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Wu D, Wu Y, Gao R, Zhang Y, Zheng R, Fang M, Li Y, Zhang Y, Guan L, Gao Y. Integrated Metabolomics and Transcriptomics Reveal the Key Role of Flavonoids in the Cold Tolerance of Chrysanthemum. Int J Mol Sci 2024; 25:7589. [PMID: 39062834 PMCID: PMC11276724 DOI: 10.3390/ijms25147589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/23/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024] Open
Abstract
Chrysanthemum (Chrysanthemum morifolium, ground-cover Chrysanthemums), one of the important garden flowers, has a high ornamental and economic value. However, its ornamental value is significantly diminished by the low temperature experienced in northeastern China. Here, metabolomics and transcriptomics were performed on three Chrysanthemum cultivars before and after a low temperature to investigate the dynamic metabolite changes and the molecular regulatory mechanisms. The results showed that 1324 annotated metabolites were detected, among which 327 were identified as flavonoids derived from Chrysanthemum. The accumulation of metabolites and gene expression related to the flavonoid biosynthesis pathway significantly increased in the three cultivars under the low temperature, indicating flavonoid metabolism actively participates in the Chrysanthemum cold response. Specifically, the content of cyanidin and pelargonidin derivatives and the expression of anthocyanin biosynthesis genes significantly increases in XHBF, providing a reasonable explanation for the change in petal color from white to purple under the low temperature. Six candidate UDP-glycosyltransferase genes involved in the glycosylation of flavonoids were identified through correlation networks and phylogenetic analysis. CmNAC1, CmbZIP3, and other transcription factors potentially regulating flavonoid metabolism and responding to low temperatures were discovered by correlation analysis and weighted gene co-expression network analysis (WGCNA). In conclusion, this study elucidated the specific response of flavonoids to low temperatures in Chrysanthemums, providing valuable insights and metabolic data for investigating cold tolerance.
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Affiliation(s)
- Di Wu
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China; (D.W.); (R.G.)
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Yingxue Wu
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China; (D.W.); (R.G.)
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Ruiqi Gao
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China; (D.W.); (R.G.)
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Yanhong Zhang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China; (D.W.); (R.G.)
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Ruiying Zheng
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Minghui Fang
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Yuhua Li
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China; (D.W.); (R.G.)
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Yang Zhang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China; (D.W.); (R.G.)
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Le Guan
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China; (D.W.); (R.G.)
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Yanqiang Gao
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China; (D.W.); (R.G.)
- College of Life Science, Northeast Forestry University, Harbin 150040, China
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Yang X, Liu D, Liu C, Li M, Yan Z, Zhang Y, Feng G. Possible melatonin-induced salt stress tolerance pathway in Phaseolus vulgaris L. using transcriptomic and metabolomic analyses. BMC PLANT BIOLOGY 2024; 24:72. [PMID: 38267871 PMCID: PMC10809447 DOI: 10.1186/s12870-023-04705-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 12/24/2023] [Indexed: 01/26/2024]
Abstract
Melatonin plays important roles in multiple stress responses; however, the downstream signaling pathway and molecular mechanism remain unclear. This study aimed to elucidate the transcriptional regulation of melatonin-induced salt stress tolerance in Phaseolus vulgaris L. and identify the key downstream transcription factors of melatonin through transcriptomic and metabolomic analyses. The melatonin-induced transcriptional network of hormones, transcription factors, and functional genes was established under both control and stress conditions. Among these, eight candidate transcription factors were identified via gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, one gene related to transmembrane transport of salts (Phvul.004G177300). These genes may play a role in maintaining the cell structure and excreting sodium ions outside the cell or transporting them to the vacuoles for storage. Melatonin regulates the Phvul.009G210332 gene and metabolites C05642 (N-acetyl-N-2-formyl-5-methoxycanurine), C05643 (6-hydroxymelatonin), C05660 (5-methoxyindoleacetic acid) involved in tryptophan metabolism. The metabolites C05642 and C05643 were identified as decomposition products of tryptophan, indicating that exogenous melatonin entered the P. vulgaris tissue and was metabolized. Melatonin promotes the synthesis and metabolism of tryptophan, which is crucial to plant metabolism, growth, maintenance, and repair.
