Non-coding RNA levels integrating analysis revealed the salt and drought stress response mechanism of miR395e-PvUXS1 pathway in switchgrass.

Soil salinization and drought are major constraints on global agricultural production, yet the shared molecular mechanisms by which forage crops respond to these stresses remain incompletedly understood. Identifying candidate genes with potential value for stress-resilient breeding is therefore an important research objective. Switchgrass (Panicum virgatum L.) is a perennial forage and bioenergy crop with adaptation to saline, semi-arid, and drought-prone environments. In this study, RNA sequencing was used to investate the responses of switchgrass to two salt-stress conditions (300mM NaCl treatment and 10‰ soil salinity). Differentially expressed (DE) mRNAs shared by the two salt-stress conditions were significantly enriched in pathways related to carbon metabolism and carbon fixation in photosynthetic organisms. Whole-transcriptome RNA sequencing further identified DE mRNAs, microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) associated with salt and drought responses. Competing endogenous RNA (ceRNA) network analysis identified four KEGG pathways commonly enriched under salt and drought stress: photosynthesis, circadian rhythm in plants, ribosome biogenesis in eukaryotes, and aminoacyl-tRNA biosynthesis. Notably, the UDP-glucuronic acid decarboxylase gene PvUXS1 (Pavir.5NG221800) involved in amino sugar and nucleotide sugar metabolism, was identified as target of miR395e. Salt and drought stress reduced miR395e expression while increasing PvUXS1 expression, and further validation showed that miR395e negatively regulates PvUXS1. Together, these results identify a previously uncharacterized miR395e-PvUXS1 regulatory pathway and provide a potential molecular target for improving stress tolerance in switchgrass.