Genome-wide transcriptome analysis of roots in two rice vari

发布时间：2023-03-04 13:42

　　Alternate wetting and drying(AWD) irrigation has been widely used as an efficient rice production method to obtain better yield without continuous flooding(CF) of the paddy field. However, how this practice affects gene expression to regulate rice physiology and morphology is largely unknown. In this study, we used two rice varieties, Nipponbare, a lowland rice cultivar, and Gaoshan 1, an upland cultivar, and found that root dry weight(RDW) and root oxidation activity(ROA) in both cultivars subs...

【文章页数】：16 页

【文章目录】：
1. Introduction
2. Materials and methods
    2.1. Plant materials and growth conditions
    2.2. Root dry weight(RDW)and root oxidation activity(ROA)
    2.3. RNA sequencing and data analysis
        2.3.1. RNA extraction and quality check
        2.3.2. Library preparation for RNA sequencing
        2.3.3. Library examination,clustering and sequencing
        2.3.4. Transcriptome analysis
    2.4. Quantitative real-time PCR validation
    2.5. Statistical analysis
3. Results
    3.1. Both rice cultivars display higher RDW and ROA under AWD
    3.2. Cultivar type was the major factor contributing to transcriptome variation followed by irrigation scheme
    3.3. Nipponbare displayed strong transcriptome modulation between different irrigation schemes
    3.4. Functional classification of the DEGs by GO and KEGG pathway analysis
    3.5. Lignin biosynthetic pathway
    3.6. Protein processing in endoplasmic reticulum(ER)pathway
    3.7. Plant hormone signal transduction pathway
    3.8. Changes in the expression profile of transcription factors(TFs)
    3.9. Expression changes from RNA-Seq and qRT-PCR strongly correlated for above mentioned candidate genes
4. Discussion
    4.1. Response of root system to AWD irrigation
    4.2. Response of protein processing in ER pathway to AWD irrigation
    4.3. Response of lignin biosynthetic pathway to AWD irrigation
    4.4. Response of plant hormones signal transduction path-ways to AWD irrigation
    4.5. Response of TFs to AWD irrigation
    4.6. Common up-and down-regulated DEGs in Nipponbare and Gaoshan 1
5. Conclusions



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