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Bakanae disease is widespread in rice cultivation areas globally, presenting a significant challenge to basmati rice farming in India. Chemical seed and seedling treatment methods are commonly employed for managing bakanae disease, however, very less information is available on spray treatments. Our study aimed to assess the effectiveness of various fungicidal spray in field conditions for managing bakanae disease and their impact on basmati rice yield and related characteristics. Seven fungicides, along with a pathogen-inoculated control, were evaluated as foliar treatments during the Kharif season of the year 2021 and 2022. A combined analysis of data from two years showed that T1 (Carbendazim 50% WP) had the lowest disease incidence at 44.68%, demonstrating a significantly high percentage disease inhibition of 44.08%. Following closely was T4 (Tebuconazole 50% + Trifloxystrobin 25% WG) with a disease incidence of 50.00% and a corresponding percentage disease inhibition of 37.37%, while, maximum disease incidence of 79.84% was recorded in control treatment (T8) followed by T5 (Copper oxychloride 50% WP). Further, significantly high grain yield was obtained in Carbendazim 50% WP treatments (219.37 g/m2) followed by Tebuconazole 50% + Trifloxystrobin 25% WG (212.00 g/m2). Additionally, a quantitative polymerase chain reaction assay on harvested grains with Fusarium fujikuroi specific marker revealed least pathogen colonization in harvested seeds of Carbendazim 50% WP treatment (T1), with a Ct value of 33.763 (copy no. 4.88E + 10), followed by Tebuconazole 50% + Trifloxystrobin 25% WG (Ct value 33.752, copy no. 4.94E + 10), conversely, Copper oxychloride (T5) demonstrated the least effectiveness with highest pathogen load (copy no. 9.44E + 13). Based on our findings, we recommend the use of Carbendazim 50% WP or Tebuconazole 50% + Trifloxystrobin 25% WG for the management of bakanae disease as foliar spray (2 sprays) treatments (First spray after 15 days of transplanting; second spray at maximum tillering stage (around 25–30 days post Ist spray)) showing low AUDPC and high yield compared to inoculated control. Further, fungicidal spray reduced the infected seed percentage and carried less inoculum in next season. Therefore, these investigations will be valuable for management of bakanae disease after symptom appearance in field conditions. Findings could be further helpful in developing and validating an integrated approach to manage bakanae disease effectively in near future. [ABSTRACT FROM AUTHOR]

A diverse set of 275 rice germplasm lines including 159 lines from global rice diversity panel, 10 Oryza glaberrima Steud accessions; 22 basmati and non-basmati varieties, 67 aromatic germplasm lines and 17 advanced breeding lines were screened along with susceptible and resistant checks for foot rot disease caused by Fusarium moniliforme Sheldon through artificial inoculation. The screening was conducted in trays under less humid condition (50% RH) in April 2019 (referred as E1) and in the field under high humid condition (72% RH) in July 2019 (referred as E2). The susceptible plants showed stunting in E1 and elongation in E2. Based on screening in E1 and E2, thirty-three lines including eighteen of global rice diversity panel, five of O. glabberrima, two aromatic and ten released varieties showed complete resistance to foot rot. Multi-locus GWAS using 159 lines of global rice diversity panel identified 11 QTLs on seven different chromosomes. In the 11 QTL regions, 40 putative genes were identified based on stringent filtering and relevance to the disease. The QTL present on chromosome 1 (qbk1) that co-localized with many studies is proposed for further studies. In addition, the expression analysis of GA-related genes, viz. OsXTH8, OsGAE1, EUI, G-alpha-(D1), GID1, GID2 and SLR1, showed no association with foot rot resistance/susceptibility. However, 24 DAS was identified as the most important stage for expression analysis. The highly resistant lines are suggested to use in the rice breeding program particularly basmati rice. Besides, the genomic region flanking the associated SNPs and the candidate genes within them could be studied further to identify underlying genes and markers associated with foot rot resistance. [ABSTRACT FROM AUTHOR]

Bakanae disease, caused by Fusarium fujikuroi, is emerging as a major threat to rice crops worldwide, posing a significant challenge to basmati rice farming in India. The difficulty in managing the disease is compounded by the morphological similarities between various pathogenic species and the limited research on its soil-borne nature, especially in the context of Indian farming conditions. This study utilized quantitative PCR (qPCR) and metagenomic approaches to monitor Fusarium fujikuroi population in soil from a rice-wheat cropping system during 2021–22 in North Indian conditions. The qPCR analysis revealed changes in Fusarium fujikuroi abundance, with the highest colonization in August 2021 (1.19 × 1010) and a notable decline by June 2022 (1.84 × 106). Metagenomic studies based abundance analysis at the phylum level showed the prevalence of ascomycetes in all the samples taken for the study. The key fungal genera observed in bakanae infected field following rice-wheat cropping system included Talaromyces, Mortierella, Trichoderma, Aspergillus, Penicillium, Emericellopsis, Fusarium, Chaetomium, Westerdykella and Amesia. Talaromyces was most abundant in September 2021 (34.40 %) which corresponded with the lowest Fusarium abundance (0.22 %) in soil samples tested. Other beneficial fungi such as Trichoderma, Penicillium and Westerdykella etc. were also detected during the evaluation, supporting their role in managing bakanae disease. The decrease in the Fusarium fujikuroi population over the study period, as revealed by quantitative PCR and metagenomics, indicates that the viability of Fusarium fujikuroi as a soil-borne pathogen is limited. This suggests the importance of maintaining a proper interval of 6–7 months between harvest and the next sowing. Further, the study emphasized the potential use of biocontrol agents to mitigate bakanae disease problem along with the promotion of sustainable and resilient rice farming systems.

