain poorly understood. In this study, genes differentially expressed were identified in control and infected plants during the early stages of the S. sisymbriifolium - G. pallida interaction. Results: Gene expression profiles were characterized for two S. sisymbriifolium cultivars, Melody and Sis6001, uninfected and infected by G. pallida. The comparative transcriptome analysis revealed a total of 4,087 and 2,043 differentially expressed genes (DEGs) in response to nematode infection in the cultivars Melody and Sis6001, respectively. Gene ontology (GO) enrichment analysis provided insights into the response of the plant to nematode infection, indicating an activation of the plant metabolism, oxidative stress leading to defence mechanism activation, and modification of the plant cell wall. Genes associated with the jasmonic and salicylic acid pathways were also found to be differentially expressed, suggesting their involvement in the plant's defence response. In addition, the analysis of NBS-LRR domain-containing transcripts that play an important role in hypersensitive response and programmed cell death led to the identification of ten transcripts that had no annotations from the databases, with emphasis on TRINITY_DN52667_C1_G1, found to be upregulated in both cultivars. Conclusions: These findings represent an important step towards understanding the molecular basis underlying plant resistance to nematodes and facilitating the development of more effective control strategies against PCN. [ABSTRACT FROM AUTHOR]

Background: Nitric oxide (NO) is pivotal in regulating the activity of NBS-LRR specific R genes, crucial components of the plant’s immune system. It is noteworthy that previous research has not included a genome-wide analysis of NO-responsive NBS-LRR genes in plants. Results: The current study examined 29 NO-induced NBS-LRR genes from Arabidopsis thaliana, along with two monocots (rice and maize) and two dicots (soybean and tomato) using genome-wide analysis tools. These NBS-LRR genes were subjected to comprehensive characterization, including analysis of their physio-chemical properties, phylogenetic relationships, domain and motif identification, exon/intron structures, cis-elements, protein-protein interactions, prediction of S-Nitrosylation sites, and comparison of transcriptomic and qRT-PCR data. Results showed the diverse distribution of NBS-LRR genes across chromosomes, and variations in amino acid number, exons/introns, molecular weight, and theoretical isoelectric point, and they were found in various cellular locations like the plasma membrane, cytoplasm, and nucleus. These genes predominantly harbor the NB-ARC superfamily, LRR, LRR_8, and TIR domains, as also confirmed by motif analysis. Additionally, they feature species-specific PLN00113 superfamily and RX-CC_like domain in dicots and monocots, respectively, both responsive to defense against pathogen attacks. The NO-induced NBS-LRR genes of Arabidopsis reveal the presence of cis-elements responsive to phytohormones, light, stress, and growth, suggesting a wide range of responses mediated by NO. Protein-protein interactions, coupled with the prediction of S-Nitrosylation sites, offer valuable insights into the regulatory role of NO at the protein level within each respective species. Conclusion: These above findings aimed to provide a thorough understanding of the impact of NO on NBS-LRR genes and their relationships with key plant species. [ABSTRACT FROM AUTHOR]

Kiwifruit bacterial canker, caused by Pseudomonas syringae pv. actinidiae (PSA), poses a grave threat to the global kiwifruit industry. In this study, we examined the role of microRNAs (miRNAs) in kiwifruit's response to PSA. Kiwifruit seedlings subjected to PSA treatment showed significant changes in both miRNA and gene expression compared to the control group. We identified 364 differentially expressed miRNAs (DEMs) and 7170 differentially expressed genes (DEGs). Further analysis revealed 180 miRNAs negatively regulating 641 mRNAs. Notably, two miRNAs from the miRNA482 family, miRNA-215-3p and miRNA-29-3p, were found to increase kiwifruit's sensitivity to PSA when overexpressed. These miRNAs were linked to the regulation of NBS-LRR target genes, shedding light on their role in kiwifruit's defence against PSA. This study offers insights into the miRNA482-NBS-LRR network as a crucial component in enhancing kiwifruit bioresistance to PSA infestation and provides promising candidate genes for further research. [ABSTRACT FROM AUTHOR]

Nucleotide-binding domain and leucine-rich repeat (NLR) immune receptor genes form a major line of defense in plants, acting in both pathogen recognition and resistance machinery activation. NLRs are reported to form large gene clusters in limber pine (Pinus flexilis), but it is unknown how widespread this genomic architecture may be among the extant species of conifers (Pinophyta). We used comparative genomic analyses to assess patterns in the abundance, diversity, and genomic distribution of NLR genes. Chromosome-level whole genome assemblies and high-density linkage maps in the Pinaceae, Cupressaceae, Taxaceae, and other gymnosperms were scanned for NLR genes using existing and customized pipelines. The discovered genes were mapped across chromosomes and linkage groups and analyzed phylogenetically for evolutionary history. Conifer genomes are characterized by dense clusters of NLR genes, highly localized on one chromosome. These clusters are rich in TNL-encoding genes, which seem to have formed through multiple tandem duplication events. In contrast to angiosperms and nonconiferous gymnosperms, genomic clustering of NLR genes is ubiquitous in conifers. NLR-dense genomic regions are likely to influence a large part of the plant's resistance, informing our understanding of adaptation to biotic stress and the development of genetic resources through breeding. [ABSTRACT FROM AUTHOR]

Fusarium wilt in Cymbidium ensifolium, caused by Fusarium oxysporum, is highly contagious and poses a severe hazard. It significantly reduces the ornamental value of C. ensifolium and causes substantial economic losses in agricultural production. Nucleotide-binding site–leucine-rich repeat (NBS-LRR) genes are key regulatory factors in plant disease resistance responses, playing vital roles in defending against pathogen invasions. In our study, we conducted a comprehensive analysis of the NBS-LRR gene family in the genome of Cymbidium ensifolium. Phylogenetic analysis identified a total of 31 NBS-LRR genes encoding NB-ARC proteins, which were categorized into five classes (CNL, CN, NL, N, RNL) based on their protein structural domains. These genes were found to be unevenly distributed across eight chromosomes. Physicochemical analysis revealed significant variances in molecular weight and sequence length among the family members. Subcellular localization results indicated that most genes primarily reside in the cytoplasm and cell membrane, suggesting that the primary sites of disease resistance responses may be the cell membrane and cyto-plasm. Furthermore, noticeable disparities were observed in gene structures and conserved motifs among different categories of family genes. Promoter analysis indicated that cis-regulatory elements are mainly associated with plant stress, jasmonic acid, gibberellin, and other development-related factors, suggesting that CeNBS-LRR genes mainly resist external stress through hormones such as abscisic acid and jasmonic acid. We characterized twenty-seven CeNBS-LRR gene expression patterns of healthy C. ensifolium at different periods after Fusarium wilt infection, and found that those genes exhibit a temporospatial expression pattern, and that their expression is also responsive to Fusarium wilt infection. By analyzing the expression pattern via transcriptome and qRT-PCR, we speculated that JL006442 and JL014305 may play key roles in resisting Fusarium wilt. This study lays the groundwork and holds considerable significance as a reference for identifying disease-resistant genes and facilitating genetic breeding in C. ensifolium. [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.

