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Accurate taxonomic classification of samples from infected host material is essential for disease diagnostics and genome analyses. Despite the importance, diagnosis of fungal pathogens causing banana leaf diseases remains challenging. Foliar diseases of bananas are mainly caused by 3 Pseudocercospora species, of which the most predominant causal agent is Pseudocercospora fijiensis. Here, we sequenced and assembled four fungal isolates obtained from necrotic banana leaves in Bohol (Philippines) and obtained a high-quality genome assembly for one of these isolates. The samples were initially identified as P. fijiensis using PCR diagnostics; however, the assembly size was consistently 30 Mb smaller than expected. Based on the internal transcribed spacer (ITS) sequences, we identified the samples as Zasmidium syzygii (98.7% identity). The high-quality Zasmidium syzygii assembly is 42.5 Mb in size, comprising 16 contigs, of which 11 are most likely complete chromosomes. The genome contains 98.6% of the expected single-copy BUSCO genes and contains 14,789 genes and 10.3% repeats. The 3 short-read assemblies are less continuous but have similar genome sizes (40.4–42.4 Mb) and contain between 96.5 and 98.4% BUSCO genes. All 4 isolates have identical ITS sequences and are distinct from Zasmidium isolates that were previously sampled from banana leaves. We thus report the first continuous genome assembly of a member of the Zasmidium genus, forming an essential resource for further analysis to enhance our understanding of the diversity of pathogenic fungal isolates as well as fungal diversity.

Foliar diseases of maize cause severe economic losses in India and around the world. The increasing severity of maize leaf blight (MLB) over the past ten years necessitates rigorous identification and characterization of MLB-causing pathogens from different maize production zones to ensure the success of resistance breeding programs and the selection of appropriate disease management strategies. Although Bipolaris maydis is the primary pathogen causing MLB in India, other related genera such as Curvularia, Drechslera, and Exserohilum, and a taxonomically distant genus, Alternaria, are known to infect maize in other countries. To investigate the diversity of pathogens associated with MLB in India, 350 symptomatic leaf samples were collected between 2016 and 2018, from 20 MLB hotspots in nine states representing six ecological zones where maize is grown in India. Twenty representative fungal isolates causing MLB symptoms were characterized based on cultural, pathogenic, and molecular variability. Internal Transcribed Spacer (ITS) and glyceraldehyde-3-phosphate dehydrogenase (GADPH) gene sequence-based phylogenies showed that the majority of isolates (13/20) were Bipolaris maydis. There were also two Curvularia papendorfii isolates, and one isolate each of Bipolaris zeicola, Curvularia siddiquii, Curvularia sporobolicola, an unknown Curvularia sp. isolate phylogenetically close to C. graminicola, and an Alternaria sp. isolate. The B. zeicola, the aforesaid four Curvularia species, and the Alternaria sp. are the first reports of these fungi causing MLB in India. Pathogenicity tests on maize plants showed that isolates identified as Curvularia spp. and Alternaria sp. generally caused more severe MLB symptoms than those identified as Bipolaris spp. The diversity of fungi causing MLB, types of lesions, and variation in disease severity by different isolates described in this study provide baseline information for further investigations on MLB disease distribution, diagnosis, and management in India.