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Affiliation(s)
- Xiaoxu Yang
- Horticulture Department, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, 74 Xuefu Road, Harbin, Heilongjiang, 150000, China
- Jiaxiang Industrial Technology Research Institute of Heilongjiang University, Jining, Shandong, 272400, China
| | - Dajun Liu
- Horticulture Department, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, 74 Xuefu Road, Harbin, Heilongjiang, 150000, China
| | - Chang Liu
- Horticulture Department, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, 74 Xuefu Road, Harbin, Heilongjiang, 150000, China
- Jiaxiang Industrial Technology Research Institute of Heilongjiang University, Jining, Shandong, 272400, China
| | - Mengdi Li
- Horticulture Department, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, 74 Xuefu Road, Harbin, Heilongjiang, 150000, China
| | - Zhishan Yan
- Horticulture Department, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, 74 Xuefu Road, Harbin, Heilongjiang, 150000, China
| | - Yu Zhang
- Horticulture Department, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, 74 Xuefu Road, Harbin, Heilongjiang, 150000, China
- Jiaxiang Industrial Technology Research Institute of Heilongjiang University, Jining, Shandong, 272400, China
| | - Guojun Feng
- Horticulture Department, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, 74 Xuefu Road, Harbin, Heilongjiang, 150000, China.
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Pei L, Gao Y, Feng L, Zhang Z, Liu N, Yang B, Zhao N. Phenolic Acids and Flavonoids Play Important Roles in Flower Bud Differentiation in Mikania micrantha: Transcriptomics and Metabolomics. Int J Mol Sci 2023; 24:16550. [PMID: 38068873 PMCID: PMC10705899 DOI: 10.3390/ijms242316550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/13/2023] [Accepted: 11/17/2023] [Indexed: 12/18/2023] Open
Abstract
Mikania micrantha is a highly invasive vine, and its ability to sexually reproduce is a major obstacle to its eradication. The long-distance dissemination of M. micrantha depends on the distribution of seeds; therefore, inhibiting M. micrantha flowering and seed production is an effective control strategy. The number of blooms of M. micrantha differs at different altitudes (200, 900, and 1300 m). In this study, we used a combination of metabolomics and transcriptomics methods to study the patterns of metabolite accumulation in the flower buds of M. micrantha. Using LC-MS/MS, 658 metabolites were found in the flower buds of M. micrantha at three different altitudes (200, 900, and 1300 m). Flavonoids and phenolic acids were found to be the main differential metabolites, and their concentrations were lower at 900 m than at 200 m and 1300 m, with the concentrations of benzoic acid, ferulic acid, and caffeic acid being the lowest. The biosynthesis pathways for flavonoids and phenolic compounds were significantly enriched for differentially expressed genes (DEGs), according to the results of transcriptome analysis. The production of flavonoid and phenolic acids was strongly linked with the expressions of phenylalanine ammonia-lyase (PAL), caffeoyl-CoA O-methyltransferase (COMT), and 4-coumarate-CoA ligase (4CL), according to the results of the combined transcriptome and metabolome analysis. These genes' roles in the regulation of distinct phenolic acids and flavonoids during M. micrantha bud differentiation are still unknown. This study adds to our understanding of how phenolic acids and flavonoids are regulated in M. micrantha flower buds at various altitudes and identifies regulatory networks that may be involved in this phenomenon, offering a new approach for the prevention and management of M. micrantha.
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Affiliation(s)
- Ling Pei
- College of Life Sciences, Southwest Forestry University, Kunming 650224, China; (L.P.); (Y.G.); (L.F.); (Z.Z.)
| | - Yanzhu Gao
- College of Life Sciences, Southwest Forestry University, Kunming 650224, China; (L.P.); (Y.G.); (L.F.); (Z.Z.)
| | - Lichen Feng
- College of Life Sciences, Southwest Forestry University, Kunming 650224, China; (L.P.); (Y.G.); (L.F.); (Z.Z.)
| | - Zihan Zhang
- College of Life Sciences, Southwest Forestry University, Kunming 650224, China; (L.P.); (Y.G.); (L.F.); (Z.Z.)
| | - Naiyong Liu
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming 650224, China;
| | - Bin Yang
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming 650224, China;
| | - Ning Zhao
- College of Life Sciences, Southwest Forestry University, Kunming 650224, China; (L.P.); (Y.G.); (L.F.); (Z.Z.)
