A study of miRNAs and lncRNAs during Lr28-mediated resistance against leaf rust in wheat (Triticum aestivum L.)

Jain, Neelu; Sinha, Nivedita; Krishna, Hari; Singh, Pradeep Kumar; Gautam, Tinku; Prasad, Pramod; Balyan, H. S.; Gupta, P. K.

doi:10.1016/j.pmpp.2020.101552

Cited by 23 publications

(14 citation statements)

References 118 publications

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“…A number of expression studies for wheat-rust pathosystem in the past suggested that the host rapidly and precisely re-program a large number of downstream signalling and defense genes for providing partial durable resistance against a broad range of fungal pathogens ,9,10,11,12,13 . This reprogramming may also involve epigenetic modi cations as shown in our own studies involving epigenetic modi cations (methylation, chromatin modi cation and ncRNA) of some downstream defense genes involved in leaf rust resistance mediated by race-speci c gene Lr28 and APR gene Lr48 12,13,14,15,16 . Among epigenetic modi cations, DNA methylation has received maximum attention, and has been shown to be involved in regulation of expression of genes involved in a variety of cellular processes, which control development and stress responses 18 .…”

Section: Introductionmentioning

confidence: 79%

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Pathogen-induced alterations in methylome during Lr48-mediated APR in wheat (Triticum aestivum L.) 

Jain¹,

Batra²,

Saripalli³

et al. 2021

Preprint

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Differential DNA methylation due to APR gene Lr48 for leaf rust resistance in wheat cv. CSP44 was examined at pre-adult plant (P-AP) susceptible stage and adult plant (AP) resistant stage. As many as 52,872 differentially methylated regions (DMRs) carrying 897 differentially methylated genes (DMGs) and many intergenic regions were identified. DMGs included exons/introns, promoters and UTRs. Little less than half of DMGs, were also compared with transcriptome data based on RNA-sEq. Susceptibility (at P-AP) was found to be governed by activation (due to hypomethylation) of relatively more genes, whereas resistance (at AP) involved silencing of relatively large number of genes. Using GO terms, DMGs were found to belong to a variety of biological processes including transcription regulation, protein synthesis, signal transduction, defense, photosynthesis, lipid and carbohydrate metabolism. The results of the present study improved our understanding of the epigenetic control of leaf rust APR in wheat.

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Section: Introductionmentioning

confidence: 79%

“…Maximum number of DMGs, which matched DEGs was observed in treatment pair R0 vs R96 (311 = 306 + 4 + 1) followed by S96 vs R96 (15), R0 vs R96 (14) and S0 vs R0 (11) ( Table 5).…”

Section: A Comparison Of Dmgs With Degsmentioning

confidence: 96%

Pathogen-induced alterations in methylome during Lr48-mediated APR in wheat (Triticum aestivum L.) 

Jain¹,

Batra²,

Saripalli³

et al. 2021

Preprint

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“…Both Sr36 and Lr45 introgression undoubtedly produced huge change in miRNA repertoire compared to their parental line HD2329. In a study by Jain et al, 2020, the differential miRNA and long non-coding RNA (lncRNA) expression were presented from HD2329 cultivar and its NIL of Lr28 [53]. Similarly, differential miRNA expression between HD2329 and its NIL with Lr24 was studied earlier [24].…”

Section: Discussionmentioning

confidence: 99%

Wheat sRNA transcriptome reveals R-gene associated distinct temporal miRNA profiles in response to stem rust and leaf rust diseases

