Integrated analyses of miRNAome and transcriptome reveal zinc deficiency responses in rice seedlings

Background: Zinc (Zn) deficiency is one of the most widespread soil constraints affecting rice productivity, but the molecular mechanisms underlying the regulation of Zn deficiency response is still limited. Here, we aim to understand the molecular mechanisms of Zn deficiency response by integrating the analyses of the global miRNA and mRNA expression profiles under Zn deficiency and resupply in rice seedlings by integrating Illumina's high-throughput small RNA sequencing and transcriptome sequencing. Results: The transcriptome sequencing identified 360 genes that were differentially expressed in the shoots and roots of Zn-deficient rice seedlings, and 97 of them were recovered after Zn resupply. A total of 68 miRNAs were identified to be differentially expressed under Zn deficiency and/or Zn resupply. The integrated analyses of miRNAome and transcriptome data showed that 12 differentially expressed genes are the potential target genes of 10 Zn-responsive miRNAs such as miR171g-5p, miR397b-5p, miR398a-5p and miR528-5p. Some miRNA genes and differentially expressed genes were selected for validation by quantitative RT-PCR, and their expressions were similar to that of the sequencing results. Conclusion: These results provide insights into miRNA-mediated regulatory pathways in Zn deficiency response, and provide candidate genes for genetic improvement of Zn deficiency tolerance in rice.