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Series GSE230023 Query DataSets for GSE230023
Status Public on Apr 20, 2023
Title Genome-wide identification of nitrate-responsive microRNAs by small RNA sequencing in the rice restorer cultivar Nanhui 511
Organism Oryza sativa
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary Rice productivity relies heavily on nitrogen fertilization, and improving nitrogen use efficiency (NUE) is important for hybrid rice breeding. Reducing nitrogen inputs is the key to achieving sustainable rice production and reducing environmental problems. Here, we analyzed the genome-wide transcriptomic changes in microRNAs (miRNAs) in the indica rice restorer cultivar NH511 (Nanhui 511) under high (HN) and low nitrogen (LN) conditions. The results showed that NH511 is sensitive to nitrogen supplies and HN conditions promoted the growth its lateral roots at the seedling stage. Furthermore, we identified 483 known miRNAs and 128 novel miRNAs by small RNA sequencing in response to nitrogen in NH511. We also detected 100 differentially expressed genes (DEGs), including 75 upregulated and 25 downregulated DEGs, under HN conditions. Among these DEGs, 43 miRNAs that exhibited a 2-fold change in their expression were identified in response to HN conditions, including 28 upregulated and 15 downregulated genes. Additionally, some differentially expressed miRNAs were further validated by qPCR analysis, which showed that miR443, miR1861b, and miR166k-3p were upregulated, whereas miR395v and miR444b.1 were downregulated under HN conditions. Moreover, the degradomes of possible target genes for miR166k-3p and miR444b.1 and expression variations were analyzed by qPCR at different time points under HN conditions. Our findings revealed comprehensive expression profiles of miRNAs responsive to HN treatments in an indica rice restorer cultivar, which advances our understanding of the regulation of nitrogen signaling mediated by miRNAs and provides novel data for high-NUE hybrid rice cultivation.
 
Overall design Comparative miRNA expression profiling analysis of RNA-seq data for rice cultivar Nanhui511 under HN and LN conditions
 
Contributor(s) Qin X, Li X, Li C, Li Y, Wu Q, Wen H, Jiang D, Tang T, Nan W, Liang Y, Zhang H
Citation(s) 37332718
Submission date Apr 18, 2023
Last update date Sep 08, 2023
Contact name Xiaojian Qin
E-mail(s) qinxiaojian@cqnu.edu.cn
Organization name Chongqing Normal University
Street address No.37, Daxuecheng Middle Road, Shapingba District, Chongqing
City Chongqing
State/province --- Select One ---
ZIP/Postal code 401331
Country China
 
Platforms (1)
GPL19290 Illumina HiSeq 2500 (Oryza sativa)
Samples (2)
GSM7184018 Nanhui511_LN [S04]
GSM7184019 Nanhui511_HN [S03]
Relations
BioProject PRJNA956981

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Supplementary file Size Download File type/resource
GSE230023_RAW.tar 10.0 Kb (http)(custom) TAR (of TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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