Characterization of microRNAs expression during maize seed development
Ontology highlight
ABSTRACT:
ORGANISM(S): Zea mays
SUBMITTER: Mingming Kang
PROVIDER: E-GEOD-37551 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
Characterization of microRNAs expression during maize seed development.
Kang Mingming M Zhao Qian Q Zhu Dengyun D Yu Jingjuan J
BMC genomics 20120801
<h4>Background</h4>MicroRNAs (miRNAs) are approximately 20-22 nt non-coding RNAs that play key roles in many biological processes in both animals and plants. Although a number of miRNAs were identified in maize, the function of miRNA in seed development was merely discussed.<h4>Results</h4>In this study, two small RNA libraries were sequenced, and a total reads of 9,705,761 and 9,005,563 were generated from developing seeds and growing leaves, respectively. Further analysis identified 125 known ...[more]
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Project description:In this study, two small RNA libraries were sequenced, and a total reads of 9,705,761 and 9,005,563 were generated from developing seeds and growing leaves, respectively. Further analysis identified 125 known miRNAs in seeds and 127 known miRNAs in leaves. 54 novel miRNAs were identified and they were not reported in other plants.
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Project description:The present study profiled and analyzed gene expression of the maize ear at four key developmental stages. Based on genome-wide profile analysis, we detected differential mRNA of maize genes. Some of the differentially expressed genes (DEGs) were predicted to be potential candidates of maize ear development. Several well-known genes were found with reported mutants analyses, such as, compact plant2 (ct2), zea AGAMOUS homolog1 (zag1), bearded ear (bde), and silky1 (si1). MicroRNAs such as microRNA156 were predicted to target genes involved in maize ear development. Antisense transcripts were widespread throughout all the four stages, and are suspected to play important roles in maize ear development. Thus, identification and characterization of important genes and regulators at all the four developmental stages will contribute to an improved understanding of the molecular mechanisms responsible for maize ear development. Seeds of the maize inbred line 18-599 (Maize Research Institute, Sichuan Agricultural University, Chengdu, China) were grown in a growth chamber at 24°C/18°C (day/night) with 12 h illumination per day. Ears were collected as described previously [10] at four developmental stages: the growth point elongation, spikelet differentiation, floret primordium differentiation, and the floret organ differentiation phases. In brief, ears were manually collected at the four developmental stages. All the samples were harvested and immediately frozen in liquid nitrogen, and stored at -80°C until used for RNA isolation.
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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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