Application of biochar, a pyrolyzed biomass from organic sources, to agricultural soils is considered a promising strategy to sustain soil fertility leading to increased plant productivity. It is also known that applications of biochar to soilless potting substrates and to soil increases resistance of plants against diseases, but also bear the potential to have inconsistent and contradictory results depending on the type of biochar feedstock and application rate. The following study examined the effect of biochar produced from maple bark on soybean resistance against Rhizoctonia foliar blight (RFB) disease caused by , and examined the underlying molecular responses of both soybean and during interaction with biochar application. Soybean plants were grown in the presence of 1, 3, or 5% (w/w) or absence of maple bark biochar for 2 weeks, and leaves were infected with AG1-IA. At lower concentrations (1 and 3%), biochar was ineffective against RFB, however at the 5% amendment rate, biochar was conducive to RFB with a significant increase in disease severity. For the first time, soybean and responsive genes were monitored during the development of RFB on detached leaves of plants grown in the absence and presence of 5% biochar at 0, 6, 12, and 24 h post-inoculation (h.p.i.). Generally, large decreases in soybean transcript abundances of genes associated with primary metabolism such as glycolysis, tricarboxylic acid (TCA) cycle, starch, amino acid and glutathione metabolism together with genes associated with plant defense and immunity such as salicylic acid (SA) and jasmonic acid pathways were observed after exposure of soybean to high concentration of biochar. Such genes are critical for plant protection against biotic and abiotic stresses. The general down-regulation of soybean genes and changes in SA hormonal balance were tightly linked with an increased susceptibility to RFB. In conjunction, genes associated with carbohydrate metabolism were up-regulated, while genes involved in redox reactions and detoxification had varying effects. In conclusion, this study presents strong evidence that maple bark biochar increased susceptibility of soybean to a foliar disease. This condition is partly mediated by the down-regulation of soybean genes leading to reduced immunity and also affecting gene expression.

Tomato is one of the major cash crops in the Golapar area of district Nainital in Uttarakhand (India), where farmers are facing the problem of diseases in tomato cultivation. In the present investigation, a survey of tomato fields in the Golapar area of Haldwani block was conducted. The survey revealed the occurrence of late blight, early blight, stem rot, and wilt diseases causing an average loss of 80% to tomato. To counter the above diseases, Trichoderma harzianum (Th43), Pseudomonas fluorescens (Pf173), Jas mycorrhiza (AMF), and the fungicide (Mancozeb) in different combinations applyed through soil application (SA), seedling treatment (ST), and foliar spray (FA) were evaluated for growth promotion and disease control in tomato at experimental and farmers’ fields. The results of the study revealed that in experimental field, the maximum plant height (43.67 cm), highest number of branches (7.33) per plant, highest weight of fruit (47 g), highest number of fruits (39) per plant, minimum plant mortality (4% at 30 DAT and 3.2% at 30–60 DAT), minimum plant disease index (6.85), maximum total yield (256.00 q/ha), and marketable yield (246.67 q/ha) were observed in Th+Pf+JM (SA) + Th+Pf (ST) + Mancozeb (FS). At farmer’s field, minimum plant mortality (7.31%) at 30 days after transplanting (DAT) (5.73%) in 30–60 DAT, minimum plant disease index (11.47), and maximum yield 249.91 q/ha were observed in Th+Pf+JM (SA) + Th+Pf (ST) + Mancozeb (FS) combination. So, it can be concluded that among all the treatments, integrated treatment comprising of soil application of T. harzianum , P. fluorescens , Jas mycorrhiza (AMF) + seedling treatment with T. harzianum and P. fluorescens  + three foliar sprays of Mancozeb was found very effective in reducing the plant mortality, promoting the plant growth, and increasing the yield at experimental field as well as at farmers’ fields.

Knowing pests and diseases that may cause injuries and are likely to affect plant health and quality is critical to minimizing the gap between attainable yield and actual yield. In this paper, we highlight concepts and strategies aimed at controlling major biotic constraints affecting wheat in intensive production systems and present emerging challenges, with a special attention to the developing world. Disease epidemics result from the combination of inoculum, favorable environment, and host susceptibility. Changes in cropping systems as a result of adoption of conservation agriculture may have serious implications. Necrotrophic pathogens such as those responsible for tan spot or septorias are likely to emerge, and Fusarium head blight may increase. However, resistance breeding combined with rotations, timely sowing, and irrigation or even fungicide utilization, if affordable, are part of integrated crop management practices that can minimize losses. In South Asia, the effect of spot blotch, a devastating foliar disease caused by Cochliobolus sativus, can be minimized by reducing physiological stress through timely sowing and adequate use of fertilizers, which demonstrates the complex relationships among crop physiology, disease resistance, and yield. Although some root rots that induce premature death of tillers in cooler high-yielding humid environments can be important, the dryland crown rot (Fusarium spp.), common root rot (C. sativus), and the cereal nematode (Heterodera spp. and Pratylenchus spp.) should not be ignored. These are all known to be much more damaging under suboptimal moisture (rainfed or supplementary irrigation), particularly where plant growth is stressed. Climate change is likely to modify the wheat disease spectrum in some regions, and pathogens or pests considered unimportant today may turn out to be potential new threats in future.

