A PCR-based Technique for Identification of Fusicoccum sp. from Pistachio and Various Other Hosts in California

PCR-based detection of Botryosphaeria canker pathogens in fig trees

Canker and dieback, caused by members of the Botryosphaeriaceae family, pose significant threats to plant productivity, food security, and natural ecosystems, particularly in economically important woody crops including fig trees. Detecting and identifying these pathogens is challenging due to their latent infections and the presence of multiple pathogens within the same host. In our study, we developed a PCR assay using three carefully selected primer pairs based on sequence differences in two protein-coding genes, β-tubulin and RNA polymerase II. The species-specific primers TUB-Bd1 (specific for Botryosphaeria dothidea), TUB-Np1 (specific for Neofusicoccum parvum), and RPB-Nd2 (specific for Neoscytalidium dimidiatum) effectively amplified target gene sequences in pure cultures and infected tissue samples using PCR and nested PCR conditions. The efficiency test results demonstrated that TUB-Bd1, TUB-Np1, and RPB-Nd2 primer pairs could detect specific DNA fragments at very low concentrations in nested PCR. Furthermore, we collected 180 symptomatic and asymptomatic fig samples from different regions of Fars Province, Iran. Applying the species-specific primer pair RPB-Nd2 in direct PCR led to the detection of N. dimidiatum in 25.5% of symptomatic woody samples and 13% of asymptomatic one-year-old branch samples of fig trees. This represents a significant improvement compared to the mere 6.67% detected using traditional culturing methods on PDA. Interestingly, neither B. dothidea nor N. parvum were detected in the 180 samples using nested PCR. Moreover, multiplex PCR enabled simultaneous DNA detection of the target Botryosphaeriaceae pathogens. Our findings emphasize the importance of molecular techniques for early detection of evident and latent infections caused by these three pathogens in fig trees.

Quadruplex and q-PCR based diagnostic assay to delineate the major quarantine and other seed-borne fungal pathogens of soybean

Soybean is one of the most important crops grown worldwide and accounting for significant global trade including transgenic soybean. The crop is attacked by several seed-borne fungal pathogens and some of them are of quarantine concern for India. Keeping in view of the risks associated with movement of soybean seeds, sensitive and reliable molecular diagnostics have been developed for precise and simultaneous detection of three pathogens of quarantine concern for India namely, Diaporthe phaseolorum (stem blight), D. longicolla (seed decay), Peronospora manshurica (downy mildew), along with Macrophomina phaseolina causing dry root rot. The targeted pathogens after isolation from imported transgenic and non-transgenic soybean seeds were identified. Quadruplex and qPCR assays were developed targeting the sequences of different genes such as Histone-3 for detection of D. longicolla and M. phaseolina. The markers DlHisF2&R2 and MpHisF1&R1 produced 265 and 309 bp amplicons for D. longicolla and M. phaseolina, respectively. Actin gene based marker DpActF1&R2 was developed for D. phaseolorum which provided 113 bp amplicon whereas, COX2 based marker PmCoxF2&R2 was developed for P. manshurica with amplified product of 152 bp. During qPCR analysis, these markers proved highly specific and sensitive for detection of these pathogens up to 0.1 pg of template DNA. Quadruplex PCR protocol was also developed by combining these specific markers which could distinguish all the targeted pathogens simultaneously in a single reaction. The developed diagnostic protocols are extremely valuable for quarantine clearance and to ensure the safe transboundary exchange and healthy conservation of germplasm in the National Genebank.

Fungi Inhabiting the Wheat Endosphere

Wheat production is influenced by changing environmental conditions, including climatic conditions, which results in the changing composition of microorganisms interacting with this cereal. The group of these microorganisms includes not only endophytic fungi associated with the wheat endosphere, both pathogenic and symbiotic, but also those with yet unrecognized functions and consequences for wheat. This paper reviews the literature in the context of the general characteristics of endophytic fungi inhabiting the internal tissues of wheat. In addition, the importance of epigenetic regulation in wheat-fungus interactions is recognized and the current state of knowledge is demonstrated. The possibilities of using symbiotic endophytic fungi in modern agronomy and wheat cultivation are also proposed. The fact that the current understanding of fungal endophytes in wheat is based on a rather small set of experimental conditions, including wheat genotypes, plant organs, plant tissues, plant development stage, or environmental conditions, is recognized. In addition, most of the research to date has been based on culture-dependent methods that exclude biotrophic and slow-growing species and favor the detection of fast-growing fungi. Additionally, only a few reports of studies on the entire wheat microbiome using high-throughput sequencing techniques exist. Conducting comprehensive research on the mycobiome of the endosphere of wheat, mainly in the context of the possibility of using this knowledge to improve the methods of wheat management, mainly the productivity and health of this cereal, is needed.