The Solanaceae family occupies a significant position, and the study of resistance genes within this family is extremely valuable. Therefore, our goal is to examine disease resistance genes based on the high-quality representative genomes of Solanaceae crops, and to develop corresponding Simple Sequence Repeat (SSR) molecular markers. Among nine representative Solanaceae species, we identified 819 NBS-LRR genes, which were further divided into 583 CC-NBS-LRR (CNL), 54 RPW8-NBS-LRR (RNL), and 182 TIR-NBS-LRR (TNL) genes. Whole genome duplication (WGD) has played a very important role in the expansion of NBS-LRR genes in Solanaceae crops. Gene structure analysis showed the striking similarity in the conserved motifs of NBS-LRR genes, which suggests a common ancestral origin, followed by evolutionary differentiation and amplification. Gene clustering and events like rearrangement within the NBS-LRR family contribute to their scattered chromosomal distribution. Our findings reveal that the majority of NBS-LRR family genes across all examined species predominantly localize to chromosomal termini. The analysis indicates the significant impact of the most recent whole genome triplication (WGT) on the NBS-LRR family genes. Moreover, we constructed Protein–Protein Interaction (PPI) networks for all 819 NBS-LRR genes, identifying 3820 potential PPI pairs. Notably, 97 genes displayed clear interactive relationships, highlighting their potential role in disease resistance processes. A total of 22,226 SSRs were detected from all genes of nine Solanaceae species. Among these SSRs, we screened 43 NBS-LRR-associated SSRs. Our study lays the foundation for further exploration into SSR development and genetic mapping related to disease resistance in Solanaceae species.

Fusarium wilt in Cymbidium ensifolium, caused by Fusarium oxysporum, is highly contagious and poses a severe hazard. It significantly reduces the ornamental value of C. ensifolium and causes substantial economic losses in agricultural production. Nucleotide-binding site–leucine-rich repeat (NBS-LRR) genes are key regulatory factors in plant disease resistance responses, playing vital roles in defending against pathogen invasions. In our study, we conducted a comprehensive analysis of the NBS-LRR gene family in the genome of Cymbidium ensifolium. Phylogenetic analysis identified a total of 31 NBS-LRR genes encoding NB-ARC proteins, which were categorized into five classes (CNL, CN, NL, N, RNL) based on their protein structural domains. These genes were found to be unevenly distributed across eight chromosomes. Physicochemical analysis revealed significant variances in molecular weight and sequence length among the family members. Subcellular localization results indicated that most genes primarily reside in the cytoplasm and cell membrane, suggesting that the primary sites of disease resistance responses may be the cell membrane and cyto-plasm. Furthermore, noticeable disparities were observed in gene structures and conserved motifs among different categories of family genes. Promoter analysis indicated that cis-regulatory elements are mainly associated with plant stress, jasmonic acid, gibberellin, and other development-related factors, suggesting that CeNBS-LRR genes mainly resist external stress through hormones such as abscisic acid and jasmonic acid. We characterized twenty-seven CeNBS-LRR gene expression patterns of healthy C. ensifolium at different periods after Fusarium wilt infection, and found that those genes exhibit a temporospatial expression pattern, and that their expression is also responsive to Fusarium wilt infection. By analyzing the expression pattern via transcriptome and qRT-PCR, we speculated that JL006442 and JL014305 may play key roles in resisting Fusarium wilt. This study lays the groundwork and holds considerable significance as a reference for identifying disease-resistant genes and facilitating genetic breeding in C. ensifolium.

The nucleotide-binding site-leucine-rich repeat (NBS-LRR) gene family is the largest group of disease resistance (R) genes in plants and is active in response to viruses, bacteria, and fungi usually involved in effector-triggered immunity (ETI). Pangenome-wide studies allow researchers to analyze the genetic diversity of multiple species or their members simultaneously, providing a comprehensive understanding of the evolutionary relationships and diversity present among them. The draft pan-genome of three Mangifera indica cultivars (Alphonso, Hong Xiang Ya, and Tommy atkins) was constructed and Presence/absence variants (PAVs) were filtered through the ppsPCP pipeline. As a result, 2823 genes and 5907 PAVs from H. Xiang Ya, and 1266 genes and 2098 PAVs from T. atkins were added to the reference genome. For the identification of CC-NBS-LRR (CNL) genes in these mango cultivars, this draft pan-genome study has successfully identified 47, 27, and 36 members in Alphonso, H. Xiang Ya, and T. atkins respectively. The phylogenetic analysis divided MiCNL proteins into four distinct subgroups. All MiCNL genes are unevenly distributed on chromosomes. Both tandem and segmental duplication events played a significant role in the expansion of the CNL gene family. These genes contain cis-elements related to light, stress, hormone, and development. The analysis of protein-protein interactions (PPI) revealed that MiCNL proteins interacted with other defense-responsive proteins. Gene Ontology (GO) analysis indicated that MiCNL genes play a role in defense mechanisms within the organism. The expression level of the identified genes in fruit peel was observed under disease and cold stress which showed that Mi_A_CNL13 and 14 were upregulated while Mi_A_CNL15, 25, 30, 31, and 40 were down-regulated in disease stress. On the other hand, Mi_A_CNL2, 14, 41, and 45 were up-regulated and Mi_A_CNL47 is down-regulated in cold stress. Subsequently, the Random Forest (RF) classifier was used to assess the multi-stress response of MiCNLs. It was found that Mi_A_CNL14 is a gene that responds to multiple stress conditions. The CNLs have similar protein structures which show that they are involved in the same function. The above findings provide a foundation for a deeper understanding of the functional characteristics of the mango CNL gene family. [ABSTRACT FROM AUTHOR]

Plants coordinately use cell‐surface and intracellular immune receptors to perceive pathogens and mount an immune response. Intracellular events of pathogen recognition are largely mediated by immune receptors of the nucleotide binding and leucine rich‐repeat (NLR) classes. Upon pathogen perception, NLRs trigger a potent broad‐spectrum immune reaction, usually accompanied by a form of programmed cell death termed the hypersensitive response. Some plant NLRs act as multifunctional singleton receptors which combine pathogen detection and immune signaling. However, NLRs can also function in higher order pairs and networks of functionally specialized interconnected receptors. In this article, we cover the basic aspects of plant NLR biology with an emphasis on NLR networks. We highlight some of the recent advances in NLR structure, function, and activation and discuss emerging topics such as modulator NLRs, pathogen suppression of NLRs, and NLR bioengineering. Multi‐disciplinary approaches are required to disentangle how these NLR immune receptor pairs and networks function and evolve. Answering these questions holds the potential to deepen our understanding of the plant immune system and unlock a new era of disease resistance breeding. [ABSTRACT FROM AUTHOR]

