Different scales of gene duplications occurring at different times have jointly shaped the NBS-LRR genes in Prunus species

In this study, genome-wide identification, phylogenetic relationships, duplication time and selective pressure of the NBS-LRR genes, an important group of plant disease-resistance genes (R genes), were performed to uncover their genetic evolutionary patterns in the six Prunus species. A total of 1946 NBS-LRR genes were identified; specifically, 589, 361, 284, 281, 318, and 113 were identified in Prunus yedoensis, P. domestica, P. avium, P. dulcis, P. persica and P. yedoensis var. nudiflora, respectively. Two NBS-LRR gene subclasses, TIR-NBS-LRR (TNL) and non-TIR-NBS-LRR (non-TNL), were also discovered. In total, 435 TNL and 1511 non-TNL genes were identified and could be classified into 30/55/75 and 103/158/191 multi-gene families, respectively, according to three different criteria. Higher Ks and Ka/Ks values were detected in TNL gene families than in non-TNL gene families. These results indicated that the TNL genes had more members involved in relatively ancient duplications and were affected by stronger selection pressure than the non-TNL genes. In general, the NBS-LRR genes were shaped by species-specific duplications, and lineage-specific duplications occurred at recent and relatively ancient periods among the six Prunus species. Therefore, different duplicated copies of NBS-LRRs can resist specific pathogens and will provide an R-gene library for resistance breeding in Prunus species.

Select and Sequence of a Segregating Sugar Beet Population Provides Genomic Perspective of Host Resistance to Seedling Rhizoctonia solani Infection

Understanding the genetic basis of polygenic traits is a major challenge in agricultural species, especially in non-model systems. Select and sequence (SnS) experiments carried out within existing breeding programs provide a means to simultaneously identify the genomic background of a trait while improving the mean phenotype for a population. Using pooled whole genome sequencing (WGS) of selected and unselected bulks derived from a synthetic outcrossing sugar beet population EL57 (PI 663212), which segregates for seedling rhizoctonia resistance, we identified a putative genomic background involved in conditioning a resistance phenotype. Population genomic parameters were estimated to measure fixation (He), genome divergence (FST), and allele frequency changes between bulks (DeltaAF). We report on the genome wide patterns of variation resulting from selection and highlight specific genomic features associated with resistance. Expected heterozygosity (He) showed an increased level of fixation in the resistant bulk, indicating a greater selection pressure was applied. In total, 1,311 biallelic loci were detected as significant FST outliers (p < 0.01) in comparisons between the resistant and susceptible bulks. These loci were detected in 206 regions along the chromosomes and contained 275 genes. We estimated changes in allele frequency between bulks resulting from selection for resistance by leveraging the allele frequencies of an unselected bulk. DeltaAF was a more stringent test of selection and recovered 186 significant loci, representing 32 genes, all of which were also detected using FST. Estimates of population genetic parameters and statistical significance were visualized with respect to the EL10.2 physical map and produced a candidate gene list that was enriched for function in cell wall metabolism and plant disease resistance, including pathogen perception, signal transduction, and pathogen response. Specific variation associated with these genes was also reported and represents genetic markers for validation and prediction of resistance to Rhizoctonia. Select and sequence experiments offer a means to characterize the genetic base of sugar beet, inform selection within breeding programs, and prioritize candidate variation for functional studies.

Use of Lentinan and Fluopimomide to Control Cotton Seedling Damping-Off Disease Caused by Rhizoctonia solani

Lentinan (LNT) is a natural and functional polysaccharide isolated from Lentinus edodes fruiting bodies, which functions in stimulating the plant immune response, improving plant disease resistance and regulating plant growth. This study explores the use of LNT as a plant growth regulator and attractant in cotton production. After treatment with LNT, the content of malondialdehyde (MDA) in cotton seeds decreased, whereas the activities of polyphenol oxidase (PPO), superoxide dismutase (SOD) and peroxidase (POD) in leaves increased significantly. LNT also promoted the growth and development of cotton plants and significantly reduced the incidence of cotton damping-off disease. The relative expression of salicylic acid pathway-related genes in cotton also increased significantly. The prevention mechanism of fluopimomide was also evaluated, and the result showed lower EC50 values and was effective in controlling cotton seedling disease caused by Rhizoctonia solani in both greenhouse experiments and field trials. The use of LNT and fluopimomide in controlling cotton seedling damping-off disease showed a synergistic effect in field trials. These results will provide a new insight into the agricultural application of LNT as a biological fungicide in the field of biological controls.

