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Jia K, Zhang X, Meng Y, Liu S, Liu X, Yang T, Wen C, Liu L, Ge S. Metabolomics and transcriptomics provide insights into the flavonoid biosynthesis pathway in the roots of developing Aster tataricus. JOURNAL OF PLANT RESEARCH 2023; 136:139-156. [PMID: 36520245 PMCID: PMC9753034 DOI: 10.1007/s10265-022-01426-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 11/09/2022] [Indexed: 06/17/2023]
Abstract
Aster tataricus (L.) is an important medicinal plant in China. Its roots are rich in flavonoids, the main medicinal components. However, the molecular basis of flavonoid biosynthesis in the roots of A. tataricus remains unclear. In this study, the content of total flavonoid of A. tataricus roots at different developmental stages was measured first, and the results showed that the content of total flavonoid gradually decreased from September to November, which may be caused by the stagnation of A. tataricus growth due to the decrease in temperature after September. Then, an integrated analysis of transcriptome and metabolome was conducted on five developing stages of A. tataricus roots to identify flavonoid compositions and potential genes involved in flavonoid biosynthesis. A total of 80 flavonoid metabolites, of which 75% were flavonols and flavonoids, were identified in metabolomic analyses, among which isorhamnetin, kaempferol, quercetin, and myricetin were the main skeletons of these flavonoids. Cluster analysis divided these 80 flavonoids into 3 clusters. The compounds in cluster I mainly accumulated in S1, S3, and S5. In cluster II, the relative content of the flavonoid metabolites showed an upward trend from S2 to S4. In cluster III, the flavonoids decreased from S1 to S5. A total of 129 structural genes, including 43 PAL, 23 4CL, 9 C4H, 4 CHS, 18 CHI, 3 F3H, 5 F3'H, 1 F3'5'H, 21 FLS, and 2 FSII, and 65 transcription factors, including 22 AP2/ERF, 7 bHLH, 5 bZIP, 8 MYB, 11 NAC, and 12 WRKY, showed significant correlation with total flavonoid content. Eighteen genes (7 4CL, 5 C4H, 2 CHI, 1 F3H, and 3 FLS) and 30 genes (5 PAL, 9 4CL, 1 C4H, 2 CHI, 1 F3H, 1 DFR, 7 3AT, 1 BZ1, and 3 UGT79B1) were identified as key structural genes for kaempferol and anthocyanins biosynthesis, respectively. Our study provides valuable information for understanding the mechanism of flavonoid biosynthesis in A. tataricus root.
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Affiliation(s)
- Kaixuan Jia
- College of Agronomy, West Campus of Hebei Agricultural University, Lianchi District, Baoding, 071000, Hebei, China
- Key Laboratory of Crop Germplasm Resources Research and Utilization in North China, Ministry of Education, Baoding, 071000, China
| | - Xiaoling Zhang
- College of Agronomy, West Campus of Hebei Agricultural University, Lianchi District, Baoding, 071000, Hebei, China
- Key Laboratory of Crop Germplasm Resources Research and Utilization in North China, Ministry of Education, Baoding, 071000, China
| | - Yijiang Meng
- Key Laboratory of Crop Germplasm Resources Research and Utilization in North China, Ministry of Education, Baoding, 071000, China
- College of Life Science, Hebei Agricultural University, Baoding, 071000, China
| | - Shuqi Liu
- College of Agronomy, West Campus of Hebei Agricultural University, Lianchi District, Baoding, 071000, Hebei, China
- Key Laboratory of Crop Germplasm Resources Research and Utilization in North China, Ministry of Education, Baoding, 071000, China
| | - Xiaoqing Liu
- College of Agronomy, West Campus of Hebei Agricultural University, Lianchi District, Baoding, 071000, Hebei, China
- Key Laboratory of Crop Germplasm Resources Research and Utilization in North China, Ministry of Education, Baoding, 071000, China
| | - Taixin Yang
- College of Agronomy, West Campus of Hebei Agricultural University, Lianchi District, Baoding, 071000, Hebei, China
- Key Laboratory of Crop Germplasm Resources Research and Utilization in North China, Ministry of Education, Baoding, 071000, China
| | - Chunxiu Wen
- Institute of Cash Crops, Medicinal Plant Research Center West of Hebei Academy of Agriculture and Forestry Sciences, Nongke Road, Xiyuan Street, Xinhua District, Shijiazhuang, 050000, Hebei, China
| | - Lingdi Liu
- Institute of Cash Crops, Medicinal Plant Research Center West of Hebei Academy of Agriculture and Forestry Sciences, Nongke Road, Xiyuan Street, Xinhua District, Shijiazhuang, 050000, Hebei, China.
| | - Shujun Ge
- College of Agronomy, West Campus of Hebei Agricultural University, Lianchi District, Baoding, 071000, Hebei, China.