NBS-LRR genes constitute one of the largest resistance gene families in plants, which play key roles in resistance to pathogens. Although the identification and characterization of the NBS-LRR gene family has been extensively reported in various species, a comprehensive analysis in eggplant has not been previously documented. In this study, a total of 269 SmNBS genes were identified in the eggplant genome. Based on domain classification and phylogenetic analysis, SmNBSs were divided into three subgroups 231 CNLs (CC-NBS-LRR), 36 TNLs (TIR-NBS-LRR), and 2 RNLs (RPW8-NBS-LRR). Chromosomal mapping analysis revealed an uneven distribution of SmNBSs in clusters across chromosomes, with a predominant presence on chromosomes 10, 11, and 12. Structural analysis identified eight conserved motifs previously reported in SmNBSs, exhibiting high conservation in both amino acid sequences and their order. Evolutionary analysis demonstrated that tandem duplication events mainly contributed to the expansion of SmNBS. Subsequently, qRT-PCR analysis demonstrated that nine SmNBSs exhibited differential expression patterns in response to R. solanacearum stress, with EGP05874.1 potentially involved in the resistance response. In conclusion, this study provides a comprehensive insight into SmNBSs, which will enhance the research on eggplant disease resistance and facilitate the breeding of new disease-resistant varieties. [ABSTRACT FROM AUTHOR]

The nucleotide-binding site-leucine-rich repeat (NBS–LRR) gene family is the largest group of disease resistance (R) genes in plants and is active in response to viruses, bacteria, and fungi usually involved in effector-triggered immunity (ETI). Pangenome-wide studies allow researchers to analyze the genetic diversity of multiple species or their members simultaneously, providing a comprehensive understanding of the evolutionary relationships and diversity present among them. The draft pan-genome of three Mangifera indica cultivars (Alphonso, Hong Xiang Ya, and Tommy atkins) was constructed and Presence/absence variants (PAVs) were filtered through the ppsPCP pipeline. As a result, 2823 genes and 5907 PAVs from H. Xiang Ya, and 1266 genes and 2098 PAVs from T. atkins were added to the reference genome. For the identification of CC-NBS-LRR (CNL) genes in these mango cultivars, this draft pan-genome study has successfully identified 47, 27, and 36 members in Alphonso, H. Xiang Ya, and T. atkins respectively. The phylogenetic analysis divided MiCNL proteins into four distinct subgroups. All MiCNL genes are unevenly distributed on chromosomes. Both tandem and segmental duplication events played a significant role in the expansion of the CNL gene family. These genes contain cis-elements related to light, stress, hormone, and development. The analysis of protein-protein interactions (PPI) revealed that MiCNL proteins interacted with other defense-responsive proteins. Gene Ontology (GO) analysis indicated that MiCNL genes play a role in defense mechanisms within the organism. The expression level of the identified genes in fruit peel was observed under disease and cold stress which showed that Mi_A_CNL13 and 14 were up-regulated while Mi_A_CNL15, 25, 30, 31, and 40 were down-regulated in disease stress. On the other hand, Mi_A_CNL2, 14, 41, and 45 were up-regulated and Mi_A_CNL47 is down-regulated in cold stress. Subsequently, the Random Forest (RF) classifier was used to assess the multi-stress response of MiCNLs. It was found that Mi_A_CNL14 is a gene that responds to multiple stress conditions. The CNLs have similar protein structures which show that they are involved in the same function. The above findings provide a foundation for a deeper understanding of the functional characteristics of the mango CNL gene family.

Arms race co‐evolution of plant–pathogen interactions evolved sophisticated recognition mechanisms between host immune receptors and pathogen effectors. Different allelic haplotypes of an immune receptor in the host mount distinct recognition against sequence or non‐sequence related effectors in pathogens. We report the molecular characterization of the Piks allele of the rice immune receptor Pik against rice blast pathogen, which requires two head‐to‐head arrayed nucleotide‐binding sites and leucine‐rich repeat proteins. Like other Pik alleles, both Piks‐1 and Piks‐2 are necessary and sufficient for mediating resistance. However, unlike other Pik alleles, Piks does not recognize any known AvrPik variants of Magnaporthe oryzae. Sequence analysis of the genome of an avirulent isolate V86010 further revealed that its cognate avirulence (Avr) gene most likely has no significant sequence similarity to known AvrPik variants. Piks‐1 and Pikm‐1 have only two amino acid differences within the integrated heavy metal‐associated (HMA) domain. Pikm‐HMA interacts with AvrPik‐A, ‐D, and ‐E in vitro and in vivo, whereas Piks‐HMA does not bind any AvrPik variants. Characterization of two amino acid residues differing Piks‐1 from Pikm‐1 reveal that Piks‐E229Q derived from the exchange of Glu229 to Gln229 in Piks‐1 gains recognition specificity against AvrPik‐D but not AvrPik‐A or ‐E, indicating that Piks‐E229Q partially restores the Pikm spectrum. By contrast, Piks‐A261V derived from the exchange of Ala261 to Val261 in Piks‐1 retains Piks recognition specificity. We conclude that Glu229 in Piks‐1 is critical for Piks breaking the canonical Pik/AvrPik recognition pattern. Intriguingly, binding activity and ectopic cell death induction is maintained between Piks‐A261V and AvrPik‐D, implying that positive outcomes from ectopic assays might be insufficient to deduce its immune activity against the relevant effectors in rice and rice blast interaction. [ABSTRACT FROM AUTHOR]

SUMMARY: The soybean Rpp1 locus confers resistance to Phakopsora pachyrhizi, causal agent of rust, and resistance is usually dominant over susceptibility. However, dominance of Rpp1‐mediated resistance is lost when a resistant genotype (Rpp1 or Rpp1b) is crossed with susceptible line TMG06_0011, and the mechanism of this dominant susceptibility (DS) is unknown. Sequencing the Rpp1 region reveals that the TMG06_0011 Rpp1 locus has a single nucleotide‐binding site leucine‐rich repeat (NBS‐LRR) gene (DS‐R), whereas resistant PI 594760B (Rpp1b) is similar to PI 200492 (Rpp1) and has three NBS‐LRR resistance gene candidates. Evidence that DS‐R is the cause of DS was reflected in virus‐induced gene silencing of DS‐R in Rpp1b/DS‐R or Rpp1/DS‐R heterozygous plants with resistance partially restored. In heterozygous Rpp1b/DS‐R plants, expression of Rpp1b candidate genes was not significantly altered, indicating no effect of DS‐R on transcription. Physical interaction of the DS‐R protein with candidate Rpp1b resistance proteins was supported by yeast two‐hybrid studies and in silico modeling. Thus, we conclude that suppression of resistance most likely does not occur at the transcript level, but instead probably at the protein level, possibly with Rpp1 function inhibited by binding to the DS‐R protein. The DS‐R gene was found in other soybean lines, with an estimated allele frequency of 6% in a diverse population, and also found in wild soybean (Glycine soja). The identification of a dominant susceptible NBS‐LRR gene provides insight into the behavior of NBS‐LRR proteins and serves as a reminder to breeders that the dominance of an R gene can be influenced by a susceptibility allele. Significance Statement: Most resistance genes are inherited dominantly, although the present study serves as a reminder to breeders that the dominance of an R gene can be influenced by a susceptibility allele. The study identified a susceptible NBS‐LRR allele that can negate the dominance of the Rpp1‐mediated resistance to Asian soybean rust. The results support suppression of resistance occurring at the protein level, possibly through the interaction between the susceptible protein and the resistance protein. [ABSTRACT FROM AUTHOR]

