Dipartimento di Scienze Agrarie Alimentari Forestali, Università di Palermo, viale delle scienze Ed. 4., Palermo, Italy.
Institute of Plant Sciences, Altenbergrain 21, University of Bern, Bern, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland.
J Plant Physiol. 2018 May-Jun;224-225:163-172. doi: 10.1016/j.jplph.2018.02.011. Epub 2018 Mar 29.
Tef [Eragrostis tef (Zucc.) Trotter], a staple food crop in the Horn of Africa and particularly in Ethiopia, has several beneficial agronomical and nutritional properties, including waterlogging and drought tolerance. In this study, we performed microRNA profiling of tef using the Illumina HiSeq 2500 platform, analyzing both shoots and roots of two tef genotypes, one drought-tolerant (Tsedey) and one drought-susceptible (Alba). We obtained more than 10 million filtered reads for each of the 24 sequenced small cDNA libraries. Reads mapping to known miRNAs were more abundant in the root than shoot tissues. Thirteen and 35 miRNAs were significantly modulated in response to drought, in Alba and Tsedey roots, respectively. One miRNA was upregulated under drought conditions in both genotypes. In shoots, nine miRNAs were modulated in common between the two genotypes and all showed similar trends of expression. One-hundred and forty-seven new miRNA mature sequences were identified in silico, 22 of these were detected in all relevant samples and seven were differentially regulated when comparing drought with normal watering. Putative targets of the miRNA regulated under drought in root and shoot tissues were predicted. Among the targets were transcription factors such as CCAAT-HAP2, MADS and NAC. Verification with qRT-PCR revealed that five of six potential targets showed a pattern of expression that was consistent with the correspondent miRNA amount measured by RNA-Seq. In general, candidate miRNAs involved in the post-transcriptional regulation of the tef response to drought could be included in next-generation breeding programs.
埃塞俄比亚画眉草（Eragrostis tef (Zucc.) Trotter）是非洲之角，尤其是埃塞俄比亚的主食作物，具有许多有益的农艺和营养特性，包括耐涝和耐旱性。在这项研究中，我们使用 Illumina HiSeq 2500 平台对画眉草进行了 microRNA 分析，分析了两个画眉草基因型（耐旱型（Tsedey）和耐旱型（Alba））的地上部和根部。我们为 24 个测序的小 cDNA 文库中的每一个获得了超过 1000 万个过滤后的读数。映射到已知 miRNA 的读数在根部组织中比在地上部组织中更为丰富。干旱胁迫分别导致 Alba 和 Tsedey 根部中 13 个和 35 个 miRNA 显著调节。一个 miRNA 在两个基因型下的干旱条件下均上调。在地上部，两个基因型之间有 9 个 miRNA 共同调节，并且所有 miRNA 的表达趋势都相似。通过计算机鉴定了 147 个新的 miRNA 成熟序列，其中 22 个在所有相关样本中均被检测到，而在比较干旱和正常浇水时，有 7 个被差异调节。预测了 miRNA 在根和地上部组织中受干旱调节的靶基因。在靶基因中，有转录因子如 CCAAT-HAP2、MADS 和 NAC。qRT-PCR 验证显示，六个潜在靶基因中的五个显示出与 RNA-Seq 测量的相应 miRNA 丰度一致的表达模式。总体而言，参与画眉草对干旱响应的转录后调控的候选 miRNA 可以包含在下一代的育种计划中。
