Search Results (31)

Introduction: Rice, a cornerstone of global food security, faces escalating demands for enhanced yield and disease resistance. We collected 300 high-quality genomes, representing both cultivated (Oryza sativa indica, O. sativa japonica, and O. sativa aus) and wild species (O. rufipogon, O. glaberrima, and O. barthii). Methods: Leveraging HMMER, NLR-Annotator, and OrthoFinder, we systematically identified 148,077 leucine-rich repeat (LRR) and 143,459 nucleotide-binding leucine-rich repeat (NLR) genes, with LRR receptor-like kinases (LRR-RLKs) dominating immune receptor proportions, followed by coiled-coil domain containing (CNL)-type NLRs and LRR receptor-like proteins (LRR-RLPs). Results: Benchmarking Universal Single-Copy Orthologs (BUSCO) assessments confirmed robust genome quality (average score: 94.78). Strikingly, 454 TIR-NB-LRR (TNL) genes—typically rare in monocots—were detected, challenging prior assumptions. Phylogenetic analysis with Arabidopsis TNLs highlighted five O. glaberrima genes clustering with dicot TNLs; these genes featured truncated PLN03210 motifs fused to nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4 (NB-ARC) and LRR domains. Conclusions: By bridging structural genomics, evolutionary dynamics, and domestication-driven adaptation, this work provides a foundation for targeted breeding strategies and advances functional studies of plant immunity in rice. Full article

Plants are challenged regularly with multiple types of biotic stress factors, such as pathogens or insect herbivores, in their environment. To detect and defend against pathogens, plants have evolved an innate immune system in which intracellular receptors in the so-called effector-triggered immunity play a vital role. In Arabidopsis thaliana the Toll/interleukin-1 receptors (TIRs) domain is related to intracellular immunity receptors, for example in TIR-NBS-LRR (TNL) proteins. Among the TIR domain carrying proteins, very little is known about the function of the TIR-X proteins. Here, we focus on the recently described TIR-X (TIRP; At5g44900) to analyze its role in phytohormone-mediated plant defense through gene expression and phytohormone quantification. Therefore, we employed two fungal pathogens, the necrotrophic Alternaria brassicicola and the hemibiotrophic Verticillium dahliae, to infect A. thaliana WT (Col-0), TIRP knock-out, and TIRP overexpressing lines for comparative analyses. Furthermore, we included the insect herbivore Spodoptera littoralis and a treatment with S. littoralis egg extract on the plants to analyze any role of TIRP during these attacks. We found that both A. brassicicola and V. dahliae infections increased TIRP gene expression systemically. The salicylic acid content was higher in the TIRP overexpressing line, corresponding to a better S. littoralis larval growth performance in feeding assays. However, since we never observed clear infection-related differences in jasmonate or salicylic acid levels between the wild type and the two transgenic Arabidopsis lines, our results rule out the possibility that TIRP acts via the regulation of phytohormone synthesis and accumulation. Full article

Background/objectives: Methyl jasmonate is a plant signaling molecule involved in a wide range of functions, including stress responses. This study investigates the relative differential expression of microRNAs and their target genes in response to methyl jasmonate treatment of Scots pine needles. Methods: A combined strategy of high-throughput sequencing and in silico prediction of potential target genes was implemented. Results: a total of 58 differentially expressed (DE) microRNAs (miRNAs) (43 up-regulated and 15 down-regulated), belonging to 29 miRNA families, were identified. The 41 DE miRNAs from 17 families were conifer-specific miRNA families—miR946, miR947, miR950, miR1312, miR1313, miR1314, miR3693, miR3107, miR11452, miR11466, miR11487, miR11490, miR11504, miR11511, miR11532, miR11544, and miR11551. The other DE miRNAs (miR159, miR164, miR169, miR396, miR397, miR398, miR408, miR535) were conserved miRNAs, which are also found in angiosperm species. Transcriptome analysis identified 389 gene transcripts with 562 miRNA-target sites targeted by 57 of the 58 DE miRNAs. Of these, 250 target genes with 138 different GO annotations were found for the 41 DE conifer-specific conserved miRNAs. Conclusions: The 26 DE miRNAs from 14 DE miRNA families, of which almost all (12 families, 24 miRNAs) are conifer specific, and were associated with 68 disease resistance and TMV resistance proteins, TIR-NBS-LRR, LRR receptor-like serine/threonine-protein kinase, putative CC-NBS-LRR protein, and putative NBS-LRR protein target transcripts with 29 target gene GO term descriptions. Some of the genes targeted by conifer-specific miRNAs have been previously reported to be targeted by other miRNAs in angiosperms, indicating that the miRNA-target gene regulation system can vary between species. Full article