DeepLRR: An Online Webserver for Leucine-Rich-Repeat Containing Protein Characterization Based on Deep Learning

Members of the leucine-rich repeat (LRR) superfamily play critical roles in multiple biological processes. As the LRR unit sequence is highly variable, accurately predicting the number and location of LRR units in proteins is a highly challenging task in the field of bioinformatics. Existing methods still need to be improved, especially when it comes to similarity-based methods. We introduce our DeepLRR method based on a convolutional neural network (CNN) model and LRR features to predict the number and location of LRR units in proteins. We compared DeepLRR with six existing methods using a dataset containing 572 LRR proteins and it outperformed all of them when it comes to overall F1 score. In addition, DeepLRR has integrated identifying plant disease-resistance proteins (NLR, LRR-RLK, LRR-RLP) and non-canonical domains. With DeepLRR, 223, 191 and 183 LRR-RLK genes in Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa ssp. Japonica) and tomato (Solanum lycopersicum) genomes were re-annotated, respectively. Chromosome mapping and gene cluster analysis revealed that 24.2% (54/223), 29.8% (57/191) and 16.9% (31/183) of LRR-RLK genes formed gene cluster structures in Arabidopsis, rice and tomato, respectively. Finally, we explored the evolutionary relationship and domain composition of LRR-RLK genes in each plant and distributions of known receptor and co-receptor pairs. This provides a new perspective for the identification of potential receptors and co-receptors.

Expression Analysis Reveals That Sorghum Disease Resistance Protein SbSGT1 Is Regulated by Auxin

SGT1 (suppressor of the skp1 G2 allele) is an important plant disease resistance-related protein, which plays an important role in plant resistance to pathogens and regulates signal transduction during the process of plant disease resistance. In this study, we analyzed the expression profile of SbSGT1 in sorghum under phytohormones treatment. Quantitative real-time PCR results showed that SbSGT1 was most expressed in sorghum leaves, and could respond to plant hormones such as auxin, abscisic acid, salicylic acid, and brassinolide. Subsequently, we determined the optimal soluble prokaryotic expression conditions for SbSGT1 and purified it using a protein purification system in order to evaluate its potential interactions with plant hormones. Microscale thermophoretic analysis showed that SbSGT1 exhibited significant interactions with indole-3-acetic acid (IAA), with a Kd value of 1.5934. Furthermore, the transient expression of SbSGT1 in Nicotiana benthamiana indicated that treatment with exogenous auxin could inhibit SbSGT1 expression, both at the transcriptional and translational level, demonstrating that there exists an interaction between SbSGT1 and auxin.

Importance of the Natural Incidence of the Fusarium Genus in Food Crops Established in Northern México

The incidence of the Fusarium genus causing root rot is reviewed in crops showing high importance for food supply and to obtain regular income by farmers in the highlands of Northern México. Pathogen incidence was evaluated under field conditions in multiple sampling locations for common beans (Phaseolus vulgaris L.) and several chili peppers (Capsicum annuum) local cultivars (landraces and bred cultivars). Five commercial plots for registered and certified seed were also evaluated in common beans to be used in the ‘seed refreshing program’ implemented for the cultivar Pinto Saltillo, considered as the main variety sown in the highlands of México. High Fusarium genus incidence and its interactions with other fungi species, such as Rhizoctonia solani and Pythium spp., cause high losses in plant population, commercial yield and seed quality in food crops grown in Northern México. The natural incidence of plant disease caused by the Fusarium genus and its negative effect on crop survival and the reduction of commercial yield and seed quality is fully reviewed. Plant disease resistance, crop breeding and the influence of the environmental conditions were also considered.

Transcriptome Analysis of Eucalyptus grandis Implicates Brassinosteroid Signaling in Defense Against Myrtle Rust (Austropuccinia psidii)