In South Asia, foliar blight of wheat (Triticum aestivum L.) is a disease complex caused by Cochliobolus sativus (the spot blotch pathogen) and Pyrenophora tritici-repentis (the tan spot pathogen) which can reduce yields by > 30 %. Little is known about the effects of wheat genotypes and their planting time on foliar blight epidemics. Field experiments were conducted to determine the infection potential and epidemic development of C. sativus and P. tritici-repentis on two susceptible (Sonalika and BL1473) and two tolerant (NL750 and Milan/Shanghai-7) wheat genotypes under optimum (November 26) and late (December 11 and December 26) planting conditions. The dynamics of airborne conidia were studied using air samplers. The highest aerial concentrations of conidia and disease incidence of both pathogens on all four wheat genotypes were detected during the first 3 weeks of March under both optimum and late seeding conditions in both years. Compared to optimum sowing time (i.e. November 26), wheat genotypes had higher disease severity when planted late on December 11 and 26. The disease complex reduced grain yield by 20.5, 27.2 and 37.3 % for November 26, December 11 and December 26 plantings, respectively in 2004. The corresponding differences were 17.7, 23.6 and 30.2 % in 2005. The findings of this study provide valuable information on the epidemiology of spot blotch and tan spot, which could help in developing strategies for managing these diseases in South Asian region through the selection of suitable genotypes and planting dates.

Spot blotch, caused by Cochliobolus sativus (Ito and Kurib.) Drechsler ex Dastur, and heat stress are two important stresses of bread wheat (Triticum aestivum L.) causing substantial yield reduction in the warm areas of South Asia. These two stresses put pressure on at least 25 million hectares of wheat areas worldwide. This study was conducted to examine variation in physiological traits and its association with heat and spot blotch. Eleven diverse bread wheat genotypes were evaluated in replicated field trials under spot blotch epidemics and heat stress conditions in 2006 and 2007 at Rampur, Nepal. Canopy temperature depression (CTD), chlorophyll fluorescence (CF), chlorophyll content, percent disease leaf area, yield and yield components were recorded. Heat and spot blotch individually reduced CTD, CF, chlorophyll content, grain yield (GRY), and thousand kernel weight (TKW), with greater reductions recorded under combined stress. Genotypes showing lower GRY or TKW loss due to spot blotch also exhibited lower yield loss due to heat stress or combined heat and disease stress, suggesting an association between tolerance mechanisms to the stresses. The physiological traits chlorophyll content, CF and CTD showed higher correlations with GRY and TKW than with area under disease progress curve (AUDPC) suggesting their potential application in screening for heat and spot blotch tolerant genotypes. Genotypes with lower disease showed the highest values for chlorophyll content, CF and CTD. Our findings provide new information on the relationship of these physiological traits with spot blotch resistance and heat tolerance when examined in the same study. The physiological traits studied have potential application in integrative indirect selection criteria for improving spot botch and heat tolerance in wheat.

