Specific PCR and real-time PCR assays for detection and quantitation of 'Candidatus Phytoplasma phoenicium'

The Efficacy of Orange Terpene and Bacillus mycoides Strain BM103 on the Control of Periwinkle Leaf Yellowing Phytoplasma

Phytoplasmas are obligate phytopathogenic bacteria belonging to the class Mollicutes. The pathogens, transmitted by insect vectors, are associated with hundreds of plant diseases worldwide. Because of the regulations banning the use of antibiotics and the limited efficacy of traditional disease management manners, an eco-friendly alternative is needed. Given that terpene and probiotics have antibiotic activity and the ability to induce systemic resistance, in this study, the effectiveness of orange terpene and a Bacillus mycoides strain, BM103, was evaluated in periwinkle plants infected with periwinkle leaf yellowing (PLY) phytoplasma derived from a shoot-tip tissue culture system. Weekly drenching of 1,000 ppm diluted orange terpene emulsion or preactivated strain BM103 liquid culture dilution exhibited the ability to inhibit PLY phytoplasma accumulation. The expression of the genes associated with plant defense response and flower development was upregulated after treatment. Moreover, pretreatment of orange terpene or strain BM103 delayed PLY infection via cleft-grafting inoculation. Although orange terpene did not suppress the symptoms, strain BM103 did result in a milder symptom expression that might partially attribute to its plant growth-promoting characteristics. Additionally, the preactivation of strain BM103 may contribute to its efficacy. Taken together, this research indicates that orange terpene and B. mycoides BM103, with the ability to rapidly induce plant defense responses, could potentially be developed into biologic control materials as preventive agents or biofertilizers.

The development of two fast genotyping assays for the differentiation of hemp from marijuana

The legalization of hemp cultivation in the United States has raised the need for reliable methods to distinguish between legal hemp and illegal marijuana. Genetic analysis has emerged as a powerful tool, surpassing traditional chemical methods in specific aspects, such as analyzing trace amounts, aged samples, and different parts of the sample. Genetic differences in cannabinoid synthase genes offer promise for precise crop type determination, particularly focusing on genes like tetrahydrocannabinolic acid synthase (THCAS), cannabidiolic acid synthase (CBDAS), and cannabichromenic acid synthase (CBCAS). However, previous research faced several challenges in developing discriminatory genetic markers, including limited sample sizes, high similarity between the synthase genes, and the presence of pseudo synthase genes. A comprehensive study using Next-Generation Sequencing (NGS) introduced a differentiation flowchart based on THCAS, CBDAS, and THCAS pseudogenes. To bridge the gap between NGS and the practical requirements of crime laboratories, two rapid genotyping assays were developed: a CE-based SNaPshot™ assay and a TaqMan™ real-time PCR assay. While the SNaPshot™ assay effectively differentiated various hemp and marijuana types, differentiation was limited with marijuana samples containing THC% close to the 0.3% legal threshold (0.3%-1%). The TaqMan™ qPCR SNP genotyping assay provided quicker results, making it an efficient choice for crime laboratories. However, this method had the same limitations as the SNaPshot™ assay with addtional challenges in differentiating edible hemp seed samples, and it did not provide additional CBD information. The study also highlighted the influence of two variants of one THCAS pseudogene on chemotype determination, emphasizing the necessity for precise genetic analysis for accurate categorization of cannabis varieties.

Preliminary Evidence of a Horizontal Transfer of Paramutation Phenomenon at the pl1 Gene in Maize (Zea mays L.)

Paramutation, a specific epigenetic phenomenon first identified in Zea mays by Alexander Brink in the 1950s, has since been observed in different plant and animal species. What sets paramutation apart from other gene silencing processes is its ability for one silenced allele (referred to as paramutagenic) to silence another allele (paramutable) in trans. The resultant silenced allele (paramutated) remains stable across generations, even after separating from the paramutagenic allele, and acquires paramutagenic properties itself. This hereditary behavior facilitates the rapid dissemination of specific gene expression patterns or phenotypes within populations, disrupting the Hardy-Weinberg equilibrium even without other evolutionary pressures. Despite extensive research, the molecular mechanisms underlying paramutation are still not fully understood, although numerous studies suggest the involvement of RNA-mediated changes in DNA methylation and in the chromatin structure of silenced genes. In this paper, we report preliminary evidence regarding horizontal paramutation transfer at the pl1 (purple plant1) regulatory gene involved in the accumulation of anthocyanin in several plant tissues such as tassel, kernel, and cob. A paramutated pl1' allele arose spontaneously in a pl1 population, and in this study, we found evidence of silencing events spatially associated in the field, suggesting a possible horizontal transfer of silencing among nearby plants.

