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

Abstract Wheat (Triticum aestivum L.) is a major crop, which is widely grown, occupying globally an area of ∼215 million hectares. The crop suffers major losses due to leaf rust caused by fungal pathogen, Puccinia triticina Eriks. and E. Henn.. When wheat plants are attacked by this fungus, hundreds of downstream genes involved in signal transduction pathways experience regulated expression. This regulation partly depends on non-coding RNAs (ncRNAs) including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). In the present study, miRNAs and lncRNAs associated with wheat-leaf rust pathosystem were identified using RNA-seq data for a pair of near-isogenic lines (NILs), which differed for the gene Lr28 in the background of wheat cultivar HD2329. The study is a continuation of our earlier transcriptome study involving the same pathosystem. A total of 50 miRNAs and 1178 lncRNAs were identified through in silico analysis of RNA-seq data; of these, 16 miRNAs and 22 lncRNAs were differentially expressed (DE). Expression of as many as 8 miRNAs was induced in resistant NIL (expression of remaining DE miRNAs induced in susceptible NIL); these DE miRNAs targeted several important genes, which include disease responsive genes. As many as 49 lncRNAs were found to be the targets for miRNAs; among these, one lncRNA functioned as a precursor of two mature miRNAs, and three lncRNAs acted as target mimics (TMs, which mimic and therefore compete with the mRNA targets for miRNA) thus regulating the expression of target genes. The results were also validated using qRT-PCR analyses. Taken together, the leaf rust responsive miRNAs, their targets along with putative TMs, and the lncRNAs, identified in the present study, should improve our understanding about the role of non-coding RNAs during response to leaf rust in wheat.