MicroRNAs (miRNAs) play essential roles in plant defense responses, although such roles have not been identified in cotton in response to the plant pathogenic fungus Verticillium dahliae. In this study, the functions of miR398b and its target genes in cotton-V. dahliae interaction were investigated. The transcript levels of miR398b were down-regulated by V. dahliae infection and miR398b overexpression in cotton made the plants more susceptible to V. dahliae. The results suggest that miR398b negatively regulates cotton resistance to V. dahliae. This may occur by miR398b repression of some CC-NBS-LRR genes via translational inhibition, interfering with defense responses and leading to cotton susceptibility to V. dahliae. Alternatively, miR398b may guide the cleavage of the mRNAs of GhCSD1, GhCSD2 and GhCCS, each of which functions in reactive oxygen species (ROS) regulation and homeostasis, thereby causing excessive ROS accumulation in miR398b-overexpressing plants in response to V. dahliae infection. This study suggests conserved and novel roles of miR398b in the cotton–V. dahliae interaction. These discoveries may be coupled with new strategies in cotton breeding programs to improve resistance to V. dahliae.

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

Introduction: Cold stress adversely affects the growth and development of plants and limits the geographical distribution of many plant species. Accumulation of spontaneous mutations shapes the adaptation of plant species to diverse climatic conditions. Methods: The genome-wide association study of the phenotypic variation gathered by a newly designed phenomic platform with the over six millions single nucleotide polymorphic (SNP) loci distributed across the genomes of 417 Arabidopsis natural variants collected from various geographical regions revealed 33 candidate cold responsive genes. Results: Investigation of at least two independent insertion mutants for 29 genes identified 16 chilling tolerance genes governing diverse genetic mechanisms. Five of these genes encode novel leucine-rich repeat domaincontaining proteins including three nucleotide-binding site-leucine-rich repeat (NBS-LRR) proteins. Among the 16 identified chilling tolerance genes, ADS2 and ACD6 are the only two chilling tolerance genes identified earlier. Discussion: The 12.5% overlap between the genes identified in this genomewide association study (GWAS) of natural variants with those discovered previously through forward and reverse genetic approaches suggests that chilling tolerance is a complex physiological process governed by a large number of genetic mechanisms. [ABSTRACT FROM AUTHOR]

Key message: Expression of the VaRPP13 in Arabidopsis and tobacco enhanced resistance to oomycete pathogens, and this enhancement is closely related to the activation of salicylic acid (SA) signaling pathway. Resistance (R) genes, which usually contain a nucleotide-binding site and a leucine-rich repeat (NBS-LRR) domain, play crucial roles in disease resistance. In this study, we cloned a CC-NBS-LRR gene VaRPP13 from Vitis amurensis 'Shuang Hong' grapevine, and investigated its function on disease resistance. VaRPP13 expression was induced by Plasmopara viticola, an oomycetes pathogen causing downy mildew disease in grapevine. Heterologous expression VaRPP13 could also enhance resistance to Hyaloperonospora arabidopsidis in Arabidopsis thaliana and Phytophthora capsici in Nicotiana benthamiana, both oomycete pathogens. Further study indicated that VaRPP13 could enhance the expression of genes in SA signal pathway, while exogenous SA could also induce the expression of VaRPP13. In conclusion, our studies demonstrated that VaRPP13 contributes to a broad-spectrum resistance to oomycetes via activating SA signaling pathway. [ABSTRACT FROM AUTHOR]

IntroductionCold stress adversely affects the growth and development of plants and limits the geographical distribution of many plant species. Accumulation of spontaneous mutations shapes the adaptation of plant species to diverse climatic conditions.MethodsThe genome-wide association study of the phenotypic variation gathered by a newly designed phenomic platform with the over six millions single nucleotide polymorphic (SNP) loci distributed across the genomes of 417 Arabidopsis natural variants collected from various geographical regions revealed 33 candidate cold responsive genes.ResultsInvestigation of at least two independent insertion mutants for 29 genes identified 16 chilling tolerance genes governing diverse genetic mechanisms. Five of these genes encode novel leucine-rich repeat domain-containing proteins including three nucleotide-binding site-leucine-rich repeat (NBS-LRR) proteins. Among the 16 identified chilling tolerance genes, ADS2 and ACD6 are the only two chilling tolerance genes identified earlier.DiscussionThe 12.5% overlap between the genes identified in this genome-wide association study (GWAS) of natural variants with those discovered previously through forward and reverse genetic approaches suggests that chilling tolerance is a complex physiological process governed by a large number of genetic mechanisms.

The nucleotide-binding site and leucine-rich repeat (NBS-LRR) genes, one of the largest gene families in plants, are evolving rapidly and playing a critical role in plant resistance to pathogens. In this study, a genome-wide search in 12 Rosaceae genomes screened out 2188 NBS-LRR genes, with the gene number varied distinctively across different species. The reconciled phylogeny revealed 102 ancestral genes (7 RNLs, 26 TNLs, and 69 CNLs), which underwent independent gene duplication and loss events during the divergence of the Rosaceae. The NBS-LRR genes exhibited dynamic and distinct evolutionary patterns in the 12 Rosaceae species due to independent gene duplication/loss events, which resulted the discrepancy of NBS-LRR gene number among Rosaceae species. Specifically, Rubus occidentalis, Potentilla micrantha, Fragaria iinumae and Gillenia trifoliata, displayed a "first expansion and then contraction" evolutionary pattern; Rosa chinensis exhibited a "continuous expansion" pattern; F. vesca had a "expansion followed by contraction, then a further expansion" pattern, three Prunus species and three Maleae species shared a "early sharp expanding to abrupt shrinking" pattern. Overall, this study elucidated the dynamic and complex evolutionary patterns of NBS-LRR genes in the 12 Rosaceae species, and could assist further investigation of mechanisms driving these evolutionary patterns. [ABSTRACT FROM AUTHOR]

Dalbergia sissoo is an important timber tree, and dieback disease poses a dire threat to it toward extinction. The genomic record of D. sissoo is not available yet on any database; that is why it is challenging to probe the genetic elements involved in stress resistance. Hence, we attempted to unlock the genetics involved in dieback resistance through probing the NBS-LRR family, linked with mostly disease resistance in plants. We analyzed the transcriptome of D. sissoo under dieback challenge through DOP-rtPCR analysis using degenerate primers from conserved regions of NBS domain-encoded gene sequences. The differentially expressed gene sequences were sequenced and in silico characterized for predicting the expressome that contributes resistance to D. sissoo against dieback. The molecular and bioinformatic analyses predicted the presence of motifs including ATP/GTP-binding site motif A (P-loop NTPase domain), GLPL domain, casein kinase II phosphorylation site, and N-myristoylation site that are the attributes of proteins encoded by disease resistance genes. The physicochemical characteristics of identified resistance gene analogs, subcellular localization, predicted protein fingerprints, in silico functional annotation, and predicted protein structure proved their role in disease and stress resistance. [ABSTRACT FROM AUTHOR]

