Fusarium basal rot (FBR) poses a serious threat to onion (Allium cepa L.) production worldwide. In South Korea, FBR is primarily associated with Fusarium oxysporum, F. commune, and F. proliferatum. To investigate the relationship between effector gene profiles and virulence, we screened 34 isolates collected from FBR-affected fields for 14 Secreted in Xylem (SIX) genes and three additional effector candidates (CRX1, CRX2, and C5). F. oxysporum isolates carrying the effector suite SIX3, SIX5, SIX7, SIX9, SIX10, SIX12, SIX14, together with CRX1, CRX2 and C5, exhibited significantly higher aggressiveness on onion seedlings and bulbs than effector-negative strains. Among F. commune isolates lacking SIX genes, those carrying both CRX1 and CRX2 tended to show greater pathogenicity than CRX-negative strains. Nevertheless, SIX-negative strains still caused substantial seedling loss and bulb-rot, indicating the involvement of SIX-independent virulence factors. All F. proliferatum isolates were comparably pathogenic to SIX-negative F. oxysporum and F. commune strains, and uniformly carried SIX2-1 and CRX2, with a subset also harboring the SIX2-2 homologue. Across all isolates, SIX9 was the most frequently detected SIX gene and was markedly enriched in strains exhibiting strong pathogenicity. We developed and validated a SIX9-targeted quantitative PCR (qPCR) assay that specifically detects SIX9-positive Fusarium isolates (mainly F. oxysporum and F. commune), with detection limits of 1 pg of DNA or 10⁴ conidia/g soil. These findings enhance our understanding of effector repertoires contributing to Fusarium pathogenicity on onion and provide a molecular tool to support FBR diagnosis.

Fusarium basal rot (FBR) severely reduces onion production by causing substantial pre- and post-harvest losses, resulting in shortage of onion during the lean period. Among many reported Fusarium species causing FBR, the Fusarium acutatum and Fusarium falciforme have become more aggressive with their increasing prevalence. The current study evaluated and compared the five different 'onion bulb inoculation methods' to induce F. acutatum and F. falciforme mediated bulb rotting under controlled laboratory conditions. The methods tested included: (1) cotton swab impregnated with spore suspension, (2) pinprick at the basal plate followed by dipping in spore suspension, (3) a combination of pinprick, dipping, and cotton swab, (4) disk inoculation, and (5) injection of spore suspension. Onion bulb rotting was monitored for 15days post-inoculation observing mycelial growth, tissue necrosis, affected bulb surface area and affected bulb tissue volume, histopathology, and disease rating. Depending upon effectiveness of methods, the bulb rot affected area ranged from 32 to 70 cm2 for F. acutatum and from 64 to 81 cm2 for F. falciforme, while the volume of affected bulb tissue ranged from 17 to 55 cm3 for F. acutatum and from 48 to 69 cm3 for F. falciforme. The affected surface area, affected volume, rotting over control and disease rating in Cotton swab method was 48 cm2, 31 cm3, 56%, 7 for F. acutatum and 80 cm2, 67 cm3, 92%, 9 for F. falciforme, respectively, which indicated the pathogenicity of F. falciforme was higher than that of F. acutatum across all five inoculation methods (Methods 1-5). Further, we observed that F. acutatum caused rot within 3days of exposure while symptoms in F. falciforme appeared on 5th day, however the extent of the tissue damage was higher. In our findings, the 'cotton swab method' was found best for creating the artificial infection on the onion bulbs followed by 'Pinprick at the basal plate and dipping in spore suspension method' in comparison to other methods. The results of this study would pave the way to onion breeders and pathologists to employ suitable screening method for mass screening of onion genotypes for FBR resistance/tolerance.

Metabolites Profiling and Bioactivity of Aspergillus-Penicillium Co-culture: Integrative GC-MS, LC-MS/MS, and in Silico Analysis for Targeting Fusarium Proliferatum in Onion Basal Rot Biocontrol

