Insights of Lr28 mediated wheat leaf rust resistance: Transcriptomic approach

Singh, Dharmendra; Kumar, Dharmender; Satapathy, Lopamudra; Pathak, Jyoti; Chandra, Saket; Riaz, Adnan; Bhaganagre, Govindraj; Dhariwal, Raman; Kumar, Manish; Prabhu, K. V.; Balyan, H. S.; Gupta, P. K.; Mukhopadhyay, Kunal

doi:10.1016/j.gene.2017.09.028

Cited by 27 publications

(18 citation statements)

References 74 publications

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“…Enzymes such as chalcone isomerase (CHI), avanone 3-hydroxylase (F3H), anthocyanidin synthase (ANS), dihydro avonol 4-reductase (DFR), avonol synthase (FLS) and avone synthase (FNS) are involved in the pathway leading to biosynthesis of major avonoid classes (Lu et al, 2017). CHS, Chalcone avanone isomerase (CFI), Chorismate synthase (CS), Iso-chorismate synthase (ICS) genes are involved in various circadian rhythms which gets activated by MYB and MYB-related TFs (Singh et al, 2017). Previous study also acknowledges that avonoid biosynthetic pathway responds to biotic and abiotic stress in maize (Chiristie et al, 1994), rice (Ithal and Reddy, 2004), Ligustrum vulgare (Guidi et al, 2008), Scutellaria baicalensis (Yuan et al, 2012), and the desert plant Reaumuria soongorica (Liu et al, 2013).…”

Section: Discussionmentioning

confidence: 99%

“…Leaf samples were collected from ve different plants of same treatment at different time points, 0 (just before inoculation), 24-, 48-, 72-and 168-hour post inoculation (hpi), ash frozen in liquid nitrogen and stored at -80°C freezers for further studies. These time points were selected based on earlier leaf rust pathogenwheat interaction studies conducted in our laboratory (Singh et al, 2017;Kumar et al, 2017). Leaf extracts were prepared from the samples collected at the above-mentioned time points from 10 g (fresh weight, FW) as mentioned in Adhikary et al (2021).…”

Section: Plant Growth Pathogen Inoculation and Leaf Sample Collectionmentioning

confidence: 99%

“…Four Serial Analysis of Gene Expression (SAGE) libraries (Short Read Archive Biosample number SRA061917) of the same wheat NILs either mock inoculated or inoculated with urediniospores of Puccinia triticina [SAGE1 (S-MI; accession number SAMN01820702), SAGE2 (S-PI; accession number SAMN01820703), SAGE3 (R-MI; accession number SAMN01820704) and SAGE4 (R-PI; accession number SAMN01820705)] were earlier prepared in this lab using SOLiD3 System SAGE kit and sequenced (Applied Biosystems, CA, USA; Chandra et al, 2016;Singh et al, 2017). The retrieved sequences were functionally annotated at KEGG (Kyoto Encyclopedia of Genes and Genomes) using KAAS (KEGG Automatic Annotation Server; https://www.genome.jp/kegg/kaas/; Chandra et al, 2016;Yuan et al, 2018).…”

Section: Gene Ontology Annotationmentioning

confidence: 99%

“…However, regulation and modi cation of expression of avonoid biosynthetic genes and their relationship to metabolite accumulation in response to pathogen infection remain an attractive target for research. In this study, data were retrieved from four SAGE (Serial Analysis of Gene Expression) libraries that were prepared from mock and leaf rust pathogen inoculated near isogenic wheat lines (NILs; with or without seedling leaf rust resistance gene Lr28) and were sequenced using the Next Generation Sequencing (NGS) tool SOLiD3 (Chandra et al, 2016;Singh et al, 2017). Our aim was to explore the role of avonoidbased defense mechanism to understand the phenomenon underlying wheat-leaf rust interaction in both susceptible and resistant wheat NILs.…”

