Unknown,Transcriptomics,Genomics,Proteomics

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Identification and Characterization of Maize MicroRNAs Involved in the Very Early Stage of Seed Germination

ABSTRACT: In this study, a small RNA library from maize seed 24 hours after imbibition was sequenced by the Solexa technology. A total of 11,338,273 reads were obtained. 1,047,447 total reads representing 431 unique sRNAs matched to known maize miRNAs. Further analysis confirmed the authenticity of 115 known miRNAs belonging to 24 miRNA families and the discovery of 167 novel miRNAs in maize. Both the known and the novel miRNAs were confirmed by sequencing of a second small RNA library constructed the same way as the one used in the first sequencing. We also found 10 miRNAs that had not been reported in maize, but had been reported in other plant species. All novel sequences had not been earlier described in other plant species. In addition, seven miRNA* sequences were also obtained. Putative targets for 106 novel miRNAs were successfully predicted. Our results indicated that miRNA-mediated gene expression regulation is present in maize imbibed seed. This study led to the confirmation of the authenticity of 115 known miRNAs and the discovery of 167 novel miRNAs in maize. Identification of novel miRNAs resulted in significant enrichment of the repertoire of maize miRNAs and provided insights into miRNA regulation of genes expressed in imbibed seed. Discovery of novel miRNAs involved in imbibed maize seed by deep sequencing 2 independent small RNA libraries

ORGANISM(S): Zea mays

SUBMITTER: Huabang Chen

PROVIDER: E-GEOD-27664 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:In plants, MicroRNAs (miRNAs) are a new class of endogenous small RNAs that play essential regulatory roles in plant growth, development and stress response. Extensive studies of miRNAs have been performed in model plants such as rice, Arabidopsis thaliana and other plants. However, the number of miRNAs discovered in maize is relatively low and little is known about miRNAs involved in the four stages during maize ear development. Here, we use deep-sequencing, miRNA microarray assays and computational methods to identify, proM-oM-,M-^Ale, and describe conserved and non-conserved miRNAs at four developmental stages. A total of 27 conserved miRNA families were identiM-oM-,M-^Aed in all four stages, In addition to known miRNAs, we also found 23 new maize-specific miRNAs together with their star strands. We have also shown that almost all of them originated from single genes. We have found that many known and new miRNAs showed temporally expression. Finally, a total of 251 transcripts (140 genes) targeted by 102 small RNAs including 98 miRNAs and 4 ta-siRNAs were identified by genomic-scale high-throughput sequencing of miRNA cleaved mRNAs.This study led to the confirmation of the authenticity of 27 conserved miRNA families and the discovery of 23 novel miRNAs in maize. In addition, we have identified 130 targets of known and new miRNAs and ta-siRNA using recently developed tools for the global identification of miRNA targets. Identification and characterization of this important class of regulatory genes in maize may improve our understanding of molecular mechanism controlling flower development. The seeds of maize inbred line B73 were first sterilized and germinated in an incubator, then grown in a controlled environment with 28M-BM-0C/21M-BM-0C (day/night) under a 16-h day/8-h night photoperiod with a relative humidity of 70%. Ear development can be divided into four stages: the growth point elongation phase, spikelet differentiation phase, the floret primordium differentiation phase and floret organ differentiation phase. Plant materials (ears) were collected as described previously. In brief, ears were manually collected at the four developmental stages according to the plant features (number of visible leaves, leaf age index, and number of unfolded and folded leaves) combined with microscopic observation.

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Identification and Characterization of Maize MicroRNAs Involved in the Very Early Stage of Seed Germination

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