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. Full article

NLR genes are crucial components of the effector-triggered immunity (ETI) system, responsible for recognizing pathogens and initiating immune responses. Although NLR genes in many plant species have been extensively studied, the diversity of NLR genes in citrus remains largely unknown. Our analysis revealed significant variations in the copy numbers of NLR genes among these species. Gene duplication and recombination were identified as the major driving forces behind this diversity. Additionally, horizontal gene transfer (HGT) emerged as the principal mechanism responsible for the increase in NLR gene copy number in A. buxifolia. The citrus NLR genes were classified into four categories: TIR-NBS-LRR (TNL), CC-NBS-LRR (CNL), RPW8-NBS-LRR (RNL), and NL. Our findings indicate that TNL, RNL, and CNL genes originated from NL genes through the acquisition of TIR and RPW8 domains, along with CC motifs, followed by the random loss of corresponding domains. Phylogenetic analysis suggested that citrus NLR genes originated alongside the species and underwent adaptive evolution, potentially playing crucial roles in the global colonization of citrus. This study provides important insights into the diversity of citrus NLR genes and serves as a foundational dataset for future research aimed at breeding disease-resistant citrus varieties. Full article

Clubroot, a significant soil-borne disease, severely impacts the productivity of cruciferous crops. The identification and development of clubroot resistance (CR) genes are crucial for mitigating this disease. This study investigated the genetic inheritance of clubroot resistance within an F₂ progeny derived from the cross of a resistant parent, designated “377”, and a susceptible parent, designated “12A”. Notably, “377” exhibited robust resistance to the “KEL-23” strain of Plasmodiophora brassicae, the causative agent of clubroot. Genetic analyses suggested that the observed resistance is controlled by a single dominant gene. Through Bulked Segregant Analysis sequencing (BSA-seq) and preliminary gene mapping, we localized the CR gene locus, designated as BraPb8.3, to a 1.30 Mb genomic segment on chromosome A08, flanked by the markers “333” and “sau332-1”. Further fine mapping precisely narrowed down the position of BraPb8.3 to a 173.8 kb region between the markers “srt8-65” and “srt8-25”, where we identified 22 genes, including Bra020861 with a TIR-NBS-LRR domain and Bra020876 with an LRR domain. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) analyses confirmed that both Bra020861 and Bra020876 exhibit increased expression levels in the resistant parent “377” following inoculation with P. brassicae, thereby underscoring their potential as key genes implicated in BraPb8.3-mediated clubroot resistance. This study not only identifies molecular markers associated with BraPb8.3 but also enriches the genetic resources available for breeding programs aimed at enhancing resistance to clubroot. Full article

The recognition of pathogen effectors through the nucleotide-binding leucine-rich repeat receptor (NLR) family is an important component of plant immunity. In addition to typical domains such as TIR, CC, NBS, and LRR, NLR proteins also contain some atypical integrated domains (IDs), the roles of which are rarely investigated. Here, we carefully screened the soybean (Glycine max) genome and identified the IDs that appeared in the soybean TNL-like proteins. Our results show that multiple IDs (36) are widely present in soybean TNL-like proteins. A total of 27 Gm-TNL-ID genes (soybean TNL-like gene encoding ID) were cloned and their antiviral activity towards the soybean mosaic virus (SMV)/tobacco mosaic virus (TMV) was verified. Two resistance (R) genes, SRA2 (SMV resistance gene contains AAA_22 domain) and SRZ4 (SMV resistance gene contains zf-RVT domain), were identified to possess broad-spectrum resistance characteristics towards six viruses including SMV, TMV, plum pox virus (PPV), cabbage leaf curl virus (CaLCuV), barley stripe mosaic virus (BSMV), and tobacco rattle virus (TRV). The effects of Gm-TNL-ID^X (the domain of the Gm-TNL-ID gene after the TN domain) on the antiviral activity of a R protein SRC7^TN (we previously reported the TN domain of the soybean broad-spectrum resistance gene SRC7) were validated, and most of Gm-TNL-ID^X inhibits antiviral activity mediated by SRC7^TN, possibly through intramolecular interactions. Yeast-two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays showed that seven Gm-TNL-ID^X interacted with SMV-component proteins. Truncation analysis on a broad-spectrum antiviral protein SRZ4 indicated that SRZ4^TIR is sufficient to mediate antiviral activity against SMV. Soybean cDNA library screening on SRZ4 identified 48 interacting proteins. In summary, our results indicate that the integration of IDs in soybean is widespread and frequent. The NLR-ID toolkit we provide is expected to be valuable for elucidating the functions of atypical NLR proteins in the plant immune system and lay the foundation for the development of engineering NLR for plant-disease control in the future. Full article

