Molecular diagnostic assay for pre-harvest detection of Tilletia indica infection in wheat plants

The current study describes a new diagnostic method for the rapid and accurate detection of Tilletia indica, the pathogen accountable for causing Karnal bunt (KB) disease in wheat. This method uses quantitative real-time polymerase chain reaction (qPCR) and a primer set derived from glyceraldehyde 3-phosphate dehydrogenase (GAPDH) gene of T. indica to identify the presence of the pathogen. The qPCR assay using this primer set was found highly sensitive, with a limit of detection (LOD) value of 4 pg of T. indica DNA. This level of sensitivity allows for the detection of the pathogen even in cases of different growth stages of wheat, where no visible symptoms of infection on the wheat plants can be seen by naked eyes. The study also validated the qPCR assay on ten different wheat cultivars. Overall, this study presents a valuable molecular tool for rapid, specific and sensitive detection of KB fungus in wheat host. This method has practical applications in disease management, screening of wheat genotypes against KB and can aid in the development of strategies to mitigate the impact of Karnal bunt disease on wheat production.

Intelligent reprogramming of wheat for enhancement of fungal and nematode disease resistance using advanced molecular techniques

Wheat (Triticum aestivum L.) diseases are major factors responsible for substantial yield losses worldwide, which affect global food security. For a long time, plant breeders have been struggling to improve wheat resistance against major diseases by selection and conventional breeding techniques. Therefore, this review was conducted to shed light on various gaps in the available literature and to reveal the most promising criteria for disease resistance in wheat. However, novel techniques for molecular breeding in the past few decades have been very fruitful for developing broad-spectrum disease resistance and other important traits in wheat. Many types of molecular markers such as SCAR, RAPD, SSR, SSLP, RFLP, SNP, and DArT, etc., have been reported for resistance against wheat pathogens. This article summarizes various insightful molecular markers involved in wheat improvement for resistance to major diseases through diverse breeding programs. Moreover, this review highlights the applications of marker assisted selection (MAS), quantitative trait loci (QTL), genome wide association studies (GWAS) and the CRISPR/Cas-9 system for developing disease resistance against most important wheat diseases. We also reviewed all reported mapped QTLs for bunts, rusts, smuts, and nematode diseases of wheat. Furthermore, we have also proposed how the CRISPR/Cas-9 system and GWAS can assist breeders in the future for the genetic improvement of wheat. If these molecular approaches are used successfully in the future, they can be a significant step toward expanding food production in wheat crops.

SCAR marker: A potential tool for authentication of agriculturally important microorganisms

Microbial inoculants are globally recommended for plant growth promotion and control of plant pathogens. These inoculants require stringent quality checks for sustainable field efficacy. Questionable regulatory frameworks constantly deteriorate the reliability of bio-inoculant technology. Existing global regulations do not involve any rapid molecular technique for the routine inspection of microbial preparations. Sequence characterized amplified region (SCAR) marker offers rapid and precise strain-level authentication of target microbes. Such advanced molecular techniques must be exploited to accurately validate the microbial formulations. Besides, the global dissemination of plant pathogenic microbes has always been an alarming threat to food security. SCAR markers could be used at the plant quarantine centers to rapidly detect catastrophic pathogens, thereby circumventing the import and export of contagious plant materials. The current review is focused on promoting the SCAR marker technology to validate commercial bio-inoculants and predict plant pandemics.

Development of droplet digital PCR for the detection of Tilletia laevis, which causes common bunt of wheat, based on the SCAR marker derived from ISSR and real-time PCR

Common bunt of wheat caused by Tilletia laevis and/or T. caries (syn. T. tritici), is a major disease in wheat-growing regions worldwide that could lead to 80% or even total loss of production. Even though T. laevis can be distinguished from T. caries on the bases of morphology of teliospores using microscopy technique. However, molecular methods could serve as an additional method to quantify the pathogen. To develop a rapid diagnostic and quantify method, we employed the ISSR molecular marker for T. laevis in this study. The primer ISSR857 generated a polymorphic pattern displaying a 1385 bp T. laevis-specific DNA fragment. A pair of specific primers (L57F/L57R) was designed to amplify a sequence-characterized amplified region (SCAR) (763 bp) for the PCR detection assay. The primers amplified the DNA fragment in the tested isolates of T. laevis but failed in the related species, including T. caries. The detection limit of the primer set (L57F/L57R) was 5 ng/µl of DNA extracted from T. laevis teliospores. A SYBR Green I real-time PCR method for detecting T. laevis with a 100 fg/µl detection limit and droplet digital PCR with a high sensitivity (30 fg/µl detection limit) were developed; this technique showed the most sensitive detection compared to the SCAR marker and SYBR Green I real-time PCR. Additionally, this is the first study related the detection of T. laevis with the droplet digital PCR method.