- Key Laboratory of Crop Germplasm Resources Research and Utilization in North China, Ministry of Education, Baoding, 071000, China.
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Xie G, Zou X, Liang Z, Wu D, He J, Xie K, Jin H, Wang H, Shen Q. Integrated metabolomic and transcriptomic analyses reveal molecular response of anthocyanins biosynthesis in perilla to light intensity. FRONTIERS IN PLANT SCIENCE 2022; 13:976449. [PMID: 36212297 PMCID: PMC9540795 DOI: 10.3389/fpls.2022.976449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/22/2022] [Indexed: 06/16/2023]
Abstract
The perilla anthocyanins have important medicinal and ornamental value, and their contents are significantly affected by light intensity. In view of their molecular mechanisms were not well understood, we integrated the metabolomic and transcriptomic analyses of the light-sensitive perilla variety under different light intensity. The perilla leave color were obviously affected under different treatments. Totally 140 flavonoid metabolites and 2461 genes showed steady change, among which 60 flavonoid metabolites were increased accumulation and 983 genes were upregulated expression under elevated light intensity treatment. Light treatment prominently affected the expression of genes involved in the main anthocyanin metabolites accumulation in perilla leaves. Using WGCNA analysis, we identified 4 key genes in anthocyanin biosynthesis pathway (CHI, DFR, and ANS) and 147 transcription factors (MYB, bHLH, bZIP, ERF, and NAC) involved in malonylshisonin biosynthesis. Among them, 6 MYBs and 4 bZIPs were predicted to play important roles in light regulation of malonylshisonin biosynthesis based on phylogenetic construction, correlation analysis, cis-acting element identification and qPCR verification. The identified key genes and regulatory factors will help us to understand the potential mechanism of photo-regulated anthocyanin accumulation in perilla.
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Yin YC, Zhang XD, Gao ZQ, Hu T, Liu Y. The Research Progress of Chalcone Isomerase (CHI) in Plants. Mol Biotechnol 2019; 61:32-52. [PMID: 30324542 DOI: 10.1007/s12033-018-0130-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Chalcone isomerase (CHI) is the second rate-limiting and the first reported enzyme involved in the biosynthetic pathway of flavonoids. It catalyzes the intramolecular cyclization reaction, converting the bicyclic chalcone into tricyclic (2S)-flavanone. In this paper, we obtained and analyzed 916 DNA sequences, 1310 mRNA sequences, and 2403 amino acid sequences of CHI registered in NCBI by Jan 2018. The full length of CHI DNA sequences ranges from 218 to 3758 bp, CHI mRNA sequences ranges from 265 to 1436 bp, and CHI amino acid sequences ranges from 35 to 465 amino acid residues. Forty representative species were selected from each family to construct the maximum likelihood tree and analyze the evolutionary relationship. According to the medicinal and agricultural use, 13 specific species were selected, and their physicochemical properties were analyzed. The molecular weight of CHI ranges from 23 to 26 kD, and the isoelectric point of CHI ranges from 4.93 to 5.85. All the half-life periods of CHI are 30 h in mammalian reticulocytes in vitro, 20 h in yeast, and 10 h in E. coli in vivo, theoretically. The consistency of the 13 CHI amino acid sequences is 63.55%. According to the similarity between each sequence, we selected four CHI sequences of Paeonia suffruticosa, Paeonia lactiflora, Taxus wallichiana, and Tradescantia hirsutiflora for secondary structure, three-dimensional protein models, conserved domains, transmembrane structure, and signal peptide prediction analysis. It was found that CHI sequences of Paeonia suffruticosa and Paeonia lactiflora owned a higher similarity; they both share the template 4doi.1.A. The four CHI all have no signal peptides, and they exert their activities in cytoplasm. Then, PubMed, Web of Science, Science Direct, and Research Gate were used as information sources through the search terms 'chalcone isomerase', 'biosynthesis', 'expression', and their combinations to get the latest and comprehensive information of CHI, mainly from the year 2010 to 2018. More than 300 papers were searched and 116 papers were reviewed in the present work. We summarized the classification of CHI, catalytic reaction mechanism of CHI, and progress of genetic engineering regarding CHI clone, expression, and exogenous stimulator regulation. This paper will lay a foundation for further studies of CHI and other functional genes involved in flavonoids biosynthetic pathway.