Onions (Allium cepa L.) are a major crop for spices in Bangladesh. The current study was conducted to assess the morphological traits, cultural effects, molecular identification, and environmentally friendly management of the pathogenic fungus isolated from onion basal rot disease. Fusarium verticillioides causes basal rot symptoms in onion at the early and mature stages. Mycelial growth of F. verticillioides was highest on the potato dextrose agar (PDA) medium (72 mm), followed by the potato sucrose agar (PSA) medium, and lowest on the yeast extract agar (YEA) medium (31 mm). F. verticillioides grew and developed mycelially best at 30°C and 6.5 pH, respectively. A blast search revealed 99% sequence match with the F. verticillioides species complex, and the internal transcribed spacer (ITS) region of the PCR products spanned 590 bp. Against the growth and development of F. verticillioides mycelium, Trichoderma harzianum exhibited the highest mycelial growth inhibition (75%), followed by T. erinaceum (64%), and T. asperellum (55%). According to the findings, T. harzianum, an antagonistic fungus, is a highly successful bio-control agent against F. verticillioides. Plant Tissue Cult. & Biotech. 35(1): 93-104, 2025 (June)

The onion (Allium cepa L.) is one of the most important vegetable crops that is cultivated worldwide. It is one of the most important vegetable cash crops of Balochistan with an area of 35.8 thousand ha and a production of 681.5 thousand tonnes. It is attacked by many diseases, which affect the yield. Among onion diseases, the basal rot of onion is one of the most important diseases of onion caused by fungus (Fusarium oxysporum f. sp. cepae) that causes heavy losses of onion production and its quality worldwide. Keeping in view the economic importance of disease, the current study was carried out at the Directorate of Vegetable Seed Production, Agricultural Research Institute, Quetta, Balochistan. In the greenhouse experiment, plant growth attributes like plant height, number of leaves, leaf length, bulb size, bulb weight, root length, and root weight were significantly increased by all treatments. The Topsin-M was found most effective at all concentrations with the highest plant biomass production and biological yield, as with maximum plant height (72.30 cm), number of leaves (13.00), leaf length (62.23 cm), bulb size (5.45 dia), bulb weight (108.00 g), root length (18.26 cm), and root weight (1.45 g) at a concentration of 1% after 130 days, followed by Cabriotop, Score, and Antracol at 1% doses, respectively. While Mencozeb+ Metalxyl was least effective with plant height (45.63 cm), number of leaves (8.00), leaf length (35.90 cm), bulb size (3.81 dia), bulb weight (64.23 g), root length (8.18 cm), and root weight (0.36 g), at a level of 0.25% after 130 days over the control.

Developing cultivars with broad-spectrum resistance to Fusarium basal rot is a major aim of onion breeding. Studies conducted between 2020–2023 to identify Fusarium spp. causing basal rot in Karnataka, India detected only F. acutatum and F. falciforme (Bhat et al., 2023). In September 2023, 34 onion bulbs with symptoms of Fusarium basal rot were collected from farmer's fields in the districts of Bagalkot, Chikkamagaluru, and Chitradurga in Karnataka (Figure 1). Single spore isolation of Fusarium from the diseased bulbs resulted in 64 cultures. Among them were 11 isolates with a colony morphology and colour on potato dextrose agar distinctly different from those previously described, prompting further investigation. Protocols used for isolation and characterisation of Fusarium were as described in Sarwadnya et al. (2023). Two isolates from the ochre-yellow (IBFB-35A and IBFB-35B) and dark purple (IBFN-41A and IBFN-41B) colour groups were cultured on synthetic nutrient-poor agar and carnation leaf agar media to study spore morphology. IBFB-35A and IBFB-35B produced microconidia with zero to one septum measuring 5.87-6.95 × 1.7-2.72 µm (n = 20) in size (Liu et al., 2023) and chlamydospores were round, single or in chains and were either terminal or intercalary in position, but macroconidia were not observed. Isolates IBFN-41A and IBFN-41B produced three-septate macroconidia, 17–32.9 × 1.43-3.71 µm (n = 20), microconidia were 6.07-7.88 × 1.43-2.69 µm (n = 20) in size and chlamydospores either solitary or in chains as described by Zhang et al. (2023) (Figures 2- 3). The internal transcribed spacer (ITS) and partial translation elongation factor 1-α (tef1) gene (O'Donnell et al., 1998) regions of the isolates were amplified and sequenced. Sequences of the four isolates (IBFB-35A, IBFB-35B, IBFN-41 and IBFN-41B) were submitted to GenBank, Accession Nos. PP981364, PP981365, PP981366, PP991501, and PP986950-PP986953 for the ITS region and tef1, respectively. Phylogenetic analysis placed isolates IBFB-35A and IBFB-35B with F. brachygibbosum (F. solani complex) and isolates IBFN-41A and IBFN-41B with F. nygamai (F. fujikuroi species complex) (Figure 4). The pathogenicity of the F. brachygibbosum and F. nygamai isolates, along with previously characterised F. acutatum (IBFA-17) and F. falciforme (IBFF-10) isolates, (Bhat et al., 2023), were tested on a susceptible onion line 16/7Y GR3. Twenty-eight-day-old seedlings, grown in sterilised cocopeat, were removed and washed with sterile water and immersed in a conidial suspension (1×104 conidia/mL) for 15 minutes before transplanting into a pre-sterilised soil mix (red soil: farmyard manure: cocopeat, 2:1:1 v/v/v). Each seedling was then treated at the base with 5 mL of the conidial suspension. Control plants were mock-inoculated with sterile water. Pots were kept in polytunnels with natural light (c. 13 hours daylight) and a day/night temperature of 27–33/16-18°C. All inoculated onion plants were dead by 40 days post-inoculation (Figure 5). However, when compared with F. acutatum and F. falciforme, the symptoms caused by F. brachygibbosum and F. nygamai took longer to develop, and inoculated plants took longer to wilt (Table 1). Fusarium brachygibbosum causing basal rot of onion has been reported in Mexico (Tirado-Ramirez et al., 2021).This is the first report of the pathogen infecting onion in India. Fusarium nygamai was reported as an endosymbiont of onion in Egypt (Sayed et al., 2021) but this is the first report as a pathogen of onion in India or globally.

