Search Results (69)

Lignocellulosic biomass may play a major role in the production of biofuels, bioplastics, sugar, paper, and various other industrial products. In addition, it is a key trait in plants due to its contribution to lodging resistance. Fiber also shows a significant negative correlation with most yield traits and all sugar traits. As the most harvested crop globally by tonnage, sugarcane is an important resource for both sugar and bioenergy production. In this study, a panel of sugarcane clones was utilized to investigate the fiber content. This panel included 17 core parental lines derived from 11 countries involved in sugarcane cultivation and breeding. It represented the genetic base of commercial sugarcane breeding programs in China and other countries. The objective of this research was to identify molecular markers and candidate genes associated with fiber content in sugarcane using genome-wide association studies (GWASs). By integrating 5,964,084 high-quality single-nucleotide polymorphisms (SNPs) with phenotypic data collected across five different environments, a total of 69 SNPs spanning 41 quantitative trait loci (QTLs) were identified. Based on functional annotations and genomic positions, these QTLs contained 52 candidate genes. These candidate genes encoded the ultraviolet-B receptor (UVR8), leucine-rich repeat receptor-like kinases (LRR-RLKs), serine/threonine kinases (STKs), cellulose synthase (CESA), vegetative cell wall protein glycoproteins1 (gp1), F-box protein, MYB transcription factor, and so on. These genes could directly or indirectly influence the fiber content in sugarcane. Furthermore, according to previous studies, among these candidate genes, five located in four QTL regions were proposed to be the most critical. They included Sspon.02G0041160-2C, encoding CESA; Sspon.03G0039010-1C and Sspon.03G0039030-1C, both encoding gp1; Sspon.06G0023090-1B, encoding an F-box protein; and Sspon.07G0019440-2C, encoding a MYB transcription factor. The genetic basis of the fiber content was explored using elite breeding lines and their derivatives from the Chinese sugarcane breeding program. These candidate genes represent promising targets for future functional studies and may contribute to the development of different types of sugarcane varieties with correspondingly suitable fiber content through marker-assisted selection. Full article

This study identifies and classifies resistance gene analogues (RGAs) in the genomes of Brassica nigra, Sinapis arvensis and Sinapis alba using the RGAugury pipeline. RGAs were categorised into four main classes: receptor-like kinases (RLKs), receptor-like proteins (RLPs), nucleotide-binding leucine-rich repeat (NLR) proteins and transmembrane-coiled-coil (TM-CC) genes. A total of 4499 candidate RGAs were detected, with species-specific proportions. RLKs were the most abundant across all genomes, followed by TM-CCs and RLPs. The sub-classification of RLKs and RLPs identified LRR-RLKs, LRR-RLPs, LysM-RLKs, and LysM-RLPs. Atypical NLRs were more frequent than typical ones in all species. Atypical NLRs were more frequent than typical ones in all species. We explored the relationship between chromosome size and RGA count using regression analysis. In B. nigra and S. arvensis, larger chromosomes generally harboured more RGAs, while S. alba displayed the opposite trend. Exceptions were observed in all species, where some larger chromosomes contained fewer RGAs in B. nigra and S. arvensis, or more RGAs in S. alba. The distribution and density of RGAs across chromosomes were examined. RGA distribution was skewed towards chromosomal ends, with patterns differing across RGA types. Sequence hierarchical pairwise similarity analysis revealed distinct gene clusters, suggesting evolutionary relationships. The study also identified homologous genes among RGAs and non-RGAs in each species, providing insights into disease resistance mechanisms. Finally, RLKs and RLPs were co-localised with reported disease resistance loci in Brassica, indicating significant associations. Phylogenetic analysis of cloned RGAs and QTL-mapped RLKs and RLPs identified distinct clusters, enhancing our understanding of their evolutionary trajectories. These findings provide a comprehensive view of RGA diversity and genomics in these Brassicaceae species, providing valuable insights for future research in plant disease resistance and crop improvement. Full article