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Affiliation(s)
- Yan-Chao Yin
- School of Life Sciences, Beijing University of Chinese Medicine, Yangguang South Street, Fangshan District, Beijing, 102401, China
| | - Xiao-Dong Zhang
- School of Life Sciences, Beijing University of Chinese Medicine, Yangguang South Street, Fangshan District, Beijing, 102401, China
| | - Zhi-Qiang Gao
- School of Life Sciences, Beijing University of Chinese Medicine, Yangguang South Street, Fangshan District, Beijing, 102401, China
| | - Ting Hu
- School of Life Sciences, Beijing University of Chinese Medicine, Yangguang South Street, Fangshan District, Beijing, 102401, China
| | - Ying Liu
- School of Life Sciences, Beijing University of Chinese Medicine, Yangguang South Street, Fangshan District, Beijing, 102401, China.
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Gutierrez-Gonzalez JJ, Wu X, Zhang J, Lee JD, Ellersieck M, Shannon JG, Yu O, Nguyen HT, Sleper DA. Genetic control of soybean seed isoflavone content: importance of statistical model and epistasis in complex traits. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 119:1069-83. [PMID: 19626310 PMCID: PMC2755750 DOI: 10.1007/s00122-009-1109-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2009] [Accepted: 06/25/2009] [Indexed: 05/07/2023]
Abstract
A major objective for geneticists is to decipher genetic architecture of traits associated with agronomic importance. However, a majority of such traits are complex, and their genetic dissection has been traditionally hampered not only by the number of minor-effect quantitative trait loci (QTL) but also by genome-wide interacting loci with little or no individual effect. Soybean (Glycine max [L.] Merr.) seed isoflavonoids display a broad range of variation, even in genetically stabilized lines that grow in a fixed environment, because their synthesis and accumulation are affected by many biotic and abiotic factors. Due to this complexity, isoflavone QTL mapping has often produced conflicting results especially with variable growing conditions. Herein, we comparatively mapped soybean seed isoflavones genistein, daidzein, and glycitein by using several of the most commonly used mapping approaches: interval mapping, composite interval mapping, multiple interval mapping and a mixed-model based composite interval mapping. In total, 26 QTLs, including many novel regions, were found bearing additive main effects in a population of RILs derived from the cross between Essex and PI 437654. Our comparative approach demonstrates that statistical mapping methodologies are crucial for QTL discovery in complex traits. Despite a previous understanding of the influence of additive QTL on isoflavone production, the role of epistasis is not well established. Results indicate that epistasis, although largely dependent on the environment, is a very important genetic component underlying seed isoflavone content, and suggest epistasis as a key factor causing the observed phenotypic variability of these traits in diverse environments.
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Affiliation(s)
- Juan Jose Gutierrez-Gonzalez
- Division of Plant Sciences, National Center for Soybean Biotechnology, University of Missouri, Life Sciences Building, Columbia, MO 65201 USA
| | - Xiaolei Wu
- Division of Plant Sciences, National Center for Soybean Biotechnology, University of Missouri, Life Sciences Building, Columbia, MO 65201 USA
| | - Juan Zhang
- Donald Danforth Plant Science Center, 975 North Warson Road, Saint Louis, MO 63132 USA
| | - Jeong-Dong Lee
- Division of Plant Sciences, National Center for Soybean Biotechnology, University of Missouri, Life Sciences Building, Columbia, MO 65201 USA
| | - Mark Ellersieck
- Department of Statistics, University of Missouri, 146 Middlebush Hall, Columbia, MO 65211 USA
| | - J. Grover Shannon
- Division of Plant Sciences, National Center for Soybean Biotechnology, University of Missouri, Life Sciences Building, Columbia, MO 65201 USA
| | - Oliver Yu
- Donald Danforth Plant Science Center, 975 North Warson Road, Saint Louis, MO 63132 USA
| | - Henry T. Nguyen
- Division of Plant Sciences, National Center for Soybean Biotechnology, University of Missouri, Life Sciences Building, Columbia, MO 65201 USA
| | - David A. Sleper
- Division of Plant Sciences, National Center for Soybean Biotechnology, University of Missouri, Life Sciences Building, Columbia, MO 65201 USA
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