Salicylic acid (SA) and methyl jasmonate (MeJA ) are plant defense elicitors with proven antimicrobial properties against various plant pathogens. Rhizoctonia solani, the pathogen responsible for rice sheath blight remains a significant challenge to rice production due to the lack of stable genetic resistance and the limitations of chemical fungicides. This study evaluated the potential of SA and MeJA as sustainable alternatives for sheath blight management in two contrasting rice genotypes, Tapaswini and CR Dhan 1014. Treatments included seed priming and foliar applications of SA and MeJA, with effects on growth, disease suppression, and yield were assessed. In vitro assays revealed that both SA and MeJA completely inhibited R. solani mycelial growth. SA also completely inhibited sclerotial formation at concentrations of 25, 50, and 100 mg, while MeJA achieved complete inhibition at 100 mg. For seedling traits, MeJA (100 mg) significantly enhanced germination in Tapaswini (95.00

Bakanae disease of rice has emerged as a major threat in the rice-growingregions of Eastern and Northeastern India. Under field conditions, Fusarium species associated with bakanae disease of rice exhibit a significant degree of variability. Characterizing the pathogen and its isolates is crucial for understanding this variability. This study aimed to assess the genetic diversity and virulence patterns among 88 Fusarium isolates, the causal agents of rice bakanae disease, collected from various locations across Eastern and Northeastern regions of India. The isolates showed a significant variation in their morphology and virulence pattern. The genetic variability among isolates was assessed using 19 microsatellite markers, all of which were successfully amplified across the isolates. The observed genetic diversity was significant, as indicated by Shannon's information index for marker alleles. Using the marker allele differences among the isolates, pathogen population was subdivided into two groups. The analysis of molecular variance among two subpopulations demonstrated lower variance among population than within population. These findings suggest that the studied pathogen population comprises genetically distinct strains, ranging from highly virulent to moderately virulent. This study enhances our understanding of the diversity and distribution of Fusarium isolates, providing valuable insights for strategic breeding programs and effective disease management strategies.

Magnaporthe oryzae, the causative agent of rice blast disease, poses a significant threat to rice yield. Aromatic rice landraces offer significant variation in disease resistance. However, the mechanisms underlying these responses remain poorly understood. Understanding how these landraces respond to blast infection can contribute to developing effective strategies for disease control. In this study, we conducted a comparative analysis of protein profiles in two aromatic rice genotypes, 'Benugopal' (resistant) and 'Kalikati 2' (susceptible), with contrasting blast resistance using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. A total of 18 protein spots were identified as differentially expressed between the two genotypes, showing significant intensity differences at 0, 24, 48, and 72 h post-inoculation with M. oryzae. These differentially expressed proteins (DEPs) were primarily associated with disease resistance, plant defense, signaling, stress response, growth, and development in rice. To validate protein expression changes at the transcript level, qRT-PCR was performed, revealing a positive correlation between mRNA levels and protein fold changes for eight selected genes. In conclusion, this study offers valuable insights into the molecular mechanisms driving the resistance of aromatic rice genotypes to M. oryzae infection.

Grain discolouration has become an important disease of rice in India. The disease causes yield loss and deteriorates the quality of rice. There is no consistent agreement on the causal organism as many researchers reported the disease to be caused by various pathogens like fungi, bacteria, environmental effects etc. For an efficient management of a disease, prior knowledge of the pathogen is indispensable. An attempt was made to understand the causal pathogen of rice grain discolouration. Rice grain showing typical brown or black spots was used for isolation of the pathogen using potato dextrose agar media. The mycelia were fast growing, brown to greyish black with a black reverse. The conidia were curved (lunate), the sub terminal cell enlarged and pale brown at both ends with 3–5 septa. The causal fungus of grain discolouration was validated as C. lunata through the fulfilment of the Koch postulates. The infected grains showed distinct degrees of darkening/browning either partially or wholly due to grain discolouration of rice. Moreover, the ITS regions were sequenced and revealed 100% similarity with Curvularia lunata . Hence, based on the analyzed samples, morphological, validation through Koch postulates and molecular assays, the pathogen causing grain discolouration was identified as Curvularia lunata .