In Burkina Faso, onions (Allium cepa L.) are one of the main vegetable crops. It is a very important source of income for producers. However, its production is subject to loss, one of the main ones being disease caused by fungal pathogens, including Fusarium falciforme, which causes onions basal rot. This study aimed to contribute to the onion production improvement through agroecological methods by setting up a pathogenicity test and an antifungal test based on essential oils of local plants against Fusarium falciforme. For the pathogenicity test, a conidial suspension of each strain was produced at 1 x 106 conidia/ml using a haematimeter. It was carried out in the Biosciences Laboratory of Joseph KI-ZERBO University and in the greenhouse. A randomized block design with 04 replicates and 06 treatments was used. For antifungal test, the method by direct contact was used. The germination rate parameter was measured in the laboratory. The rate of emergence and damping-off were assessed in the greenhouse. The pathogenicity test results showed that the impact of Fusarium falciforme on onion seeds was relatively high in all pots. As regards the antifungal test, results showed a significant inhibitory effect of the essential oils used on the mycelial growth of Fusarium falciforme. All the essential oil concentrations of Cymbopogon citratus and Cymbopogon nardus were able to completely inhibit the fungus' growth. In contrast, the essential oil of Eucalyptus camaldulensis showed little mycelial growth at 1 %, 2 % and 3 % concentrations of 1.05 to 2.85 cm, with an inhibition rate of 63.83 % to 86.68 %. Based on these results, biopesticide-based biocontrol of Fusarium falciforme is therefore possible for onions basal rot management.

One of Egypt’s most notable and historically significant vegetable crops is the Liliaceae plant, Allium cepa L. In this study, the effectiveness of methanolic extracts of Artemisia absinthium leaves, Calotropis procera latex, Moringa oleifera seeds, and Syzygium aromaticum clove was investigated in vitro and, in a greenhouse, setting against Fusarium oxysporum, the pathogen that causes onion basal rot in Assiut Governorate, Egypt. The S. aromaticum extract exhibited the inhibition peak (63.3%), whereas the A. absinthium extract had the lowest inhibition impact against F. oxysporum growth (41.1%). The gas chromatography-mass spectroscopy (GC–MS) analysis revealed that 82 important compounds, with abundances ranging from low to high, were present in the tested S. aromaticum’s methanolic extract. The primary components were acetaldehyde, hydroxy- and 2-propanone, 1,1,3,3-tetrachloro-(42.71%), 1,2-ethanediol, and methyl alcohol (34.01%). In comparison to the infected control, the disease severity was significantly reduced by 20% with the use of a plant extracts mixture and Dovex 50% and increased by 62.22% with the use of an extract from A. absinthium. When compared to the infected control, onion plant fresh weight and dry weight were considerably higher under the clove extract therapy. The plant extracts used in this study’s testing contain a number of active ingredients, including amino acids, vitamins, minerals, antioxidants, and enzymes, which is probably why they have such positive impacts. The application of a combination of plant extracts was suggested as a feasible strategy for improving the growth and productivity of onion plants by the study’s findings. More research is needed to comprehend the mechanisms by which plant extracts promote plant development and to optimize the concentration and timing of administration.