Peanuts (Arachis hypogaea L.) are important high-protein and oil-containing legume crops adapted to arid to semi-arid regions. The yield and quality of peanuts are complex quantitative traits that show high environmental influence. In this study, a recombinant inbred line population (RIL) (Valencia-C × JUG-03) was developed and phenotyped for nine traits under two environments. A genetic map was constructed using 1323 SNP markers spanning a map distance of 2003.13 cM. Quantitative trait loci (QTL) analysis using this genetic map and phenotyping data identified seventeen QTLs for nine traits. Intriguingly, a total of four QTLs, two each for 100-seed weight (HSW) and shelling percentage (SP), showed major and consistent effects, explaining 10.98% to 14.65% phenotypic variation. The major QTLs for HSW and SP harbored genes associated with seed and pod development such as the seed maturation protein-encoding gene, serine-threonine phosphatase gene, TIR-NBS-LRR gene, protein kinase superfamily gene, bHLH transcription factor-encoding gene, isopentyl transferase gene, ethylene-responsive transcription factor-encoding gene and cytochrome P450 superfamily gene. Additionally, the identification of 76 major epistatic QTLs, with PVE ranging from 11.63% to 72.61%, highlighted their significant role in determining the yield- and quality-related traits. The significant G × E interaction revealed the existence of the major role of the environment in determining the phenotype of yield-attributing traits. Notably, the seed maturation protein-coding gene in the vicinity of major QTLs for HSW can be further investigated to develop a diagnostic marker for HSW in peanut breeding. This study provides understanding of the genetic factor governing peanut traits and valuable insights for future breeding efforts aimed at improving yield and quality. Full article

Fire blight, caused by Erwinia amylovora, is one of the most devastating apple diseases. The selection of cultivars of low susceptibility and the study of the genetic mechanisms of the disease play important roles in fire blight management. The susceptibility level to fire blight was evaluated in 102 accessions originating from Asturias, a cider-producing region located in the north of Spain with a wide apple germplasm. Evaluations took place under quarantine conditions using artificial inoculations of grafted plants. The results revealed wide variation in susceptibility responses and low-susceptible cultivars were identified. In addition, 91 cultivars were genotyped using the Affymetrix Axiom^® Apple 480 K SNP array to conduct genome-wide association studies (GWAS). A statistically significant signal was detected on chromosome 10 using the multi-locus mixed model (MLMM). Two genes were identified as major putative candidate genes: a TIR-NBS-LRR class disease protein and a protein containing a development and cell death (DCD) domain. The outcomes of this study provide a promising source of information, particularly in the context of cider apples, and set a starting point for future genetic and breeding approaches. Full article

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. Full article

Roses, which are one of the world’s most important ornamental plants, are often damaged by pathogens, resulting in serious economic losses. As a subclass of the disease resistance gene family of plant nucleotide-binding oligomerization domain (NOD)-like receptors, TIR-NBS-LRR (TNL) genes play a vital role in identifying pathogen effectors and activating defense responses. However, a systematic analysis of the TNL gene family is rarely reported in roses. Herein, 96 intact TNL genes were identified in Rosa chinensis. Their phylogenies, physicochemical characteristics, gene structures, conserved domains and motifs, promoter cis-elements, microRNA binding sites, and intra- and interspecific collinearity relationships were analyzed. An expression analysis using transcriptome data revealed that RcTNL genes were dominantly expressed in leaves. Some RcTNL genes responded to gibberellin, jasmonic acid, salicylic acid, Botrytis cinerea, Podosphaera pannosa, and Marssonina rosae (M. rosae); the RcTNL23 gene responded significantly to three hormones and three pathogens, and exhibited an upregulated expression. Furthermore, the black spot pathogen was identified as M. rosae. After inoculating rose leaves, an expression pattern analysis of the RcTNL genes suggested that they act during different periods of pathogen infection. The present study lays the foundations for an in-depth investigation of the TNL gene function and the mining of disease resistance genes in roses. Full article

