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Transcriptome and Phenotype Integrated Analysis Identifies Genes Controlling Ginsenoside Rb1 Biosynthesis and Reveals Their Interactions in the Process in Panax ginseng
Genes are the keys to deciphering the molecular mechanism underlying a biological trait and designing approaches desirable for plant genetic improvement. Ginseng is an important medicinal herb in which ginsenosides have been shown to be the major bioactive component; however, only a few genes involv...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9698431/ https://www.ncbi.nlm.nih.gov/pubmed/36430494 http://dx.doi.org/10.3390/ijms232214016 |
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author | Jiang, Yue Liu, Sizhang Li, Li Zang, Kaiyou Wang, Yanfang Zhao, Mingzhu Wang, Kangyu Zhu, Lei Chen, Ping Lei, Jun Wang, Yi Zhang, Meiping |
author_facet | Jiang, Yue Liu, Sizhang Li, Li Zang, Kaiyou Wang, Yanfang Zhao, Mingzhu Wang, Kangyu Zhu, Lei Chen, Ping Lei, Jun Wang, Yi Zhang, Meiping |
author_sort | Jiang, Yue |
collection | PubMed |
description | Genes are the keys to deciphering the molecular mechanism underlying a biological trait and designing approaches desirable for plant genetic improvement. Ginseng is an important medicinal herb in which ginsenosides have been shown to be the major bioactive component; however, only a few genes involved in ginsenoside biosynthesis have been cloned through orthologue analysis. Here, we report the identification of 21 genes controlling Rb1 biosynthesis by stepwise ginseng transcriptome and Rb1 content integrated analysis. We first identified the candidate genes for Rb1 biosynthesis by integrated analysis of genes with the trait from four aspects, including gene transcript differential expression between highest- and lowest-Rb1 content cultivars, gene transcript expression–Rb1 content correlation, and biological impacts of gene mutations on Rb1 content, followed by the gene transcript co-expression network. Twenty-two candidate genes were identified, of which 21 were functionally validated for Rb1 biosynthesis by gene regulation, genetic transformation, and mutation analysis. These genes were strongly correlated in expression with the previously cloned genes encoding key enzymes for Rb1 biosynthesis. Based on the correlations, a pathway for Rb1 biosynthesis was deduced to indicate the roles of the genes in Rb1 biosynthesis. Moreover, the genes formed a strong co-expression network with the previously cloned Rb1 biosynthesis genes, and the variation in the network was associated with the variation in the Rb1 content. These results indicate that Rb1 biosynthesis is a process of correlative interactions among Rb1 biosynthesis genes. Therefore, this study provides new knowledge, 21 new genes, and 96 biomarkers for Rb1 biosynthesis useful for enhanced research and breeding in ginseng. |
format | Online Article Text |
id | pubmed-9698431 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-96984312022-11-26 Transcriptome and Phenotype Integrated Analysis Identifies Genes Controlling Ginsenoside Rb1 Biosynthesis and Reveals Their Interactions in the Process in Panax ginseng Jiang, Yue Liu, Sizhang Li, Li Zang, Kaiyou Wang, Yanfang Zhao, Mingzhu Wang, Kangyu Zhu, Lei Chen, Ping Lei, Jun Wang, Yi Zhang, Meiping Int J Mol Sci Article Genes are the keys to deciphering the molecular mechanism underlying a biological trait and designing approaches desirable for plant genetic improvement. Ginseng is an important medicinal herb in which ginsenosides have been shown to be the major bioactive component; however, only a few genes involved in ginsenoside biosynthesis have been cloned through orthologue analysis. Here, we report the identification of 21 genes controlling Rb1 biosynthesis by stepwise ginseng transcriptome and Rb1 content integrated analysis. We first identified the candidate genes for Rb1 biosynthesis by integrated analysis of genes with the trait from four aspects, including gene transcript differential expression between highest- and lowest-Rb1 content cultivars, gene transcript expression–Rb1 content correlation, and biological impacts of gene mutations on Rb1 content, followed by the gene transcript co-expression network. Twenty-two candidate genes were identified, of which 21 were functionally validated for Rb1 biosynthesis by gene regulation, genetic transformation, and mutation analysis. These genes were strongly correlated in expression with the previously cloned genes encoding key enzymes for Rb1 biosynthesis. Based on the correlations, a pathway for Rb1 biosynthesis was deduced to indicate the roles of the genes in Rb1 biosynthesis. Moreover, the genes formed a strong co-expression network with the previously cloned Rb1 biosynthesis genes, and the variation in the network was associated with the variation in the Rb1 content. These results indicate that Rb1 biosynthesis is a process of correlative interactions among Rb1 biosynthesis genes. Therefore, this study provides new knowledge, 21 new genes, and 96 biomarkers for Rb1 biosynthesis useful for enhanced research and breeding in ginseng. MDPI 2022-11-13 /pmc/articles/PMC9698431/ /pubmed/36430494 http://dx.doi.org/10.3390/ijms232214016 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Jiang, Yue Liu, Sizhang Li, Li Zang, Kaiyou Wang, Yanfang Zhao, Mingzhu Wang, Kangyu Zhu, Lei Chen, Ping Lei, Jun Wang, Yi Zhang, Meiping Transcriptome and Phenotype Integrated Analysis Identifies Genes Controlling Ginsenoside Rb1 Biosynthesis and Reveals Their Interactions in the Process in Panax ginseng |
title | Transcriptome and Phenotype Integrated Analysis Identifies Genes Controlling Ginsenoside Rb1 Biosynthesis and Reveals Their Interactions in the Process in Panax ginseng |
title_full | Transcriptome and Phenotype Integrated Analysis Identifies Genes Controlling Ginsenoside Rb1 Biosynthesis and Reveals Their Interactions in the Process in Panax ginseng |
title_fullStr | Transcriptome and Phenotype Integrated Analysis Identifies Genes Controlling Ginsenoside Rb1 Biosynthesis and Reveals Their Interactions in the Process in Panax ginseng |
title_full_unstemmed | Transcriptome and Phenotype Integrated Analysis Identifies Genes Controlling Ginsenoside Rb1 Biosynthesis and Reveals Their Interactions in the Process in Panax ginseng |
title_short | Transcriptome and Phenotype Integrated Analysis Identifies Genes Controlling Ginsenoside Rb1 Biosynthesis and Reveals Their Interactions in the Process in Panax ginseng |
title_sort | transcriptome and phenotype integrated analysis identifies genes controlling ginsenoside rb1 biosynthesis and reveals their interactions in the process in panax ginseng |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9698431/ https://www.ncbi.nlm.nih.gov/pubmed/36430494 http://dx.doi.org/10.3390/ijms232214016 |
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