Differential Symptomology, Susceptibility, and Titer Dynamics Manifested by Phytoplasma-Infected Periwinkle and Tomato Plants

Phytoplasmas are intracellular pathogenic bacteria that infect a wide range of plant species, including agriculturally important crops and ornamental trees. However, our understanding of the relationship between symptom severity, disease progression, and phytoplasma concentration remains limited due to the inability to inoculate phytoplasmas mechanically into new plant hosts. The present study investigated phytoplasma titer dynamics and symptom development in periwinkle and tomato, both infected with the same potato purple top (PPT) phytoplasma strain using a small seedling grafting approach. Virescence, phyllody, and witches'-broom (WB) symptoms sequentially developed in periwinkle, while in tomato plants, big bud (BB, a form of phyllody), cauliflower-like inflorescence (CLI), and WB appeared in order. Results from quantitative polymerase chain reaction (qPCR) targeting the PPT phytoplasma's 16S rRNA gene revealed that in both host species, phytoplasma titers differed significantly at different infection stages. Notably, the highest phytoplasma concentration in periwinkles was observed in samples displaying phyllody symptoms, whereas in tomatoes, the titer peaked at the BB stage. Western blot analysis, utilizing an antibody specific to PPT phytoplasma, confirmed substantial phytoplasma presence in samples displaying phyllody and BB symptoms, consistent with the qPCR results. These findings challenge the conventional understanding that phytoplasma infection dynamics result in a higher titer at later stages, such as WB (excessive vegetative growth), rather than in the early stage, such as phyllody (abnormal reproductive growth). Furthermore, the PPT phytoplasma titer was markedly higher in periwinkles than in tomato plants, indicating differing susceptibilities between the hosts. This study reveals distinct host responses to PPT phytoplasma infection, providing valuable insights into phytoplasma titer dynamics and symptom development, with implications for the future management of agricultural disease.

Modified "Allele-Specific qPCR" Method for SNP Genotyping Based on FRET

The proposed method is a modified and improved version of the existing "Allele-specific q-PCR" (ASQ) method for genotyping of single nucleotide polymorphism (SNP) based on fluorescence resonance energy transfer (FRET). This method is similar to frequently used techniques like Amplifluor and Kompetitive allele specific PCR (KASP), as well as others employing common universal probes (UPs) for SNP analyses. In the proposed ASQ method, the fluorophores and quencher are located in separate complementary oligonucleotides. The ASQ method is based on the simultaneous presence in PCR of the following two components: an allele-specific mixture (allele-specific and common primers) and a template-independent detector mixture that contains two or more (up to four) universal probes (UP-1 to 4) and a single universal quencher oligonucleotide (Uni-Q). The SNP site is positioned preferably at a penultimate base in each allele-specific primer, which increases the reaction specificity and allele discrimination. The proposed ASQ method is advanced in providing a very clear and effective measurement of the fluorescence emitted, with very low signal background-noise, and simple procedures convenient for customized modifications and adjustments. Importantly, this ASQ method is estimated as two- to ten-fold cheaper than Amplifluor and KASP, and much cheaper than all those methods that rely on dual-labeled probes without universal components, like TaqMan and Molecular Beacons. Results for SNP genotyping in the barley genes HvSAP16 and HvSAP8, in which stress-associated proteins are controlled, are presented as proven and validated examples. This method is suitable for bi-allelic uniplex reactions but it can potentially be used for 3- or 4-allelic variants or different SNPs in a multiplex format in a range of applications including medical, forensic, or others involving SNP genotyping.

Duplex TaqMan Real-Time PCR for Rapid Quantitative Analysis of a Phytoplasma in Its Host Plant without External Standard Curves

The chapter describes a simple quantitative approach to assess phytoplasma load in samples obtained from "Candidatus Phytoplasma mali"-infected apple plants without the use of external standard curves. The assay is based on the simultaneous detection of a gene of the pathogen and a gene of the host plant in a duplex single-tube real-time PCR reaction using TaqMan chemistry. The quantity of the phytoplasma, relative to its host plant, is determined as the difference between the C_T values of the two target genes (ΔC_T). A critical data analysis step, affecting the inter-assay reproducibility between different amplification runs, is the setting of the threshold level, which is achieved by the recurrent analysis of a calibrator sample. The relative quantification procedure allows analyzing 45 DNA samples in duplicates on a 96-well reaction plate, in addition to the control and calibrator samples, and thus contributes to a substantial increase of analysis throughput and decrease of reagent/consumable costs per sample.

Real-Time PCR Protocol for Phytoplasma Detection and Quantification

Phytoplasmas are mollicutes restricted to plant phloem tissue and are normally present at very low concentrations. Real-time polymerase chain reaction (qPCR) offers several advantages over conventional PCR. It is a fast, sensitive, and reliable detection technique amenable to high throughput. Two fluorescent chemistries are available, intercalating dyes or hybridization probes. Intercalating dyes are relatively less expensive than TaqMan^® hybridization probes but the latter chemistry is the most commonly used for phytoplasma detection. qPCR may be designed for universal detection of phytoplasma, group or subgroup specific detection, or for simultaneous detection of up to three or four phytoplasmas (multiplexing). qPCR may be used for relative or absolute quantification in host plants and in insect vectors. Therefore, qPCR plays an important role in phytoplasma detection as well as in host-pathogen interaction and in epidemiological studies. This chapter outlines the protocols followed in qPCR assay for phytoplasma detection and quantification, focusing mainly on the use of TaqMan^® probes.

