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

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.