Development and Validation of a Real-Time PCR Assay for the Quantification of Verticillium dahliae in Potato

Comparison of different screening methods for the selection of Ascochyta blight disease on chickpea (Cicer arietinum L.) genotypes

Chickpea (Cicer arietinum L.) is the second most important edible food grain legume, widely grown all over the world. However, the cultivation and production of chickpea are mainly affected by the Ascochyta blight (AB) disease, which causes losses of up to 100% in areas with high humidity and warm temperature conditions. Various screening methods are used in the selection of chickpea genotypes for resistance to AB disease. These methods are natural field condition (NFC), artificial epidemic field condition (AEC), marker-assisted selection (MAS), and real-time PCR (RT-PCR). The study was conducted with 88 chickpea test genotypes between the 2014 and 2016 growing seasons. The results of the screening were used to sort the genotypes into three categories: susceptible (S), moderately resistant (MR), and resistant (R). Using MAS screening, 13, 21, and 54 chickpea genotypes were identified as S, MR, and R, respectively. For RT-PCR screening, 39 genotypes were S, 31 genotypes were MR, and 18 genotypes were R. In the AEC method for NFC screening, 7, 17, and 64 genotypes were S, MR, and R, while 74 and 6 genotypes were S and MR, and 8 genotypes were R-AB disease. As a result of screening chickpea genotypes for AB disease, it was determined that the most effective method was artificial inoculation (AEC) under field conditions. In the study, Azkan, ICC3996, Tüb-19, and Tüb-82 were determined as resistant within all methods for Pathotype 1.

A droplet digital PCR assay for detection and quantification of Verticillium nonalfalfae and V. albo-atrum

Verticillium nonalfalfae and V. albo-atrum are notorious pathogenic fungi that cause a destructive vascular disease called Verticillium wilt worldwide. Thus, timely and quantitative monitoring of fungal progression is highly desirable for early diagnosis and risk assessment. In this study, we developed a droplet digital polymerase chain reaction (ddPCR) assay to detect and quantify V. nonalfalfae and V. albo-atrum. The performance of this assay was validated in comparison with that of a quantitative real-time polymerase chain reaction (qPCR) assay. The standard curve analysis of the ddPCR assay showed good linearity. The ddPCR assay indicated similar detection sensitivity to that of qPCR on pure genomic DNA, while it enhanced the positive rate for low-abundance fungi, especially in alfalfa stems. Receiver operating characteristic analysis revealed that ddPCR provided superior diagnostic performance on field tissues compared to qPCR, and the area under curve values were 0.94 and 0.90 for alfalfa roots and stems, respectively. Additionally, the quantitative results of the two methods were highly concordant (roots: R² = 0.91; stems: R² = 0.76); however, the concentrations determined by ddPCR were generally higher than those determined by qPCR. This discrepancy was potentially caused by differing amplification efficiencies for qPCR between cultured and field samples. Furthermore, the ddPCR assays appreciably improved quantitative precision, as reflected by lower coefficients of variation. Overall, the ddPCR method enables sensitive detection and accurate quantification of V. nonalfalfae and V. albo-atrum, providing a valuable tool for evaluating disease progression and enacting effective disease control.

Detection and quantification of Verticillium dahliae and V. longisporum by droplet digital PCR versus quantitative real-time PCR

Vascular wilt, caused by Verticillium dahliae and V. longisporum, limits the quality and yield of agricultural crops. Although quantitative real-time PCR (qPCR) has greatly improved the diagnosis of these two pathogens over traditional, time-consuming isolation methods, the relatively poor detection sensitivity and high measurement bias for traceable matrix-rich samples need to be improved. Here, we thus developed a droplet digital PCR (ddPCR) assay for accurate, sensitive detection and quantification of V. dahliae and V. longisporum. We compared the analytical and diagnostic performance in detail of ddPCR and the corresponding qPCR assay against the genomic DNA (gDNA) of the two fungi from cultures and field samples. In our study, the species specificity, quantification linearity, analytical sensitivity, and measurement viability of the two methods were analyzed. The results indicated that ddPCR using field samples enhanced diagnostic sensitivity, decreased quantification bias, and indicated less susceptibility to inhibitors compared with qPCR. Although ddPCR was as sensitive as qPCR when using gDNA from cultures of V. dahliae and V. longisporum, its detection rates using field samples were much higher than those of qPCR, potentially due to the inhibition from residual matrix in the extracts. The results showed that digital PCR is more sensitive and accurate than qPCR for quantifying trace amounts of V. dahliae and V. longisporum and can facilitate management practices to limit or prevent their prevalence.

