Characterization and Pathogenicity of Rhizoctonia solani Isolates Affecting Pisum sativum in North Dakota

Assessment of Genetic Variability and Evolutionary Relationships of Rhizoctonia solani Inherent in Legume Crops

Rhizoctonia solani is one of the most common soil-borne fungal pathogens of legume crops worldwide. We collected rDNA-ITS sequences from NCBI GenBank, and the aim of this study was to examine the genetic diversity and phylogenetic relationships of various R. solani anastomosis groups (AGs) that are commonly associated with grain legumes (such as soybean, common bean, pea, peanut, cowpea, and chickpea) and forage legumes (including alfalfa and clover). Soybean is recognized as a host for multiple AGs, with AG-1 and AG-2 being extensively investigated. This is evidenced by the higher representation of sequences associated with these AGs in the NCBI GenBank. Other AGs documented in soybean include AG-4, AG-7, AG-11, AG-5, AG-6, and AG-9. Moreover, AG-4 has been extensively studied concerning its occurrence in chickpea, pea, peanut, and alfalfa. Research on the common bean has been primarily focused on AG-2, AG-4, and AG-1. Similarly, AG-1 has been the subject of extensive investigation in clover and cowpea. Collectively, AG-1, AG-2, and AG-4 have consistently been identified and studied across these diverse legume crops. The phylogenetic analysis of R. solani isolates across different legumes indicates that the distinct clades or subclades formed by the isolates correspond to their specific anastomosis groups (AGs) and subgroups, rather than being determined by their host legume crop. Additionally, there is a high degree of sequence similarity among isolates within the same clade or subclade. Principal coordinate analysis (PCoA) further supports this finding, as isolates belonging to the same AGs and/or subgroups cluster together, irrespective of their host legume. Therefore, the observed clustering of R. solani AGs and subgroups without a direct association with the host legume crop provides additional support for the concept of AGs in understanding the genetic relationships and evolution of R. solani.

Leguminous Seedborne Pathogens: Seed Health and Sustainable Crop Management

Pulses have gained popularity over the past few decades due to their use as a source of protein in food and their favorable impact on soil fertility. Despite being essential to modern agriculture, these species face a number of challenges, such as agronomic crop management and threats from plant seed pathogens. This review's goal is to gather information on the distribution, symptomatology, biology, and host range of seedborne pathogens. Important diagnostic techniques are also discussed as a part of a successful process of seed health certification. Additionally, strategies for sustainable control are provided. Altogether, the data collected are suggested as basic criteria to set up a conscious laboratory approach.

Global distribution, traditional and modern detection, diagnostic, and management approaches of Rhizoctonia solani associated with legume crops

Sustainable development relies heavily on a food system that is both safe and secure. Several approaches may lead to sustainability and food safety. An increase in the cultivation of legume crops is one of the approaches for enhancing agricultural viability and ensuring adequate food supply. Legumes may increase daily intake of fiber, folate, and protein as substitutes for meat and dairy. They are also crucial in various intercropping systems worldwide. However, legume production has been hampered by Rhizoctonia solani due to its destructive lifestyle. R. solani causes blights, damping off, and rotting diseases in legume crops. Our knowledge of the global distribution of R. solani associated with legume crops (alfalfa, soybean, chickpea, pea, lentil, common bean, and peanut), detection, diagnosis, and management of legume crops diseases caused by R. solani is limited. Traditional approaches rely on the incubation of R. solani, visual examination of symptoms on host legume crops, and microscopy identification. However, these approaches are time-consuming, require technical expertise, fail to detect a minimal amount of inoculum, and are unreliable. Biochemical and molecular-based approaches have been used with great success recently because of their excellent sensitivity and specificity. Along with conventional PCR, nested PCR, multiplex PCR, real-time PCR, magnetic-capture hybridization PCR, and loop-mediated isothermal amplification have been widely used to detect and diagnose R. solani. In the future, Next-generation sequencing will likely be used to a greater extent to detect R. solani. This review outlines global distribution, survival, infection and disease cycle, traditional, biochemical, molecular, and next-generation sequencing detection and diagnostic approaches, and an overview of the resistant resources and other management strategies to cope with R. solani.

