Leaf rust (Puccinia triticina) mediated RNAi in wheat (Triticum aestivum L.) prompting host susceptibility

Dutta, Summi; Jha, Shailendra K.; Prabhu, K. V.; Kumar, Manish; Mukhopadhyay, Kunal

doi:10.1007/s10142-019-00655-6

Cited by 14 publications

(6 citation statements)

References 49 publications

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“…These results are challenging to obtain and frequently require follow-up studies to confirm functionality and role of a proposed mi/milRNA [58]. Evidence of cleavage found in degradome and 5'-RACE experiments hints that fungal mi/milRNAs may function more similarly to plants [31,[59][60][61][62][63][64][65], as this evidence indicates directed cleavage of a target RNA. However, much more information is needed to develop a detailed view of these dynamics, especially in terms of base-pairing requirements [66] or distinct mechanisms of different AGOs [11].…”

Section: Discussionmentioning

confidence: 99%

Comprehensive re-analysis of hairpin RNAs in fungi reveals ancestral links

Johnson

Larrondo

Álvarez

et al. 2022

Preprint

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RNA interference is an ancient mechanism with many regulatory roles in eukaryotic genomes, with small RNAs acting as their functional element. While there is a wide array of classes of small-RNA-producing loci, those resulting from stem-loop structures (hairpins) have received profuse attention. Such is the case of microRNAs (miRNAs), which have distinct roles in plants and animals. Fungi also produce small RNAs, and several publications have identified miRNAs and miRNA-like (mi/milRNA) hairpin RNAs in diverse fungal species using deep sequencing technologies. Despite this relevant source of information, relatively little is known about mi/milRNA-like features in fungi, mostly due to a lack of established criteria for their annotation. To systematically assess mi/miRNA-like characteristics and annotation confidence, we searched for publications describing mi/milRNA loci and re-assessed the annotations for 40 fungal species. We extracted and normalized the annotation data for 1,677 reported mi/milRNA-like loci and determined their abundance profiles, concluding that less than half of the reported loci passed basic standards used for hairpin RNA discovery. We found that fungal mi/milRNA are generally more similar in size to animal miRNAs and were frequently associated with protein-coding genes. The compiled genomic analyses identified 18 mi/milRNA loci conserved in multiple species. Our pipeline allowed us to build a general hierarchy of locus quality, identifying around 200 loci with high-quality annotations. We provide a centralized annotation of identified mi/milRNA hairpin RNAs in fungi which will serve as a resource for future research and advance in understanding the characteristics and functions of mi/milRNAs in fungal organisms.

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Section: Discussionmentioning

confidence: 99%

Comprehensive re-analysis of hairpin RNAs in fungi reveals ancestral links

Johnson

Larrondo

Álvarez

et al. 2022

Preprint

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“…Following the finding of milRNAs in the model N. crassa system, milRNA sRNAs have since been reported in a number of agronomically important fungal pathogens, including Puccinia triticina [95], Puccinia striiformis [96], Sclerotinia sclerotiorum [97], V. dahliae [90], and F. graminearum [98]. Furthermore, computational methods for predicting milRNA sRNAs and their precursors in fungi have more recently become available [99].…”

Section: The Fungal Mirna Pathwaymentioning

confidence: 99%

“…In the leaf rust pathogen P. triticina, three putative fungal milRNA precursor transcripts were detected bioinformatically using the ShortStack tool [100] and Vienna RNA folding predictions [101]. One of these milRNAs, PtmilR2, was upregulated during infection, which correlated with a downregulation of its putative targets in wheat plants, including a calcium-modulated protein and the CALMODULIN (CAM) and MITOGEN ACTIVATED PROTEIN (MAP) kinases [95]. Similarly, milR1 in the stripe rust pathogen P. striiformis has been identified as a potential milRNA-based pathogenicity factor that putatively targets the wheat gene PATHOGENESIS-RELATED2 (PR2) [96].…”