Over the past decade, there have been accumulating reports from researchers, farmers, and field extension personnel on the increasing incidence and spread of onion basal rot in India. Onion basal rot disease is mainly caused by Fusarium spp. This study aimed to validate the information on the active prevalence of F. falciforme and F. acutatum causing Fusarium basal rot (FBR) in Maharashtra. A survey was conducted, and the infected plants/bulbs were collected from fields of 38 locations comprising five districts of Maharashtra, namely, Nashik, Aurangabad, Solapur, Ahmednagar, and Pune, in 2023. This disease was prevalent in high-moisture and high-oil-temperature conditions and the symptoms were observed in most of the fields, with the FBR incidence ranging from 17 to 41%. The available data of basal rot incidence from 1998 to 2022 were analyzed, based on which the prevalence of FBR was 11–50%. Tissue from the infected samples of onion bulbs was used for the isolation. The identification was performed based on colony morphology and microscopic features and confirmed through molecular markers using ITS and Tef-1α gene primers. Of the ten Fusarium isolates collected from selected locations, six species were confirmed as F. acutatum and four as F. falciforme. The pathogenicity tests performed with onion seedlings and bulbs under moist conditions proved that both F. acutatum and F. falciforme independently could cause basal rot disease symptoms but with different degrees of virulence. Koch’s postulates were confirmed by reisolating the same pathogens from the infected plants. Thus, the active prevalence of FBR was confirmed in Maharashtra and also, to the best of our knowledge, this is the first report of F. falciforme and F. acutatum causing basal rot of onion independently in Maharashtra, India.

Fusarium basal rot of onions causes large losses during storage of commercial production of onion bulbs, which in turn adversely affects the food market situation in the off-season period. There are no data on the composition of Fusarium spp., which causes onion basal rot in the Russian Federation. Therefore, our research was aimed at Fusarium spp. causing onion basal rot in the Moscow Region of the Russian Federation and studying the pathogenicity of these species for the host plant. We studied 20 isolates of Fusarium spp. collected from affected mature bulbs and seed bulbs. Species identification of the isolates was carried out using analysis of the nucleotide sequences of the three genetic loci ITS, tef1 and rpb2, as well as was based on the macro- and micromorphological characteristics of these isolates. As a result, the species F. annulatum (F. fujikuroi species complex), F. oxysporum (F. oxysporum species complex), F. acuminatum (F. tricinctum species complex) and F. solani (F. solani species complex) were identified to involve in the pathogenesis of Fusarium basal rot. We have shown for the first time that the species F. annulatum and F. acuminatum are highly aggressive and capable of causing onion basal rot. The predominant species were F. annulatum and F. oxysporum. The proportion of these species in the total number of analyzed isolates was 60% and 25%, respectively. The largest proportion (33%) of highly aggressive on mature bulbs isolates was found in the species F. annulatum. The data obtained provide practical insights for developing strategies to manage Fusarium fungi responsible for onion basal rot Moscow Region of the Russian Federation. In addition, data about species composition and aggressive isolates may be used in onion breeding for resistance to Fusarium basal rot.

onion basal rot poses a serious threat to onion production in the Upper east region of Ghana.a survey was conducted in 2022 in three purposefully sampled districts and a municipality in the region to determine the incidence and severity of the disease and to assess the perception and knowledge of farmers on the spread and control of the disease in the region.in each district/municipality, three communities were purposefully selected for the study.a questionnaire was administered to 180 onion farmers randomly selected to assess the farmers' perceptions, knowledge, and agronomic practices.Fifteen onion fields, from each district/municipality, were randomly selected for the assessment of the incidence and severity of the disease.Symptomatic onion plants were collected for pathogen isolation using potato dextrose agar.the causal organism was identified as Fusarium oxysporum f. sp.cepae based on morphological characteristics and confirmed by pathogenicity test.Under irrigated conditions, the incidence of onion bulb rot was highest in Bansi (28.92%) and lowest in Kuka (19.47%).the disease severity index, on the other hand, was highest and lowest at Yalugu (44.25%) and Bugri Corner (30.15%), respectively.the disease incidence was significantly higher in the rainy season than in the dry season.