Pistia stratiotes (Araceae), commonly referred to as water lettuce, is one of the most notorious weeds that cause severe damage to the economy and natural ecosystems of infested areas. In order to explore the mechanism of its rapid invasion, here, we assembled a high‐quality chromosome‐level genome for P. stratiotes based on the Illumina sequencing, PacBio sequencing, and Hi‐C scaffolding technology. The assembled genome is 311.87 Mb in size with a contig N50 of 1.08 Mb. The contigs were further anchored on 14 pseudochromosomes with a scaffold N50 of 21.21 Mb. A total of 20,356 protein‐coding genes were predicted, of which 79.35% were functionally annotated here. Evolutionary analysis showed that P. stratiotes and Colocasia esculenta were clustered together as sister lineages that diverged approximately 61 Ma. The synteny analyses indicated that two whole‐genome duplication (WGD) events occurred within a short period in P. stratiotes. Moreover, comparative genome analysis indicated that the expansion of gene families corresponding to disease resistance might contribute to rapid invasion in P. stratiotes. Also, we analysed the disease‐resistance gene family (NBS‐LRR) involved in plant defence. A genome‐wide search in P. stratiotes genome identified 85 NBS‐LRR genes in this study. In conclusion, this study provides some new insights into the evolution of the invasive aquatic plant P. stratiotes. Our reference genome will also provide valuable resources for future invasion genomic research programmes. [ABSTRACT FROM AUTHOR]

The vast majority of plant disease resistance (R) genes encode nucleotide binding site-leucine-rich repeat (NBS-LRR) proteins, which specifically determine the plant immune response and have been demonstrated to be targets of several microRNA (miRNA) families. The fungus Fusarium oxysporum f. sp. lycopersici (FOL) causes vascular wilt disease in tomato worldwide. Here, we explored a possible role for FGR3 in tomato defense against FOL. FRG3 is a predicted NBS-LRR like gene that is targeted by slmiR482e-3p, a member of slmiR482 miRNA family. Northern blot data demonstrated that all seven members of the slmiR482 family were regulated in diverse ways after infection by FOL. The ability of FRG3 to be regulated by slmiR482e-3p was confirmed at the transcript level by co-expression studies in Nicotiana benthamiana. A virus-induced gene silencing (VIGS) approach revealed that FRG3 confers resistance to the Motelle tomato cultivar. Taken together, our study has identified a novel R gene, FRG3, which is targeted by slmiR482e-3p at the transcript level, and is necessary for resistance to tomato wilt disease in planta.

Verticillium wilt caused by Verticillium dahliae results in severe losses in cotton, and is economically the most destructive disease of this crop. Improving genetic resistance is the cleanest and least expensive option to manage Verticillium wilt. Previously, we identified the island cotton NBS-LRR-encoding gene GbaNA1 that confers resistance to the highly virulent V. dahliae isolate Vd991. In this study, we expressed cotton GbaNA1 in the heterologous system of Arabidopsis thaliana and investigated the defense response mediated by GbaNA1 following inoculations with V. dahliae. Heterologous expression of GbaNA1 conferred Verticillium wilt resistance in A. thaliana. Moreover, overexpression of GbaNA1 enabled recovery of the resistance phenotype of A. thaliana mutants that had lost the function of GbaNA1 ortholog gene. Investigations of the defense response in A. thaliana showed that the reactive oxygen species (ROS) production and the expression of genes associated with the ethylene signaling pathway were enhanced significantly following overexpression of GbaNA1. Intriguingly, overexpression of the GbaNA1 ortholog from Gossypium hirsutum (GhNA1) in A. thaliana did not induce the defense response of ROS production due to the premature termination of GhNA1, which lacks the encoded NB-ARC and LRR motifs. GbaNA1 therefore confers Verticillium wilt resistance in A. thaliana by the activation of ROS production and ethylene signaling. These results demonstrate the functional conservation of the NBS-LRR-encoding GbaNA1 in a heterologous system, and the mechanism of this resistance, both of which may prove valuable in incorporating GbaNA1-mediated resistance into other plant species.

Dalbergia sissoo is an important timber tree, and dieback disease poses a dire threat to it toward extinction. The genomic record of D. sissoo is not available yet on any database; that is why it is challenging to probe the genetic elements involved in stress resistance. Hence, we attempted to unlock the genetics involved in dieback resistance through probing the NBS-LRR family, linked with mostly disease resistance in plants. We analyzed the transcriptome of D. sissoo under dieback challenge through DOP-rtPCR analysis using degenerate primers from conserved regions of NBS domain-encoded gene sequences. The differentially expressed gene sequences were sequenced and in silico characterized for predicting the expressome that contributes resistance to D. sissoo against dieback. The molecular and bioinformatic analyses predicted the presence of motifs including ATP/GTP-binding site motif A (P-loop NTPase domain), GLPL domain, casein kinase II phosphorylation site, and N-myristoylation site that are the attributes of proteins encoded by disease resistance genes. The physicochemical characteristics of identified resistance gene analogs, subcellular localization, predicted protein fingerprints, in silico functional annotation, and predicted protein structure proved their role in disease and stress resistance.

• A total of 97 NBS-LRR genes were identified in Musa acuminata , through genome-wide identification. • Key differentially expressed genes (MaNBS85, MaNBS89 and MaNBS92) were screened by analysis the transcriptome changes between the mild resistant and susceptible cultivar at three time points post Foc infection. • RNA interference assays demonstrated that MaNBS89 contributed to pathogen resistance. • MaNBS89 will be a desirable target for future molecular breeding of disease resistance. Nucleotide binding site-leucine-rich repeat (NBS-LRR) genes are the most abundant known plant resistance (R) genes and are essential for plant stress tolerance. Fusarium oxysporum f. sp. cubense (Foc) is the causal agent of Banana Fusarium vascular wilt that threatens global banana production, yet, the role of NBS-LRR in disease resistance is unknown. We performed a genome-wide identification and analysis of NBS-LRR genes in M. acuminata and revealed a total of 97 NBS-LRR genes, of which 71 were divided into 17 clusters. Analyses of phylogenetic and conserved motifs indicated that NBS-LRR genes in the same cluster were conserved. Transcriptomic analysis revealed divergent functions of the NBS-LRR genes; genes within cluster 17 were activated in a moderately disease-resistant cultivar but repressed in a susceptible cultivar, especially the MaNBS89 gene. Transcriptional silencing of MaNBS89 led to more serious leaf injury compared to control plants. Overall, our study comprehensively revealed the expression profiles of NBS-LRR genes in an economically important plant and suggested a strong candidate gene (MaNBS89) for future use in resistance breeding in Musa diseases. [ABSTRACT FROM AUTHOR]

