Functional divergence of LncRNAs in wheat-fungal interactions: insights from stem rust-responsive wheat transcriptomes.

Stem rust of wheat, caused by the fungal pathogen Puccinia graminis f. sp. tritici (Pgt), is an economically significant disease affecting wheat production globally. The recent progress in high-throughput sequencing technology has uncovered the crucial role of non-coding RNAs, an emerging yet influential regulatory genetic element modulating plant response against abiotic and biotic stresses. Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) are prominent regulatory nRNAs, renowned for their ability to finely tune plant gene expression across transcriptional, post-transcriptional, and epigenetic layers. The current study adopts a comprehensive transcriptome sequencing approach to identify stem rust-responsive lncRNAs from near isogenic lines of wheat introgressed with resistance gene Sr36, along with their susceptible variety, HD2329. A meticulous lncRNA selection criterion yielded a total of 948 Pgt-responsive lncRNAs. The detection of 11 lncRNAs acting as miRNA precursors, along with 590 miRNA-lncRNA target interactions further highlights the dynamic interplay between miRNAs and lncRNAs during Pgt infection in wheat. Moreover, the functional annotation of lncRNA targets unveiled the prevalence of genes such as LRR receptor-like serine/threonine-protein kinases, disease resistance protein RPM1-like, chitin elicitor receptor kinase, nudix hydrolases and NAC transcription factors, that are involved in discrete biological pathways crucial for plant stress responses. Detection of 37 SSR marker-bearing lncRNAs along with the interaction of lncRNAs with disease-associated transcription factors such as C2H2, ERF, GATA and Dof, further elevate the significance of the study. The study unveils potential functional divergence within lncRNAs and serves as a fine resource that can be harnessed to elucidate the interplay of coding and non-coding RNAs governing wheat-fungal interactions. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12298-025-01599-x.