Rhizoctonia solani AG-1 IA causes leaf blight on soybean and rice. Despite the fact that R. solani AG-1 IA is a major pathogen affecting soybean and rice in Brazil and elsewhere in the world, little information is available on its genetic diversity and evolution. This study was an attempt to reveal the origin, and the patterns of movement and amplification of epidemiologically significant genotypes of R. solani AG-1 IA from soybean and rice in Brazil. For inferring intraspecific evolution of R. solani AG-1 IA sampled from soybean and rice, networks of ITS-5.8S rDNA sequencing haplotypes were built using the statistical parsimony algorithm from Clement et al. (2000) Molecular Ecology 9: 1657-1660. Higher haplotype diversity (Nei M 1987, Molecular Evolutionary Genetics Columbia University Press, New york: 512p.) was observed for the Brazilian soybean sample of R. solani AG-1 IA (0.827) in comparison with the rest of the world sample (0.431). Within the south-central American clade (3-2), four haplotypes of R. solani AG-1 IA from Mato Grosso, one from Tocantins, one from Maranhao, and one from Cuba occupied the tips of the network, indicating recent origin. The putative ancestral haplotypes had probably originated either from Mato Grosso or Maranhao States. While 16 distinct haplotypes were found in a sample of 32 soybean isolates of the pathogen, the entire rice sample (n=20) was represented by a single haplotype (haplotype 5), with a worldwide distribution. The results from nested-cladistic analysis indicated restricted gene flow with isolation by distance (or restricted dispersal by distance in nonsexual species) for the south-central American clade (3-2), mainly composed by soybean haplotypes.

Wheat (Triticum aestivum L.) cultivars for the warm regions of South Asia must produce high yields and possess resistance to spot blotch (Cochliobolus sativus), early maturity and high kernel weight. A study was conducted to determine the effectiveness of selecting for high grain yield based on a selection index for spot blotch resistance, maturity and kernel weight in four wheat crosses involving a susceptible cultivar and resistant genotypes. Initial selection of 40 progeny lines in each cross had been made using a selection index based on disease severity, days to heading and kernel weight as reported by Sharma and Duveiller [{Crop Sci 43 (2003) 2031}]. The five highest grain-yielding progeny lines from among the 40 lines in each cross, their parents and five popular commercial cultivars were evaluated in field trials at two sites in Nepal in the 2002 and 2003 wheat seasons. Multiple spot blotch assessments were made to determine the area under disease progress curve (AUDPC). Grain yield, thousand-kernel weight (TKW), days to heading and plant height were examined. The wheat genotypes in the farmer's field were also ranked on the basis of cultivar preference criteria by the local farmers. The 20 progeny lines always showed a higher (+11 to +125%) grain yield and heavier (+10 to +44%) kernels than their parents and a lower (-83 to -89%) AUDPC than the susceptible parent. The progeny lines showed 98-100% grain yield, 97-100% TKW and 66-78% AUDPC compared to the highest grain-yielding commercial cultivar. Based on the farmers' preference criteria for a desirable wheat genotype, the best progeny lines ranked from 3rd to 5th, whereas the two commercial cultivars ranked 1st (Gautam) and 2nd (BL 1473). Results indicated that selection was effective in combining adaptation genes present in a local cultivar with some level of tolerance to spot blotch and resistance genes from exotic genotypes, which translated into improved agronomic performance and disease resistance. The selection index and farmer participatory approach used in this study could serve as a guideline in breeding efforts targeted for high yielding genotypes for wheat-growing conditions in South Asia where spot blotch is a serious biotic constraint to yield.[PUBLICATION ABSTRACT]

One thousand three hundred and eighty-seven spring wheat germplasm (Triticum aestivum L.) lines belonging to the Indian and CIMMYT wheat programmes were evaluated for their tolerance to foliar blight disease for three consecutive years i.e., from 1994 to 1997. Disease severity at six different growth stages, beginning from tillering to late milk stage, was recorded. None of the genotypes showed immunity to the disease. Of 43 lines showing resistant reaction, a major proportion (25) was represented by CIMMYT material. Comparatively, Indian germplasm lines tended to be more susceptible at more advanced growth stages. Area Under Disease Progress Curve (AUDPC) and Apparent Infection Rate (r) values of resistant lines were much lower than those of susceptible ones, but lower AUDPC in some of the resistant lines did not correspond to a lower 'r' value. Most of the resistant lines were derived from Seri, Myna, Bau, kauz, Hork 's' and Aegilops tauschii Coss.