Diversity and Aggressiveness of Rhizoctonia spp. from Nebraska on Soybean and Cross-Pathogenicity to Corn and Wheat

Rhizoctonia and Rhizoctonia-like species of fungi that cause disease are known to have varying host ranges and aggressiveness. Accurate identification of these species causing disease is important for soybean disease management that relies upon crop rotation. The anamorphic genus Rhizoctonia contains several diverse species and anastomosis groups (AGs) including some known soybean pathogens, such as Rhizoctonia solani, whereas for others the ability to cause disease on soybean has not been well described. The present study was conducted to identify the predominant species and AG of Rhizoctonia from soybean, corn, and wheat fields that are pathogenic on soybean and characterize cross-pathogenicity to common rotational crops, corn and wheat. We surveyed for Rhizoctonia spp. in Nebraska; isolates were identified to species and AG, and aggressiveness was assessed. A total of 59 R. zeae isolates, 49 R. solani, nine binucleate Rhizoctonia, three R. circinata, and two R. oryzae isolates were collected in 2016 and 2017 from a total of 29 fields in 15 counties. The most abundant R. solani AGs were AG-4, AG-1 IB, AG-2-1, AG-3, and AG-5. R. solani AG-4 and R. zeae were found in all three regions of the state (west, central, and eastern). Some isolates that were most aggressive to soybean seedlings were cross-pathogenic on both wheat and corn. In addition, R. zeae was pathogenic on soybean when evaluated at 25°C, which is warmer than temperatures used previously, and isolates were identified that were aggressive on soybean and cross-pathogenic on both corn and wheat.

Root rot a silent alfalfa killer in China: Distribution, fungal, and oomycete pathogens, impact of climatic factors and its management

Alfalfa plays a significant role in the pasture ecosystems of China's north, northeast, and northwest regions. It is an excellent forage for livestock, improves soil structure, prevents soil erosion, and has ecological benefits. Presently root rot is a significant threat to the alfalfa productivity because of the survival of the pathogens as soil-borne and because of lack of microbial competition in the impoverished nutrient-deficient soils and resistant cultivars. Furthermore, these regions' extreme ecological and environmental conditions predispose alfalfa to root rot. Moisture and temperature, in particular, have a considerable impact on the severity of root rot. Pathogens such as Fusarium spp. and Rhizoctonia solani are predominant, frequently isolated, and of major concern. These pathogens work together as disease complexes, so finding a host genotype resistant to disease complexes is challenging. Approaches to root rot control in these regions include mostly fungicides treatments and cultural practices and very few reports on the usage of biological control agents. As seed treatment, fungicides such as carbendazim are frequently used to combat root rot; however, resistance to fungicides has arisen. However, breeding and transgenic approaches could be more efficient and sustainable long-term control strategies, especially if resistance to disease complexes may be identified. Yet, research in China is mainly limited to field investigation of root rot and disease resistance evaluation. In this review, we describe climatic conditions of pastoral regions and the role of alfalfa therein and challenges of root rot, the distribution of root rot in the world and China, and the impact of root rot pathogens on alfalfa in particular R. solani and Fusarium spp., effects of environmental factors on root rot and summarize to date disease management approach.

Ascophyllum nodosum Extract and Mycorrhizal Colonization Synergistically Trigger Immune Responses in Pea Plants against Rhizoctonia Root Rot, and Enhance Plant Growth and Productivity

Rhizoctonia root rot is one of the most destructive diseases affecting pea crops, resulting in up to 75% loss. In this study, the biocontrol activity of seaweed (Ascophyllum nodosum) extract at 1, 2, and 3% and/or mycorrhization of pea roots was investigated against Rhizoctonia root rot under greenhouse conditions. In addition, their effects on the transcriptional, physiological, ultrastructural, and growth status of pea plants were also studied. The results showed that the mycorrhizal colonization of pea roots and the application of the seaweed extract at 3% synergistically overexpressed the responsive factor (JERF3) recording 18.2-fold, and the defense-related genes peroxidase (23.2-fold) and chitinase II (31.8-fold). In addition, this treatment improved the activity of the antioxidant enzymes POD and PPO, increased the phenolic content in pea roots, and triggered multiple hypersensitivity reactions at the ultrastructural level of the cell, leading to a 73.1% reduction in disease severity. Moreover, a synergistic growth-promoting effect on pea plants was also observed. The photosynthetic pigments in pea leaves were enhanced in response to this dual treatment, which significantly improved their yield (24 g/plant). The inducing effect of mycorrhizal colonization on plant resistance and growth has been extensively studied. However, developing improved and synergistically acting biological agents for plant disease control and growth promotion as alternatives to the chemical fungicides is crucial for safety and food security. Based on these results, it can be concluded that the mycorrhizal colonization of pea roots and soaking their seeds in the A. nodosum extract at 3% have a promising and improved biocontrol activity against R. solani, and a growth-promoting effect on pea plants. However, field applications should be evaluated prior to any use recommendations.