Bakanae, caused by Fusarium fujikuroi, is a serious seed-borne disease affecting rice production worldwide. Herein, we investigated the potential of propolis, a natural honeybee product, collected from three geographic locations in Egypt: North (Menofia), Middle (Cairo), and South (Sohag), and extracted with four different solvents (ethanol, olive oil, hexane, and water) as a sustainable eco-friendly alternative to control the Bakanae disease in rice. In vitro experiments showed that propolis extracts exhibited antifungal activity against F. fujikuroi and significantly suppressed its mycelial growth and sporulation. The antifungal activity of propolis extracts was associated with its chemical composition which varied depending on geographical origin, and the extraction solvents. Moreover, SEM-based analysis revealed that ethanolic extract of northern propolis prominently altered the microconidia morphology of F fujikuroi, which shrunken and seemed to lose their viability. These findings were further confirmed in vivo under greenhouse conditions. Soaking F fujikuroi-inoculated rice seeds in 1000 ppm of propolis extract significantly reduced the bakanae disease incidence, and disease severity index compared to mock-treated controls. Although infection with F fujikuroi induced the accumulation of H2O2, the application of propolis extracts alleviated oxidative stress and significantly reduced the H2O2 levels within infected rice seedlings. Moreover, propolis extracts enhanced the profile of enzymatic antioxidants (guaiacol-dependent peroxidase [POX] and polyphenol oxidase [PPO]) in F. fujikuroi-infected rice seedlings. Finally, Propolis extracts-treated rice seedlings exhibited higher transcript levels of three PTI-marker genes including nonexpressor of pathogenesis-related genes 1 (OsNPR1), WRKY transcription factor 21(OsWRKY21), and phenylalanine ammonia-lyase (OsPAL1), which are associated with systemic acquired resistance (SAR) and crucial for the plant's defense response against pathogens. Collectively, these findings suggest that propolis might be a promising sustainable, eco-friendly alternative to control bakanae disease and other fungal seed-borne phytopathogens due to its antifungal properties and ability to induce a complex multilayered defense system within infected plants.

Gibberellic acid (GA3) is a tetracyclic diterpenoid carboxylic acid synthesized by the secondary metabolism of Fusarium fujikuroi. This phytohormone is widely studied due to the advantages it offers as a plant growth regulator, such as growth stimulation, senescence delay, flowering induction, increased fruit size, and defense against abiotic or biotic stress, which improve the quality and yield of crops. Therefore, GA3 has been considered as an innovative strategy to improve agricultural production. However, the yields obtained at large scale are insufficient for the current market demand. This low productivity is attributed to the lack of adequate parameters to optimize the fermentation process, as well as the complexity of its regulation. Therefore, this article describes the latest advances for potentializing the GA3 production process, including an analysis of its origins from crops, the benefits of its application, the related biosynthetic metabolism, the maximum yields achieved from production processes, and their association with genetic engineering techniques for GA3 producers. This work provides a new perspective on the critical points of the production process, in order to overcome the limits surrounding this modern line of bioengineering. [ABSTRACT FROM AUTHOR]

Bakanae is one of the important diseases of rice in Bangladesh that causes substantial yield loss every year. We collected thirty isolates of Fusarium spp. from bakanae-infected rice plants from different agroecological zones of Bangladesh and investigated the variations in cultural and morphological characteristics and pathogenicity. Diversity was found in cultural characteristics, viz., colony features, phialide, chlamydospore formation, shape, and size of macro- and microconidia. Three variants of Fusarium species such as F. moniliforme, F. fujikuroi, and F. proliferatum were identified on PDA media based on their cultural and morphological characteristics. Isolate FM10 (F. moniliforme) exhibited the highest disease aggressiveness in developing elongated plants (26.50 cm), the highest number of chlorotic leaves (5.75), and a lower germination percentage. We evaluated different bioagents against the virulent isolate of F. moniliforme to develop a rice bakanae disease management approach. Four bioagents, viz., Trichoderma spp., Bacillus subtilis, Pseudomonas fluorescens, and Achromobacter spp., were evaluated for growth suppression of F. moniliforme. Among the bioagents, Achromobacter spp. and B. subtilis (BS21) showed 73.54% and 71.61% growth suppression, respectively. The investigation revealed that the application of Achromobacter spp. and B. subtilis (BS21) would be a potential candidate for effective and eco-friendly management of the bakanae disease of rice. [ABSTRACT FROM AUTHOR]

Bakanae disease caused by Fusarium fujikuroi is emerging in India. In this work, fungicides and biocontrol agents were evaluated as seed, seedling treatment, and foliar spray(s) against bakanae disease in rice under field conditions. Carbendazim (50% WP) was found to be the most effective fungicide for seed and seedling root dip treatments. Soil drenching with 0.25% carbendazim (50% WP) 5 days before transplanting of seedlings was effective for large scale treatments. Foliar spray of 0.1% tebuconazole 50%+ trifloxystrobin 25% w/w (75 WG) significantly reduced the percentage of infected seeds (7.17%) compared with the control (32.50%). The minimum disease incidence (31%) was observed when seeds were treated with Talaromyces flavus. Individual treatments were integrated in the form of six management modules and evaluated under the field conditions of New Delhi (India) and Pusa Bihar (India) with the susceptible cultivars ‘Pusa Basmati 1121’ and ‘Pusa 1176’. Bakanae disease incidence was lower in the modules tested compared with the inoculated control or the individual treatment. The most favorable results at two locations achieved the lowest disease incidence of 7% and 2.41%.

Bakanae disease caused by Fusarium fujikuroi is an emerging disease of rice causing losses in all rice-growing regions around the world. A BC2F2 population was developed by backcrossing the recurrent parent Pusa Basmati 1121 (PB1121) with the recombinant inbred line RIL28, which harbors a major quantitative trait locus (QTL) governing resistance to bakanae, qBK1.2. MassARRAY-based single-nucleotide polymorphism (SNP) assays targeting the genomic region of qBK1.2 helped in fine mapping the QTL to a region of 130 kb between the SNP markers rs3164311 and rs3295562 using 24 recombinants. In-silico mining of the fine-mapped region identified 11 putative candidate genes with functions related to defense. The expression analysis identified two significantly differentially expressed genes, that is, LOC_Os01g06750 and LOC_Os01g06870, between the susceptible genotype PB1121 and the resistant genotypes Pusa1342 and R-NIL4. Furthermore, the SNPs identified in LOC_Os01g06750 produced minor substitutions of amino acids with no major effect on the resistance-related functional motifs. However, LOC_Os01g06870 had 21 amino acid substitutions, which led to the creation of the leucine-rich repeat (LRR) domain in the resistant genotype Pusa1342, thereby making it a potential candidate underlying the major bakanae-resistant QTL qBK1.2. The markers used in the fine mapping program are of immense utility in marker-assisted breeding for bakanae resistance in rice. [ABSTRACT FROM AUTHOR]

