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

Xu, Tongshuo; Yao, Zhaoqun; Liu, Jianjian; Zhang, Han; Din, Ghulam Muhae Ud; Zhao, Shiying; Chen, Wanquan; Liu, Taiguo; Gao, Li

doi:10.1038/s41598-020-72976-7

Cited by 13 publications

(10 citation statements)

References 42 publications

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“…As there is an increasing interest in the ecological and evolutionary dynamics in tripartite systems in microbial communities such as hosts, helper viruses and satellite viruses, the presented methods for multiplex ddPCR should be considered for other systems as well. This method can help the study of the role of virophage-giant virus interactions, and has the potential to be used for a wide range of disciplines, for clinical samples to identify drug-resistant subpopulations [ 36 ], agricultural evaluation of pest resistance [ 37 ], and field surveying of viruses [ 29 ] among others.…”

Section: Discussionmentioning

confidence: 99%

Simultaneous Giant Virus and Virophage Quantification Using Droplet Digital PCR

Arco

Fischer

Becks

2022

Viruses

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Viruses are an abundant component of aquatic systems, but their detection and quantification remain a challenge. Virophages co-replicate with giant viruses in the shared host cell, and can inhibit the production of new giant virus particles, thereby increasing the survival of the infected host population. Here, we present a protocol for Droplet Digital PCR (ddPCR) to quantify simultaneously giant virus and virophage in a mixed sample, enabling the rapid, culture-free and high throughput detection of virus and virophage. As virophage can be present as free virus particles or integrated into the virus host’s genome as well as associated with organic particles, we developed a simple method that enables discrimination between free and particle-associated virophages. The latter include aggregated virophage particles as well as virophage integrated into the host genome. We used, for our experiments, a host-virus-virophage system consisting of Cafeteria burkhardae, CroV and mavirus. Our results show that ddPCR can be an efficient method to quantify virus and virophage, and we discuss potential applications of the method for studying ecological and evolutionary processes of virus and virophages.

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Section: Discussionmentioning

confidence: 99%

Simultaneous Giant Virus and Virophage Quantification Using Droplet Digital PCR

Arco

Fischer

Becks

2022

Viruses

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“…The grains were sterilized and vernalized, and ten wheat seedlings were transplanted into every pot. Based on morphological characterization of teliospores of T. laevis ( Supplementary Figure 1 ) and specific band and sequence of SCAR marker of T. laevis ( Supplementary Figure 2 ), we identified the pathogen of T. laevis based on the previous reports ( Xu et al, 2020 ; Qin et al, 2021 ). Then, the identified T. laevis was use in this study.…”

Section: Methodsmentioning

confidence: 99%

Transcriptomics Analysis of Wheat Tassel Response to Tilletia laevis Kühn, Which Causes Common Bunt of Wheat

Ren

Muhae-Ud-Din

et al. 2022

Front. Plant Sci.

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Tilletia laevis Kühn [synonym T. foetida (Wallr.) Liro] can lead to a wheat common bunt, which is one of the most serious diseases affecting kernels, a serious reduction in grain yield, and losses can reach up to 80% in favorable environments. To understand how wheat tassels respond to T. laevis, based on an RNA-Seq technology, we analyzed a host transcript accumulation on healthy wheat tassels and on tassels infected by the pathogen. Our results showed that 7,767 out of 15,658 genes were upregulated and 7,891 out of 15,658 genes were downregulated in wheat tassels. Subsequent gene ontology (GO) showed that differentially expressed genes (DEGs) are predominantly involved in biological processes, cellular components, and molecular functions. Additionally, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that 20 pathways were expressed significantly during the infection of wheat with T. laevis, while biosynthesis of amino acids, carbon metabolism, and starch and sucrose metabolism pathways were more highly expressed. Our findings also demonstrated that genes involved in defense mechanisms and myeloblastosis (MYB) transcription factor families were mostly upregulated, and the RNA-seq results were validated by quantitative real-time polymerase chain reaction (qRT-PCR). This is the first report on transcriptomics analysis of wheat tassels in response to T. laevis, which will contribute to understanding the interaction of T. laevis and wheat, and may provide higher efficiency control strategies, including developing new methods to increase the resistance of wheat crops to T. laevis-caused wheat common bunt.

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“…A droplet digital PCR (ddPCR) sensing system for detecting common bunt disease (caused by Tilletia laevis) in wheat was reported in [42]. The ddPCR exhibited superior detection limit of 30 fg/µL as compared to qPCR (100 fg/µL).…”

Section: Pcr-based Methodsmentioning

confidence: 99%

Sensing Methodologies in Agriculture for Monitoring Biotic Stress in Plants Due to Pathogens and Pests

Kashyap

Kumar

2021

Inventions

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Reducing agricultural losses is an effective way to sustainably increase agricultural output efficiency to meet our present and future needs for food, fiber, fodder, and fuel. Our ever-improving understanding of the ways in which plants respond to stress, biotic and abiotic, has led to the development of innovative sensing technologies for detecting crop stresses/stressors and deploying efficient measures. This article aims to present the current state of the methodologies applied in the field of agriculture towards the detection of biotic stress in crops. Key sensing methodologies for plant pathogen (or phytopathogen), as well as herbivorous insects/pests are presented, where the working principles are described, and key recent works discussed. The detection methods overviewed for phytopathogen-related stress identification include nucleic acid-based methods, immunological methods, imaging-based techniques, spectroscopic methods, phytohormone biosensing methods, monitoring methods for plant volatiles, and active remote sensing technologies. Whereas the pest-related sensing techniques include machine-vision-based methods, pest acoustic-emission sensors, and volatile organic compound-based stress monitoring methods. Additionally, Comparisons have been made between different sensing techniques as well as recently reported works, where the strengths and limitations are identified. Finally, the prospective future directions for monitoring biotic stress in crops are discussed.

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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

Cited by 13 publications

References 42 publications

Simultaneous Giant Virus and Virophage Quantification Using Droplet Digital PCR

Simultaneous Giant Virus and Virophage Quantification Using Droplet Digital PCR

Transcriptomics Analysis of Wheat Tassel Response to Tilletia laevis Kühn, Which Causes Common Bunt of Wheat

Sensing Methodologies in Agriculture for Monitoring Biotic Stress in Plants Due to Pathogens and Pests

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