In this study, 96 rice germplasm lines were shortlisted for the constitution of a panel containing genotypes with varying reactions to false smut resistance ranging from highly resistant to highly susceptible. The panel populations were screened for false smut phenotypically and using the resistance-linked SSR markers to validate the QTLs and markers linked to the disease resistance. Phenotypic data were compared with genotypic data to validate markers for false smut resistance. Twelve SSR markers associated with eight QTLs revealed 54 resistance alleles across the panel population. The SSR markers, RM216, RM222, RM307, RM271, RM254, RM6091, and RM6374 showed resistance-specific bands in certain genotypes. Genotyping results confirmed the flanking markers RM216 and RM222, for the QTL, qFSR-10-2, while RM307 (qFSR-4-1) produced a resistance-specific 150 bp band in the resistant genotypes, Geetanjali and Maichikan. The markers, RM324 and RM6374 showed linkage with the QTLs, qFSR-2-4 and qFSR2b, respectively producing resistance-specific bands in some germplasm lines. Cluster analysis divided the germplasm lines into two major clusters, subdivided into seven clusters based on false smut resistance response. Notably, the widely grown but susceptible genotype Pooja grouped within a mixed-resistance cluster, highlighting its vulnerability to false smut. These findings validate the specific SSR markers for selecting resistant genotypes for marker-assisted breeding to improve false smut resistance in rice.

Rice blast, caused by the fungal pathogen Magnaporthe oryzae, is one of the most destructive diseases affecting rice, leading to significant global yield losses. Investigation on genetic diversity and population structure of 108 aromatic rice (Oryza sativa L.) landraces from Odisha, India were made using a set of 20 major blast resistance (R) genes. Phenotypic evaluation classified these landraces into resistant (17 landraces), moderately resistant (17 landraces), and susceptible (74 landraces) groups based on their disease response. The frequency of the 20 R genes across the landraces varied widely, ranging from 2.78 % to 100 %, with each landrace carrying 7 to 18 positive R-gene alleles. In population structure analysis, two sub-populations (K = 2) were found with considerable admixture. Principal coordinate analysis (PCoA) further demonstrated distinct clustering patterns, separating the resistant and moderately resistant landraces. Molecular variance analysis (AMOVA) indicated that the majority of genetic diversity (57 %) was found within populations, while a smaller proportion (6 %) occurred between populations. Among the eight significant markers identified, YL155/YL87 (Pita gene, R2 = 7.8 %), Pita3 (R2 = 5.1 %), and Pikh (Pi54 gene, R2 = 4.0 %) exhibited the strongest associations with blast resistance, highlighting their potential for marker-assisted selection in breeding programs.

Among the diseases of rice, false smut is one of the major emerging diseases that reduce the quality and yield of rice (Bag et al., 2021).The disease is caused by Ustilaginoidea virens (teleomorph -Villosiclava virens) which is a flower-infecting fungus.False smut has become an important disease as it appears in many rice-growing areas of the world in mild to alarming proportions.The disease is greatly influenced by prevailing weather conditions and has been occurring in many rice-growing regions of the world.Yield loss due to false smut varied from 0.5-75%, depending on the genotypes and weather conditions (Upadhyay and Singh, 2013;Baite et al., 2020).The disease is harmful to both humans and animals due to poisonous mycotoxins produced by the fungus (Sun et al., 2017;Wang et al., 2019).As false smut is increasingly encountered in many rice-growing regions, it was important to carry out a survey find out the status of false smut in the coastal rice ecosystem.Therefore, a study was carried out at Naira, Andhra Pradesh to monitor the incidence of false smut in rice.

In this study, we evaluated the efficacy of Bacillus strains for plant growth promotional activities under in vitro and in vivo conditions. The results indicated that Bacillus megaterium BS11 was superior in enhancing the plant growth and yield of rice plants compared to other Bacillus strains. Currently, there is no information available on the molecular mechanism of Rice– B. megaterium interaction for plant growth promotion. Thus, the present study was undertaken to understand the molecular basis of Rice– B. megaterium interaction at the proteome level using the two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) approach. Proteomic results revealed that a total of 17 proteins were differentially expressed in response to BS11 inoculation. The application of BS11 up-regulated most of the identified proteins involved in plant metabolism, transcription, transporter, signaling, defense, and stress responses, which may underlie the improvement of rice plant growth. Furthermore, the proteomic results were validated at the mRNA level by Quantitative Real-Time PCR (qPCR) analysis. The abundances of proteins and transcripts were positively correlated for all genes except LOC_Os01g68620. Overall, our results suggest that B. megaterium strain BS11 may promote plant growth by improving various metabolism in rice plants.