Section: The Fungal Mirna Pathwaymentioning

confidence: 99%

RNA-Based Control of Fungal Pathogens in Plants

Mann

Sawyer

Gardiner

et al. 2023

IJMS

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Our duty to conserve global natural ecosystems is increasingly in conflict with our need to feed an expanding population. The use of conventional pesticides not only damages the environment and vulnerable biodiversity but can also still fail to prevent crop losses of 20–40% due to pests and pathogens. There is a growing call for more ecologically sustainable pathogen control measures. RNA-based biopesticides offer an eco-friendly alternative to the use of conventional fungicides for crop protection. The genetic modification (GM) of crops remains controversial in many countries, though expression of transgenes inducing pathogen-specific RNA interference (RNAi) has been proven effective against many agronomically important fungal pathogens. The topical application of pathogen-specific RNAi-inducing sprays is a more responsive, GM-free approach to conventional RNAi transgene-based crop protection. The specific targeting of essential pathogen genes, the development of RNAi-nanoparticle carrier spray formulations, and the possible structural modifications to the RNA molecules themselves are crucial to the success of this novel technology. Here, we outline the current understanding of gene silencing pathways in plants and fungi and summarize the pioneering and recent work exploring RNA-based biopesticides for crop protection against fungal pathogens, with a focus on spray-induced gene silencing (SIGS). Further, we discuss factors that could affect the success of RNA-based control strategies, including RNA uptake, stability, amplification, and movement within and between the plant host and pathogen, as well as the cost and design of RNA pesticides.

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“…Total RNA was isolated using TRI Reagent (Sigma-Aldrich) from the mock and pathogen inoculated leaves of both wheat NILs sampled at varied infection time points (Dutta et al, 2019). Complementary DNA was prepared from 1µg of isolated RNA using RevertAid First Strand cDNA synthesis kit (Thermo sher) as suggested by the manufacturer.…”

Section: Gene Expression Analysis Using Quantitative Real-time Pcrmentioning

confidence: 99%

Identification and molecular characterization of flavonoid biosynthetic genes and their expression analysis in wheatgrass (Triticum aestivum L.) during leaf rust infection

Adhikary,

Deb,

Sarkar

et al. 2023

Preprint

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Wheat (Triticum aestivum L.) is a major staple food worldwide. Puccinia triticina. forms infectious urediniospores causing leaf rust disease in bread wheat leading to an annual yield loss of ~15% globally. Evolution of new virulent strains and ability of urediniospores to traverse long distances in air pose a challenge on the prevailing leaf rust control techniques. Therefore, significant knowledge is required about the genes in wheat plants that can restrict disease development.Contemporary studies indicate that flavonoid biosynthetic genes are involved in transcriptional and post-transcriptional gene regulation, growth, responses to environmental stimuli and signal transduction. We were able to identify flavonoids like apigenin and luteolin that were synthesized in wheat plants only after leaf rust infection In silico identification of contigs from four SOLiD-SAGE libraries and their functional annotation depicted the involvement of secondary metabolism pathways in retort to the disease development. The flavonoid biosynthetic pathway was discerned through KEGG mapping of the identified contigs and the key genes like Chalcone synthase, Flavanone 3-dioxygenase and Anthocyanidin synthase were characterized. Expression analysis of these genes at varied time points post pathogen infection on both resistant and susceptible wheat Near-Isogenic Lines, revealed their association with development, metabolism, and defense response regulation. Expression of these genes decreased significantly during pathogenesis in susceptible wheat plants compared to the resistant plants, indicating the transition in expression of flavonol accumulation possibly to combat leaf rust disease progression. Consequently, this study focuses on investigating flavonoid biosynthetic genes in wheat and their response during leaf-rust pathogenesis.

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Leaf rust (Puccinia triticina) mediated RNAi in wheat (Triticum aestivum L.) prompting host susceptibility

Cited by 14 publications

References 49 publications

Comprehensive re-analysis of hairpin RNAs in fungi reveals ancestral links

Comprehensive re-analysis of hairpin RNAs in fungi reveals ancestral links

RNA-Based Control of Fungal Pathogens in Plants

Identification and molecular characterization of flavonoid biosynthetic genes and their expression analysis in wheatgrass (Triticum aestivum L.) during leaf rust infection

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