Bakanae disease caused by Fusarium fujikuroi is an emerging disease of rice causing losses in all rice-growing regions around the world. A BC2F2 population was developed by backcrossing the recurrent parent Pusa Basmati 1121 (PB1121) with the recombinant inbred line RIL28, which harbors a major quantitative trait locus (QTL) governing resistance to bakanae, qBK1.2. MassARRAY-based single-nucleotide polymorphism (SNP) assays targeting the genomic region of qBK1.2 helped in fine mapping the QTL to a region of 130 kb between the SNP markers rs3164311 and rs3295562 using 24 recombinants. In-silico mining of the fine-mapped region identified 11 putative candidate genes with functions related to defense. The expression analysis identified two significantly differentially expressed genes, that is, LOC_Os01g06750 and LOC_Os01g06870, between the susceptible genotype PB1121 and the resistant genotypes Pusa1342 and R-NIL4. Furthermore, the SNPs identified in LOC_Os01g06750 produced minor substitutions of amino acids with no major effect on the resistance-related functional motifs. However, LOC_Os01g06870 had 21 amino acid substitutions, which led to the creation of the leucine-rich repeat (LRR) domain in the resistant genotype Pusa1342, thereby making it a potential candidate underlying the major bakanae-resistant QTL qBK1.2. The markers used in the fine mapping program are of immense utility in marker-assisted breeding for bakanae resistance in rice.

Bakanae disease caused by Fusarium fujikuroi is emerging in India. In this work, fungicides and biocontrol agents were evaluated as seed, seedling treatment, and foliar spray(s) against bakanae disease in rice under field conditions. Carbendazim (50% WP) was found to be the most effective fungicide for seed and seedling root dip treatments. Soil drenching with 0.25% carbendazim (50% WP) 5 days before transplanting of seedlings was effective for large scale treatments. Foliar spray of 0.1% tebuconazole 50%+ trifloxystrobin 25% w/w (75 WG) significantly reduced the percentage of infected seeds (7.17%) compared with the control (32.50%). The minimum disease incidence (31%) was observed when seeds were treated with Talaromyces flavus. Individual treatments were integrated in the form of six management modules and evaluated under the field conditions of New Delhi (India) and Pusa Bihar (India) with the susceptible cultivars 'Pusa Basmati 1121' and 'Pusa 1176'. Bakanae disease incidence was lower in the modules tested compared with the inoculated control or the individual treatment. The most favorable results at two locations achieved the lowest disease incidence of 7% and 2.41%. [ABSTRACT FROM AUTHOR]

Background: Fusarium fujikuroi causing bakanae is one of the most significant pathogens of rice and much responsible for yield losses thereby emerging as a major risk to food security. Methods: In the present study transcriptomic analysis was conducted between two contrasting resistant (C101A51) and susceptible (Rasi) genotypes of rice with the combinations of C101A51 control (CC) vs. C101A51 inoculated (CI); Rasi control (RC) vs. Rasi inoculated (RI) and C101A51 inoculated (CI) vs. Rasi inoculated (RI). Results: In CC vs. CI commonly expressed genes were 12,764. Out of them 567 (4%) were significantly upregulated and 1399 (9%) genes were downregulated. For the RC vs. RI 14, 333 (79%) genes were commonly expressed. For CI vs. RI 13,662 (72%) genes were commonly expressed. Genes related to cysteine proteinase inhibitor 10, disease resistance protein TAO1-like, oleosin 16 kDa-like, pathogenesis-related protein (PR1), (PR4), BTB/POZ and MATH domain-containing protein 5-like, alpha-amylase isozyme were upregulated in resistant genotype C101A51. Whereas, genes related to GDSL esterase/lipase, serine glyoxylate aminotransferase, CASP-like protein 2C1, WAT1-related protein, Cytoplasmic linker associated proteins, xyloglucan endotransglucosylase/hydrolase protein and β-D xylosidase 7 were upregulated in susceptible genotype Rasi. Gene ontology analysis showed functions related to defence response (GO:0006952), regulation of plant hypersensitive type response (GO:0010363), Potassium ion transmembrane activity (GO:0015079), chloroplast (GO:0009507), response to wounding (GO:0009611), xylan biosynthetic process (GO:0045492) were upregulated in resistant genotype C101A51 under inoculated conditions. Conclusion: Real time PCR based validation of the selected DEGs showed that the qRT-PCR was consistent with the RNA-Seq results. This is the first transcriptomic study against bakanae disease of rice in Indian genotypes. Further, functional studies on identified genes and their utilization through different methodology will be helpful for the development of bakanae disease management strategies. [ABSTRACT FROM AUTHOR]

Bakanae disease is an emerging problem for the Basmati rice cultivation in India. Forty-seven endophytes isolated earlier along with three Talaromyces flavus isolates evaluated against Fusaium fujikuroi [Nirenberg] bakanae pathogen [isolate F250] through dual culture and enzymatic assays. Out of 50 isolates, 6 isolates namely, Tf1, Tf2, Tf3, Fusarium equiseti, Fusarium sp. and Trichoderma sp. produced good inhibitory results under in vitro conditions and were proceeded with in planta studies and conducted microscopic studies and real-time PCR assays. Microscopic studies revealed that the defense response system of plants was activated to a longer extent in bioagent treatments, since the number of live nuclei (DAPI staining) and green stained live plant cells (FDA staining) were higher as seen in treated plants when compared to pathogen-inoculated and uninoculated control when observed under confocal laser scanning microscopy. The analysis of cell cycle-related genes expressed during the ROS activity showed increased expression of the cell cycle-related genes involved. The selected isolates were also tested under glasshouse for disease inhibition studies. F. equiseti, Fusarium sp. and Trichoderma sp. gave a disease inhibition of, 87%, 66% and 94%, respectively. Tf2 and Tf1 isolate dominantly inhibited the disease with 95% whereas Tf3 also inhibited successfully with 70%. Through the results of our study, we can deduce that the T. flavus (Tf1, Tf2, Tf3) isolates and the endophytes F. equiseti, Fusarium sp. and Trichoderma sp. may represent an important biocontrol agent to control the bakanae disease of rice and also implicated that could further be befitting to capitalize them for field evaluations. [ABSTRACT FROM AUTHOR]