Fusarium basal rot (FBR) places a significant limitation on Allium production worldwide. The damage caused by the disease can be observed throughout the entire crop cycle. This research aimed to further our understanding of the impact of FBR on the cultivation of onions (Allium cepa) in northeast Israel. It focused on studying the composition and incidence of Fusarium species involved in disease outbursts in two representative fields, one in Galilee (Hula Valley) and the second in the Golan Heights, where the disease incidences reached 8%. Using colony morphology, microscopic taxonomic keys, and molecular methods, a new, unreported Neocosmospora (previously Fusarium solani) species complex (SC, mostly N. falciformis) was discovered as a wildly spread member of the Fusarium pathobiome community. This species complex appeared more generalist in its nature since it was found in all three onion cultivars’ samples. It was also less virulent in seed germination (42–52% higher sprout biomass, p < 0.05) and bulb pathogenicity tests (41–45% less necrotic) than Fusarium acutatum. Whereas the Galilee yellow Orlando (Riverside) onion cultivar bulbs sampled were colonized by Neocosmospora SC (70%) and two other, less abundant species, F. oxysporum f. sp. cepae and F. acutatum (15% each), the Golan Heights field’s Fusarium community showed host specificity. In the Golan Heights field, F. oxysporum f. sp. cepae inhabited the red Ha2 onion cultivar bulbs, whereas F. acutatum colonized the yellow Ha1 cultivar (40% and 50% prevalence along with Neocosmospora SC). A better understanding of the complexity of this disease caused by different Fusarium species and with a divergence in host susceptibility and virulence is critical for developing disease management strategies. Since each Fusarium species reacts differently to pest control treatments, changes in the species composition may require specifically adapted management solutions.

Onion basal rot (Fusarium oxysporum f. sp. cepae) disease exerts serious threats on global onion (Allium cepa L.) production and trade. Present breeding programs mostly focus on development of cultivars resistant to onion basal rot disease. Characterization of breeding material in breeding gene pool is the first step of breeding. This study was conducted to determine the susceptibility of 4 onion cultivars, 30 long-day, 1 intermediate-day and 21 short-day onion genotypes to onion basal rot disease. Significant differences were seen in disease susceptibility of the genotypes (P<0.01 ) in both onion seedling and bulb tests. Onion seedling and bulb tests revealed that resistance was not detected in short and intermediate-day onion genotypes and cultivars, while two of long-day onion genotypes (ACLD 7 and 8) were found to be tolerant. Based on present finding, 3 cultivars, 28 long-day, 1 intermediate-day and 21 short-day genotypes were identified as sensitive. ACLD 7 and 8 long-day onion genotypes, which were identified as promising in seedling tests, were also identified as tolerant in bulb tests and such findings proved the compliance of seedling and bulb tests. Bulbs were obtained from the long-day onion lines (ACLD 7-8 genotypes) that were found to be promising and survived in seedling tests and seeds were obtained from these genotypes to ensure progress of generation and they were included in breeding gene pool.

<i>Fusarium oxysporum</i> is the main pathogen causing Fusarium basal rot in onion (<i>Allium cepa</i> L.), which incurs significant yield losses before and after harvest. Among management strategies, biological control is an environmentally safe and sustainable alternative to chemical control. In this study, we isolated and screened bacteria for antifungal activity against the basal rot pathogen <i>F. oxysporum</i>. Isolates 23-045, 23-046, 23-052, 23-055, and 23-056 significantly inhibited <i>F. oxysporum</i> mycelial growth and conidial germination. Isolates 23-045, 23-046, 23-052, and 23-056 suppressed the development of Fusarium basal rot in both onion seedlings and bulbs in pot and spray inoculation assays. Isolate 23-055 was effective in onion seedlings but exhibited weak inhibitory effect on onion bulbs. Based on analyses of the 16S rRNA and <i>rpoB</i> gene sequences together with morphological analysis, isolates 23-045, 23-046, 23-052, and 23-055 were identified as <i>Bacillus thuringiensis</i>, and isolate 23-056 as <i>Bacillus toyonensis</i>. All five bacterial isolates exhibited cellulolytic, proteolytic, and phosphate-solubilizing activity, which may contribute to their antagonistic activity against onion basal rot disease. Taken together <i>B. thuringiensis</i> 23-045, 23-046, 23-052, and 23-055 and <i>B. toyonensis</i> 23-056 have potential for the biological control of Fusarium basal rot in onion.