Detection and Typing of "Candidatus Phytoplasma " spp. in Host DNA Extracts Using Oligonucleotide-Coupled Fluorescent Microspheres

The use of oligonucleotide-coupled fluorescent microspheres is a rapid, sequencing-independent, and reliable way to diagnose bacterial diseases. Previously described applications of oligonucleotide-coupled fluorescent microspheres for the detection and identification of bacteria in human clinical samples have been successfully adapted to detect and differentiate "Ca. Phytoplasma" species using as a target the chaperonin 60-encoding gene. In this chapter, we describe in detail the design and validation of oligonucleotide capture probes, and their application in the assay aiming to differentiate phytoplasma strains infecting Brassica napus and Camelina sativa plants grown in the same geographic location at the same time.

Advantages of Amplifluor-like SNP markers over KASP in plant genotyping

BACKGROUND

KASP (KBioscience Competitive Allele Specific PCR) and Amplifluor (Amplification with fluorescence) SNP markers are two prominent technologies based upon a shared identical Allele-specific PCR platform.

METHODS

Amplifluor-like SNP and KASP analysis was carried out using published and own design of Universal probes (UPs) and Gene-specific primers (GSPs).

RESULTS

Advantages of the Amplifluor-like system over KASP include the significantly lower costs and much greater flexibility in the adjustment and development of 'self-designed' dual fluorescently-labelled UPs and regular GSPs. The presented results include optimisation of 'tail' length in UPs and GSPs, protocol adjustment, and the use of various fluorophores in different qPCR instruments. The compatibility of the KASP Master-mix in both original and Amplifluor-like systems has been demonstrated in the presented results, proving their similar principles. Results of SNP scoring with rare alleles in addition to more frequently occurring alleles are shown.

CONCLUSIONS

The Amplifluor-like system produces SNP genotyping results with a level of sensitivity and accuracy comparable to KASP but at a significantly cheaper cost and with much greater flexibility for UPs with self-designed GSPs.

General phytoplasma detection by a q-PCR method using mycoplasma primers

Phytoplasmas and mycoplasmas are bacteria belonging to the class Mollicutes. In this study, a fine tuning of quantitative polymerase chain reaction (qPCR) with a universal mycoplasma primer pair (GPO3F/MGSO) targeting the 16S rRNA gene was carried out on phytoplasmas. The dissociation curves of DNAs from Catharanthus roseus phytoplasma-infected micropropagated shoots and from phytoplasma field-infected plant samples showed a single peak at 82.5 °C (±0.5) specifically detecting phytoplasmas belonging to several ribosomal groups. Assay specificity was determined with DNA of selected bacteria: 'Candidatus Liberibacter solanacearum', Xylella fastidiosa, Ralstonia solanacearum and Clavibacter michiganensis. No amplification curves were observed with any of these tested bacteria except 'Ca. L. solanacearum' that was amplified with a melting temperature at 85 °C. Absolute quantification of phytoplasma titer was calculated using standard curves prepared from serial dilutions of plasmids containing the cloned fragment GPO3F/MGSO from European stone fruit yellows phytoplasma. Phytoplasma copy number ranged from 10⁶ to 10³ according with the sample. The sensitivity evaluated comparing plasmid serial dilutions resulted 10^-6 for conventional PCR and 10^-7 for qPCR. The latter method resulted therefore able to detect very low concentrations of phytoplasma in plant material.

Comparing qPCR and Nested PCR Diagnostic Methods for Aster Yellows Phytoplasma in Aster Leafhoppers

The aster yellows phytoplasma (AYp) is a wall-less bacterium that causes damage in multiple crops. They are spread primarily by the aster leafhopper, Macrosteles quadrilineatus (Hemiptera: Cicadellidae). A total of 3,156 aster leafhoppers were collected during the 2014 and 2015 growing seasons in Michigan celery and carrot fields using sweep nets. The objective of this study was to test previously developed 16S rDNA phytoplasma gene primers to find the most reliable and least time-consuming method for AYp detection in leafhoppers. Nested polymerase chain reaction (PCR) was performed with universal primers P1/P7 and R16F2n/R16R2, and then, restriction enzymes AluI, MseI, and HhaI identified the phytoplasma to subgroup. Over the two years, 2.2% of samples were phytoplasma positive with nested PCR, classified in subgroups 16SrI-A or 16SrI-B. All samples were also tested with a TaqMan quantitative qPCR assay with universal phytoplasma primers and probe and 4.6% tested positive. A subset of samples were also tested with AYp-specific SYBR green qPCR, showing a >93% similarity between SYBR green and TaqMan qPCR assay results. The qPCR assays were more than two times faster than nested PCR. However, qPCR assays likely have specificity issues that need to be addressed before they can be used as a reliable method of detection for AYp in leafhoppers.