Bakanae disease of rice caused by Fusarium fujikuroi is a significant disease of rice worldwide. The use of inoculum free seeds works well to act against this seed borne disease. Increased restrictions by the environmental protection agency (EPA) on the use of chemical seed-dressing products have made this disease a major concern among seed producers. In the present studies, 1,2,4-triazole derivatized with dithiocarbamate was further conjugated on silver nanoparticles to get 1,2,4-triazolyldithiocarbamate conjugated silver nanoparticles (TDTC-AgNPs) and its in vitro antifungal evaluation against F. fujikuroi (carbendazim as a standard fungicide) revealed its significant potential at a low dose. Double staining of hyphae with calcofluor white and propidium iodide (PI) revealed the disruption of cell membrane on treatment with TDTC-AgNPs which was further confirmed by ultramicroscopic details. Abrupt soluble protein leakage (250 μg/g) was observed within 50 min of in vitro treatment on test fungus which was further supported by the hyphal distortion as their mode of action. Priming of rice seeds revealed TDTC-AgNPs as promising materials for the development of novel antifungal agents against F. fujikuroi. Field evaluation studies of novel synthesized TDTC-AgNPs revealed that percent disease incidence was minimum (1.89 and 5.90) in the plots where seed priming with TDTC-AgNPs was given during cropping seasons 2018 and 2019 in both the varieties (PUSA 1509 and PUSA 1121) used in the experiments. Percent disease incidence (3.5 and 12.82; 6.78 and 11.46 on PUSA 1509 and PUSA 1121 during 2018 and 2019, respectively) was even less than that obtained with seed treatment with standard fungicide (carbendazim) treated seeds. Seed yield was also maximum (11.25 and 10.45; 13.30 and 12.20 q/acre for PUSA 1509 and PUSA 1121 during 2018 and 2019, respectively) in plots where seedlings obtained from TDTC-AgNPs primed seeds were transplanted. [ABSTRACT FROM AUTHOR]

Abstract Background Bakanae disease is an important fungal disease caused by Gibberella fujikuroi. Incidence of rice bakanae disease creates serious problems in the foremost rice growing countries, and no rice variety has been found to be completely resistant to this disease. However, breeding rice varieties resistant to bakanae disease may be a cost-saving solution preferable to the application of fungicides. In this study, we aimed to determine the exact position and the candidate gene for qBK1, a major resistant quantitative trait locus (QTLs) for bakanae disease. Results The genotypes/phenotypes of recombinants selected from backcrossed recombinant inbred lines of two rice varieties, Shingwang (resistant) and Ilpum (susceptible), indicated that the locus qBK1, conferring resistance to bakanae disease in Shingwang, was delimited to a 35-kb interval delimited by InDel 18 (23.637 Mbp) and InDel 19–14 (23.672 Mbp). Sequence analysis of this 35-kb region revealed four candidate genes, LOC_Os01g41770, LOC_Os01g41780, LOC_Os01g41790, and LOC_Os01g41800. There were many non-synonymous SNPs in LOC_Os01g41770 and the transcript of LOC_Os01g41790 was early terminated in Shingwang, whereas there were no differences in both LOC_Os01g41780 and LOC_Os01g41800 sequences between Ilpum and Shingwang. Expression profiling of the four candidate genes showed the up-regulation of LOC_Os01g41770, LOC_Os01g41780, and LOC_Os01g41790 in Ilpum and of LOC_Os01g41800 in Shingwang after inoculation of G. fujikuroi. Conclusion Utilization of marker-assisted selection (MAS) with a precise molecular marker on qBK1 could provide an effective tool for breeding rice varieties resistant to bakanae disease. To our knowledge, this is the first report on fine mapping and candidate gene approaches for identifying the gene for qBK1.

Root knot nematode, Meloidogyne graminicola Golden and Birchfield is widely distributed and considered a serious soil borne pathogen reducing the productivity of rice crop. In India, it is reported that root knot nematode is responsible to cause17-30% yield losses. On other hand, bakanae disease is also emerging as a serious disease of basmati rice. Precise information on losses caused by this disease (15%) was reported in India. In order to identify resistant source against root knot nematode, 20 rice varieties were tested in nematode sick plots. After 30 and 60 days of seed sowing, galls per root were recorded. To know the incidence of bakanae disease in screened rice varieties, an overall view of the rice crop was made for general observations for the presence or absence of disease symptoms. Among the screened rice varieties, Centuri Patna showed very mild intensity of root knot nematode. Three rice varieties viz., Type-3, PS-3 and PS-15 were observed with mild intensity of root knot nematode. Whereas, seven rice varieties viz., PB-1121, Tarauri Basmati, Bas-386, VB-22, VB-24, Punjab Basmati and PB-6 were observed with severe intensity. An overall view of the rice crop, bakanae disease symptoms were observed only in three rice varieties i.e. PB-1121, PB-1509 and VB-21. [ABSTRACT FROM AUTHOR]