Onion (Allium cepa L.) is a globally important crop worldwide including Saudi Arabia. In November 2020, 2-month-old onion plants (cv. Redwing) in commercial fields within the Sajir area of Riyadh region (∼ 1.4 ha), showed symptoms of yellowing, wilting, stunting, bulb discoloration, rot in the basal parts of bulb and decrease in roots. In the advanced stages, the affected plants collapsed and died. The incidence of symptomatic plants ranged from 30 to 65% in the surveyed fields. To isolate the pathogen, symptomatic onion plants (n =20) were sampled. Diseased tissues from roots and bulbs were cut into small pieces (4 × 4 mm), sanitized with 1% sodium hypochlorite solution for 2 min, submerged in 70% alcohol for 20 s, then rinsed with sterile water, before plating on potato dextrose agar (PDA) medium. The plates were incubated at 25°C for 6 days. Subcultures of the mycelia grown out of the diseased tissues produced purplish pink fungal colonies on PDA. On carnation leaf agar, cultures were characteristic of Fusarium oxysporum as described by Leslie and Summerell (2006), with the presence of unicellular microconidia (3.8 to 7.8 × 1.7 to 2.5 μm, n= 50) without septa in false heads or short monophialides and slightly curved macroconidia (16.3 to 28 × 4.2 to 6.1 μm, n= 50) with two to four septa. Older mycelia developed many chlamydospores that were single or in short chains. To further confirm the pathogen identification, DNA was extracted from single-spore cultures of three representative isolates using the DNeasy Plant Mini kit (QIAGEN, Hilden, Germany). Three different fungal nuclear regions of internal transcribed spacer (ITS), elongation factor 1-α, (TEF1-α) and the second largest subunit of DNA-directed RNA polymerase II (RPB2) DNA were amplified by PCR and sequenced with the following primers: ITS4 and ITS5 (White et al. 1990); EF-1 and EF-2 (O'Donnell et al. 2008); and fRPB2-5F and fRPB2-7cR (Liu et al. 1999), respectively. Phylogenetic analysis based on the alignment of the ITS, TEF1-α, and RPB2 sequences using MEGA7 placed these isolates in the F. oxysporum clade. The ITS, TEF1-α, and RPB2 sequences of an isolate FOC-OR9 were submitted to GenBank (OL721757, OL764494, and OL764495 respectively). To confirm the forma specialis cepae, a fragment of the F. oxysporum f. sp. cepae gene Secreted In Xylem 3 (SIX3) was amplified by PCR (Kalman et al. 2020). The SIX3 amplicon (∼ 277-bp) was sent for sequencing, and the sequence was submitted to GenBank (OL828265). BLASTn analysis of the sequences showed 100% identity with F. oxysporum f. sp. cepae (KP746408). To fulfill Koch's postulates, pathogenicity tests were performed with healthy onion bulbs cv. "Redwing" of 100-150 g each. Prior to inoculation of onion bulbs, the dry bulb scales, one of the fleshy inner scales, as well as the roots were removed. Bulbs were then surface sterilized (as described above) and injected with 20 µl of a conidial suspension (106 spores/ ml) into the basal plate of each bulb and approximately 1 cm deep into the tissue. Six bulbs were inoculated for each isolate, placed in a mesh bag, and incubated at 28 °C in the dark. Six bulbs injected with sterile water and six non-inoculated bulbs served as controls. At the 4th week post inoculation, necrotic rot symptoms and brown discoloration were observed on the basal plates of these inoculated bulbs (similar symptoms to those observed in the field), while control treatments showed no symptoms. The pathogen was re-isolated from the basal plates onto PDA and identified morphologically and molecularly as F. oxysporum f. sp. cepae, thus fulfilling Koch's postulates. The test was repeated twice. This pathogen was previously reported causing onion basal rot in United Kingdom (Taylor, et al., 2013). To our knowledge, this is the first report of basal rot in onion caused by F. oxysporum f. sp. cepae in Saudi Arabia. It is recommended that preventive management should be considered as this disease may cause significant economic losses for onion growers in Saudi Arabia. Also, Fusarium mycotoxin contamination of onion bulb could pose a public health risk.