Fungal Pathogens Associated With Canker Diseases of Almond in California

Almond canker diseases are destructive and can reduce the yield as well as the lifespan of almond orchards. These diseases may affect the trunk and branches of both young and mature trees and can result in tree death soon after orchard establishment in severe cases. Between 2015 and 2018, 70 almond orchards were visited throughout the Central Valley of California upon requests from farm advisors for canker disease diagnosis. Two major canker diseases were identified, including Botryosphaeriaceae cankers and Ceratocystis canker. In addition, five less prevalent canker diseases were identified, including Cytospora, Eutypa, Diaporthe, Collophorina, and Pallidophorina canker. Seventy-four fungal isolates were selected for multilocus phylogenetic analyses of internal transcribed spacer region ITS1-5.8S-ITS2 and part of the translation elongation factor 1-α, β-tubulin, and glyceraldehyde 3-phosphate dehydrogenase gene sequences; 27 species were identified, including 12 Botryosphaeriaceae species, Ceratocystis destructans, five Cytospora species, Collophorina hispanica, four Diaporthe species, two Diatrype species, Eutypa lata, and Pallidophorina paarla. The most frequently isolated species were Ceratocystis destructans, Neoscytalidium dimidiatum, and Cytospora californica. Pathogenicity experiments on almond cultivar Nonpareil revealed that Neofusicoccum parvum, Neofusicoccum arbuti, and Neofusicoccum mediterraneum were the most virulent. Botryosphaeriaceae cankers were predominantly found in young orchards and symptoms were most prevalent on the trunks of trees. Ceratocystis canker was most commonly found in mature orchards and associated with symptoms found on trunks or large scaffold branches. This study provides a thorough examination of the diversity and pathogenicity of fungal pathogens associated with branch and trunk cankers of almond in California.

A Review of Conventional PCR Assays for the Detection of Selected Phytopathogens of Wheat

Infection of phyllosphere (stems, leaves, husks, and grains) by pathogenic fungi reduces the wheat yield and grain quality. Detection of the main wheat pathogenic fungi provides information about species composition and allows effective and targeted plant treatment. Since conventional procedures for the detection of these organisms are unreliable and time consuming, diagnostic DNA-based methods are required. Nucleic acid amplification technologies are independent of the morphological and biochemical characteristics of fungi. Microorganisms do not need to be cultured. Therefore, a number of PCR-based methodologies have been developed for the identification of key pathogenic fungi, such as <i>Fusarium</i> spp., <i>Puccinia</i> spp., <i>Zymoseptoria tritici</i>, <i>Parastagonospora nodorum</i>,<i> Blumeria graminis </i>f. sp.<i> tritici</i>, and<i> Pyrenophora tritici-repentis</i>. This article reviews frequently used DNA regions for fungus identification and discusses already known PCR assays for detection of the aforementioned wheat pathogens. We demonstrate that PCR-based wheat pathogen identification assays require further research. In particular, the number of diagnostic tests for <i>Fusarium graminearum</i>, <i>Puccinia</i> spp., and <i>P. tritici-repentis</i> are insufficient.

Specific and Sensitive Detection of Venturia nashicola, the Scab Fungus of Asian Pears, by Nested PCR

The fungus Venturia nashicola is the causal agent of scab on Asian pears. For the rapid and reliable identification as well as sensitive detection of V. nashicola, a PCR-based technique was developed. DNA fingerprints of three closely related species, V. nashicola, V. pirina, and V. inaequalis, were obtained by random amplified polymorphic DNA (RAPD) analysis. Two RAPD markers specific to V. nashicola were identified by PCR, after which two pairs of sequence characterized amplified region (SCAR) primers were designed from the nucleotide sequences of the markers. The SCAR primer pairs, designated as D12F/D12R and E11F/E11R, amplified 535-bp and 525-bp DNA fragments, respectively, only from genomic DNA of V. nashicola. The specificity of the primer sets was tested on strains representing three species of Venturia and 20 fungal plant pathogens. The nested PCR primer pair specific to V. nashicola was developed based on the sequence of the species-specific 525-bp DNA fragment amplified by primer set E11F/E11R. The internal primer pair Na11F/Na11R amplified a 235-bp fragment from V. nashicola, but not from any other fungal species tested. The nested PCR assay was sensitive enough to detect the specific fragment in 50 fg of V. nashicola DNA.