Bakanae is the emerging disease threating the rice cultivation globally. Yield reduction of 4–70% is recorded in different parts of the world. A total of 119 Fusarium isolates were collected from rice plants at different geographical locations and seeds of different rice cultivars. The isolates were evaluated for morphological, biochemical and pathogenic diversity. The amplification of TEF-1α gene was carried out for exploring the species spectrum associated with the cultivated and pre-released rice varieties. The production of gibberellin varied from 0.53 to 2.26 µg/25 ml, while as that of Indole acetic acid varied from 0.60 to 3.15 µg/25 ml among the Fusarium isolates. The phylogenetic analysis identified 5 different species of the genus Fusarium viz. Fusarium fujikuroi, F. proliferatum, F. equiseti, F.oxysporum and F. persicinum after nucleotide blasting in NCBI. Only two Fusarium spp. F. fujikuroi and F. proliferatum were found to be pathogenic under virulence assays of the isolates. The isolates showed a considerable variation in morphological and pathogenic characters. The isolates were divided into different groups based on morphology and pathogenicity tests. The isolates showed a considerable variation in morphology, phytohormone profile and virulence indicative of population diversity. Three species F. equiseti, F.oxysporum and F. persicinum which have not been reported as pathogens of rice in India were found to be associated with bakanae disease of rice, however their pathogenicity could not be established. [ABSTRACT FROM AUTHOR]

Bakanae, caused by the hemibiotrophic fungus Fusarium fujikuroi, is one of the most important diseases of rice and is attributed to up to 75% of losses, depending on the strain and environmental conditions. Some strains cause elongation and thin leaves, whereas others induce stunting and chlorotic seedlings. Differences in symptoms are attributed to genetic differences in the strains. F. fujikuroi strains Augusto2, CSV1, and I1.3 were sequenced with Illumina MiSeq, and pathogenicity trials were conducted on rice cultivar Galileo, which is susceptible to bakanae. By performing gene prediction, single nucleotide polymorphism (SNP) calling, and structural variant analysis with a reference genome, we show how an extremely limited number of polymorphisms in genes not commonly associated with bakanae disease can cause strong differences in phenotype. CSV1 and Augusto2 were particularly close, with only 21,887 SNPs between them, but they differed in virulence, reaction to temperature, induced symptoms, colony morphology and color, growth speed, fumonisin, and gibberellin production. Genes potentially involved in the shift in phenotype were identified. Furthermore, we show how temperature variation may result in different symptoms even in rice plants inoculated with the same F. fujikuroi strain. Moreover, all of the F. fujikuroi strains became more virulent at higher temperatures. Significant differences were likewise observed in gibberellic acid production and in the expression of both fungal and plant gibberellin biosynthetic genes. [ABSTRACT FROM AUTHOR]

Bakanae disease caused by Gibberella fujikuroi, Sawada, Wollenworth (teleomorph) (anamorph: Fusarium fujikuroi Nirenberg), is emerging as a serious disease of rice in India. Histopathological study of plant tissue during infection can provide valuable insight for understanding the pathogenesis and the mechanism of resistance. The early infection process of F. fujikuroi in rice was observed at microscopic level using light microscopes and scanning electron microscope (SEM). In seed, the pathogen was observed in the husk, embryo and endosperm with maximum colonization in the husk region. Different infectious structures such as swollen tip hyphae, infectious hyphae, appressorium and infection cushion were observed in F. fujikuroi-rice interactions. The estimates of per cent (%) transmission of inoculum (seed-seed; seedlings-seed and florets-seed) revealed maximum transmission of F. fujikuroi through florets followed by seedlings and seed. The present study established that the infection of rice plants by F. fujikuroi can occur through three routes namely seed, seedlings (soil) and florets (air). The information generated in the present study will be valuable for providing an understanding on the pathogenesis and help to device effective strategies for management of bakanae disease of rice. [ABSTRACT FROM AUTHOR]

Abstract Background Bakanae or foot rot disease is a prominent disease of rice caused by Gibberella fujikuroi. This disease may infect rice plants from the pre-emergence stage to the mature stage. In recent years, raising rice seedlings in seed boxes for mechanical transplanting has increased the incidence of many seedling diseases; only a few rice varieties have been reported to exhibit resistance to bakanae disease. In this study, we attempted to identify quantitative trait loci (QTLs) conferring bakanae disease resistance from the highly resistant japonica variety Wonseadaesoo. Results A primary QTL study using the genotypes/phenotypes of the recombinant inbred lines (RILs) indicated that the locus qBK1 WD conferring resistance to bakanae disease from Wonseadaesoo was located in a 1.59 Mb interval delimited on the physical map between chr01_13542347 (13.54 Mb) and chr01_15132528 (15.13 Mb). The log of odds (LOD) score of qBK1 WD was 8.29, accounting for 20.2% of the total phenotypic variation. We further identified a gene pyramiding effect of two QTLs, qBK WD and previously developed qBK1. The mean proportion of healthy plant for 31 F4 RILs that had no resistance genes was 35.3%, which was similar to that of the susceptible check variety Ilpum. The proportion of healthy plants for the lines with only qBK WD or qBK1 was 66.1% and 55.5%, respectively, which was significantly higher than that of the lines without resistance genes and that of Ilpum. The mean proportion of the healthy plant for 15 F4 RILs harboring both qBK WD and qBK1 was 80.2%, which was significantly higher than that of the lines with only qBK WD or qBK1. Conclusion Introducing qBK WD or pyramiding the QTLs qBK WD and qBK1 could provide effective tools for breeding rice with bakanae disease resistance. To our knowledge, this is the first report on a gene pyramiding effect that provides higher resistance against bakanae disease.

Fusarium fujikuroi, causing bakanae disease, is one of the most important seedborne pathogens of rice, the detection of which is paramount for seed certification and for preventing field infections. Molecular tests—qPCR and loop-mediated isothermal amplification (LAMP)—are replacing the blotter test in seed health procedures, due to higher sensitivity, specificity, fast turnaround results delivery, on-site application and the possibility of quantifying endophytic seed infections. A LAMP test, which had been previously developed with primers designed to target the elongation factor 1-α sequence of F. fujikuroi, was validated according to the international validation standard (EPPO, PM7/98) on thirty-four rice seed lines of different levels of susceptibility to the disease, thus comparing it to the blotter test and with two different DNA extraction procedures. The use of crude extracted DNA provided more sensitive results than the DNA extracted with the commercial kit Omega E.Z.N.A® Plant DNA kit. The results showed that the endophytic infection of F. fujikuroi is essential for the development of the disease in the field and that the minimum amount of the pathogen necessary for the development of the disease corresponds to 4.17 × 104 cells/µL. This study confirms the applicability of the LAMP technique on-site on rice seeds with fast and quantitative detection of the pathogen.