Untangling the Pea Root Rot Complex Reveals Microbial Markers for Plant Health

Plant health is recognised as a key element to ensure global food security. While plant breeding has substantially improved crop resistance against individual pathogens, it showed limited success for diseases caused by the interaction of multiple pathogens such as root rot in pea (Pisum sativum L.). To untangle the causal agents of the pea root rot complex and determine the role of the plant genotype in shaping its own detrimental or beneficial microbiome, fungal and oomycete root rot pathogens, as well as previously identified beneficials, i.e., arbuscular mycorrhizal fungi (AMF) and Clonostachys rosea, were qPCR quantified in diseased roots of eight differently resistant pea genotypes grown in four agricultural soils under controlled conditions. We found that soil and pea genotype significantly determined the microbial compositions in diseased pea roots. Despite significant genotype x soil interactions and distinct soil-dependent pathogen complexes, our data revealed key microbial taxa that were associated with plant fitness. Our study indicates the potential of fungal and oomycete markers for plant health and serves as a precedent for other complex plant pathosystems. Such microbial markers can be used to complement plant phenotype- and genotype-based selection strategies to improve disease resistance in one of the world's most important pulse crops of the world.

Genotypes and Genomic Regions Associated With Rhizoctonia solani Resistance in Common Bean

Rhizoctonia solani Kühn (teleomorph Thanatephorus cucumeris) is an important root rot pathogen of common bean (Phaseolus vulgaris L.). To uncover genetic factors associated with resistance to the pathogen, the Andean (ADP; n = 273) and Middle American (MDP; n = 279) diversity panels, which represent much of the genetic diversity known in cultivated common bean, were screened in the greenhouse using R. solani anastomosis group 2-2. Repeatability of the assay was confirmed by the response of five control genotypes. The phenotypic data for both panels were normally distributed. The resistance responses of ∼10% of the ADP (n = 28) and ∼6% of the MDP (n = 18) genotypes were similar or higher than that of the resistant control line VAX 3. A genome-wide association study (GWAS) was performed using ∼200k single nucleotide polymorphisms to discover genomic regions associated with resistance in each panel, For GWAS, the raw phenotypic score, and polynomial and binary transformation of the scores, were individually used as the input data. A major QTL peak was observed on Pv02 in the ADP, while a major QTL was observed on Pv01 with the MDP. These regions were associated with clusters of TIR-NB_ARC-LRR (TNL) gene models encoding proteins similar to known disease resistance genes. Other QTL, unique to each panel, were mapped within or adjacent to a gene model or cluster of related genes associated with disease resistance. This is a first case study that provides evidence for major as well as minor genes involved in resistance to R. solani in common bean. This information will be useful to integrate more durable root rot resistance in common bean breeding programs and to study the genetic mechanisms associated with root diseases in this important societal legume.

Insights to plant-microbe interactions provide opportunities to improve resistance breeding against root diseases in grain legumes

Root and foot diseases severely impede grain legume cultivation worldwide. Breeding lines with resistance against individual pathogens exist, but these resistances are often overcome by the interaction of multiple pathogens in field situations. Novel tools allow to decipher plant-microbiome interactions in unprecedented detail and provide insights into resistance mechanisms that consider both simultaneous attacks of various pathogens and the interplay with beneficial microbes. Although it has become clear that plant-associated microbes play a key role in plant health, a systematic picture of how and to what extent plants can shape their own detrimental or beneficial microbiome remains to be drawn. There is increasing evidence for the existence of genetic variation in the regulation of plant-microbe interactions that can be exploited by plant breeders. We propose to consider the entire plant holobiont in resistance breeding strategies in order to unravel hidden parts of complex defence mechanisms. This review summarizes (a) the current knowledge of resistance against soil-borne pathogens in grain legumes, (b) evidence for genetic variation for rhizosphere-related traits, (c) the role of root exudation in microbe-mediated disease resistance and elaborates (d) how these traits can be incorporated in resistance breeding programmes.

Identifying and Managing Root Rot of Pulses on the Northern Great Plains

Pulse crops (annual grain legumes such as field pea, lentil, dry bean, and chickpea) have become an important component of the cropping system in the northern Great Plains of North America over the last three decades. In many areas, the intensity of damping-off, seedling blight, root rot, and premature ripening of pulse crops is increasing, resulting in reduction in stand establishment and yield. This review provides a brief description of the important pathogens that make up the root rot complex and summarizes root rot management on pulses in the region. Initially, several specific Fusarium spp., a range of Pythium spp., and Rhizoctonia solani were identified as important components of the root rot disease complex. Molecular approaches have recently been used to identify the importance of Aphanomyces euteiches on pulses, and to demonstrate that year-to-year changes in precipitation and temperature have an important effect on pathogen prevalence. Progress has been made on management of root rot, but more IPM tools are required to provide effective disease management. Seed-treatment fungicides can reduce damping-off and seedling blight for many of the pathogens in this disease complex, but complex cocktails of active ingredients are required to protect seedlings from the pathogen complex present in most commercial fields. Partial resistance against many of the pathogens in the complex has been identified, but is not yet available in commercial cultivars. Cultural practices, especially diversified cropping rotations and early, shallow seeding, have been shown to have an important role in root rot management. Biocontrol agents may also have potential over the long term. Improved methods being developed to identify and quantify the pathogen inoculum in individual fields may help producers avoid high-risk fields and select IPM packages that enhance yield stability.

