Next-generation sequencing and micro RNAs analysis reveal SA/MeJA1/ABA pathway genes mediated systemic acquired resistance (SAR) and its master regulation via production of phased, trans-acting siRNAs against stem rot pathogen Macrophomina phaseolina in a

•A RIL population of jute was developed for resistance to Macrophomina phaseolina.•A number of defense genes involved in the defense-response were identified.•Major defense genes belonged to ROS, SA, ethylene, JA, ABA, HR and PCD pathways.•Study revealed that Trans-acting siRNAs negatively regulate the target transcripts.

A RIL population of jute was developed by crossing one resistant accession CIM 036 and a susceptible variety JRC 412. Two cDNA libraries were constructed using pool of mRNA from healthy as well as infected seedlings from all the 177 RIL lines. A significant number of defense genes involved in the defense-response were identified viz. cell wall biosynthesis, reactive oxygen species (ROS), salicylic acid (SA), ethylene, jasmonic acid (JA), abscissic acid (ABA), hormone signaling, hypersensitive response (HR) and programmed cell death (PCD) pathways. Furthermore, microRNA analysis revealed that Trans-acting siRNAs (tasiRNAs) negatively regulate these target transcripts and are characterized by siRNAs spaced in 21-nucleotide (nt) “phased” intervals. We identified highly abundant 22-nt miRNA families that target conserved domains in these SA/JA/ABA precursors and trigger the production of trans-acting siRNAs. SA and JA1 transcripts were found to be cleaved by these 22-nt miRNA generating phasiRNA, suggesting silencing pathogenicity pathway of Macrophomina phaseolina. Gene function annotation was studied in jute-M. phaseolina interaction in each of the 177 lines of a RIL population. tasiRNA based SAR regulation demonstrated master regulator of a large gene family. It is the first report of studying resistance mechanism in jute against M. phaseolina in a RIL population through transcript and miRNA analysis.