Dry Bean and Anthracnose Development From Seeds With Varying Symptom Severity

Anthracnose, caused by the fungal pathogen Colletotrichum lindemuthianum, is a damaging seed-transmitted disease of dry beans that causes reduced seed quality and yield. Seed-to-seedling transmission of C. lindemuthianum has been documented as high as 15% in asymptomatic seeds under greenhouse conditions. Increasing pathogen colonization in seeds has been correlated with increasing anthracnose seed symptoms via quantitative PCR (qPCR), but stem colonization has not been quantified. Previous studies also have characterized seed yield and quality losses caused by planting C. lindemuthianum-infected seeds, but none evaluated the effect of growing asymptomatic seeds on disease and plant development under field conditions. A real-time qPCR assay was developed in this study and used to detect C. lindemuthianum in the stems of seedlings as early as 15 days after planting. Field trials measured the seed-to-seedling transmission of C. lindemuthianum across levels of anthracnose symptoms in seeds ranging from healthy to severely discolored. Results from these two field trials indicated that emergence and yield decreased and foliar symptoms, pathogen detection, and incidence of symptoms on progeny seeds increased as the severity of infection in planted seeds increased. In both years, planting asymptomatic seeds resulted in higher anthracnose severity than planting healthy seeds. Yield, seed weight, and incidence of symptoms on progeny seeds were not higher in asymptomatic seeds than in healthy seeds in 2014, when moderate disease pressure was observed. However, these factors were significantly different in 2015, when anthracnose severity was driven up to 75% by conducive weather conditions. This serves as a strong warning to growers that planting seed grown in a field where anthracnose was present, even if those seeds are asymptomatic, can result in yield and quality losses. Planting certified dry bean seed is always recommended.

Triplex Real-Time PCR Approach for the Detection of Crucial Fungal Berry Pathogens-Botrytis spp., Colletotrichum spp. and Verticillium spp

Phytopathogens cause undeniably serious damage in agriculture by harming fruit cultivations and lowering harvest yields, which as a consequence substantially reduces food production efficiency. Fungi of the Botrytis, Colletotrichum and Verticillium genera are a main concern in berry production. However, no rapid detection method for detecting all of these pathogens simultaneously has been developed to date. Therefore, in this study, a multiplex real-time PCR assay for this purpose was established. Universal fungal primers for the D2 region of the large subunit ribosomal DNA and three multiplexable fluorogenic probes specific for the chosen fungi were designed and deployed. The triplex approach for the molecular detection of these fungi, which was developed in this study, allows for the rapid and effective detection of crucial berry pathogens, which contributes to a more rapid implementation of protective measures in plantations and a significant reduction in losses caused by fungal diseases.

Alternative Molecular-Based Diagnostic Methods of Plant Pathogenic Fungi Affecting Berry Crops-A Review

Increasing consumer awareness of potentially harmful pesticides used in conventional agriculture has prompted organic farming to become notably more prevalent in recent decades. Central European countries are some of the most important producers of blueberries, raspberries and strawberries in the world and organic cultivation methods for these fruits have a significant market share. Fungal pathogens are considered to be the most significant threat to organic crops of berries, causing serious economic losses and reducing yields. In order to ameliorate the harmful effects of pathogenic fungi on cultivations, the application of rapid and effective identification methods is essential. At present, various molecular methods are applied for fungal species recognition, such as PCR, qPCR, LAMP and NGS.

Initial stages of endophytic colonization by Metarhizium involves rhizoplane colonization

Here we assessed the time course of rhizoplane colonization by the endophytic insect pathogenic fungus Metarhizium robertsii. We describe a method of quantifying root colonization of bean plants by M. robertsii using quantitative polymerase chain reaction (qPCR). Results of this method were compared to the standard plate count method using colony-forming units (c.f.u.). Both the c.f.u. and qPCR methods were used to monitor the time-course of haricot bean (Phaseolus vulgaris) colonization by a strain of M. robertsii that expresses the green fluorescent protein (ARSEF 2575-GFP) for colony verification. There was a strong correlation between the results of the c.f.u. and qPCR methods, indicating that both methods are well suited for the determination of colonization of P. vulgaris roots by M. robertsii. Primers for a catalase gene (cat) amplified DNA from M. robertsii, M. brunneum and M. guizhouense. Primers for a nitrogen response-regulator (nrr) additionally detected M. acridum and M. flavoviride, whereas Metarhizium perilipin-like protein (mpl) primers were specific to M. robertsii alone. However, cat was the only target that specifically amplified Metarhizium in experiments utilizing non-sterile soil. Endophytic colonization of P. vulgaris at 60 days post-inoculation with M. robertsii was detected from surface-sterilized roots with more sensitivity using our qPCR technique over the c.f.u. method. Our results suggest that there is a prolonged period of rhizoplane colonization by Metarhizium with transient, low-level endophytic colonization of the root system of P. vulgaris that persists for the entirety of the plant life cycle.