Abstract Background Bakanae disease, caused by seed-borne Fusarium species, mainly F. fujikuroi, is a rice disease whose importance is considerably increasing in several rice growing countries, leading to incremental production losses. Results A germplasm collection of japonica rice was screened for F. fujikuroi resistance, allowing the identification of accessions with high-to-moderate levels of resistance to bakanae. A GWAS approach uncovered two genomic regions highly associated with the observed phenotypic variation for response to bakanae infection on the short arm of chromosome 1 (named as qBK1_628091) and on the long arm of chromosome 4 (named as qBK4_31750955). High levels of phenotypic resistance to bakanae were associated to the cumulated presence of the resistant alleles at the two resistance loci, suggesting that they can provide useful levels of disease protection in resistance breeding. A fine comparison with the genomic positions of qBK1_628091 and qBK4_31750955 with respect to the QTLs for bakanae resistance reported in the literature suggests that the resistant loci here described represent new genomic regions associated to F. fujikuroi resistance. A search for candidate genes with a putative role in bakanae resistance was conducted considering all the annotated genes and F. fujikuroi-related DEGs included in the two genomic regions highlighting several gene functions that could be involved in resistance, thus paving the way to the functional characterization of the resistance loci. Conclusions New effective sources for bakanae resistance were identified on rice chromosomes 1 and 4 and tools for resistance breeding are provided.

Bakanae caused by Fusarium fujikuroi (Nirenberg) is an emerging disease of rice in India. Although, two other pathogens are closely associated with the disease (F. proliferatum and F. verticillioides), F. fujikuroi is considered the major pathogen of this disease. Correct diagnosis and identification of the pathogen is the key to the successful management of plant diseases. PCR and loop mediated isothermal amplification (LAMP) based assays were developed for the detection of F. fujikuroi. Based on the unique sequences (NRPS31 gene) of F. fujikuroi obtained from GenBank accession KY953210, a specific marker BMFf1900 was developed for the amplification of F. fujikuroi with a sensitivity of 10 pg. For precise quantification of the inoculum, real time primers (NRPS31RT-F and NRPS31RT-R) were designed and sensitivity of the assay was increased to 10 fg. For the visualization of results under isothermal conditions, the LAMP assay was standardized. These PCR and LAMP based assays have been validated under field conditions, seed testing and in resistance evaluation of rice genotypes. The diagnostics developed are efficient, rapid and sensitive for the detection of F. fujikuroi which would be useful for testing seed health, validating varietal resistance and monitoring the pathogen inoculum. [ABSTRACT FROM AUTHOR]

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Paddy (Oryza sativa L.) growing areas of Haryana indicated that the incidence of bakanae caused by Fusarium moniliforme Sheld. In India, bakanae disease incidence has been increasing considerably and low to moderate disease incidences have been reported. The major constraint for low productivity of basmati rice in the Ambala District of Haryana is lack of awareness about the management of bakanae disease and non adoption of recommended package of practices of improved cultivation. Currently, seed treatment with Carbendazim @ 2.0 g/kg or Carbendazim + Thiram (1:1) @ 2.5 g/kg seed is the most important disease management strategy used by the farmers in worldwide after the use of resistant varieties. To replace this old age disease management strategy Krishi Vigyan Kendra, Ambala Haryana suggested one foliar spray of Sixer (Mancozeb 63% + Carbendazim 12%) W.P. fungicide @ 600gr/acre at booting stage of rice after following seed treatment strategy. KVK conducted 20 front line demonstrations on high yielding variety of basmati rice (PB 1121) during kharif season 2014 and 2015. An average yield of PB 1121 in FLDs ranged from 41.12 to 43.25 q/ha whereas in local practices 36.00 and 37.50 q/ha during 2014 and 2015, respectively and percent incidence of bakanae disease also recorded in demonstration plots ranged from 7% to 5% in compression to local check 19% to 12% during 2014 and 2015, respectively. It was recorded that the percentage increase yield with high in demonstration plots over local check was recorded in range of 14.5% to 13.29%. Similarly, the extension gap ranged between 5.12 to 5.75 q/ha during the years 2014 and 2015, respectively. [ABSTRACT FROM AUTHOR]

Fusarium species are important seedborne pathogens that cause rice bakanae disease (RBD). In this study, 421 strains were isolated from 25 rice samples collected from Zhejiang, Anhui, and Jiangxi provinces of China. Furthermore, 407 isolates were identified as F. fujikuroi (80.05% isolation frequency), F. proliferatum (8.31%), F. equiseti (5.94%), F. incarnatum (2.61%), F. andiyazi (0.95%), and F. asiaticum (0.48%) based on morphology and translation elongation factor 1-alpha (TEF1-α) gene. Phylogenetic analysis of combined sequences of the RNA polymerase II largest subunit (RPB1), RNA polymerase II second largest subunit (RPB2), TEF1-α gene, and ribosomal DNA (rDNA) internal transcribed spacer (ITS) showed that 17 representative strains were attributed to six species. Pathogenicity tests showed that representative isolates possessed varying ability to cause symptoms of bakanae on rice seedlings. Moreover, the seed germination assay revealed that six isolates had different effects, such as inhibition of seed germination, as well as seed and bud rot. The loop mediated isothermal amplification (LAMP)-based assay were developed for the detection of F. fujikuroi. According to sequences of desaturase-coding gene promoter, a species-specific marker desM231 was developed for the detection of F. fujikuroi. The LAMP assay using seeds collected from field was validated, and diagnostics developed are efficient, rapid, and sensitive.

