Summary of Signatures that Match Various RNAs.

<p>Summary of Signatures that Match Various RNAs.</p

Genome-Wide Identification and Characterization of microRNAs in Developing Grains of <i>Zea mays</i> L.

<div><p>The development and maturation of maize kernel involves meticulous and fine gene regulation at transcriptional and post-transcriptional levels, and miRNAs play important roles during this process. Although a number of miRNAs have been identified in maize seed, the ones involved in the early development of grains and in different lines of maize have not been well studied. Here, we profiled four small RNA libraries, each constructed from groups of immature grains of <i>Zea mays</i> inbred line Chang 7–2 collected 4–6, 7–9, 12–14, and 18–23 days after pollination (DAP). A total of 40 known (containing 111 unique miRNAs) and 162 novel (containing 196 unique miRNA candidates) miRNA families were identified. For conserved and novel miRNAs with over 100 total reads, 44% had higher accumulation before the 9^th DAP, especially miR166 family members. 42% of miRNAs had highest accumulation during 12–14 DAP (which is the transition stage from embryogenesis to nutrient storage). Only 14% of miRNAs had higher expression 18–23 DAP. Prediction of potential targets of all miRNAs showed that 165 miRNA families had 377 target genes. For miR164 and miR166, we showed that the transcriptional levels of their target genes were significantly decreased when co-expressed with their cognate miRNA precursors <i>in vivo</i>. Further analysis shows miR159, miR164, miR166, miR171, miR390, miR399, and miR529 families have putative roles in the embryogenesis of maize grain development by participating in transcriptional regulation and morphogenesis, while miR167 and miR528 families participate in metabolism process and stress response during nutrient storage. Our study is the first to present an integrated dynamic expression pattern of miRNAs during maize kernel formation and maturation.</p></div

Relative expression levels of 14 miRNAs and their target genes at four time points during maize seed development.

<p><i>U6</i> and <i>TUBULIN</i> were used as internal controls for miRNAs and target genes, respectively. DAP: days after pollination. Maize miRNAs are indicated by dark gray bars; target genes are indicated by light gray bars.</p

Coexpression of miRNA precursors and their target genes in a transient expression system in <i>N</i>. <i>benthamiana</i> cells.

<p>(A) Relative expression levels of NAM gene coexpressed with miR164 precursor in <i>N</i>. <i>benthamiana</i>. (B) Relative expression levels of unknown gene coexpressed with miR166 precursor in <i>N</i>. <i>benthamiana</i>. Target genes were also coexpressed with an unrelated <i>GFP</i> construct as a control. Tobacco 18s rRNA was used as an internal control for normalization.</p

Expression Pattern of Known miRNAs in Maize Grain Development.

<p>Expression Pattern of Known miRNAs in Maize Grain Development.</p

Northern blot analysis of selected maize miRNAs.

<p><b>Maize</b><i>U6</i> RNA was used as an internal control. DAP: days after pollination.</p