Histochemical Analyses Reveal That Stronger Intrinsic Defenses in Gossypium barbadense Than in G. hirsutum Are Associated With Resistance to Verticillium dahliae

Verticillium wilt, caused by Verticillium dahliae Kleb., is a serious threat to cotton (Gossypium spp.) crop production. To enhance our understanding of the plant's complex defensive mechanism, we examined colonization patterns and interactions between V. dahliae and two cotton species, the resistant G. barbadense and the susceptible G. hirsutum. Microscopic examinations and grafting experiments showed that the progression of infection was restricted within G. barbadense. At all pre- and postinoculation sampling times, levels of salicylic acid (SA) were also higher in that species than in G. hirsutum. Comparative RNA-Seq analyses indicated that infection induced dramatic changes in the expression of thousands of genes in G. hirsutum, whereas those changes were fewer and weaker in G. barbadense. Investigations of the morphological and biochemical nature of cell-wall barriers demonstrated that depositions of lignin, phenolic compounds, and callose were significantly higher in G. barbadense. To determine the contribution of a known resistance gene to these processes, we silenced GbEDS1 and found that the transformed plants had decreased SA production, which led to the upregulation of PLASMODESMATA-LOCATED PROTEIN (PDLP) 1 and PDLP6. This was followed by a decline in callose deposition in the plasmodesmata, which then led to increased pathogen susceptibility. This comparison between resistant and susceptible species indicated that both physical and chemical mechanisms play important roles in the defenses of cotton against V. dahliae.

Effect of Verticillium dahliae Soil Inoculum Levels on Spinach Seed Infection

Verticillium dahliae is a soilborne pathogen and a threat to spinach seed production. The aim of this study was to understand the relation between V. dahliae soil inoculum and infection in harvested seed. Quantitative polymerase chain reaction was used for quantification of the pathogen. Semifield experiments in which spinach was grown in soils with different inoculum levels enabled us to determine a threshold level for V. dahliae DNA of 0.003 ng/g of soil for seed infection to occur. Soils from production fields were sampled in 2013 and 2014 during and before planting, as well as the harvested seed. Seed from plants grown in infested soils were infected with V. dahliae in samples from both the semifield and open-field experiments. Lower levels of pathogen were found in seed from spinach grown in soils with a scattered distribution of V. dahliae (one or two positive of three soil subsamples) than in soils with a uniform distribution of the pathogen (three of three positive soil subsamples). Our results showed that infection of V. dahliae in harvested seed strongly depended on the presence of pathogen inoculum in the soil.

Comparative Transcriptome Analysis of White and Purple Potato to Identify Genes Involved in Anthocyanin Biosynthesis

INTRODUCTION

The potato (Solanum tuberosum) cultivar 'Xin Daping' is tetraploid with white skin and white flesh, while the cultivar 'Hei Meiren' is also tetraploid with purple skin and purple flesh. Comparative transcriptome analysis of white and purple cultivars was carried out using high-throughput RNA sequencing in order to further understand the mechanism of anthocyanin biosynthesis in potato.

METHODS AND RESULTS

By aligning transcript reads to the recently published diploid potato genome and de novo assembly, 209 million paired-end Illumina RNA-seq reads from these tetraploid cultivars were assembled on to 60,930 transcripts, of which 27,754 (45.55%) are novel transcripts and 9393 alternative transcripts. Using a comparison of the RNA-sequence datasets, multiple versions of the genes encoding anthocyanin biosynthetic steps and regulatory transcription factors were identified. Other novel genes potentially involved in anthocyanin biosynthesis in potato tubers were also discovered. Real-time qPCR validation of candidate genes revealed good correlation with the transcriptome data. SNPs (Single Nucleotide Polymorphism) and indels were predicted and validated for the transcription factors MYB AN1 and bHLH1 and the biosynthetic gene anthocyanidin 3-O-glucosyltransferase (UFGT).

CONCLUSIONS

These results contribute to our understanding of the molecular mechanism of white and purple potato development, by identifying differential responses of biosynthetic gene family members together with the variation in structural genes and transcription factors in this highly heterozygous crop. This provides an excellent platform and resource for future genetic and functional genomic research.

