Identification and Validation of Leaf Rust Responsive Wheat isomiRs and their Target Genes in both Wheat and Puccinia triticina
- 486 Downloads
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.
KeywordsisomiR Leaf rust miRNA modifications SNP_isomiR Triticum aestivum L
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.
- Baev V, Milev I, Naydenov M, Vachev T, Apostolova E, Mehterov N, Gozmanva M, Minkov G, Sablok G, Yahubyan G (2014) Insight into small RNA abundance and expression in high-and low-temperature stress response using deep sequencing in Arabidopsis. Plant Physiol Biochem 84:105-114. PMID: 25261853; https://doi.org/10.1016/j.plaphy.2014.09.007 CrossRefGoogle Scholar
- Dean R, Van Kan JA, Pretorius ZA, Hammond-Kosack KE, Di Pietro A, Spanu PD, Rudd JJ, Dickman M, Kahmann R, Ellis J, Foster GD (2012) The top 10 fungal pathogens in molecular plant pathology. Mol Plant Pathol 13:414–430. PMID: 22471698; https://doi.org/10.1111/j.1364-3703.2011.00783.x CrossRefGoogle Scholar
- Ding G, Che P, Ilarslan H, Wurtele ES, Nikolau BJ (2012) Genetic dissection of methylcrotonyl CoA carboxylase indicates a complex role for mitochondrial leucine catabolism during seed development and germination. Plant J 70:562–577. PMID: 22211474; https://doi.org/10.1111/j.1365-313X.2011.04893.x CrossRefGoogle Scholar
- Dutta S, Kumar D, Jha S, Prabhu KV, Kumar M, Mukhopadhyay K (2017) Identification and molecular characterization of a trans-acting small interfering RNA producing locus regulating leaf rust responsive gene expression in wheat (Triticum aestivum L.). Planta 246:939–957. PMID: 28710588; https://doi.org/10.1007/s00425-017-2744-2 CrossRefGoogle Scholar
- FAOSTAT (2018) FAOSTAT statistical database. http://www.fao.org/india/fao-in-india/india-at-a-glance/en. Accessed Sept. 2018
- Hackenberg M, Huang PJ, Huang CY, Shi BJ, Gustafson P, Langridge P (2012) A comprehensive expression profile of microRNAs and other classes of non-coding small RNAs in barley under phosphorous-deficient and-sufficient conditions. DNA Res 20:109–125. PMID: 23266877; https://doi.org/10.1093/dnares/dss037 CrossRefGoogle Scholar
- International Wheat Genome Sequencing Consortium (IWGSC) (2014) A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 345(6194):1251788Google Scholar
- Jeong DH, Park S, Zhai J, Gurazada SG, De Paoli E, Meyers BC, Green PJ. Massive analysis of rice small RNAs: mechanistic implications of regulated microRNAs and variants for differential target RNA cleavage. Plant Cell 2011; 23: 4185–4207; PMID: 22158467; https://doi.org/10.1105/tpc.111.089045 CrossRefGoogle Scholar
- Jeong DH, Thatcher SR, Brown RS, Zhai J, Park S, Rymarquis LA, Meyers BC, Green PJ (2013) Comprehensive investigation of microRNAs enhanced by analysis of sequence variants, expression patterns, ARGONAUTE loading, and target cleavage. Plant Physiol 162: 1225−1245. PMID: 23709668; https://doi.org/10.1104/pp.113.219873 CrossRefGoogle Scholar
- Kumar D, Dutta S, Singh D, Prabhu KV, Kumar M, Mukhopadhyay K (2017) Uncovering leaf rust responsive miRNAs in wheat (Triticum aestivum L.) using high-throughput sequencing and prediction of their targets through degradome analysis. Planta 245:161–182. PMID: 27699487; https://doi.org/10.1007/s00425-016-2600-9 CrossRefGoogle Scholar
- Liu H, Guo Z, Gu F, Ke S, Sun D, Dong S, Liu W, Huang M, Xiao W, Yang G, Liu Y (2017) 4-coumarate-CoA ligase-like gene OsAAE3 negatively mediates the rice blast resistance, floret development and lignin biosynthesis. Front Plant Sci 7:2041. PMID: 28119718; https://doi.org/10.3389/fpls.2016.02041
- Shahrtash M (2013) Plant glutathione s-transferases function during environmental stresses: a review article. Rom J Biol-Plant Biol 58:19–25Google Scholar
- Shivaprasad PV, Chen HM, Patel K, Bond DM, Santos BA, Baulcombe DC (2012) A microRNA superfamily regulates nucleotide binding site–leucine-rich repeats and other mRNAs. Plant Cell 24:859–874. PMID: 22408077; https://doi.org/10.1105/tpc.111.095380