Integrated small RNA and Degradome sequencing provide insights into salt tolerance in sesame ( Sesamum indicum L.)

MicroRNAs (miRNAs) exhibit important regulatory roles in the response to abiotic stresses by post-transcriptionally regulating the target gene expression in plants. However, their functions in sesame response to salt stress are poorly known. To dissect the complex mechanisms underlying salt stress response in sesame, miRNAs and their targets were identified from two contrasting sesame genotypes by a combined analysis of small RNAs and degradome sequencing. A total of 351 previously known and 91 novel miRNAs were identified from 18 sesame libraries. Comparison of miRNA expressions between salt-treated and control groups revealed that 116 miRNAs were involved in salt stress response. Using degradome sequencing, potential target genes for some miRNAs were also identified. The combined analysis of all the differentially expressed miRNAs and their targets identified miRNA–mRNA regulatory networks and 21 miRNA–mRNA interaction pairs that exhibited contrasting expressions in sesame under salt stress. This comprehensive integrated analysis may provide new insights into the genetic regulation mechanism of miRNAs underlying the adaptation of sesame to salt stress.