Characterization of a vacuolar processing enzyme expressed in Arachis diogoi in resistance responses against late leaf spot pathogen, Phaeoisariopsis personata

Vacuolar processing enzymes are cysteine proteases responsible for maturation of vacuolar proteins. They have been shown to possess caspase-1-like activity, mediate cell death and display increased activity during pathogen infections. A transcript derived fragment corresponding to VPE was found to be up-regulated in a cDNA-AFLP analysis of host responses of a wild peanut, Arachis diogoi upon challenge from the late leaf spot pathogen Phaeoisariopsis personata, which was subsequently validated by q-PCR in a time course analysis, where susceptible peanut did not show its upregulation. In transient conditional and constitutive expression studies in tobacco leaves using agroinfiltration, we have observed that expression of AdVPE was associated with hypersensitive response (HR) like cell death. AdVPE expression was found to be high at 24 h post estradiol application and this was associated with the enhanced co-expression of molecular markers of HR cell death genes and genes for pathogenesis related proteins indicating that AdVPE positively regulates defense responses and its estradiol induced expression is sufficient for HR-like cell death in tobacco. We found that AdVPE expression was very strongly induced in response to sodium nitroprusside, which indicates its involvement in stress signaling. Induced expression of AdVPE in response to jasmonic acid and ethylene also indicates its involvement in an interconnected network of signaling. Transgenic tobacco plants ectopically expressing AdVPE exhibited enhanced resistance against Phytophthora parasitica var. nicotianae, Alternaria alternata var.  nicotianae and Rhizoctonia solani. To our knowledge, this is the first report on the heterologous expression of a pathogen induced VPE enhancing resistance to fungal pathogens with cell death phenomenon under transient expression.

Unraveling the Wheat Stem Rust Infection Process on Barley Genotypes Through Relative qPCR and Fluorescence Microscopy

The infection process of wheat stem rust (Puccinia graminis f. sp. tritici) on barley (Hordeum vulgare) is often observed as a mesothetic infection type at the seedling stages, and cultivars containing the same major resistance genes often show variation in the level of resistance provided against the same pathogen race or isolate. Thus, robust phenotyping data based on quantification of fungal DNA can improve the ability to elucidate host-pathogen interaction, especially at early time points of infection when disease symptoms are not yet evident. Quantitative real-time polymerase chain reaction (qPCR) was used to determine the amount of fungal DNA relative to host DNA in infected tissue, providing new insights about fungal development and host resistance during the infection process in this pathosystem. The stem rust susceptible 'Steptoe', resistant cultivars containing only Rpg1 ('Beacon', 'Morex', and 'Chevron'), and the resistant line Q21861 containing Rpg1 and the rpg4/Rpg5 complex were evaluated using the traditional 0-to-4 rating scale, fluorescence microscopy, and qPCR. Statistical differences (P<0.05) were observed in fungal development as early as 24 h postinoculation using the qPCR assay. Fungal development observed using fluorescence microscopy displayed the same hierarchal ordering observed using the qPCR assay. The fungal development occurring at 24 and 48 h postinoculation was vastly different than what was expected using the traditional disease phenotyping methodology; with Steptoe appearing more resistant than the barley lines harboring the known Rpg1 and rpg4/Rpg5 resistance complex. These data indicate potential early prehaustorial resistance contributions in a cultivar considered susceptible based on infection type. Moreover, the temporal differences in resistance suggest pre- and post-haustorial resistance mechanisms in the barley-wheat stem rust infection process, indicating potential host genotype contributions related to basal defense during the wheat stem rust infection process.

Accurate detection and quantification of the fish viral hemorrhagic Septicemia virus (VHSv) with a two-color fluorometric real-time PCR assay

Viral Hemorrhagic Septicemia virus (VHSv) is one of the world's most serious fish pathogens, infecting >80 marine, freshwater, and estuarine fish species from Eurasia and North America. A novel and especially virulent strain - IVb - appeared in the Great Lakes in 2003, has killed many game fish species in a series of outbreaks in subsequent years, and shut down interstate transport of baitfish. Cell culture is the diagnostic method approved by the USDA-APHIS, which takes a month or longer, lacks sensitivity, and does not quantify the amount of virus. We thus present a novel, easy, rapid, and highly sensitive real-time quantitative reverse transcription PCR (qRT-PCR) assay that incorporates synthetic competitive template internal standards for quality control to circumvent false negative results. Results demonstrate high signal-to-analyte response (slope = 1.00±0.02) and a linear dynamic range that spans seven orders of magnitude (R(2) = 0.99), ranging from 6 to 6,000,000 molecules. Infected fishes are found to harbor levels of virus that range to 1,200,000 VHSv molecules/10(6) actb1 molecules with 1,000 being a rough cut-off for clinical signs of disease. This new assay is rapid, inexpensive, and has significantly greater accuracy than other published qRT-PCR tests and traditional cell culture diagnostics.