Background Rice (Oryza sativa) is one of the most dominating cereal crop and half of the global people have chosen it as staple food. Rice production has increased significantly but the productivity is not increased significantly to combat the global need. One of the major constraints of low productivity is biotic stresses faced by rice growers. Some of the important biotic stresses of rice are major diseases like brown spot, bacterial blight, blast, sheath blight and, few emerging but significant diseases like false smut, bakanae and sheath rot play crucial role in reducing yield per unit area and quality of rice. Host plant resistance is the most effective, economic and eco-friendly approach of mitigating disease like biotic stress problem. Objective The objective of this review is to compile data related to resistance in rice against various major and emerging diseases as well as their application to develop gene pyramided varieties that increase resistance to those pathogens to achieve durable resistance. Methods Diseases are one of the most important constraints for sustainable or demanding production level as well as maintaining different quality parameters of the rice. Different management practices including majority by chemical means are not always solution as it add production cost many times vis-à-vis cause pollution in every aspect. Thus, development of durable resistant varieties are the best approaches. Result An array of robust molecular markers and genetic map of the crop has made application of marker assisted selection possible for the traits controlled by resistant genes or quantitative trait loci (QTLs) to induce durable resistance in the crop. Conclusion A comprehensive assessment on identification, sources and deployment of resistance genes/QTLs of major and emerging diseases of rice will help in development of varieties of rice with durable resistant to major and emerging disease-causing pathogens.

Rice (Oryza sativa L) being one of the imperative food crops of the word contributes immensely to the food and nutritional security of India. The cultivation of rice is changed over the decades from a simple cultivation practices to the advanced cultivation to increase yield. Increased in rice yields especially after 1960s is mainly due to the introduction of high yielding semi-dwarf varieties which requires more inputs like chemical fertilizers, water and other resources. As a result, India achieved self sufficiency in rice and currently producing more than 115 MT of rice to meet country’s demand. Now India is exporting rice to other nations and earning foreign returns. With the change in rice cultivation practices, problems also aroused side by side. A number of biotic and abiotic stresses emerged as major constraints for rice cultivation in diverse agro-climatic conditions and growing ecologies. Diseases are the major biotic constraints to rice which can reduce the yields by 20–100% based on severity. Major diseases like blast, brown spot, bacterial blight, sheath blight and tungro still causing more damage and new minor diseases like bakanae, false smut, grain discoloration, early seedling blight, narrow brown spot, sheath rot have emerged as major problems. The losses due to these diseases may 1–100% based on the growing conditions, varietal susceptibility etc.., At present no significant source of resistance available for any of the above emerging diseases. But looking into the severity of these diseases, it is very important to address them by following integrated management practices like cultural, mechanical, biological and finally chemical control. But more emphasis has to be given to screen gerrmplasm against these diseases and identify stable source of resistance. Finally utilizing these sources in resistance breeding program by employing molecular breeding tools like marker assisted selection (MAS), marker assisted back cross breeding (MABB), gene pyramiding and transgenic tools. The present chapter discusses the importance of these emerging minor diseases of rice, the losses and possible management measures including resistance breeding.

In the past decades to meet the increases in population demand, farmers have utilized huge amount of agrochemicals to increase the crop production. However, in the present era, there is an awareness regarding the adverse consequences posed by the agrochemicals to human health and the environment. Such concerns are driving the search for more environmentally friendly methods to control plant disease that will contribute to the goal of sustainability in agriculture. Plant growth promoting rhizobacteria (PGPR) are found to be a potential alternative to chemical pesticides with an ability to antagonize and prevent plant disease. Fluorescent pseudomonads are one of the common PGPR which have received much attention in recent years as biocontrol agent. Fluorescent pseudomonads are known for its production of diverse microbial metabolites including antibiotics, siderophores and volatile compounds such as HCN. Moreover, it also possesses plant growth-promoting traits such as nitrogen fixation, phosphate solubilization, iron chelation, and phytohormone production. Hence, this chapter will give an importance and overview of the Fluorescent pseudomonads as a potential biostimulant for sustainable crop production.

Traditional agricultural practices exclusively based on the synthetic fertilizers and pesticides. Although chemicals show promising results in crop management, there are several major issues concerning pesticide residues, human health predicaments and environmental pollution. To minimize these effects, an alternative approaches are highly essential. One such approach is the utilization of beneficial microbes residing in the plant rhizosphere. Among Plant Growth Promoting Rhizobacteria (PGPRs), the sporulating Gram-positive bacteria like Bacillus spp. have been well studied, especially production of versatile antibiotics, lytic enzymes, antagonistic effect, plant growth promotion and induction of systemic resistance. Despite this, only less information is available for their effect on crop production. Many Bacilli rhizobacteria and their multifaceted benefits are still unexploited. This chapter will give an overview of the Bacilli rhizobacteria and their multifarious benefits for agricultural sustainability and environmental safety.

