High‐throughput deep sequencing shows that micro RNA s play important roles in switchgrass responses to drought and salinity stress

Summary Micro RNA s (mi RNA s) are an important class of small regulatory RNA s. The goal of this study was to analyse stress‐responsive mi RNA s in switchgrass ( P anicum virgatum ), the emerging biofuel crop, to facilitate choosing gene targets for improving biomass and biofuel yield. After sequencing three small RNA libraries constructed from control, salt‐ and drought‐treated switchgrass using Illumina sequencing technology, we identified 670 known mi RNA families from a total of more than 50 million short reads. A total of 273 mi RNA s were identified with precursors: 126 conserved mi RNA s and 147 novel mi RNA s. Of them, 265 mi RNA s were found to have their opposite sequences (mi RNA *) with 2‐nt overhang on the 3′ end. Of them, 194 were detected in switchgrass transcriptome sequences generated from 31 high‐throughput RNA sequencing ( RNA ‐Seq) data sets in NCBI . Many mi RNA s were differentially or uniquely expressed during salinity or drought stress treatment. We also discovered 11 mi RNA clusters containing 29 mi RNA s. These identified mi RNA s potentially targeted 28 549 genes with a various function, including transcription factors, stress‐response proteins and cellulose biosynthesis‐related proteins. Gene ontology ( GO ) and K yoto E ncyclopedia of G enes and G enomes ( KEGG ) analysis showed that the identified mi RNA s and their targets were classified to 3779 GO terms including 1534 molecular functions, 1851 biological processes and 394 cellular components and were enriched to 147 KEGG pathways. Interestingly, 195 mi RNA families and 450 targets were involved in the biosynthesis pathways of carbon, glucose, starch, fatty acid and lignin and in xylem formation, which could aid in designing next‐generation switchgrass for biomass and biofuel.