Fusarium basal rot is an important pre- and post-harvest disease of onion (Allium cepa) worldwide. Karnataka state produces around 10% of the onions grown in India and the incidence of this disease varies from 10 to 70%, depending on the area, season and year. The incidence is lowest during the dry season and in fields with loamy soils, and highest in areas with high rainfall, during the rainy season, and on black soils. Fusarium oxysporum f. sp. cepae has been reported to be the major pathogen causing Fusarium basal rot of onion in India (Ilhe et al., 2013) The aetiology of the disease was investigated during a survey of onion fields in Karnataka from 2020 to 2022. Three to five bulbs with symptoms of Fusarium bulb rot were collected from each of 25 fields in the Bangalore, Bagalkot, Chitradurga and Hassan districts of Karnataka during 2020–22 (Fig. 1). Pathogen diagnosis was done as described by Sarwadnya et al. (2023). Single spores were plated on potato dextrose agar, synthetic nutrient-poor agar and carnation leaf agar media. Culture morphology (Figs. 2, 3) and molecular analysis of the internal transcribed spacer (ITS) of 26 isolates confirmed that all belonged to Fusarium. Partial sequencing of the translation elongation factor 1-α (tef1) gene (O'Donnell et al., 1998) and multi locus BLAST analysis in the Fusarioid -ID database (Crous et al., 2021) revealed that 14 isolates belonged to F. falciforme (Sarwadnya et al., 2023) and 12 belonged to F. acutatum. part of the F. fujikuroi species complex (Yilmaz et al., 2021). Phylogenetic analysis of tef1 fragments showed clustering of isolates with F. acutatum and F. falciforme (Fig. 4). ITS and partial tef1 gene sequences of F. acutatum isolates IBFA-13 and IBFA-17 were submitted to GenBank (Accession Nos. OQ402722, OQ411015 and OQ402724, OQ411016 respectively). The virulence of nine F. falciforme and eleven F. acutatum isolates were tested on seedlings of a susceptible yellow onion cultivar (16/7Y GR3) (Table 1). Twenty-eight-day old seedlings grown on sterilised cocopeat were uprooted, washed with sterile water, dipped into conidial suspension (1×104 conidia/ml) for 15 minutes and transplanted into a pre-sterilised soil mix (red soil:farmyard manure:cocopeat, 2:1:1 v/v/v) in plastic pots. Each seedling was then drenched at the base with 5 ml of conidial suspension diluted with sterile water (1:1, v/v). Control plants were mock inoculated with sterile water. Pots were housed in polytunnels under natural light (c. 13 hours daylight) and temperature conditions (day 27–33°C; night 16–18°C) and watered by hand with a with a watering can rose. All F. acutatum isolates were highly virulent, whereas there was a range of virulence amongst F. falciforme isolates (Table 1., Fig. 5). The pathogen re-isolated from inoculated plants were similar in morphology and and partial tef1 sequence to the original isolates, thus fulfilling Koch's postulates. Fusarium acutatum causing onion basal rot has been reported from Israel (Kalman et al., 2020) and Burkina Faso (Sogoba et al., 2021). Although reported to cause root rot on legumes (Gautam et al., 2016), this is the first report of onion infecting F. acutatum from India and it appears to be a major cause of basal rot rather than F. oxysporum as reported previously. The widespread occurrence, high virulence and mycotoxigenic potential of this previously unreported species demands systematic investigation into the diversity and geographical spread of different Fusarium species in India to breed for resistant cultivars yielding better quality produce.