False smut, caused by Ustilaginoidea virens, is one of the emerging diseases of rice in the world. The fungi show a high degree of morphological and cultural variability and produce diverse symptoms. India is a vast country with 44-million-ha rice production area and has only one report on genetic diversity and population analysis of U. virens from the eastern and north-eastern region. Ten polymorphic RAPD and 21 SSR markers were used to analyse the genetic diversity and population structure of 81 isolates of U. virens from northern India, the second largest rice-growing region. In this study, higher Polymorphic Information Content (PIC) and Quality Nature of Data (QND) data in simple-sequence repeats (SSR) markers over random amplified polymorphic DNA (RAPD) revealed its higher efficacy; thus, SSR markers are highly informative and can help to dissect the genetic structures of U. virens. All markers yielded a total of 180 alleles with 1.0 effective alleles per loci. Genetic diversity ranged from 0.1 to 0.39. The principal coordinate analysis (PCoA), and structure analysis identified two genetic clusters of U. virens isolates with some degree of distinctness according to locations. But clusters, PCoA and structure analysis did not group the isolates according to their geographical origin and this may be due to high gene flow (Nm = 1.14).

Brown spot disease, caused by Bipolaris oryzae, is one of the several disastrous diseases affecting rice. The brown spot fungus illustrates substantial pathogenic and genetic variability. To the best of our knowledge, extensive analysis utilizing specific SSR primers for B. oryzae genome is quite inadequate for the population structure and genetic diversity of Indian B. oryzae isolates. A total of 84 brown spot isolates were collected from rice-cultivating areas across southern and eastern Indian states, viz., Tamil Nadu, Andhra Pradesh, Odisha and Chhattisgarh. The pathogenicity and virulence characteristics of these isolates were assessed with the susceptible cultivar CR Dhan 201. Twelve genome-specific SSR markers of B. oryzae warranted the investigation of the population structure and genetic diversity among the isolates. These isolates were categorized based on their disease grade as highly virulent isolates (4 nos.), virulent isolates (8 nos.), moderately virulent isolates (47 nos.) and less virulent isolates (25 nos.). PCR amplification and DNA sequencing confirmed the isolates to be B. oryzae. PCR amplification and DNA sequencing confirmed the isolates to be B. oryzae. The SSR markers produced a total of 35 alleles with 1 to 4 alleles per locus with a gene diversity ranging between 0.00 and 0.687 and a major allele frequency variation of 0.425–0.975. The PIC value ranged from 0.00 to 0.638 having a mean value of 0.34. Cluster analysis technique was applied to group the brown spot isolates into four distinct clusters. Principal coordinate and structure analysis identified two genetic clusters of B. oryzae isolates for individual states with some degree of distinctness complying with their virulence. Analysis of molecular variance revealed more genetic variation within populations and less among populations. The study outcome would expedite the comprehension of genetic diversity of B. oryzae across the southern and eastern states of India. Furthermore, we anticipate its guidance in the development of more effective disease management strategies as well as in the generation of novel resistant varieties through marker-assisted breeding.

False smut caused by the flower-infecting fungus, Ustilaginoidea virens has become an important disease of rice seriously hampering production worldwide. An experiment on the eco-friendly method of biological control of false smut was conducted both in vitro and in field conditions to evaluate the ability of biocontrol agents to control the disease. The in vitro evaluation revealed maximum inhibition of U. virens by Trichoderma harzianum (66.88%) followed by Trichoderma atroviride (51.16%), Dendryphiella sp. (41.50%), Bacillus amyloliquefaciens (36.56%) and Bacillus subtilis (36.40%). The mechanisms of action observed during in vitro tests for T. harzianum and T. atroviride were parasitism and production of volatile metabolites. Whereas B. subtilis produced volatile metabolites to control U. virens. All the plants treated with biocontrol agents showed reduced disease incidence relative to the control demonstrating their ability to suppress false smut under field conditions. Besides disease suppression, the biocontrol agents were found to be beneficial to rice as evident from the increased number of grains per panicle in treated plants. Moreover, the chaffiness that reduces rice production, was much lower in all treatments except for plants treated with Dendryphiella sp. Therefore, B. subtilis and T. harzianum have maximum potential to control false smut of rice.

