논문 (학술지)
Transcriptome analysis for identifying possible gene regulations during maize root emergence and formation at the initial growth stage
| 등록번호 | RPMS-2018-0090689165 | SCI 구분
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※구분 : SCI(SCIE포함), 비SCI |
SCI |
|---|---|---|---|
| 저자명 (주·공동저자) | Hwang Sun-Goo; Kim Kyung-Hee; Lee Byung-Moo; Moon Jun-Cheol | ||
| 논문구분 | 국내전문학술지 | 학술지명 | GENES & GENOMICS |
| ISSN | 1976-9571 | 학술지 출판일자 | - |
| 학술지 볼륨번호 | 40 | 논문페이지 | 755 ~ 766 |
| 학술지 임팩트팩터 | 0.566 | 기여율 | 50 % |
| DOI | 10.1007/s13258-018-0687-z | ||
| 초록 | The root plays an important role during plant development and growth, i.e., the plant body maintenance, nutrient storage, absorption of water, oxygen and nutrient from the soil, and storage of water and carbohydrates, etc. The objective of this study was attempted to determine root-specific genes at the initial developmental stages of maize by using network-based transcriptome analysis. The raw data obtained using RNA-seq were filtered for quality control of the reads with the FASTQC tool, and the filtered reads were pre-proceed using the TRIMMOMATIC tool. The enriched BINs of the DEGs were detected using PageMan analysis with the ORA_FISHER statistical test, and genes were assigned to metabolic pathways by using the MapMan tool, which was also used for detecting transcription factors (TFs). For reconstruction of the co-expression network, we used the algorithm for the reconstruction of accurate cellular networks (ARACNE) in the R package, and then the reconstructed co-expression network was visualized using the Cytoscape tool. RNA-seq. was performed using maize shoots and roots at different developmental stages of root emergence (6–10 days after planting, VE) and 1 week after plant emergence (V2). A total of 1286 differentially expressed genes (DEGs) were detected in both tissues. Many DEGs involved in metabolic pathways exhibited altered mRNA levels between VE and V2. In addition, we observed gene expression changes for 113 transcription factors and found five enriched cis-regulatory elements in the 1-kb upstream regions of both DEGs. The network-based transcriptome analysis showed two modules as co-expressed gene clusters differentially expressed between the shoots and roots during plant development. The DEGs of one module exhibited gene expressional coherence in the maize root tips, suggesting that their functional relationships are associated with the initial developmental stage of the maize root. Finally, we confirmed reliable mRNA levels of the hub genes in the potential sub-network related to initial root development at the different developmental stages of VE, V2, and 2 weeks after plant emergence. | ||
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