Atherosclerosis (AS), a progressive inflammatory disease of coronary arteries, the aorta, and the internal carotid artery, is considered one of the main contributors to cardiovascular disorders. Blood flow is restricted by accumulating lipid-rich macrophages (foam cells), calcium, fibrin, and cellular debris into plaques on the intima of arterial walls. Butyrate maintains gut barrier integrity and modulates immune responses. Butyrate regulates G-protein-coupled receptor (GPCR) signaling and activates nuclear factor kappa-B (NF-κB), activator protein-1 (AP-1), and interferon regulatory factors (IFRs) involved in the production of proinflammatory cytokines. Depending on the inflammatory stimuli, butyrate may also inactivate NF-κB, resulting in the suppression of proinflammatory cytokines and the stimulation of anti-inflammatory cytokines. Butyrate modulates mitogen-activated protein kinase (MAPK) to promote or suppress macrophage inflammation, muscle cell growth, apoptosis, and the uptake of oxidized low-density lipoprotein (ox-LDL) in macrophages. Activation of the peroxisome proliferator-activated receptor γ (PPARγ) pathway plays a role in lipid metabolism, inflammation, and cell differentiation. Butyrate inhibits interferon γ (IFN-γ) signaling and suppresses NOD-, LRR-, and pyrin domain-containing protein 3 (NLRP3) involved in inflammation and scar tissue formation. The dual role of butyrate in AS is discussed by addressing the interactions between butyrate, intestinal epithelial cells (IECs), endothelial cells (ECs) of the main arteries, and immune cells. Signals generated from these interactions may be applied in the diagnosis and intervention of AS. Reporters to detect early AS is suggested. This narrative review covers the most recent findings published in PubMed and Crossref databases. Full article

Wheat (Triticum aestivum L.), a staple crop of global significance, faces constant biotic stress threats, with powdery mildew caused by Blumeria graminis f. sp. tritici (Bgt) being particularly damaging. In this study, a multi-year single-site experiment was conducted to minimize the environmental impacts, and a five-level classification system was used to assess powdery mildew resistance. A 660K SNP array genotyped 204 wheat germplasms, followed by GWAS. SNP loci with a −log₁₀(p) > 3.0 were screened and validated across repeats to identify those associated with powdery mildew (Pm) resistance. Twelve SNPs were consistently associated with Pm resistance across multiple years. Of these, three colocalized with previously reported Pm-resistance gene or QTL regions, and the remaining nine represented potentially novel loci. The candidate genes identified included leucine-rich repeat (LRR) and NB-ARC immune receptors, as well as pathogen-related, thioredoxin, and serine threonine-protein kinase genes. Overall, the SNP loci and candidate genes identified in this study provide a basis for further fine mapping and cloning of the genes involved in relation to Pm resistance. Full article

Leucine-rich repeat receptor-like kinases (LRR-RLKs) have evolved to perceive environmental changes. Among LRR-RLKs, PEPR1 perceives the pep1 peptide and triggers defense signal transduction in Arabidopsis thaliana. In the present study, we focused on PEPR1 and PEPR2, which are the receptors of pep1, to understand the role of tyrosine phosphorylation. PEPR1-CD (cytoplasmic domain) recombinant protein exhibited strong tyrosine autophosphorylation, including threonine autophosphorylation. We subjected all tyrosine residues in PEPR1-CD to site-directed mutagenesis. The recombinant proteins were purified along with PEPR1-CD, and Western blotting was performed using a tyrosine-specific antibody. Among the 13 tyrosine residues in PEPR1-CD, the PEPR1(Y995F)-CD recombinant protein showed significantly reduced tyrosine autophosphorylation intensity compared to PEPR1-CD and other tyrosine mutants, despite little change in threonine autophosphorylation. To confirm the autophosphorylation site, we generated a phospho-specific peptide Ab, pY995. As a result, Tyr-995 of PEPR1-CD was a major tyrosine autophosphorylation site in vitro. To understand the function of tyrosine phosphorylation in vivo, we generated transgenic plants, expressing PEPR1-Flag, PEPR1(Y995F)-Flag, and PEPR1(Y995D)-Flag in a pepr1/2 double mutant background. Interestingly, the root growths of PEPR1(Y995F)-Flag and PEPR1(Y995D)-Flag were not inhibited by pep1 peptide treatment, compared to Col-0 and PEPR1-Flag (pepr1/2) transgenic plants. Also, we analyzed downstream components, which included PROPEP1, MPK3, WRKY33, and RBOHD gene expressions in four different genotypes (Col-0, PEPR1-Flag, PEPR1(Y995F)-Flag, and PEPR1(Y995D)-Flag) of plants in the presence of the pep1 peptide. Interestingly, the expressions of PROPEP1, MPK3, WRKY33, and RBOHD were not regulated by pep1 peptide treatment in PEPR1(Y995F)-Flag and PEPR1(Y995D)-Flag transgenic plants, in contrast to Col-0 and PEPR1-Flag. These results suggest that specific tyrosine residues play an important role in vivo in the plant receptor function. Full article