Genetic diversity assessment and population structure analysis are essential for characterization of pathogens and their isolates. Markers are essential tools for exploring genetic variation among the isolates. False smut of rice caused by Ustilaginoidea virens, formerly Villosiclava virens, is a major emerging disease of rice in India. A high level of variability is observed at the field level, but no information is available from India on genetic diversity and population structure. This is the first report of genetic diversity and population structure of U. virens from India that included 63 isolates distributed across the vast geographical area of eastern and north-eastern India (18.9 to 26.7 degrees N and 82.6 to 94.2 degrees E). Seventeen RAPDs and 14 SSRs were identified as polymorphic and a total of 140 alleles were detected across the populations. The average number of alleles per locus for each primer was 4.5. All the isolates were grouped into two major clusters, with partial geographical segregation that was supported by principal coordinate analysis. Mantel test suggested genetic distance within the isolates increased with increasing geographical distance. Analysis of molecular variation showed more genetic variation within populations and less among populations. This outcome will help in understanding genetic diversity of U. virens from eastern and north-eastern India and in planning effective management strategies.

Rice (Oryza sativa L.) is the most important food crop of the developing world. Among the biotic stresses of false smut is an emerging disease caused by Ustilaginoidea virens. The disease reduces both the quality and quantity of rice. The pathogen produces mycotoxins that are harmful to animals and humans. The disease is severe when favorable environmental conditions like high humidity (more than 80%) and temperature ranging from 25 to 30°C, late sowing and high soil fertility as well as using high amount of nitrogen. It has gained the status of a major disease of rice and causing varying yield loss depending on the weather conditions during the crop-growing period and the genotypes. Therefore, the primary concern of the farmers is the disease management methods, which are effective, simple and practical. Since, there is no single effective management strategy for false smut, we have discussed about the potential management options available depending upon the economic status and adoption capacity of the farmers. In the Plant Pathologists point of view, eco-friendly methods of disease management like cultural, biological and use of resistant variety should be advocated for sustainability of agriculture and human being.

False smut caused by Ustilaginoidea virens is currently an important disease of rice. The disease regularly occurs in many parts of India resulting in significant economic losses. To find an eco-friendly method of false smut management, the effect of staggered rice sowing and flowering on false smut incidence were evaluated in 2018 and 2019 seasons. Six rice varieties were sown at 15-day intervals from 24th May to 20th August in both the years. Most varieties developed false smut when their flowering occurred during September and October in both seasons of 2018 and 2019 irrespective of their sowing dates. The relative humidity showed positive correlation with Pooja and Sarala but negatively correlated with Anjali, Durga, Geetanjali and Naveen. Therefore, avoiding the flowering period during the critical months can considerably limit the false smut severity and help to manage the disease.

This study is a unique report of the utilization of Trichoderma strains collected from even tree barks for rice plant growth, its health management, and paddy straw degradation. Seven different spp. of Trichoderma were characterized according to morphological and molecular tools. Two of the isolated strains, namely Trichoderma hebeiensis and Trichoderma erinaceum, outperformed the other strains. Both of the strains controlled four important rice pathogens, i.e., Rhizoctonia solani (100%), Sclerotium oryzae (84.17%), Sclerotium rolfsii (66.67%), and Sclerotium delphinii (76.25%). Seed bio-priming with respective Trichoderma strains reduced the mean germination time, enhanced the seedling vigor and total chlorophyll content which could be related to the higher yield observed in two rice varieties; Annapurna and Satabdi. All the seven strains accelerated the decomposition of rice straw by producing higher straw degrading enzymes like total cellulase (0.97–2.59 IU/mL), endoglucanase (0.53–0.75 IU/mL), xylanase (145.35–201.35 nkat/mL), and laccase (2.48–12.60 IU/mL). They also produced higher quantities of indole acetic acid (19.19–46.28 μg/mL), soluble phosphate (297.49–435.42 μg/mL), and prussic acid (0.01–0.37 μg/mL) which are responsible for plant growth promotion and the inhibition of rice pathogen populations. Higher expression of defense enzymes like catalase (≥250% both in shoot and root), peroxidase (≥150% in root and ≥100% in shoot), superoxide dismutase (≥ 150% in root and ≥100% in shoot), polyphenol oxidase (≥160% in shoot and ≥120% in shoot), and total phenolics (≥200% in root and ≥250% in shoot) as compared to the control indicates stress tolerance ability to rice crop. The expression of the aforementioned enzymes were confirmed by the expression of corresponding defense genes like PAL (>3-fold), DEFENSIN (>1-fold), POX (>1.5-fold), LOX (>1-fold), and PR-3 (>2-fold) as compared to the non-treated control plants. This investigation demonstrates that Trichoderma strains obtained from tree bark could be considered to be utilized for the sustainable health management of rice crop.