Abstract
Small RNA sequencing (sRNA-seq) and degradome analysis were used for the identification of miRNAs and their target host genes in a pair of near-isogenic lines (NILs), which differed for the presence of leaf rust resistance gene Lr28. The study led to identification of (i) 506 known and 346 novel miRNAs; and (ii) 5054 target genes including 4557 in silico predicted and 497 degradome-based genes using 105 differentially expressed (DE) miRNAs. A subset of 128 targets (67 in silico + 61 degradome-based) was differentially expressed in RNA-seq data that was generated by us earlier using the same pair of NILs; among these 128 targets, 58 target genes exhibited an inverse relationship with the DE miRNAs (expression of miRNAs and activation/suppression of target genes). Eight miRNAs which belonged to the conserved miRNA families and were known to be induced in response to fungal diseases in plants included the following: miR156, miR158, miR159, miR168, miR169, miR172, miR319, miR396. The target genes belonged to the following classes of genes known to be involved in downstream disease resistance pathways; peroxidases, sugar transporters, auxin response signaling, oxidation–reduction, etc. It was also noticed that although a majority of miRNAs and target genes followed the above classical inverse relationship, there were also examples, where no such relationship was observed. Among the target genes, there were also 51 genes that were not only regulated by miRNAs, but were also differentially methylated at sequences including the following segments: promotors, introns, TSS, exons. The results of the present study suggest a complex interplay among miRNA genes, target genes, and various epigenetic controls, which regulate the expression of genes involved in downstream pathways for disease resistance.
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Data availability
The raw sequence reads data that support the findings of this study are available as Sequence Read Archive of NCBI under accession number PRJNA881058.
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Acknowledgements
We are grateful to NASF, ICAR for providing financial assistance for this study (grant no. NASF/ABP-6006/2016-17). The first author acknowledges the valuable guidance received from Dr. K V Prabhu, Chairman, PPVFRA, India, during this study. HSB was awarded positions of INSA Senior Scientist and later INSA Honorary Scientist during the period of the study.
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The study was supported by financial assistance from the National Agriculture Science Fund, ICAR under grant no. NASF/ABP-6006/2016–17.
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NJ, HSB, and PKG conceived and designed research, wrote and finalized the manuscript. AS, NS carried out wet lab experiments and data analyses, HK, PKS carried out the rust phenotyping work, PP maintained and provided inoculum for leaf rust pathotype 77–5. All authors have read and approved the final manuscript.
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Jain, N., Shiv, A., Sinha, N. et al. Leaf rust responsive miRNA and their target genes in wheat. Funct Integr Genomics 23, 14 (2023). https://doi.org/10.1007/s10142-022-00928-7
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DOI: https://doi.org/10.1007/s10142-022-00928-7