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

Leucine-rich repeat receptor-like kinases (LRR-RLKs) are involved in the regulation of various biological processes, including plant growth, development, and responses to biotic and abiotic stresses. Foxtail millet (Setaria italica), an important cereal crop, has been extensively studied for its stress tolerance mechanisms. In this study, we performed a comprehensive phylogenetic analysis and chromosomal mapping of LRR-RLK genes in Setaria italica. A total of 285 SiLRR-RLK genes were identified and classified into 12 subfamilies based on phylogenetic relationships. Chromosome localization analysis revealed that SiLRR-RLK genes are unevenly distributed across the chromosomes, with certain regions showing gene clusters. Functional analysis of these genes under biotic and abiotic stress conditions suggested that several SiLRR-RLK family members are involved in key stress response pathways. Expression profiling indicated differential expression patterns of SiLRR-RLK genes in response to various stresses, including drought, salinity, and pathogen infection, highlighting their potential roles in stress adaptation. In conclusion, the phylogenetic and functional analysis of the SiLRR-RLK gene family in Setaria italica provides valuable insights into their roles in stress responses and lays the groundwork for future studies aimed at enhancing stress tolerance in foxtail millet. Full article

As one of the largest gene families in plants, the Leucine-Rich Repeat Receptor-Like Kinase (LRR-RLK) genes are involved in important biological processes, such as plant growth and development and response to bio-/abiotic stresses. The rubber tree (Hevea brasiliensis Müll. Arg.) is the primary commercial source of natural rubber globally. In this study, 274 LRR-RLK genes were comprehensively identified and classified into 21 subclades of the rubber tree genome. Members belonging to the same subclade exhibited comparable gene structures and possessed conserved protein motifs. Gene duplication analysis detected 35 tandem duplication genes and 81 segmental duplication genes. Cis-element analysis of HbLRR-RLK promoters identified light, hormone, stress, and development-related cis-elements. Tissue-specific expression profiling revealed that 73% (200/274) of HbLRR-RLKs were expressed in at least one of seven analyzed tissues. Protein–protein interaction (PPI) network identified 584 potential interactions among the HbLRR-RLKs. Additionally, subcellular localization analysis suggested that HbPSKR2 (HbLRR-RLK174) is a plasma membrane-localized receptor, and the gene could restore the short-root phenotype of the atpskr mutant in Arabidopsis. These results provide a comprehensive structure to facilitate analysis of the evolution and functional diversification of LRR-RLKs in the rubber tree. Full article

Salt stress is an environmental factor that limits plant seed germination, growth, and survival. We performed a comparative RNA sequencing transcriptome analysis during germination of the seeds from two cultivars with contrasting salt tolerance responses. A transcriptomic comparison between salt-tolerant cotton cv Jin-mian 25 and salt-sensitive cotton cv Su-mian 3 revealed both similar and differential expression patterns between the two genotypes during salt stress. The expression of genes related to aquaporins, kinases, reactive oxygen species (ROS) scavenging, trehalose biosynthesis, and phytohormone biosynthesis and signaling that include ethylene (ET), gibberellin (GA), abscisic acid (ABA), jasmonic acid (JA), and brassinosteroid (BR) were systematically investigated between the cultivars. Despite the involvement of these genes in cotton’s response to salt stress in positive or negative ways, their expression levels were mostly similar in both genotypes. Interestingly, a PXC2 gene (Ghir_D08G025150) was identified, which encodes a leucine-rich repeat receptor-like protein kinase (LRR-RLK). This gene showed an induced expression pattern after salt stress treatment in salt-tolerant cv Jin-mian 25 but not salt-sensitive cv Su-mian 3. Our multifaceted transcriptome approach illustrated a differential response to salt stress between salt-tolerant and salt-sensitive cotton. 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

