Centenary of Soil and Air Borne Wheat Karnal Bunt Disease Research: A Review

Genome sequencing, phylogenomics, and population analyses of Tilletia, with recognition of one common bunt species, T. caries (synonym T. laevis), distinct from dwarf bunt, T. controversa

Some species of Tilletia are responsible for diseases in economically important crops, such as wheat and rice. In this study, we sequenced, assembled, and annotated 22 new genomes for Tilletia, with a focus on species causing dwarf bunt (DB; T. controversa), common bunt (CB; T. caries and T. laevis), and rice kernel smut (RKS; T. horrida). We present the first genomes for four other species (T. bromi, T. fusca, T. goloskokovii, and T. rugispora), resulting in the largest and most diverse sample of Tilletia genomes studied to date. Depending on the species and strain, the assembly size ranged from 24.3 to 30.5 Mb and gene prediction resulted in 7138 to 8261 gene models per genome. Phylogenomic analyses with hundreds to thousands of genes revealed significant support for the relationships among certain Tilletia taxa and validated findings of previous molecular studies that employed a small number of genes. Further population-level analyses showed two distinct populations of DB and CB: T. controversa (DB) as a single population and another intermixed population of T. caries and T. laevis (CB). No evidence of geographic isolation was observed within these populations. Our phylogenomic analyses also supported previous multigene hypotheses that multiple lineages of Tilletia may cause RKS. Collectively, our results suggest that taxonomic revisions are needed for the RKS-causing pathogens and provide convincing evidence for formally recognizing the CB-causing taxa as one species, named T. caries (synonym T. laevis). Overall, our study significantly enhances genomic resources for Tilletia, offers insights into phylogenetic relationships and population structure, and provides whole genome sequences for future studies.

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.

Comparative analysis of nine Tilletia indica genomes for the development of novel microsatellite markers for genetic diversity and population structure analysis

Karnal bunt (KB; Tilletia indica) is the prime quarantine concern for quality wheat production throughout the world. The most effective approach to dealing with this biotic stress is to breed KB-resistant wheat varieties, which warrants a better understanding of T. indica genome architecture. In India, the North Western Plain Zone is the prime hot spot for KB disease, but only limited efforts have been made to decipher T. indica diversity at the genomic level. Microsatellites offer a powerful and robust typing system for the characterization and genetic diversity assessment of plant pathogens. At present, inadequate information is available with respect to the development of genome-derived markers for revealing genetic variability in T. indica populations. In current research, nine complete genome sequences of T. indica (PSWKBGH_1, PSWKBGH_2, PSWKBGD_1_3, RAKB_UP_1, TiK_1, Tik, DAOMC236408, DAOMC236414, and DAOMC236416) that exist in the public domain were explored to know the dynamic distribution of microsatellites. Comparative genome analysis revealed a high level of relative abundance and relative density of microsatellites in the PSWKBGH_1 genome in contrast to other genomes. No significant correlation between microsatellite distribution for GC content and genome size was established. All the genomes showed the dominance of tri-nucleotide motifs, followed by mono-, di-, tetra-, hexa-, and penta-nucleotide motifs. Out of 50 tested markers, 36 showed successful amplification in T. indica isolates and produced 52 different alleles. A PCR assay along with analysis of the polymorphic information content (PIC) revealed 10 markers as neutral and polymorphic loci (PIC 0.37). The identified polymorphic SSR loci grouped a geographically distinct T. indica population of 50 isolates representing seven Indian regions (Jammu, Himachal Pradesh, Punjab, Haryana, Uttarakhand, Uttar Pradesh, and Rajasthan) into four distinct clusters. The results of the analysis of molecular variance identified 94% genetic variation within the population and 6% among the population. Structure analysis also confirmed the existence of four genetically diverse groups containing admixtures of T. indica isolates across populations. In nutshell, the current study was successful in identifying novel, neutral and polymorphic microsatellite markers that will be valuable in offering deep insight into the evolutionary relationship and dynamics of the T. indica population for devising effective KB management strategies in wheat.

Non-targeted screening and trimethylamine determination in Tilletia foetida-infected wheat using HS-SPME-GC-MS

Common bunt disease of wheat in China is caused mainly by Tilletia foetida. However, reliable approaches for determining disease-associated biochemical markers are rarely reported. Here, a headspace-solid-phase microextraction coupled with headspace GC-tandem mass spectrometry (HS-SPME-GC-MS) was used to screen volatile substances in infected wheat, and an optimal chemical marker was selected to establish analytical methods for disease determination. Non-targeted screening of 13 volatile compounds unique to diseased wheat allowed a metabolite with rotten fish-like smell, trimethylamine (TMA), to be selected as the inspection marker. Subsequently, two analytical methodologies, HS-SPME-GC-MS and headspace gas chromatography with flame ionization detection (HS-GC-FID), were established to determinate the TMA content in wheat. The linear relationship, recovery and reproducibility of the methods were validated. The limit of detection (LOD) was 0.02 µg/kg for the former method, 5000-fold lower than that for the latter. When analysing samples, HS-SPME-GC-MS showed excellent sensitivity and allowed for the determination of 0.05% infected kernels among whole wheat grains. Therefore, TMA determination using HS-SPME-GC-MS is an effective alternative method to detect wheat common bunt disease occurring at extremely low infection rate.

Rapid sensing ofTilletia indica - Teliospore in wheat extractby apiezoelectric label free immunosensor

'Tilletia indica', a fungal pathogen causes Karnal bunt disease in wheat. It has been renowned as a quarantine pest in more than 50 countries, therefore, urged a threat to wheat in the international market. To date, conventional methods employed to detect the disease involve the tentative identification of spores (teliospores) based on morphology. For effective and specific disease control, it is essential to get the specific protein of the analyte (teliospore) to target. In present study, a label-free immunosensor has been developed to detect Karnal bunt disease. A specifically synthesized anti-teliosporic monoclonal antibody (mAb) was immobilized on a self-assembled monolayer of 11-mercaptoundecanoic acid (11-MUA) to detect teliospore. All modified electrodes were morphologically characterized by scanning electron microscopy (SEM), atomic force microscopy(AFM), Fourier transform infra-red spectroscopy (FT-IR) techniques and analytically characterized by quartz crystal microbalance (QCM) and cyclic voltammetry (CV). The linearity range was 19 pg mL^-1-10 ng mL^-1, while the detection limit (LOD) was 4.4 pg mL^-1 and 12.5 pg mL^-1, respectively. The stability, reproducibility, and repeatability of the immunoelectrode was examined by CV, and found stable upto 18 days with negligible variation. The binding affinity (association constant (K_a)) of the developed immunoelectrode was 1.9 × 10^-2 ng mL^-1. The real sample has been tested in spiked wheat samples and found about 95-103 % recovery with 2.8-4.4 % relative error.