Fusarium fujikuroi, the causal organism of bakanae disease, is mainly seed borne pathogen on rice. The response of different rice varieties have more concern to understand pathogenesis process and host pathogen interaction complex. Therefore, the present study had some objectives: to determine response of some rice genotypes to bakanae infection and Gibberellic acid (GA3) treatment through morphological, anatomical and plant hormones changes. The highly virulent isolate no. 10 of F. Fujikuroi was used in evaluation of three rice cultivars; Sakha 101, Giza 179 and promising line GZ 10101-5-1-1-1. Changes in all morphological, anatomical traits and plant hormones activities Gibberellic acid (GA3), Indol Acetic acid (IAA) and Abscisic Acid (ABA) with bakanae infection and GA3 treatment were assessed from 15-60 days after inoculation and GA3 treatment during season 2018. Results indicated that bakanae infection caused severe morphological changes as abnormal elongation, degradation of chlorophyll and seedling death. Morphological changes were associated with wide anatomical changes of leaf as deformation of motor cell, mesophyll layer. For stem, infection and GA3 induced significant increase in the No. of aerenchyma and their diameter and increase pith diameter, and stem elongation. As well as, anatomical changes in roots were significant increase in diameter of epidermis, cortex layers, vascular cylinder, and reduction in diameter of xylem vessels. Out of anatomical results, Fusarium fujikuroi prefer to grow in aerenchyma, pith, cortex, vascular bundle of both sheath and stem. There is a significant increase in plant hormones Gibberellic acid (GA3), Indol Acetic acid (IAA) and Abscisic Acid (ABA) with bakanae infection and GA3 treatment combined with bakanae infection and GA3 treatment. GZ 10101-5-1-1-1 was recorded the lowest response to GA3 treatment with the lowest infection % and stem elongation%. While Sakha 101 and Giza 179 were the highly susceptible cultivars to bakanae with the highest infection %, stem elongation% and response to GA3. The fast and highest stem elongation %, No. of nodes and internode length was considered as remarkable phenotypic markers it can be used as valuable and early selection marker of susceptibility in breeding program to bakanae disease. GZ 10101-5-1-1-1 as new promising line and high tolerant to bakanae and low response to GA3 could be used as a good source in bakanae resistance breeding program. [ABSTRACT FROM AUTHOR]

In this study, we evaluated the potential of seed priming with plant growth substances on morpho-physiological and yield attributes of bakanae infected seedlings of aromatic rice varieties Pusa Basmati 1121 and Pusa Basmati 1509. The study involved laboratory and field examination of seed priming for 6 h in SA at 5 mg L−1 &10 mg L−1 concentration, MeSA at 50 mg L−1 and 100 mg L−1 concentration, Prohexadione-Ca at 100 mg L−1 and 200 mg L−1 concentration, BABA at 5 mg L−1 and 10 mg L−1 concentration, followed by inoculation with the fourteen-day-old pure culture of Fusarium fujikuroi. The positive (inoculated hydroprimed seeds) and negative controls (un-inoculated untreated seeds) were maintained for both varieties simultaneously and the growth and physiological observations were made at 7, 14 and 21 DAG. The seed priming treatments recorded enhancement in germination, fresh and dry weight, vigour index, total chlorophyll and carotenoid content over the positive control. The optimum dose of each plant growth substance from laboratory evaluation was selected for the field studies. The procedure for priming and inoculation was same for field trial and observations were recorded at tillering, booting and anthesis stage. The seed priming treatments resulted in reduction in percent disease incidence and visible symptomology of bakanae concomitant with an enhancement in field emergence, biochemical attributes under field conditions. The study can be further used to decipher the biochemical and molecular mechanism underlying cross talk of plant growth substances during bakanae infestation in rice in order to design a disease management strategy. • Induction of systemic acquired resistance (SAR) via seed priming with SAR inducers (SA, MeSA, Prohexadione-Ca and BABA). • Enhanced germination, vigour, biochemical attributes along with reduced seed rot and seedling mortality. • Treated seedlings showed reduced disease incidence along with enhanced activities of defence enzymes. [ABSTRACT FROM AUTHOR]

Fusarium fujikuroi causing bakanae disease has emerged as one of the major pathogen of rice across the world. The study aims to comparative genomic analysis of Fusarium fujikuroi isolates and identification of the secretary proteins of the fungus involved in rice pathogenesis. In the present study, F. fujikuroi isolate “F250” was sequenced with an assembly size of 42.47 Mb providing coverage of 96.89% on reference IMI58289 genome. A total of 13,603 protein-coding genes were predicted from genome assembly. The average gene density in the F. fujikuroi genome was 315.10 genes per Mb with an average gene length of 1.67 kb. Additionally, 134,374 single nucleotide polymorphisms (SNPs) are identified against IMI58289 isolate, with an average SNP density of 3.11 per kb of genome. Repetitive elements represent approximately 270,550 bp, which is 0.63% of the total genome. In total, 3,109 simple sequence repeats (SSRs), including 302 compound SSRs are identified in the 8,656 scaffolds. Comparative analysis of the isolates of F. fujikuroi revealed that they shared a total of 12,240 common clusters with F250 showing higher similarity with IMI58289. A total of 1,194 secretory proteins were identified in its genome among which there were 356 genes encoding carbohydrate active enzymes (CAZymes) capable for degradation of complex polysaccharides. Out of them glycoside hydrolase (GH) families were most prevalent (41%) followed by carbohydrate esterase (CE). Out of them CE8 (4 genes), PL1 (10 genes), PL3 (5 genes), and GH28 (8 genes) were prominent plant cell wall degrading enzymes families in F250 secretome. Besides this, 585 genes essential for the pathogen–host interactions were also identified. Selected genes were validated through quantitative real-time PCR analyses in resistant and susceptible genotypes of rice at different days of inoculation. The data offers a better understanding of F. fujikuroi genome and will help us enhance our knowledge on Fusarium fujikuroi–rice interactions.