Blackgram is an important short-duration grain legume, but its yield is highly affected by various stresses. Among biotic stresses, yellow mosaic disease (YMD) is known as a devastating disease that leads to 100% yield loss under severe conditions. The cultivated lines possess resistance, but exploring more diverse sources of resistance may be useful for pyramiding to improve the durability of said resistance. Some wild Vigna species have potentially demonstrated a high level of resistance. R-genes, including gene families of leucine-rich repeats (LRRs) and leucine-rich repeat receptor-like kinases (LRR-RLKs), are known for modulating the resistance in plants against various biotic stresses. The first comprehensive analysis of the LRR and LRR-RLK gene families in mungbean is reported in the present study. A total of forty-six candidate genes were identified and grouped into eight clades. Protein motif analysis showed that the “Pkinase domain” and “LRR domains” were conserved in most of the R-proteins. The expression of candidate genes viz. VrNBS_TNLRR-8, VrLRR_RLK-20, VrLRR_RLK-17, and VrLRR_RLK-19 demonstrated significantly up-regulated expression upon YMD infection in control and salicylic acid-primed (SA-primed) plants. The analysis provides insight into the diversity and robust candidate genes for functional studies modulating YMD resistance altered by salicylic acid. Full article

Verticillium dahliae is a soil-borne phytopathogenic fungus causing destructive Verticillium wilt disease that greatly threats cotton production worldwide. The mechanism of cotton resistance to Verticillium wilt is very complex and requires further research. In this study, RNA-sequencing was used to investigate the defense responses of cotton leaves using varieties resistant (Zhongzhimian 2, or Z2) or susceptible (Xinluzao 7, or X7) to V. dahliae. The leaf samples were collected at 48 and 72 hpi (hours post infection) from the two varieties infected by V. dahliae (strain Vd991) or treated by water. Compared to X7, Z2 had less genes responsive to V. dahliae infection at 72 hpi and had no DEGs (differentially expressed genes) at 48 hpi. WGCNA (Weighted Gene Co-Expression Network Analysis) revealed seven key gene modules which were responsible for the resistance of Z2 and susceptibility of X7. KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis of these modules found that several reported disease resistance pathways were found to be up-regulated in Z2, with some of those pathways down-regulated in X7. Unexpectedly, several photosynthesis-related pathways were significantly up-regulated in the leaves of X7 infected by V. dahliae, leading to different profiles of glucose content, which was significantly decreased at 72 hpi and 48 hpi in X7 and Z2, respectively. These results suggest that the leaves of resistant varieties have a slower and different response to V. dahliae compared to those of the susceptible variety, as well as that the translocation of sugars produced by photosynthesis in cotton leaves might vary between the two varieties. Additionally, several HUB genes regulating disease response were identified, including NDR1/HIN1-like protein 12, DELLA protein, cytochrome P450 family protein and LRR receptor-like serine/threonine-protein kinase genes, which have been reported to be related to disease resistance in other plants, which might serve as potential candidates for breeding cotton disease resistance. Full article