First Report of Wheat Common Bunt Caused by Tilletia laevis in Henan Province, China

Wheat common bunt is a serious disease that may lead to yield losses of 75-80% in many wheat regions of the world (Mathre 1996). The disease may reduce yield and flour quality by producing trimethylamine, a compound that smells like rotting fish (Castlebury et al. 2005; Hoffmann 1981; Mathre 1996). Two closely related basidiomycete species, Tilletia caries (DC.) Tul. & C. Tul. [syn. T. tritici (Bjerk.) Wint.] and T. laevis J. G. Kühn [syn. T. foetida (Wallr.) Liro], cause wheat common bunt. Teliospore morphology is used to differentiate the two species. Teliospores of T. caries have reticulates on the surface while teliospores of T. laevis have a smooth surface (Pieczul et al. 2018). T. laevis was reported in Liaoning, Shaanxi, Shandong, Beijing, Hebei, Shanxi, Jilin, Heilongjiang, Jiangsu, Gansu, Xinjiang, Sichuan, Yunnan, Inner Mongolia, and Tibet (Guo 2011; Wang 1963), but not in Henan, the biggest wheat production province in China, before the present study. In July 2019, we found wheat common bunt in three fields grown with cultivar Zhengmai 618 in Yugong Mountain, Henan province. The diseased wheat heads had bunt balls filled with black powder with fishy smell. The disease incidences in these fields were 20-50%, but no common bunt was found in other nearby fields. About 200 diseased heads were sampled from the three fields. Teliospores from each head were observed under a microscope, and they all had smooth surface. Observations using a scanning electron microscope also showed smooth-surfaced teliospores. Teliospores were measured 13.5 to 18.5 μm in diameter. After surface sterilization of diseased heads using 0.25% NaClO for 5 min, teliospore suspension (1×106/ml) was made using sterilized distilled water and spread on water agar (200 μl per plate), and the plates were kept at 15°C with 24 h light (Goates and Hoffman 1987). On the 6th days, teliospores were germinated. Based on the disease symptoms, teliospore morphology, and germination, the bunt fungus was identified as T. laevis. To fulfill Koch's postulates, 1 ml of germinating teliospore suspension at the concentration of 106 spores/ml was injected into the heads of susceptible wheat cultivar (Dongxuan 3) at the boot stage with a syringe, and the plants injected with sterile ddH2O were used as control. The inoculated plants were grown in a growth chamber at 17°C with 50% humidity and 24 h light (300 μmol/m2/s). After one month at the ripening stage, the kernels of the inoculated plants were filled with black teliospores releasing fishy smell, and the control plants did not have bunt heads. Under a scanning electron microscope, teliospores from the inoculated heads had smooth surface and were measured 13.5 to 18.5 μm in diameter, similar to the teliospores of bunt heads from the fields. The fungus was also confirmed through molecular characterization using sequence characterized amplification region (SCAR) markers specific for T. laevis, and the expected 660 bp (Yao et al., 2019) and 286 bp (Zhang et al. 2012) bands were obtained separately from the teliospore samples from both the fields and growth chamber. The collection named as CGMCC 3.20112 was deposited in China General Microbiological Culture Collection Center. To the best of our knowledge, this is the first report of T. laevis causing wheat common bunt in Henan Province of China. Because the pathogen is seedborne and soilborne, the disease may become a high risk to wheat production in Henan and other provinces of China.

Establishment of an Agrobacterium tumefaciens-mediated transformation system for Tilletia foetida

Tilletia foetida causes wheat common smut disease with severe loss of yield production and seed quality. In this study, a low-cost, rapid, and efficient Agrobacterium tumefaciens-mediated transformation (ATMT) system for T. foetida mutagenesis was constructed: Transformants were screened with hygromycin B at 100 μg/ml, cefotaxime sodium concentrations with 200 μg/ml, Acetosyringone (AS) concentration at 200 μmol/l, 1 × 10⁶ T. foetida hypha cells/ml, co-cultivation at 22 °C with 24 h and culture was incubated at 16 °C up to day 7. Fourteen transformants were randomly selected and confirmed using the specific primers to amplify the fragment of hygromycin phosphotransferase gene. At the same time, PCR analysis was performed to detect Agrobacterium tumefaciens Vir gene to eliminate false positives. The transformants were cultivated up to 8 generations on hygromycine B-containing complete medium (CM) and confirmed by PCR. The results indicated that 80% of T. foetida transformants were hygromycine B resistant. In conclusion, our analyses identified an efficient T-DNA insertion system for T. foetida and the results will be useful for further understanding the pathogenic mechanism via generation of the insertional mutants.

Development of SCAR markers for rapid and specific detection of Pseudomonas syringae pv. morsprunorum races 1 and 2, using conventional and real-time PCR

Specific primers were developed to detect the causal agent of stone fruit bacterial canker using conventional and real-time polymerase chain reaction (PCR) methods. PCR melting profile (PCR MP) used for analysis of diversity of Pseudomonas syringae strains, allowed to pinpoint the amplified fragments specific for P. syringae pv. morsprunorum race 1 (Psm1) and race 2 (Psm2), which were sequenced. Using obtained data, specific sequence characterised amplified region (SCAR) primers were designed. Conventional and real-time PCRs, using genomic DNA isolated from different bacterial strains belonging to the Pseudomonas genus, confirmed the specificity of selected primers. Additionally, the specificity of the selected DNA regions for Psm1 and Psm2 was confirmed by dot blot hybridisation. Conventional and real-time PCR assays enabled accurate detection of Psm1 and Psm2 in pure cultures and in plant material. For conventional PCR, the detection limits were the order of magnitude ~10(0) cfu/reaction for Psm1 and 10(1) cfu/reaction for Psm2 in pure cultures, while in plant material were 10(0)-10(1) cfu/reaction using primers for Psm1 and 3 × 10(2) cfu/reaction using primers for Psm2. Real-time PCR assays with SYBR Green I showed a higher limit of detection (LOD) - 10(0) cfu/reaction in both pure culture and in plant material for each primer pairs designed, which corresponds to 30-100 and 10-50 fg of DNA of Psm1 and Psm2, respectively. To our knowledge, this is the first PCR-based method for detection of the causal agents of bacterial canker of stone fruit trees.