Comparative Biochemical and Transcriptome Analyses Reveal Potential Candidate Genes Related to Pericarp Browning in Red Rice
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials
2.2. 4-Dimethylaminocinnamaldehyde Staining
2.3. Quantification of Total Phenolic and Tannin Content
2.4. RNA Extraction and Sequencing
2.5. Identification of Differentially Expressed Genes and Enrichment Analysis
2.6. Validation of Gene Expression via Quantitative Reverse Transcription Polymerase Chain Reaction
2.7. Statical Analysis of Experimental Data
3. Results
3.1. Pericarp Color Change and Proanthocyanidin Accumulation during Grain Development
3.2. RNA Sequencing-Based Transcriptome Profiling and Detection of Differentially Expressed Genes
3.3. Gene Ontology and Kyoto Encyclopedia of Genes and Genome Pathway Enrichment Analysis
3.4. Expression Profile of Rice PA Biosynthesis-Related Genes
3.5. Potential Candidate Genes Related to Pericarp Browning
3.6. Quantitative Reverse Transcription-Polymerase Chain Reaction Validation of RNA Sequencing-Based Expression Data
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Stage | DEG Set | KEGG ID | Pathway Name | Count | Expected Count | FDR |
---|---|---|---|---|---|---|
14 DAF | Upregulated | dosa00941 | Flavonoid biosynthesis | 6 | 41 | 7.12 × 10−7 |
Upregulated | dosa03030 | DNA replication | 4 | 57 | 1.09 × 10−3 | |
Downregulated | dosa04141 | Protein processing in endoplasmic reticulum | 20 | 210 | 3.91 × 10−15 | |
28 DAF | Upregulated | dosa00904 | Diterpenoid biosynthesis | 4 | 41 | 4.25 × 10−2 |
Downregulated | dosa04141 | Protein processing in endoplasmic reticulum | 27 | 210 | 2.95 × 10−14 | |
Downregulated | dosa04626 | Plant-pathogen interaction | 10 | 192 | 2.75 × 10−2 |
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Lee, G.; Park, J.W.; Park, J.; Han, A.-R.; Hong, M.J.; Jo, Y.D.; Kim, J.-B.; Kim, S.H.; Choi, H.-I. Comparative Biochemical and Transcriptome Analyses Reveal Potential Candidate Genes Related to Pericarp Browning in Red Rice. Agriculture 2023, 13, 183. https://doi.org/10.3390/agriculture13010183
Lee G, Park JW, Park J, Han A-R, Hong MJ, Jo YD, Kim J-B, Kim SH, Choi H-I. Comparative Biochemical and Transcriptome Analyses Reveal Potential Candidate Genes Related to Pericarp Browning in Red Rice. Agriculture. 2023; 13(1):183. https://doi.org/10.3390/agriculture13010183
Chicago/Turabian StyleLee, Gileung, Jae Wan Park, Jisu Park, Ah-Reum Han, Min Jeong Hong, Yeong Deuk Jo, Jin-Baek Kim, Sang Hoon Kim, and Hong-Il Choi. 2023. "Comparative Biochemical and Transcriptome Analyses Reveal Potential Candidate Genes Related to Pericarp Browning in Red Rice" Agriculture 13, no. 1: 183. https://doi.org/10.3390/agriculture13010183