Rice (Oryza sativa L.) feeds half the world’s population and serves as one of the most vital staple food crops globally. The brown planthopper (BPH, Nilaparvata lugens Stål), a major piercing–sucking herbivore specific to rice, accounts for large yield losses annually in rice-growing areas. Developing rice varieties with host resistance has been acknowledged as the most effective and economical approach for BPH control. Accordingly, the foremost step is to identify BPH resistance genes and elucidate the resistance mechanism of rice. More than 70 BPH resistance genes/QTLs with wide distributions on nine chromosomes have been identified from rice and wild relatives. Among them, 17 BPH resistance genes were successfully cloned and principally encoded coiled-coil nucleotide-binding leucine-rich repeat (CC-NB-LRR) protein and lectin receptor kinase (LecRK), as well as proteins containing a B3 DNA-binding domain, leucine-rich repeat domain (LRD) and short consensus repeat (SCR) domain. Multiple mechanisms contribute to rice resistance against BPH attack, including transcription factors, physical barriers, phytohormones, defense metabolites and exocytosis pathways. Plant hormones, including jasmonic acid (JA), salicylic acid (SA), ethylene (ET), abscisic acid (ABA), gibberellins (GAs), cytokinins (CKs), brassinosteroids (BRs) and indoleacetic-3-acid (IAA), play crucial roles in coordinating rice defense responses to the BPH. Here, we summarize some recent advances in the genetic mapping, cloning and biochemical mechanisms of BPH resistance genes. We also review the latest studies on our understanding of the function and crosstalk of phytohormones in the rice immune network against BPHs. Further directions for rice BPH resistance studies and management are also proposed. Full article

Alternative splicing (AS) is a prevalent post-transcriptional regulatory mechanism in eukaryotes and plays a crucial role in plant disease resistance. Here, we used the Illumina Novaseq sequencing platform to conduct transcriptome sequencing on canola (Brassica napus) leaves infected with the blackleg pathogen (Leptosphaeria biglobosa strain nm⁻¹) at 0 h, 72 h, 120 h, and 168 h post-inoculation to investigate the mechanism of AS coordination with transcriptional regulation in canola’s response to blackleg disease. The rMATS software (4.1.0) was employed to analyze different AS events in samples taken at 72 h, 120 h, and 168 h. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed to elucidate the biological functions of differentially spliced genes at various time points, while Weighted Gene Co-expression Network Analysis (WGCNA) was used to identify key modules and hub genes. As a result, our analysis reveals 16908 AS events across three time points, with 221 being differently spliced. Intron retention (RI) was the most common AS event, accounting for approximately 55% of all events, while alternative 5′ splice site events were least common, comprising only 2%. Furthermore, a total of 213 significantly differentially spliced genes were identified, which were enriched in functions related to protein kinase activity, transferase activity, and pathways such as MAPK signaling pathway—plant and plant hormone signal transduction. WGCNA identified three key modules and ten hub genes, including calcium-binding transcription activator 1, LRR class receptor serine/threonine protein kinase FEI 2, PLATZ transcription factor family proteins, serine/threonine protein kinase PRP4, and E3 ubiquitin ligase SUD1, all of which are associated with canola resistance to L. biglobosa. Thus, this study provides a theoretical basis for identifying disease-resistance genes involved in AS and for exploring the functions of AS gene isoforms in canola. Full article

Cotton is one of the world’s leading fiber crops, but climate change, drought, heat, and salinity have significantly decreased its production, consequently affecting the textile industries globally. To acclimate to these environmental challenges, a number of gene families involved in various molecular, physiological, and hormonal mechanisms play crucial roles in improving plants response to various abiotic stresses. One such gene family is the GhSRF, a Strubbelig-Receptor family (SRF), and member of the leucine-rich repeat (LRR-V) group. This family encodes leucine-rich repeat transmembrane receptor-like kinases (LRR-RLKs) and have not yet been explored in cotton. Arabidopsis thaliana Strubbelig-Receptor gene sequences were used as queries to identify the homologs in cotton, with subsequent support from the literature and functional prediction through online data. In the current study, a comprehensive genome-wide analysis of cotton was conducted, identifying 22 SRF putative proteins encoded by 22 genes. We performed the detailed analysis of these proteins, including phylogeny, motif and gene structure characterization, promoter analysis, gene mapping on chromosomes, gene duplication events, and chromosomal sub-cellular localization. Expression analysis of putative genes was performed under drought and heat stress conditions using publicly available RNAseq data. The qRT-PCR results showed elevated expression of GhSRF2, GhSRF3, GhSRF4, GhSRF10, and GhSRF22 under drought and heat stress. So, it could be speculated that these genes may play a role in drought and heat tolerance in cotton. These findings could be helpful in cotton breeding programs for the development of climate-resilient cultivars. Full article