Blast disease is a major production constraint in cereal crops worldwide. Genome regions associated with blast resistance in rice were used in homology-based prediction of resistance gene orthologs across cereals. Seventy-four Resistance Gene Analogs (RGAs) that were collocated with rice QTLs (Quantitative Trait Loci) associated with blast resistance, predicted 89 orthologs from cereals,including 61 from finger millet. The RGA orthologs found hits in cereal transcriptomes derived from blast-infected tissues. Over 92% of the putative RGAs encoded NBS-LRR (Nucleotide Binding Site -Leucine Rich Repeat) proteins. Despite conserved primary protein structures, NBS-LRRs were variable in the encoding genes. Primers designed on conserved NBS-LRRs motifs amplified multiple fragments in PCR indicating the presence of highly similar paralogs in genomes. Rice chromosomes 1, 2, 4, 6, and 11 dock clusters of RGAs and syntenic clusters of orthologous RGAs were predicted from other cereal genomes identifying genome hotspots for resistance gene cassettes. RGAs in such cassettes were tightly linked with 50 %–90 % within-cluster similarity. Local finger millet germplasm identified multi-modes of resistance, and lack of correlation between the resistance traits points to independent expression of resistance mechanisms and associated genes in different tissues and development stages. The significant diversity, genomic abundance, and potential functional redundancy complicate use of RGAs for resistance breeding in given host genetic backgrounds, pathogen pools and agro-climates; therefore, robust technology pipelines that enable system-level analysis of expression and effectiveness can increase the practical use of RGAs. • Seventy-four RGAs that were collocated with rice QTLs associated with blast disease resistance predicted 89 orthologs from related cereals. • Over 92% of RGAs encoded NBS-LRR proteins that were similar in primary protein structure, but the encoding genes expressed a degree of variability. • RGAs aggregate in syntenic clusters across cereal genomes identifying genome hotspots for resistance gene cassettes. • Leaf blast resistance is expressed independently from neck and finger blast resistance, indicating diverse associated genes and mechanisms. [ABSTRACT FROM AUTHOR]

The soybean aphid poses a severe threat to soybean quality and yield by sucking phloem sap and transmitting plant viruses. An early-maturing and highly resistant soybean landrace, Fangzheng Moshidou, with markedly reduced aphid colonization has been identified by screening of aphid-resistant soybean accessions. In a population derived from the cross of Fangzheng Moshidou with the susceptible cultivar Beifeng 9, resistance was conferred by a single dominant gene. Three linked markers, Satt114, Satt334, and Sct_033, on chromosome 13 were identified by bulked-segregant analysis. Additional simple-sequence repeat and single-nucleotide polymorphism (SNP) markers were developed for gene mapping. The resistance of Fangzheng Moshidou was fine-mapped to the interval between the SNP markers YCSNP20 and YCSNP80, corresponding to 152.8 kb in the Williams 82 assembly 2 genome. This region was near the reported loci Rag2 and Rag5 but did not overlap the interval containing them. A unique haplotype is described for Fangzheng Moshidou that distinguishes it from soybean accessions PI 587972, PI 594879, and PI 567301B in the interval containing Rag2 and Rag5. These results indicate that Fangzheng Moshidou harbors a novel gene at a tightly linked resistance locus, designated as RagFMD. Fourteen candidate genes were annotated in the fine-mapping region, including seven NBS-LRR genes, which are usually considered resistance genes in plant defense. Most of these candidate genes showed variations distinguishing the resistant and susceptible parents and some genes also showed differences in expression between the two parental lines and at several times after aphid infestation. Isolation of RagFMD would advance the study of molecular mechanisms of soybean aphid resistance and contribute to precise selection of resistant soybeans. [ABSTRACT FROM AUTHOR]

The soybean aphid poses a severe threat to soybean quality and yield by sucking phloem sap and transmitting plant viruses. An early-maturing and highly resistant soybean landrace, Fangzheng Moshidou, with markedly reduced aphid colonization has been identified by screening of aphid-resistant soybean accessions. In a population derived from the cross of Fangzheng Moshidou with the susceptible cultivar Beifeng 9, resistance was conferred by a single dominant gene. Three linked markers, Satt114, Satt334, and Sct_033, on chromosome 13 were identified by bulked-segregant analysis. Additional simple-sequence repeat and single-nucleotide polymorphism (SNP) markers were developed for gene mapping. The resistance of Fangzheng Moshidou was fine-mapped to the interval between the SNP markers YCSNP20 and YCSNP80, corresponding to 152.8 kb in the Williams 82 assembly 2 genome. This region was near the reported loci Rag2 and Rag5 but did not overlap the interval containing them. A unique haplotype is described for Fangzheng Moshidou that distinguishes it from soybean accessions PI 587972, PI 594879, and PI 567301B in the interval containing Rag2 and Rag5. These results indicate that Fangzheng Moshidou harbors a novel gene at a tightly linked resistance locus, designated as RagFMD. Fourteen candidate genes were annotated in the fine-mapping region, including seven NBS-LRR genes, which are usually considered resistance genes in plant defense. Most of these candidate genes showed variations distinguishing the resistant and susceptible parents and some genes also showed differences in expression between the two parental lines and at several times after aphid infestation. Isolation of RagFMD would advance the study of molecular mechanisms of soybean aphid resistance and contribute to precise selection of resistant soybeans.

High expression of plant nucleotide binding site leucine-rich repeat (NBS-LRR) defense genes is often lethal to plant cells, a phenotype perhaps associated with fitness costs. Plants implement several mechanisms to control the transcript level of NBS-LRR defense genes. As negative transcriptional regulators, diverse miRNAs target NBS-LRRs in eudicots and gymnosperms. To understand the evolutionary benefits of this miRNA-NBS-LRR regulatory system, we investigated the NBS-LRRs of 70 land plants, coupling this analysis with extensive small RNA data. A tight association between the diversity of NBS-LRRs and miRNAs was found. The miRNAs typically target highly duplicated NBS-LRRs In comparison, families of heterogeneous NBS-LRRs were rarely targeted by miRNAs in Poaceae and Brassicaceae genomes. We observed that duplicated NBS-LRRs from different gene families periodically gave birth to new miRNAs. Most of these newly emerged miRNAs target the same conserved, encoded protein motif of NBS-LRRs, consistent with a model of convergent evolution for these miRNAs. By assessing the interactions between miRNAs and NBS-LRRs, we found nucleotide diversity in the wobble position of the codons in the target site drives the diversification of miRNAs. Taken together, we propose a co-evolutionary model of plant NBS-LRRs and miRNAs hypothesizing how plants balance the benefits and costs of NBS-LRR defense genes.

