Identification and Profiling of microRNAs and Their Target Genes in Tibetan Hulless Barley in Response to Barley Leaf Stripe (BLS) Infection

Background Tibetan hulless barley is widely grown on the Qinghai-Tibet Plateau, where it has served as a staple food for Tibetan people since the 5th century CE. Barley leaf stripe (BLS) is one of the most severe fungal diseases affecting the yield and quality of Tibetan hulless barley. Results Here, we compared the miRNA profiles before and after BLS in two Tibetan hulless barley genotypes: Z1141, a BLS-sensitive wild variety, and Kunlun14, a BLS-tolerant hybrid variety. A total of 36 conserved and 56 novel miRNAs were identified. Of these, 10 conserved and 10 novel miRNAs exhibited significantly changed expression between the normal and infected leaves of Kunlun14, respectively, while 3 conserved and 5 novel miRNAs exhibited significantly changed expression between the normal and infected leaves of Z1141, respectively. A total of 24 miRNAs were found in Z1141 and Kunlun14, and a further 546 putative target genes were predicted. Transcriptome sequencing analysis showed that among the 546 candidate genes, 131 had significant differences in expression between the normal and infected leaves of Kunlun14 and Z1141. Gene ontology, pathway, and Blast analyses indicated 10 candidate target genes that were involved in the barley disease resistance. These 10 candidate target genes may be regulated by 7 miRNAs. According to quantitative real-time PCR results, the 10 targets were negatively correlated with their corresponding miRNAs after infection with BLS. Conclusions The miRNAs and their target genes expressed in Tibetan hulless barley were identified and found to be associated with BLS resistance. Thus, these miRNAs and their target genes may be exploited via breeding programs or genetic engineering to improve BLS resistance in Tibetan hulless barley.