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.

中文翻译：

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miRNAome 和转录组的综合分析揭示了水稻幼苗的缺锌反应。

背景锌（Zn）缺乏是影响水稻生产力的最普遍的土壤限制因素之一，但锌缺乏反应调节的分子机制仍然有限。在这里，我们的目标是通过整合 Illumina 的高通量小 RNA 测序和转录组测序，对水稻幼苗缺锌和补给下的全局 miRNA 和 mRNA 表达谱进行分析，以了解缺锌反应的分子机制。结果转录组测序鉴定出360个在缺锌水稻幼苗地上部和根部差异表达的基因，其中97个基因在补锌后恢复。总共 68 个 miRNA 被鉴定出在缺锌和/或补充锌的情况下差异表达。miRNAome和转录组数据的综合分析显示，12个差异表达基因是miR171g-5p、miR397b-5p、miR398a-5p和miR528-5p等10个Zn响应miRNA的潜在靶基因。选择部分miRNA基因和差异表达基因进行定量RT-PCR验证，其表达与测序结果相似。结论这些结果提供了对缺锌反应中miRNA介导的调控途径的见解，并为水稻缺锌耐受性的遗传改良提供了候选基因。