Section: Introductionmentioning

confidence: 99%

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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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Section: Discussionmentioning

confidence: 99%

Section: Plant Growth Pathogen Inoculation and Leaf Sample Collectionmentioning

confidence: 99%

Section: Gene Ontology Annotationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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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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“…A recent study compared the transcriptional differences in wheat line carrying the Lr57 gene between compatible and incompatible interactions [14]. Using a serial analysis of gene expression (SAGE) technique, genes regulated by the Lr28 gene were initially explored [15]. In the other study, the transcriptional responses in wheat to infections of multiple fungal pathogens, including Puccinia striiformis f. sp.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Expression Profiling of Genes Associated with the Lr47-Mediated Wheat Resistance to Leaf Rust (Puccinia triticina)

Gao

et al. 2019

IJMS

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Puccinia triticina (Pt), the causal agent of wheat leaf rust, is one of the most destructive fungal pathogens threatening global wheat cultivations. The rational utilization of leaf rust resistance (Lr) genes is still the most efficient method for the control of such diseases. The Lr47 gene introgressed from chromosome 7S of Aegilops speltoides still showed high resistance to the majority of Pt races collected in China. However, the Lr47 gene has not been cloned yet, and the regulatory network of the Lr47-mediated resistance has not been explored. In the present investigation, transcriptome analysis was applied on RNA samples from three different wheat lines (“Yecora Rojo”, “UC1037”, and “White Yecora”) carrying the Lr47 gene three days post-inoculation with the epidemic Pt race THTT. A comparison between Pt-inoculated and water-inoculated “Lr47-Yecora Rojo” lines revealed a total number of 863 upregulated (q-value < 0.05 and log2foldchange > 1) and 418 downregulated (q-value < 0.05 and log2foldchange < −1) genes. Specifically, differentially expressed genes (DEGs) located on chromosomes 7AS, 7BS, and 7DS were identified, ten of which encoded receptor-like kinases (RLKs). The expression patterns of these RLK genes were further determined by a time-scale qRT-PCR assay. Moreover, heatmaps for the expression profiles of pathogenesis-related (PR) genes and several transcription factor gene families were generated. Using a transcriptomic approach, we initially profiled the transcriptional changes associated with the Lr47-mediated resistance. The identified DEGs, particularly those genes encoding RLKs, might serve as valuable genetic resources for the improvement of wheat resistance to Pt.

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The F-box protein encoding genes of the leaf-rust fungi Puccinia triticina: genome-wide identification, characterization and expression dynamics during pathogenesis

Gidhi,

Jha,

Kumar

et al. 2024

Arch Microbiol

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Aim -This study was aimed at identifying F-box genes in Puccinia triticina, the causal organism for the leaf rust disease in wheat and inferring their role in pathogenicity in susceptible wheat plants.Methods and results -Genome-wide analysis revealed 10 F-box genes and were characterized using in silico approaches for revealing phylogenetic relationships, gene structures, gene ontology, protein properties, sequence analysis and gene expression studies. Domain analysis predicted functional domains like WD40 and LRR at C-terminus along with the obvious presence of F-box motif in N-terminal. MSA showed amino acid replacements, which might be due to nucleotide substitution during replication. Phylogenetic analysis revealed the F-box proteins with similar domains to be clustered together while some were spread out in different clades, might be due to functional diversity. The clustering of GG705409 and TaAFB4/TaAFB5 in a single clade suggested the possibilities of horizontal gene transfer during the coevolution between Pucciniaand wheat. Gene ontological annotation categorized them into three classes and were functionally involved in protein degradation through the protein ubiquitination pathway. Protein-protein interaction network revealed F-box proteins to interact with other components of SCF complex involved in protein ubiquitination. Relative expression analysis of ve F-box genes in a time course experiment denoted their role in pathogenicity in leaf rust susceptible wheat plants.Conclusion-This study provides information on structure elucidation of F-box proteins of a basidiomycetes plant pathogenic fungi and their role during pathogenesis. A total of 10 F-box genes were predicted in Puccinia triticina genome sequences that revealed conserved phylogenetic relationship among different Pucciniaspecies. Expression analysis imparted their role in pathogenicity.

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Insights of Lr28 mediated wheat leaf rust resistance: Transcriptomic approach

Cited by 27 publications

References 74 publications

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

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

Genome-Wide Expression Profiling of Genes Associated with the Lr47-Mediated Wheat Resistance to Leaf Rust (Puccinia triticina)

The F-box protein encoding genes of the leaf-rust fungi Puccinia triticina: genome-wide identification, characterization and expression dynamics during pathogenesis

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