Nair

Kumar

Jyothsna

et al. 2021

Preprint

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Wheat rusts, the dreadful fungal diseases caused by members of the Puccinia genus remain as a major threat to global wheat production and food security. The R-gene mediated resistance has been employed as an efficient approach to develop rust resistant varieties. However, evolution of new fungal races and infection strategies put forward the urgency of unravelling novel genomics assisted molecular players, including non-coding RNAs for rust disease management. MicroRNAs are crucial regulators of genes associated with plant growth, development, abiotic and biotic stress responses. In this study, high throughput small RNA sequencing was performed on susceptible and resistant wheat near-isogenic lines inoculated with stem rust and leaf rust, together with mock inoculated controls. While miRNA mining in stem rust inoculated libraries revealed a total of twenty-six known and seven novel miRNAs, the search in leaf rust libraries culminated with twenty-two known and four novel miRNAs. The identified candidate miRNAs constituted both guide and passenger miRNA strands along with their isomiRs. Temporal expression pattern of differentially expressed miRNAs pinpoints their possible role during the progress of infection. Comparative analysis provides a better understanding of altered miRNA profiles associated with Sr36 and Lr45 disease resistance genes in response to stem rust and leaf rust, respectively. Also, the disclosure of guide strand, passenger strand and a variant of novel-Tae-miR02 with various sub-genomal origins might serve as an important common link between stem rust and leaf rust defense mechanisms downstream to the respective R-genes. Further, cis-regulatory elements that modulate MIR genes, targets of identified miRNAs related to various signal transduction pathways, and miR-SSRs which might be useful for rust disease control, are the emphasized attributes of our results. The outcome from this simultaneous study of miRNA profiles among two rust diseases and further characterization of the identified miRNAs can contribute to the expanding rust disease management programs.

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“…Transcriptional regulation during wheat–fungi interaction can also be mediated by lncRNAs [ 151 , 152 , 153 , 154 ]. This group of non-coding RNAs exceed 200 nt in length and do not contain the significant open reading frame (ORF).…”

Section: Molecular Interaction Between Endophytic Fungi and Wheatmentioning

confidence: 99%

Fungi Inhabiting the Wheat Endosphere

2021

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Wheat production is influenced by changing environmental conditions, including climatic conditions, which results in the changing composition of microorganisms interacting with this cereal. The group of these microorganisms includes not only endophytic fungi associated with the wheat endosphere, both pathogenic and symbiotic, but also those with yet unrecognized functions and consequences for wheat. This paper reviews the literature in the context of the general characteristics of endophytic fungi inhabiting the internal tissues of wheat. In addition, the importance of epigenetic regulation in wheat–fungus interactions is recognized and the current state of knowledge is demonstrated. The possibilities of using symbiotic endophytic fungi in modern agronomy and wheat cultivation are also proposed. The fact that the current understanding of fungal endophytes in wheat is based on a rather small set of experimental conditions, including wheat genotypes, plant organs, plant tissues, plant development stage, or environmental conditions, is recognized. In addition, most of the research to date has been based on culture-dependent methods that exclude biotrophic and slow-growing species and favor the detection of fast-growing fungi. Additionally, only a few reports of studies on the entire wheat microbiome using high-throughput sequencing techniques exist. Conducting comprehensive research on the mycobiome of the endosphere of wheat, mainly in the context of the possibility of using this knowledge to improve the methods of wheat management, mainly the productivity and health of this cereal, is needed.

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A study of miRNAs and lncRNAs during Lr28-mediated resistance against leaf rust in wheat (Triticum aestivum L.)

Cited by 23 publications

References 118 publications

Pathogen-induced alterations in methylome during Lr48-mediated APR in wheat (Triticum aestivum L.)

Pathogen-induced alterations in methylome during Lr48-mediated APR in wheat (Triticum aestivum L.)

Wheat sRNA transcriptome reveals R-gene associated distinct temporal miRNA profiles in response to stem rust and leaf rust diseases

Fungi Inhabiting the Wheat Endosphere

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A study of miRNAs and lncRNAs during Lr28-mediated resistance against leaf rust in wheat (Triticum aestivum L.)

Cited by 23 publications

References 118 publications

Pathogen-induced alterations in methylome during Lr48-mediated APR in wheat (Triticum aestivum L.)&nbsp;

Pathogen-induced alterations in methylome during Lr48-mediated APR in wheat (Triticum aestivum L.)&nbsp;

Wheat sRNA transcriptome reveals R-gene associated distinct temporal miRNA profiles in response to stem rust and leaf rust diseases

Fungi Inhabiting the Wheat Endosphere

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Pathogen-induced alterations in methylome during Lr48-mediated APR in wheat (Triticum aestivum L.)

Pathogen-induced alterations in methylome during Lr48-mediated APR in wheat (Triticum aestivum L.)