The adult‐plant leaf rust resistant gene Lr22a confers broadly effective resistance against the fungal pathogen Puccinia triticina Eriks. (Pt) in wheat that has not been extensively utilized in wheat cultivars. The objective of this study was to develop robust functional molecular markers using the Lr22a gene sequence to facilitate integration of Lr22a in breeding programmes. The Lr22a coding sequence was used to identify isolated SNPs and four kompetitive allele specific polymerase chain reaction (PCR) (KASP) markers were developed. For marker testing, a F2:3 population was developed by crossing a near‐isogenic line RL4495 (Lr22a carrier) with Thatcher and phenotyped with Pt race TDBJ and genotyped with a 90K iSelect SNP array, four KASP markers and two SSR markers. A linkage map of chromosome arm 2DS that included Lr22a was constructed. The KASP markers co‐segregated with Lr22a and were validated for cross‐applicability on a panel of wheat lines. KASP markers Kwh636, Kwh637 and Kwh638 reliably detected the presence or absence of Lr22a. The markers developed in this study will facilitate Lr22a selection in breeding programmes. [ABSTRACT FROM AUTHOR]

Leaf rust is one of the most devastating wheat diseases worldwide, to which many resistance genes have been successfully introgressed from wheat wild relatives. Though the Thinopyrum ponticum‐derived leaf rust resistance gene Lr19 is widely effective, and previous studies have shown its likely presence in Aegilops tauschii, no thorough investigation has been conducted to confirm this. The current study examined the presence of Lr19 in Ae. tauschii using molecular and bioinformatic analyses. Accordingly, the wheat cultivar Thatcher was used as a susceptible control, and the Lr19‐carrying genotypes; Thatcher + Lr19 (TcLr19) and Agatha were used as resistant controls. Phenotyping using pathotype CDHLQ accompanied with genotyping using two DNA markers verified previous results of the likely presence of an orthologue for Lr19 on chromosome 7DL of Ae. tauschii (AtLr19). Sequencing of the STS GB marker products from Ae. tauschii and TcLr19 showed 99% homology between the corresponding fragments, confirming the phenotyping and genotyping results. Both sequenced fragments matched to the melatonin biosynthesis gene, O‐methyltransferase‐2 (OMT2). A hierarchical gene network was reconstructed using all identified putative genes within a genomic region containing 2.5 cM upstream and downstream of OMT2. Results indicated that numerous important biotic stress‐responsive genes such as RPM1, RGA2, TRIUR3, BURP12 and myosin‐11, were located downstream of melatonin as a master regulator molecule through the OMT2 node. To our knowledge, this is the first report of the identification of an orthologue for Lr19 in Ae. tauschii, which provides insights into the possible regulatory route of this gene. [ABSTRACT FROM AUTHOR]

Main conclusion: We advanceUlva’s genetic tractability and highlight its value as a model organism by characterizing its APAF1_C/WD40 domain-encoding gene, which belongs to a family that bears homology to R genes. The multicellular chlorophyte alga Ulva mutabilis (Ulvophyceae, Ulvales) is native to coastal ecosystems worldwide and attracts both high socio-economic and scientific interest. To further understand the genetic mechanisms that guide its biology, we present a protocol, based on adapter ligation-mediated PCR, for retrieving flanking sequences in U. mutabilis vector-insertion mutants. In the created insertional library, we identified a null mutant with an insertion in an apoptotic protease activating factor 1 helical domain (APAF1_C)/WD40 repeat domain-encoding gene. Protein domain architecture analysis combined with phylogenetic analysis revealed that this gene is a member of a subfamily that arose early in the evolution of green plants (Viridiplantae) through the acquisition of a gene that also encoded N-terminal nucleotide-binding adaptor shared by APAF-1, certain R-gene products and CED-4 (NB-ARC) and winged helix-like (WH-like) DNA-binding domains. Although phenotypic analysis revealed no mutant phenotype, gene expression levels in control plants correlated to the presence of bacterial symbionts, which U. mutabilis requires for proper morphogenesis. In addition, our analysis led to the discovery of a putative Ulva nucleotide-binding site and leucine-rich repeat (NBS-LRR) Resistance protein (R-protein), and we discuss how the emergence of these R proteins in green plants may be linked to the evolution of the APAF1_C/WD40 protein subfamily. [ABSTRACT FROM AUTHOR]

Summary: MicroRNAs (miRNAs) are a class of 21–24 nucleotides (nt) noncoding small RNAs ubiquitously distributed across the plant kingdom. miR482/2118, one of the conserved miRNA superfamilies originating from gymnosperms, has divergent main functions in core‐angiosperms. It mainly regulates NUCLEOTIDE BINDING SITE‐LEUCINE‐RICH REPEAT (NBS‐LRR) genes in eudicots, functioning as an essential component in plant disease resistance; in contrast, it predominantly targets numerous long noncoding RNAs (lncRNAs) in monocot grasses, which are vital for plant reproduction. Usually, miR482/2118 is 22‐nt in length, which can trigger the production of phased small interfering RNAs (phasiRNAs) after directed cleavage. PhasiRNAs instigated from target genes of miR482/2118 enhance their roles in corresponding biological processes by cis‐regulation on cognate genes and expands their function to other pathways via trans activity on different genes. This review summarizes the origin, biogenesis, conservation, and evolutionary characteristics of the miR482/2118 superfamily and delineates its diverse functions in disease resistance, plant development, stress responses, etc. [ABSTRACT FROM AUTHOR]

Abstract Background Bacterial fruit blotch (BFB), a disease caused by Acidovorax citrulli, results in significant economic losses in melon. The causal QTLs and genes for resistance to this disease have yet to be identified. Resistance (R)-genes play vital roles in resistance to plant diseases. Since the complete genome sequence of melon is available and genome-wide identification of R-genes has been performed for this important crop, comprehensive expression profiling may lead to the identification of putative candidate genes that function in the response to BFB. Results We identified melon accessions that are resistant and susceptible to BFB through repeated bioassays and characterized all 70 R-genes in melon, including their gene structures, chromosomal locations, domain organizations, motif distributions, and syntenic relationships. Several disease resistance-related domains were identified, including NBS, TIR, LRR, CC, RLK, and DUF domains, and the genes were categorized based on the domains of their encoded proteins. In addition, we profiled the expression patterns of the genes in melon accessions with contrasting levels of BFB resistance at 12 h, 1 d, 3 d, and 6 d after inoculation with A. citrulli. Six R-genes exhibited consistent expression patterns (MELO3C023441, MELO3C016529, MELO3C022157, MELO3C022146, MELO3C025518, and MELO3C004303), with higher expression levels in the resistant vs. susceptible accession. Conclusion We identified six putative candidate R-genes against BFB in melon. Upon functional validation, these genes could be targeted for manipulation via breeding and biotechnological approaches to improve BFB resistance in melon in the future.

Cassava bacterial blight (CBB) caused by Xanthomonas axonopodis pv. manihotis (Xam) seriously affects cassava yield. Genes encoding nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domains are among the most important disease resistance genes in plants that are specifically involved in the response to diverse pathogens. However, the in vivo roles of NBS-LRR remain unclear in cassava (Manihot esculenta). In this study, we isolated four MeLRR genes and assessed their expression under salicylic acid (SA) treatment and Xam inoculation. Four MeLRR genes positively regulate cassava disease general resistance against Xam via virus-induced gene silencing (VIGS) and transient overexpression. During cassava-Xam interaction, MeLRRs positively regulated endogenous SA and reactive oxygen species (ROS) accumulation and pathogenesis-related gene 1 (PR1) transcripts. Additionally, we revealed that MeLRRs positively regulated disease resistance in Arabidopsis. These pathogenic microorganisms include Pseudomonas syringae pv. tomato, Alternaria brassicicola, and Botrytis cinerea. Our findings shed light on the molecular mechanism underlying the regulation of cassava resistance against Xam inoculation.

