Plant Biotechnology Institute, National Research Council of Canada, 110 Gymnasium Place, Saskatoon S7N 0W9, Canada.
BMC Genomics. 2013 Feb 28;14:140. doi: 10.1186/1471-2164-14-140.
MicroRNAs (miRNAs) are 20-21 nucleotide RNA molecules that suppress the transcription of target genes and may also inhibit translation. Despite the thousands of miRNAs identified and validated in numerous plant species, only small numbers have been identified from the oilseed crop plant Brassica napus (canola) - especially in seeds.
Using next-generation sequencing technologies, we performed a comprehensive analysis of miRNAs during seed maturation at 9 time points from 10 days after flowering (DAF) to 50 DAF using whole seeds and included separate analyses of radicle, hypocotyl, cotyledon, embryo, endosperm and seed coat tissues at 4 selected time points. We identified more than 500 conserved miRNA or variant unique sequences with >300 sequence reads and also found 10 novel miRNAs. Only 27 of the conserved miRNA sequences had been previously identified in B. napus (miRBase Release 18). More than 180 MIRNA loci were identified/annotated using the B. rapa genome as a surrogate for the B.napus A genome. Numerous miRNAs were expressed in a stage- or tissue-specific manner suggesting that they have specific functions related to the fine tuning of transcript abundance during seed development. miRNA targets in B. napus were predicted and their expression patterns profiled using microarray analyses. Global correlation analysis of the expression patterns of miRNAs and their targets revealed complex miRNA-target gene regulatory networks during seed development. The miR156 family was the most abundant and the majority of the family members were primarily expressed in the embryo.
Large numbers of miRNAs with diverse expression patterns, multiple-targeting and co-targeting of many miRNAs, and complex relationships between expression of miRNAs and targets were identified in this study. Several key miRNA-target expression patterns were identified and new roles of miRNAs in regulating seed development are suggested. miR156, miR159, miR172, miR167, miR158 and miR166 are the major contributors to the network controlling seed development and maturation through their pivotal roles in plant development. miR156 may regulate the developmental transition to germination.
microRNAs (miRNAs) 是 20-21 个核苷酸的 RNA 分子，可抑制靶基因的转录，也可能抑制翻译。尽管在许多植物物种中已经鉴定和验证了数千种 miRNAs，但在油料作物油菜（油菜）中只鉴定出了少数几种 - 尤其是在种子中。
使用下一代测序技术，我们在开花后 10 天（DAF）至 50 DAF 的 9 个时间点，使用全种子对种子成熟过程中的 miRNAs 进行了全面分析，并在 4 个选定时间点对胚根、下胚轴、子叶、胚、胚乳和种皮组织进行了单独分析。我们鉴定了超过 500 个具有 >300 个序列读数的保守 miRNA 或变体独特序列，还发现了 10 个新的 miRNAs。在油菜中，只有 27 个保守 miRNA 序列之前已经被鉴定（miRBase Release 18）。使用油菜的 Brassica rapa 基因组作为替代物，鉴定/注释了超过 180 个 MIRNA 基因座。许多 miRNAs 以阶段或组织特异性的方式表达，表明它们具有与种子发育过程中转录物丰度的精细调节相关的特定功能。使用微阵列分析预测了油菜中的 miRNA 靶标，并对其表达模式进行了分析。miRNA 和它们的靶标的表达模式的全局相关性分析揭示了种子发育过程中复杂的 miRNA-靶基因调控网络。miR156 家族是最丰富的，大多数家族成员主要在胚胎中表达。
在这项研究中，鉴定了大量具有不同表达模式的 miRNAs，许多 miRNAs 具有多靶向和共靶向作用，miRNAs 和靶标之间的表达关系复杂。鉴定了几个关键的 miRNA-靶标表达模式，并提出了 miRNAs 在调节种子发育中的新作用。miR156、miR159、miR172、miR167、miR158 和 miR166 是通过在植物发育中的关键作用控制种子发育和成熟的网络的主要贡献者。miR156 可能通过调节发育过渡到萌发来调节发育。
