Identification of microRNAs responding to salt stress in barley by high-throughput sequencing and degradome analysis

Abstract

A deep understanding of the mechanisms underlying salt tolerance should be helpful for breeding of salt-tolerant crop cultivars. Our previous study identified some wild barley accessions with high salt tolerance. In this study, small RNA and degradome sequencing was performed to identify salt-responsive microRNAs (miRNAs) and their target genes in a Tibetan wild barley accession XZ16 and a cultivar Golden Promise (GP), differing in salt tolerance. Under salt stress, XZ16 showed higher salt tolerance than GP in terms of biomass and shoot Na+ accumulation. A total of 278 and 320 miRNAs were found in roots and shoots of both genotypes, respectively. Among them, 40 and 51 miRNAs were salt-responsive in roots and shoots, respectively. In roots, miR156d, miR164a, miR393a, miR319a and miR172b targeting UGTs, NAC079, HvAFB2/HvTIR1, TCP4 and HvAP2, respectively, are probably responsible for salt tolerance. In shoots, miR159a, miR169i, miR319a/miR396e module and miR172b regulating MYB33, NHX1/LEA7, TCP4, GRFs and HvAP2, respectively, might contribute to salt tolerance. Compared with GP, XZ16 showed differential expression of miR156d, miR164a, miR169i, miR172b, miR319a, miR393a and a novel miRNA PC-miR124. We proposed that these differentially expressed miRNAs could account for the difference in salt tolerance of the two genotypes and drawn up a putative regulatory network of miRNAs to reveal molecular mechanisms of salt tolerance in barley.