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]

Cassava bacterial blight (CBB) caused by Xanthomonas axonopodis pv. manihotis (Xam) seriously affects cassava yield. Genes encoding nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domains are among the most important disease resistance genes in plants that are specifically involved in the response to diverse pathogens. However, the in vivo roles of NBS-LRR remain unclear in cassava (Manihot esculenta). In this study, we isolated four MeLRR genes and assessed their expression under salicylic acid (SA) treatment and Xam inoculation. Four MeLRR genes positively regulate cassava disease general resistance against Xam via virus-induced gene silencing (VIGS) and transient overexpression. During cassava- Xam interaction, MeLRRs positively regulated endogenous SA and reactive oxygen species (ROS) accumulation and pathogenesis-related gene 1 (PR1) transcripts. Additionally, we revealed that MeLRRs positively regulated disease resistance in Arabidopsis. These pathogenic microorganisms include Pseudomonas syringae pv. tomato , Alternaria brassicicola , and Botrytis cinerea. Our findings shed light on the molecular mechanism underlying the regulation of cassava resistance against Xam inoculation. [ABSTRACT FROM AUTHOR]

Bacterial blight caused by Xanthomonas oryzae pv. oryzae is the most destructive bacterial disease in rice production, and cultivating new disease-resistance variety by mining and utilizing the novel disease resistance genes is one of the most effective ways to control this disease. In our study, a population of 139 recombinant inbred lines (RILs) derived from super hybrid rice Xieyou 9308, between the parents of which there was genetic difference in resistance to bacterial blight, were inoculated with four Xoo strains. A genome-wide association study (GWAS) was carried out using 476,505 SNPs for the lesion length as a quantitative phenotype. The result revealed that a total of 109 significant SNPs including two genes encoding NBS-LRR containing proteins were detected to be significantly difference at P < 1x10-4 for four Xoo strains-treated lesions, accounting for phenotype variation of 59.78%-63.29%, respectively. Furthermore, 25 SNPs located in/nearby 19 candidate genes were identified by the CR4 inoculation, accounting for 61.00%. Relative expression analysis of two selected candidate genes, LOC_Os11g43420 and LOC_Os11g45930, demonstrated their higher expression levels in the resistant cultivar Zhonghui 9308 than in the susceptible variety Xieqingzao B, suggesting that these two genes might positively regulated bacterial blight resistance. Phylogenetic tree analysis indicated that these two genes were different from the previous cloned resistant genes in evolution, suggesting they were novel disease resistance genes. These results lays a theoretical basis and provides genetic resources for future resistant breeding in rice. [ABSTRACT FROM AUTHOR]

Ubiquitination is a pivotal post-translational modification that regulates turnover of nucleotide-binding site and leucine-rich repeat receptors (NLRs). As a RING-type E3 ligase, BOI (Botrytis susceptible1 interactor) has been reported to interact with different proteins, and function in the nucleus. New studies have identified that BOI can interact and ubiquitinate L5 (AT1G12290), a CC-NBS-LRR protein in vitro , and mediate the proteasomal degradation of L5 in Nicotiana benthamiana and Arabidopsis thaliana. However, there still remains an unanswered question about where the degradation occurs at the subcellular level. In this study, the ubiquitination of L5 by BOI was determined in N. benthamiana. Meanwhile, we discovered that BOI exhibited nucleocytoplasmic localization and mediated the degradation of the plasma membrane localized L5 outside the nucleus. BOI and its homologs BRG1 and BRG3 function redundantly in negatively regulate the protein level of L5. Overall, this report reveals BOI and its homologs have multiple targets and function at different subcellular locations. • E3 ligase BOI exhibited nucleo-cytoplasmic localization. • BOI mediated the degradation of the plasma membrane localized L5 outside the nucleus. • BOI and its homologs BRG1 and BRG3 function redundantly in negatively regulate the protein level of L5. [ABSTRACT FROM AUTHOR]

Nucleotide-binding site and leucine-rich repeat receptors (NLRs) play pivotal roles in plant immunity. The regulation of NLR stability is essential to ensure effective immunity, whereas the exact mechanism is largely unclear. The Arabidopsis CC-NBS-LRR protein L5 (At1g12290) can induce cell death in Nicotiana benthamiana , but not in Arabidopsis thaliana. We screened the interactors of L5 by yeast two-hybrid, and found that the BOI can interact with the CC domain of L5. Transiently expressed BOI reduced the protein level of L5, and suppressed the auoactivity of L5 in N. benthamiana. BOI can interact and ubiquitinate L5 in vitro , and mediate the proteasomal degradation of L5 in N. benthamiana and Arabidopsis. The Lys425 in the NBS domain of L5 is the critical unbiquitin site for the degradation. In conclusion, our results reveal a mechanism for the control of the stability of L5 protein and for the suppressed of L5-triggered cell death by a RING-type E3 ligase through the ubiquitin proteasome system. • E3 ligase BOI can interact with and ubiquitinate L5. •BOI mediates the proteasomal degradation of L5 in N. benthamiana and A. thaliana. •The Lys425 in the NBS domain of L5 is the critical unbiquitin site for the degradation. [ABSTRACT FROM AUTHOR]

Plants are frequently attacked by a variety of pathogens and thus have evolved a series of defense mechanisms, one important mechanism is resistance gene (R gene)-mediated disease resistance, but its expression is tightly regulated. NBS-LRR genes are the largest gene family of R genes. microRNAs (miRNAs) target to a number of NBS-LRR genes and trigger the production of phased small interfering RNAs (phasiRNAs) from these transcripts. phasiRNAs cis or trans regulate NBS-LRR genes, which can result in the repression of R gene expression. In this study, we screened for upregulated miR482 in the susceptible apple cultivar 'Golden Delicious' (GD) after inoculation with the fungal pathogen Alternaria alternata f. sp. mali (ALT1). Additionally, through combined degradome sequencing, we identified a gene targeted by miR482, named MdTNL1 , a gene encoding a TIR-NBS-LRR (Toll/interleukin1 receptor-nucleotide binding site-leucine-rich repeat) protein. This gene exhibited a significant down-regulation post ALT1 inoculation, suggesting an impact on gene expression mediated by miRNA regulation. miR482 could cleave MdTNL1 and generate phasiRNAs at the cleavage site. We found that overexpression of miR482 inhibited the expression of MdTNL1 and thus reduced the disease resistance of GD, while silencing of miR482 increased the expression of MdTNL1 and thus improved the disease resistance of GD. This work elucidates key mechanisms underlying the immune response to Alternaria infection in apple. Identification of the resistance genes involved will enable molecular breeding for prevention and control of Alternaria leaf spot disease in this important fruit crop. • MdTNL1 belonging to the TIR type significantly down-regulated after infection with ALT1. • miR482 generates phasi RNAs after cleavage of MdTNL1. • miR482- MdTNL1 pathway involved in apple resistance to apple Alternaria leaf spot disease. • Overexpression of MdTNL1 or silencing of miR482 improves apple resistance to Alternaria leaf spot disease. [ABSTRACT FROM AUTHOR]