Nucleotide-binding leucine-rich repeat sequence (NBS-LRR) protein is the main immune receptor in plants and participates in plant resistance to pathogens. When the NBS-LRR protein is activated by the pathogen’s effector protein, its conformation changes from an inhibitory state to an activated state, then it activates downstream signal transduction and initiates defense responses to inhibit the growth of pathogens. The NBS-LRR protein has major three domains: NBS, LRR and TIR/CC, which all play a certain role in the immune response induced by it. In this paper, the NBS-LRR protein domains and their functions, molecular mechanism of the induced immune response and its application in disease resistance breeding are reviewed. Full article

Cucurbits powdery mildew (CPM) is one of the main limiting factors of melon cultivation worldwide. Resistance to races 1, 2, and 5 has been reported in the African accession TGR-1551, whose resistance is controlled by a dominant–recessive epistasis. The dominant and recessive quantitative trail loci (QTL) have previously been located in chromosomes 5 and 12, respectively. We used several densely genotyped BC₃ families derived from the cross between TGR-1551 and the susceptible cultivar ‘Bola de Oro’ to finely map these resistance regions. The further phenotyping and genotyping of the selected BC₅, BC₅S₁, BC₅S₂, BC₄S₁, BC₄xPS, and (BC₄xPS) S₁ offspring allowed for the narrowing of the candidate intervals to a 250 and 381 kb region in chromosomes 5 and 12, respectively. Moreover, the temperature effect over the resistance provided by the dominant gene has been confirmed. High resolution melting markers (HRM) were tightly linked to both resistance regions and will be useful in marker-assisted selection programs. Candidate R genes with variants between parents that caused a potential modifier impact on the protein function were identified within both intervals. These candidate genes provide targets for future functional analyses to better understand the resistance to powdery mildew in melons. Full article

The green peach aphid (GPA), Myzus persicae, is an important pest of the peach crop. Three major dominant resistance genes have already been detected, Rm1 in the Weeping Flower Peach (WFP) clone, Rm2 in the Rubira clone, and Rm3 in the Fen Shouxing clone. In this study, after NGS resequencing of WFP and Rubira, we found that their genomic sequences in the Rm1 and Rm2 region were similar but very different from that of the susceptible reference peach Lovell. We constructed a BAC library for the GPA-resistant WFP and screened four BAC clones to sequence the target region. The new sequence was 61.7 Kb longer than Lovell and was annotated with four different TIR_NBS_LRR genes. Among them, the TNL1 gene was very overexpressed in WFP leaves 24 h after GPA infestation. This gene was also present and expressed in the Rubira clone and had the same sequence as the candidate Rm3 gene, supporting the hypothesis that the three genes share the same origin. In addition, we identified a second TNL, TNL2, located at 35.4 Kb from TNL1 and slightly overexpressed after GPA infestation. Kasp and size molecular markers were designed for use in marker-assisted selection and were validated in a peach segregating population. Full article

Orobanche cumana is a root alloparasitic plant that drastically reduces sunflower (Helianthus annuus) production. In this study, transcriptomic changes of O. cumana-resistant (HZ2399) and O. cumana-sensitive (SQ25) sunflower seedlings were investigated at six time points (0–72 h) following O. cumana infection. The process of resistance to O. cumana was similar in HZ2399 and SQ25 seedlings, however, significantly higher regulatory activity was observed in the resistant plants. In HZ2399, most of the 54 upregulated genes were involved in phenylpropanoid biosynthesis, plant–pathogen interaction, and plant hormone signal transduction pathways. These genes were mainly associated with antioxidant responses, responses to stress, stimulation responses, and metabolic processes. The expression level of the three most significantly upregulated genes in HZ2399 (4CL2, EDS1, and TGA3) was significantly higher than that of SQ25, suggesting that they may be the main causes of O. cumana immunity in HZ2399. It is hypothesized that sunflower resistance to O. cumana parasitism is dependent on salicylic acid (SA), a disease resistance protein (TIR-NBS-LRR class) family (RPS4), and EDS1. The results of this study contribute to elucidating the mechanism of O. cumana resistance in sunflower and for the molecular breeding of O. cumana resistance. Full article