Tropical Plant Biology

, Volume 12, Issue 4, pp 318–335 | Cite as

Identification and Validation of Leaf Rust Responsive Wheat isomiRs and their Target Genes in both Wheat and Puccinia triticina

  • Summi Dutta
  • Manish Kumar
  • Kunal MukhopadhyayEmail author


MicroRNAs as regulators of gene expression have been known for over a decade and have been correlated with various types of abiotic and biotic stresses. IsomiRs are modified forms of typical miRNAs altered by one or few nucleotides as a result of post transcriptional modifications of miRNAs at terminals or SNPs containing miRNA sequences producing 5′/3′ isomiRs or SNP_isomiRs. These isoforms function exactly like miRNAs, but sometimes alter the target gene preference particularly when they differ in sequences within seed region. Existence of isomiRs was considered earlier as errors in sequencing techniques due to unavailability of proper detection tools. Bread wheat is the most cultivated cereal crop globally with a strong hold on world’s economy. Wheat production is frequently affected by rust diseases. Leaf rust, caused by Puccinia triticina, severely affects grain filling. Four small RNA libraries were prepared from leaves of two wheat Near Isogenic Lines, HD2329 (susceptible) and HD2329 + Lr24 (resistant) both under mock- and pathogen-inoculated conditions and sequenced using Illumina NGS. Several novel miRNAs were detected from these sequences. The present study focuses on identification of isomiRs derived from these miRNAs and their target genes. In total, 66 and 38 unique 5′ and 3′ isomiRs respectively were identified from 37 miRNAs. IsomiRs targeted genes with functions like amino acid metabolism, replication, transport, chelation of reactive oxygen species in wheat while genes with SunT and Structural Maintenance of Chromosome domain of Puccinia. This study will provide a basis for exploitation of isomiRs for genetic improvements in wheat.


isomiR Leaf rust miRNA modifications SNP_isomiR Triticum aestivum



The authors are thankful to BTISNet SubDIC (BT/BI/04/065/04) for providing bioinformatics facilities. SD acknowledges Innovation in Science Pursuit for Inspired Research (INSPIRE), Government of India, Ministry of Science and Technology, New Delhi [IF140725] for fellowship. We also thank Dr. Dhananjay Kumar for preparation of small RNA libraries.

Author contribution statement

KM conceived and designed the research, MK supervised the research. SD executed the research. SD, MK and KM wrote the manuscript. All authors read and approved the manuscript.

Compliance with Ethical Standards

Conflict of Interest

The authors have declared that no competing interests exist.

Supplementary material

12042_2019_9235_MOESM1_ESM.doc (5.3 mb)
ESM 1 (DOC 5415 kb)


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of Bio-EngineeringBirla Institute of TechnologyRanchiIndia

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