Characterization and PCR-based detection of benzimidazole-resistant isolates of Monilinia laxa in California

Monilinia laxa is a pathogen of brown rot of stone fruit and almond in California, causing blossom blights and fruit rots. In this study, low-level resistance to the benzimidazole fungicides benomyl and thiophanate-methyl was detected in field isolates of M laxa collected from stone fruits and almonds in California. Low-resistant (LR) isolates grew in potato dextrose agar (PDA) plates amended with benomyl and thiophanate-methyl at 1 and 5 microg ml(-1), respectively, but not in plates amended with benomyl at 5 microg ml(-1) or thiophanate-methyl at 50 microg ml(-1). The benzimidazole LR isolates were characterized by temperature sensitivity and the DNA sequence of the beta-tubulin gene. The LR isolates showed high-temperature sensitivity, being sensitive to 1 microg ml(-1) of benomyl at 28 degrees C but resistant at 8-24 degrees C. Analysis of the DNA sequence of the beta-tubulin gene showed that the LR isolates had a point mutation at the amino-acid position 240, causing substitution of leucine by phenylalanine. Based on the point mutation, a pair of allele-specific PCR primers was developed for rapid detection of LR isolates of M laxa. In addition, a pair of PCR primers specific to M laxa was developed on the basis of the differences in the DNA sequence of the intron 6 of beta-tubulin gene from M laxa, M fructicola and other fungal species. The primer pair amplified the expected 376-bp DNA fragment from all M laxa isolates tested, but not from 14 other fungal species isolated from stone fruit and almond crops. The restriction endonuclease BsmA I recognized the sequence GTCTCC in the PCR products from sensitive (S) isolates only, but not the GTTTCC sequence in the PCR products from LR isolates. The endonuclease digested the 376-bp PCR products from S isolates to produce two bands (111 and 265 bp) on agarose gels. Thus, both allele-specific PCR and the PCR-restriction fragment length polymorphism (PCR-RFLP) methods could be useful for rapidly detecting benzimidazole-resistant isolates of M laxa from stone fruit and almond crops in California.

Spatiotemporal Changes in the Population Structure of Botryosphaeria dothidea from California Pistachio Orchards

ABSTRACT Spatiotemporal changes in the population structure of Botryosphaeria dothidea, causal agent of panicle and shoot blight of pistachio, were analyzed by using microsatellite-primed polymerase chain reaction (MPPCR), partial sequences of the RNA polymerase II (RPB2) gene, and vegetative compatibility groups (VCGs). We examined 390 isolates, 378 recovered from pistachio in seven counties of California from 1990 to 2001 and 12 recovered from peach, apple, and sycamore in Georgia, North Carolina, South Carolina, Illinois, and Pennsylvania. Six microsatellite primers generated 116 polymorphic bands. Based on MP-PCR data, we observed very high (>98%) levels of genetic identity among populations of B. dothidea collected from the commercial pistachio orchards in California. The near identity of these populations was supported by VCGs and partial sequences of the RBP2 gene. These findings suggest that populations of B. dothidea from commercial pistachio orchards are spatially and temporally stable, at least in the past 5 years.

Identification and characterization of benzimidazole resistance in Monilinia fructicola from stone fruit orchards in California

Low and high levels of resistance to the benzimidazole fungicides benomyl and thiophanate-methyl were observed in field isolates of Monilinia fructicola, which is the causative agent of brown rot of stone fruit. Isolates that had low levels of resistance (hereafter referred to as LR isolates) and high levels of resistance (hereafter referred to as HR isolates) were also cold and heat sensitive, respectively. Results from microsatellite DNA fingerprints showed that genetic identities among the populations of sensitive (S), LR, and HR isolates were very high (>0.96). Analysis of DNA sequences of the beta-tubulin gene showed that the LR isolates had a point mutation at codon 6, causing a replacement of the amino acid histidine by tyrosine. Codon 198, which encodes a glutamic acid in S and LR isolates, was converted to a codon for alanine in HR isolates. Based on these point mutations in the beta-tubulin gene, allele-specific PCR assays were developed for rapid detection of benzimidazole-resistant isolates of M. fructicola from stone fruit.