Onion (Allium cepa, L) is a very important vegetable crop in India. India is the second largest producer of onion in the world and the crop is grown on more than 1.22 million hectares. Fusarium Basal Rot (FBR) is an economically important diseasef onion that causes considerable losses in onion production up to 50% in field and 30-40% during post-harvest storage of bulbs (Gupta and Gupta 2013; Rajamohan et al. 2019). Onion plants showing chlorosis, twisting, wilting, necrosis, bulb discoloration, rot in the basal parts of bulb and roots typical to FBR were observed, in a field trial of 36 onion cultivars during October 2020 in Bangalore, Karnataka. FBR incidence varied from 30-100% in this field (Fig 1 a-d). Symptomatic bulbs were washed with water, basal plate and fleshy leaves cut into 0.5 to 1 cm-size, surface disinfected with 1.5% sodium hypochlorite (NaOCl) for 3 min, and rinsed with sterile distilled water. Twenty pieces were placed on potato dextrose agar (PDA) in Petri plates and incubated at 25°C for 7 days. Colonies from single-spore isolates on PDA showed abundant white aerial mycelium. Colonies showed light pink or purple coloration on the reverse side of the culture plate with brown center (Fig 1e-f). Macroconidia were 19.13 to 28.35 (mean= 24.2) × 4.29 to 6.06 (mean= 5.05) µm, hyaline, falcate, with slightly curved apexes, and three to five septa. Microconidia were cylindrical to ellipsoid, aseptate, hyaline 8.20 to 12 (mean=10.0) × 3.55 to 4.79 (mean= 4.29) µm (Fig 1g). Chlamydospores were round, intercalary, hyaline, single or in chains (Fig 1h). Two isolates (IBFF-09 & IBFF-10) were analyzed for internal transcribed spacer-ITS (White et al. 1990) and translation elongation factor 1-α (tef1) gene (O'Donnell et al. 1998) by polymerase chain reaction (PCR) and sequenced. ITS and partial tef1 gene sequences of isolates IBFF-09 and IBFF-10 were submitted to the NCBI database (GenBank accession # ON394614&ON026859; # ON409480, ON093166 respectively). Phylogenetic analysis of tef1 gene placed the isolates with F. falciforme (Fig 1i). A pathogenicity test was performed by dipping roots of 28 days old healthy onion seedlings of a susceptible genotype 16/7Y GR3 into a conidial suspension (1 × 104 conidia/ml) of isolate IBFF-10 for 15 min and then transplanting the plants into pots containing sterilized potting mix. Inoculated plants developed typical symptoms of FBR and were all dead by 20 days post inoculation (Fig 1j) while the non-inoculated controls remained healthy. Pathogen was re-isolated from infected plants and showed the same morphology, ITS and tef1 sequence similarity as the original isolate, thus fulfilling Koch's postulates. Basal rot of onion by F. falciforme is reported from Mexico (Tirado-Ramírez et al. 2021). Till date, only F .oxysporum, F. proliferatum and F. solani have been implicated in onion FBR in India (Lee et al. 2021; Rathore and Patil, 2019). F. falciforme however, i prevalent in India and is reported to infect other crops (Gangaraj et al. 2022; Gupta et al. 2019; Homa et al. 2018). There is a high probability that this pathogen is contributing significantly to basal rot disease but it has not been reported yet. To our knowledge, this is the first report of F. falciforme infecting onions in India. In order to develop FBR resistant onion cultivars it is critical to identify and study the response of onion genotypes to different Fusarium spp causing the disease.

T raditionally, three major red onions (Allium cepa L.) landraces such as Jaffna local, Vallari, and Vethalam have been cultivated as a major cash crop in the Northern part of Sri Lanka and used as a condiment, vegetable, and medicine based

<p><strong>Background</strong>: Species of the <em>Fusarium</em> genus are considered as devastating phytopathogens of onion crops around the world. <strong>Objective</strong>: This work aimed to know the causal agent of basal rot in onion crops from Puebla-México recorded in 2019. <strong>Methodology</strong>: The causal agent was isolated from diseased samples by tissue incubation in Potato Dextrose Agar medium (PDA) and the pathogenicity tests were done with the causal agent to demonstrate its involvement in basal rot. Monosporic cultures of the causal agent were generated for further microscopic characterization and molecular identification by Internal Transcribed Spacers ITS1 and ITS2. <strong>Results</strong>: According to the pathogenicity tests, the causal agent produced apical constriction and necrosis in the radicle and leaves accompanied by brown spots surrounded by yellowing as those observed in natural conditions. A 533 bp amplicon of the causative agent was obtained by partial amplification of the 5.8S rDNA gene. The sequence of the amplicon was compared with the sequences deposited in the database of the National Center for Biotechnology Information (NCBI) showing 100% homology with <em>Fusarium equiseti</em>. <strong>Implications</strong>: Our investigation reveals <em>F. equiseti</em> as an emergent causal agent of onion basal rot in crops from the community of “La Soledad” Puebla, México. <strong>Conclusion</strong>: Herein we report for the first time <em>F. equiseti</em> as a new phytopathogen of onion and further strategies should be considered for its control.</p>

Molecular characterization of Zn(II)2Cys6 cluster gene family and their association with pathogenicity of the onion basal rot pathogen, Fusarium oxysporum f. sp. cepae