Background: Bakanae or foot rot disease is a prominent disease of rice caused by Gibberella fujikuroi. This disease may infect rice plants from the pre-emergence stage to the mature stage. In recent years, raising rice seedlings in seed boxes for mechanical transplanting has increased the incidence of many seedling diseases; only a few rice varieties have been reported to exhibit resistance to bakanae disease. In this study, we attempted to identify quantitative trait loci (QTLs) conferring bakanae disease resistance from the highly resistant japonica variety Wonseadaesoo. Results: A primary QTL study using the genotypes/phenotypes of the recombinant inbred lines (RILs) indicated that the locus qBK1 conferring resistance to bakanae disease from Wonseadaesoo was located in a 1.59 Mb interval delimited on the physical map between chr01_13542347 (13.54 Mb) and chr01_15132528 (15.13 Mb). The log of odds (LOD) score of qBK1 was 8.29, accounting for 20.2% of the total phenotypic variation. We further identified a gene pyramiding effect of two QTLs, qBK and previously developed qBK1. The mean proportion of healthy plant for 31 F RILs that had no resistance genes was 35.3%, which was similar to that of the susceptible check variety Ilpum. The proportion of healthy plants for the lines with only qBK or qBK1 was 66.1% and 55.5%, respectively, which was significantly higher than that of the lines without resistance genes and that of Ilpum. The mean proportion of the healthy plant for 15 F RILs harboring both qBK and qBK1 was 80.2%, which was significantly higher than that of the lines with only qBK or qBK1. Conclusion: Introducing qBK or pyramiding the QTLs qBK and qBK1 could provide effective tools for breeding rice with bakanae disease resistance. To our knowledge, this is the first report on a gene pyramiding effect that provides higher resistance against bakanae disease. [ABSTRACT FROM AUTHOR]

Fungi possess diverse photosensory proteins that allow them to perceive different light wavelengths and to adapt to changing light conditions in their environment. The biological and physiological roles of the green light-sensing rhodopsins in fungi are not yet resolved. The rice plant pathogen Fusarium fujikuroi exhibits two different rhodopsins, CarO and OpsA. CarO was previously characterized as a light-driven proton pump. We further analyzed the pumping behavior of CarO by patch-clamp experiments. Our data show that CarO pumping activity is strongly augmented in the presence of the plant hormone indole-3-acetic acid and in sodium acetate, in a dose-dependent manner under slightly acidic conditions. By contrast, under these and other tested conditions, the Neurospora rhodopsin (NR)-like rhodopsin OpsA did not exhibit any pump activity. Basic local alignment search tool (BLAST) searches in the genomes of ascomycetes revealed the occurrence of rhodopsin-encoding genes mainly in phyto-associated or phytopathogenic fungi, suggesting a possible correlation of the presence of rhodopsins with fungal ecology. In accordance, rice plants infected with a CarO-deficient F. fujikuroi strain showed more severe bakanae symptoms than the reference strain, indicating a potential role of the CarO rhodopsin in the regulation of plant infection by this fungus. [ABSTRACT FROM AUTHOR]

Bakanae occurs throughout rice growing regions of the world including Asia, Africa, America and Europe. So far the pathogen causing bakanae on rice has been widely known as F. fujikuroi in the Korean peninsula. However, previous studies have shown that Fusarium species within the Gibberella fujikuroi species complex are commonly associated with bakanae. Therefore the objective of this study is to determine the genetic diversity of the Fusarium species responsible for bakanae. Using morphological approaches and translation of DNA sequences belonging to elongation factor 1 α (TEF), histone H3 and calmodulin genes, the pathogen was identified and characterized. A total 590 isolates of Fusarium species were recovered from the rice plants with typical symptoms of bakanae and rice seeds. Out of one set of the 100 Fusarium isolates, the phylogenetic tree of 90 isolates amplified and constructed from DNA sequences of TEF gene consisted of three main clades. Futher it was observed that of the 89 Fusarium isolates amplified and constructed from 474 bp of DNA sequences of histone H3 gene, consisted of F. fujikuroi and F. proliferatum groups. Lastly, based on DNA sequences of clamodulin gene, 89 isolates including F. fujikuroi and F. proliferatum formed one clade with each reference strain. It could be again sub divided into F. proliferatum group and 2 F. fujikuroi groups. As clearly demonstrated in this study, identifying Fusarium species associated with bakanae only depending on morphological investigation is a highly challenging task, owing to its diverse characteristics. Moreover, other Fusarium species such as F. proliferatum, and F. andiyazi besides F. fujikuroi are also capable of causing bakanae. And also besides these there are other non-pathogenic F. fujikuroi which are hard to distinguish even with molecular identification protocols. [ABSTRACT FROM AUTHOR]

Fusarium fujikuroi causing bakanae disease has emerged as one of the major pathogen of rice across the world. The study aims to comparative genomic analysis of Fusarium fujikuroi isolates and identification of the secretary proteins of the fungus involved in rice pathogenesis. In the present study, F. fujikuroi isolate "F250" was sequenced with an assembly size of 42.47 Mb providing coverage of 96.89% on reference IMI58289 genome. A total of 13,603 protein-coding genes were predicted from genome assembly. The average gene density in the F. fujikuroi genome was 315.10 genes per Mb with an average gene length of 1.67 kb. Additionally, 134,374 single nucleotide polymorphisms (SNPs) are identified against IMI58289 isolate, with an average SNP density of 3.11 per kb of genome. Repetitive elements represent approximately 270,550 bp, which is 0.63% of the total genome. In total, 3,109 simple sequence repeats (SSRs), including 302 compound SSRs are identified in the 8,656 scaffolds. Comparative analysis of the isolates of F. fujikuroi revealed that they shared a total of 12,240 common clusters with F250 showing higher similarity with IMI58289. A total of 1,194 secretory proteins were identified in its genome among which there were 356 genes encoding carbohydrate active enzymes (CAZymes) capable for degradation of complex polysaccharides. Out of them glycoside hydrolase (GH) families were most prevalent (41%) followed by carbohydrate esterase (CE). Out of them CE8 (4 genes), PL1 (10 genes), PL3 (5 genes), and GH28 (8 genes) were prominent plant cell wall degrading enzymes families in F250 secretome. Besides this, 585 genes essential for the pathogen--host interactions were also identified. Selected genes were validated through quantitative real-time PCR analyses in resistant and susceptible genotypes of rice at different days of inoculation. The data offers a better understanding of F. fujikuroi genome and will help us enhance our knowledge on Fusarium fujikuroi--rice interactions. [ABSTRACT FROM AUTHOR]