Eucalyptus grandis, in its native Australian range, varies in resistance to Austropuccinia psidii (syn. Puccinia psidii). The biotrophic rust fungus, A. psidii is the causal agent of myrtle rust and poses a serious threat to Australian biodiversity. The pathogen produces yellow pustules of urediniospores on young leaves and shoots, resulting in shoot tip dieback, stunted growth, and death. Dissecting the underlying mechanisms of resistance against this pathogen will contribute to improved breeding and control strategies to mitigate its devastating effects. The aim of this study was to determine the molecular dialogue between E. grandis and A. psidii, using an RNA-sequencing approach. Resistant and susceptible E. grandis seedlings grown from seed collected across its natural range were inoculated with the pandemic biotype of A. psidii. The leaf tissue was harvested at 12-h post inoculation (hpi), 1-day post inoculation (dpi), 2-dpi and 5-dpi and subjected to RNA-sequencing using Illumina 50 bp PE reads to a depth of 40 million reads per sample. Differential gene expression and gene ontology enrichment indicated that the resistant seedlings showed controlled, coordinated responses with a hypersensitive response, while the susceptible seedlings showed no systemic response against myrtle rust. Brassinosteroid signaling was apparent as an enriched term in the resistant interaction at 2-dpi, suggesting an important role of this phytohormone in defense against the pathogen. Brassinosteroid mediated signaling genes were also among the candidate genes within two major disease resistance loci (Puccinia psidii resistance), Ppr3 and Ppr5. While brassinosteroids have been tagged as positive regulators in other plant disease resistance interactions, this is the first report in the Eucalyptus – Austropuccinia psidii interaction. Furthermore, several putative resistance genes, underlying known resistance loci and implicated in the interaction have been identified and highlighted for future functional studies. This study provided further insights into the molecular interactions between E. grandis and A. psidii, contributing to our understanding of this pathosystem.

Fungal oxysterol-binding protein-related proteins promote pathogen virulence and activate plant immunity

Oxysterol-binding protein-related proteins (ORPs) are a conserved class of lipid transfer proteins that are closely involved in multiple cellular processes in eukaryotes but their roles in plant-pathogen interactions are mostly unknown. We showed that transient expression of ORPs of Magnaporthe oryzae (MoORPs) in Nicotiana benthamina plants triggered oxidative burst and cell death; treatment of tobacco Bright Yellow-2 suspension cells with recombinant MoORPs elicited the production of reactive oxygen species. Despite that ORPs are normally described as intracellular proteins, we detected MoORPs in fungal cultural filtrates and intercellular fluids from barley plants infected with the fungus. More importantly, infiltration of Arabidopsis plants with recombinant Arabidopsis or fungal ORPs activated oxidative burst, callose deposition, PR1 gene expression, and enhanced plant disease resistance, implying that ORPs may function as endogenous and exogenous danger signals triggering plant innate immunity. Extracellular application of fungal ORPs exerted an opposite impact on salicylic acid and jasmonic acid/ethylene signaling pathways. The Brassinosteroid Insensitive 1-associated Kinase 1 was dispensable for the ORP-activated defense. Besides, simultaneous knockout of MoORP1 and MoORP3 abolished fungal colony radial growth and conidiation, whereas double knockout of MoORP1 and MoORP2 compromised fungal virulence on barley and rice plants. These observations collectively highlight the multifaceted role of MoORPs in the modulation of plant innate immunity and promotion of fungal development and virulence in M. oryzae.

Ubiquitin Ligase SmDDA1b of Eggplant (Solanum melongena) Enhances Bacterial Wilt Resistance via SmNAC Degradation

Bacterial wilt (BW) is a soil-borne disease that severely impacts plant growth and productivity globally. Ubiquitination plays a crucial role in disease resistance. Our previous research indicated that NAC transcription factor SmNAC negatively regulates BW resistance in eggplant (Solanum melongena). However, whether the ubiquitin/26S proteasome system (UPS) participates in this regulation is unknown.This study used SmNAC as a bait to screen eggplant cDNA library and obtained SmDDA1b, an E3 ubiquitin ligase. Subcellular location and bimolecular fluorescence complementation assays revealed that SmDDA1b could interact with SmNAC in the nucleus. The in vivo and in vitro ubiquitination experiments indicated that SmDDA1b can degrade SmNAC through UPS. However, the discovery of negative regulation of SmDDA1b expression by SmNAC showed that there was a negative feedback loop between SmNAC and SmDDA1b in eggplant.The SmDDA1b-overexpressed lines showed a higher BW resistance associated with high expression levels of salicylic acid (SA)-related genes and SA content than the wild-type lines. However, SmDDA1b-silencing lines showed the opposite results, indicating that SmDDA1b is a positive regulatory gene for BW resistance.This study provides a candidate gene that can enhance BW resistance in eggplants. In addition, it provides insight into a mechanism that promotes plant disease resistance via the SmDDA1b-SmNAC-SA pathway.