Identification of PgRg1-3 Gene for Ginsenoside Rg1 Biosynthesis as Revealed by Combining Genome-Wide Association Study and Gene Co-Expression Network Analysis of Jilin Ginseng Core Collection
Abstract
:1. Introduction
2. Materials and Methods
2.1. Databases
2.2. Identification of Candidate Genes for Ginsenoside Rg1 Biosynthesis
2.2.1. Genome-Wide Association Study (GWAS)
Statistical Analysis of Ginsenoside Rg1 Content in Core Germplasm Resource Population
Genome-Wide Association Study Using Single-Locus Models
Multi-Locus Model Genome-Wide Association Study
Determination of Genes within Significantly Associated Intervals in Genome-Wide Association Study
2.2.2. Weighted Gene Co-Expression Network Analysis (WGCNA)
2.2.3. Study on the Effect of Gene Mutations on Rg1 Content through SNP-Rg1 Content Association Analysis
2.2.4. Gene Co-Expression Network Analysis
2.3. Functional Validation of Key Candidate Genes for Rg1
2.3.1. Validation of MeJA-Induced Regulation
2.3.2. Validation with RNA Interference (RNAi)
2.4. Exploration of the Molecular Mechanism of the PgRg1-3 Gene in Rg1 Biosynthesis
2.4.1. Functional Annotation of the PgRg1-3 Gene by GO and KEGG Pathway Localization, and Homology Analysis with Ginseng CYP Genes
2.4.2. Gene Expression Patterns at Different Times and in Different Cultivars
2.4.3. The Impacts of Gene Co-Expression Network Variations on Rg1 Biosynthesis
2.4.4. Genetic Effects of SNP Mutations in the PgRg1-3 Gene on Rg1 Biosynthesis
3. Results
3.1. Identification of Candidate Genes and Key Candidate Genes for Ginsenoside Rg1 Biosynthesis
3.1.1. Genome-Wide Association Study
Statistical Analysis of Ginsenoside Rg1 Content
Genome-Wide Association Study of Ginsenoside Rg1 Content Using Single-Locus Models
Genome-Wide Association Study of Ginsenoside Rg1 Content Using Multi-Locus Models
Identification of Genes in Significantly Associated Regions through Genome-Wide Association Study
3.1.2. WGCNA Analysis
3.1.3. Association Analysis of SNPs with Rg1 Content Investigating the Impact of Gene Mutations on Rg1 Content
3.1.4. Network Analysis of Candidate Genes III for Rg1 Biosynthesis and 15 Key Enzyme Gene Transcripts Involved in Ginsenoside Biosynthesis
3.2. Functional Validation of the PgRg1-3 Key Candidate Gene for Rg1 Biosynthesis
3.2.1. MeJA-Induced Regulation
3.2.2. Genetic Transformation RNA Interference (RNAi)
3.3. Exploration of the Molecular Mechanism of the PgRg1-3 Gene in Rg1 Biosynthesis
3.3.1. Functional Annotation of PgRg1-3 Gene by GO, KEGG Localization, and Homology Comparison with Ginseng CYP Genes
3.3.2. Gene Expression Patterns at Different Spatiotemporal Points and in Different Cultivars
3.3.3. Impact of the Changes in Gene Co-Expression Networks on Rg1 Biosynthesis
3.3.4. Analysis of the Impact and Genetic Effects of SNP Mutations in the PgRg1-3 Gene on Rg1 Biosynthesis
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Liu, S.; Chen, X.; Zhao, T.; Yu, J.; Chen, P.; Wang, Y.; Wang, K.; Zhao, M.; Jiang, Y.; Wang, Y.; et al. Identification of PgRg1-3 Gene for Ginsenoside Rg1 Biosynthesis as Revealed by Combining Genome-Wide Association Study and Gene Co-Expression Network Analysis of Jilin Ginseng Core Collection. Plants 2024, 13, 1784. https://doi.org/10.3390/plants13131784
Liu S, Chen X, Zhao T, Yu J, Chen P, Wang Y, Wang K, Zhao M, Jiang Y, Wang Y, et al. Identification of PgRg1-3 Gene for Ginsenoside Rg1 Biosynthesis as Revealed by Combining Genome-Wide Association Study and Gene Co-Expression Network Analysis of Jilin Ginseng Core Collection. Plants. 2024; 13(13):1784. https://doi.org/10.3390/plants13131784
Chicago/Turabian StyleLiu, Sizhang, Xiaxia Chen, Tianqi Zhao, Jinghui Yu, Ping Chen, Yanfang Wang, Kangyu Wang, Mingzhu Zhao, Yue Jiang, Yi Wang, and et al. 2024. "Identification of PgRg1-3 Gene for Ginsenoside Rg1 Biosynthesis as Revealed by Combining Genome-Wide Association Study and Gene Co-Expression Network Analysis of Jilin Ginseng Core Collection" Plants 13, no. 13: 1784. https://doi.org/10.3390/plants13131784
APA StyleLiu, S., Chen, X., Zhao, T., Yu, J., Chen, P., Wang, Y., Wang, K., Zhao, M., Jiang, Y., Wang, Y., & Zhang, M. (2024). Identification of PgRg1-3 Gene for Ginsenoside Rg1 Biosynthesis as Revealed by Combining Genome-Wide Association Study and Gene Co-Expression Network Analysis of Jilin Ginseng Core Collection. Plants, 13(13), 1784. https://doi.org/10.3390/plants13131784