Characterization and Pathogenicity of Rhizoctonia and Rhizoctonia-Like spp. From Pea Crops in the Columbia Basin of Oregon and Washington

Isolates of Rhizoctonia and Rhizoctonia-like spp. (n = 179) were baited selectively from soil and plant samples collected from irrigated pea crops in the semiarid Columbia Basin of Oregon and Washington from 2011 to 2013, and characterized to species, subspecies, and anastomosis groups (AG) based on sequences of the internal transcribed spacer region of ribosomal DNA. Rhizoctonia solani comprised 76% of all isolates, and included isolates of AG 4 (31% of all isolates), AG 2-1 (18%), AG 3 (10%), AG 8 (8%), AG 5 (5%), AG 10 (3%), and AG 9 (1%). The isolates of Ceratobasidium spp. (20%) comprised four AGs: AG K (11%), AG A (6%), AG I (2%), and AG I-like (1%). Waitea circinata isolates (4%) comprised two subspecies: W. circinata var. circinata (approximately 4%) and W. circinata var. zeae (<1%). Repeated pathogenicity tests of isolates of the 10 most frequently detected AGs and subspecies on 'Serge' pea at 15°C revealed that R. solani AG 2-1 caused the greatest reduction in pea emergence, followed by R. solani AG 4. R. solani AG 4 caused the most severe root rot, stunting, and reduction in pea seedling biomass, followed by isolates of AG 2-1. R. solani AG 8 did not affect emergence, plant height, and total biomass compared with noninoculated control plants; however, root rot caused by isolates of AG 8 was ranked the third most severe among isolates of the 10 Rhizoctonia subgroups, after that caused by isolates of AG 4 and AG 2-1. Isolates of other AGs and subspecies were either weakly virulent or nonpathogenic on pea. The most common AGs (AG 4 and AG 2-1) detected in pea fields in the Columbia Basin were also the most virulent. In a growers' pea crop grown for seed ('Prevail') planted 5 days after herbicide application and incorporation of a preceding winter wheat crop, severe stunting caused by Rhizoctonia spp. resulted in an average 75% yield loss within patches of stunted plants. In contrast, the yield of processing pea from a green pea crop of Serge did not differ significantly for plants sampled within versus outside patches of stunted plants; however, plants within patches were significantly more mature. In the Prevail seed crop, a greater frequency of R. solani AG 8 was detected than AG 2-1 or AG 4 from within patches of stunted plants, indicating that isolates of AG 8 may be associated with the root rot complex in some pea crops in the Columbia Basin.

Wide variation in virulence and genetic diversity of binucleate Rhizoctonia isolates associated with root rot of strawberry in Western Australia

Strawberry (Fragaria×ananassa) is one of the most important berry crops in the world. Root rot of strawberry caused by Rhizoctonia spp. is a serious threat to commercial strawberry production worldwide. However, there is no information on the genetic diversity and phylogenetic status of Rhizoctonia spp. associated with root rot of strawberry in Australia. To address this, a total of 96 Rhizoctonia spp. isolates recovered from diseased strawberry plants in Western Australia were characterized for their nuclear condition, virulence, genetic diversity and phylogenetic status. All the isolates were found to be binucleate Rhizoctonia (BNR). Sixty-five of the 96 BNR isolates were pathogenic on strawberry, but with wide variation in virulence, with 25 isolates having high virulence. Sequence analysis of the internal transcribed spacers of the ribosomal DNA separated the 65 pathogenic BNR isolates into six distinct clades. The sequence analysis also separated reference BNR isolates from strawberry or other crops across the world into clades that correspond to their respective anastomosis group (AG). Some of the pathogenic BNR isolates from this study were embedded in the clades for AG-A, AG-K and AG-I, while other isolates formed clades that were sister to the clades specific for AG-G, AG-B, AG-I and AG-C. There was no significant association between genetic diversity and virulence of these BNR isolates. This study demonstrates that pathogenic BNR isolates associated with root rot of strawberry in Western Australia have wide genetic diversity, and highlights new genetic groups not previously found to be associated with root rot of strawberry in the world (e.g., AG-B) or in Australia (e.g., AG-G). The wide variation in virulence and genetic diversity identified in this study will be of high value for strawberry breeding programs in selecting, developing and deploying new cultivars with resistance to these multi-genetic groups of BNR.