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming 650224, China;
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Li C, Wan Y, Shang X, Fang S. Integration of transcriptomic and metabolomic analysis unveils the response mechanism of sugar metabolism in Cyclocarya paliurus seedlings subjected to PEG-induced drought stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107856. [PMID: 37354727 DOI: 10.1016/j.plaphy.2023.107856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 06/26/2023]
Abstract
Cyclocarya paliurus (Batal.) Iljinskaja is a multiple function tree species used for functional food and valued timber production. Carbohydrates, especially water-soluble carbohydrates, play an important role in osmotic protection, signal transduction and carbon storage. Under the circumstance of global climate change the abiotic stress would restrict the development of C. paliurus plantation, whereas there is few knowledge on the regulatory mechanisms of sugar metabolism under drought stress in C. paliurus. To investigate the drought response of C. paliurus at molecular level, we conducted an integrated analysis of transcriptomic and metabolomic of C. paliurus at three PEG-induced drought stress levels (0%: control; 15%: moderate drought; 25%: severe drought) in short term. Both moderate and severe drought treatments activated the chemical defense with lowering relative water content, and enhancing the contents of soluble protein, proline and malondialdehyde in the leaves. Meanwhile, alterations in the expression of differentially expressed genes and carbohydrate metabolism profiles were observed among the treatments. Weighted gene co-expression network analysis (WGCNA) showed 3 key modules, 8 structural genes (such as genes encoding beta-fructofuranosidase (INV), sucrose synthase (SUS), raffinose synthase (RS)) and 14 regulatory transcription factors were closely linked to sugar metabolism. Our results provided the foundation to understand the response mechanism of sugar metabolism in C. paliurus under drought stress, and would drive progress in breeding of drought-tolerant varieties and plantation development of the species.
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Affiliation(s)
- Chenhui Li
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Yifeng Wan
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Xulan Shang
- College of Forestry, Nanjing Forestry University, Nanjing, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Shengzuo Fang
- College of Forestry, Nanjing Forestry University, Nanjing, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China.
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Qu Y, Shang X, Zeng Z, Yu Y, Bian G, Wang W, Liu L, Tian L, Zhang S, Wang Q, Xie D, Chen X, Liao Z, Wang Y, Qin J, Yang W, Sun C, Fu X, Zhang X, Fang S. Whole-genome Duplication Reshaped Adaptive Evolution in A Relict Plant Species, Cyclocarya paliurus. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:455-469. [PMID: 36775057 PMCID: PMC10787019 DOI: 10.1016/j.gpb.2023.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 11/07/2022] [Accepted: 02/05/2023] [Indexed: 02/12/2023]
Abstract
Cyclocarya paliurus is a relict plant species that survived the last glacial period and shows a population expansion recently. Its leaves have been traditionally used to treat obesity and diabetes with the well-known active ingredient cyclocaric acid B. Here, we presented three C. paliurus genomes from two diploids with different flower morphs and one haplotype-resolved tetraploid assembly. Comparative genomic analysis revealed two rounds of recent whole-genome duplication events and identified 691 genes with dosage effects that likely contribute to adaptive evolution through enhanced photosynthesis and increased accumulation of triterpenoids. Resequencing analysis of 45 C. paliurus individuals uncovered two bottlenecks, consistent with the known events of environmental changes, and many selectively swept genes involved in critical biological functions, including plant defense and secondary metabolite biosynthesis. We also proposed the biosynthesis pathway of cyclocaric acid B based on multi-omics data and identified key genes, in particular gibberellin-related genes, associated with the heterodichogamy in C. paliurus species. Our study sheds light on evolutionary history of C. paliurus and provides genomic resources to study the medicinal herbs.
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Affiliation(s)
- Yinquan Qu
- Nanjing Forestry University, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing 210037, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xulan Shang
- Nanjing Forestry University, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing 210037, China
| | - Ziyan Zeng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Yanhao Yu
- Nanjing Forestry University, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing 210037, China
| | - Guoliang Bian
- Nanjing Forestry University, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing 210037, China
| | - Wenling Wang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Li Liu
- Nanjing Forestry University, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing 210037, China
| | - Li Tian
- Nanjing Forestry University, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing 210037, China
| | - Shengcheng Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Qian Wang
- Nanjing Forestry University, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing 210037, China
| | - Dejin Xie
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xuequn Chen
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhenyang Liao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Yibin Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Jian Qin
- Nanjing Forestry University, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing 210037, China
| | - Wanxia Yang
- Nanjing Forestry University, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing 210037, China
| | - Caowen Sun
- Nanjing Forestry University, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing 210037, China
| | - Xiangxiang Fu
- Nanjing Forestry University, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing 210037, China.
| | - Xingtan Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
| | - Shengzuo Fang
- Nanjing Forestry University, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing 210037, China.
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Wang Q, Qu Y, Yu Y, Mao X, Fu X. Genome-wide identification and comparative analysis of DNA methyltransferase and demethylase gene families in two ploidy Cyclocarya paliurus and their potential function in heterodichogamy. BMC Genomics 2023; 24:287. [PMID: 37248459 DOI: 10.1186/s12864-023-09383-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/16/2023] [Indexed: 05/31/2023] Open
Abstract
BACKGROUND DNA methylation is one of the most abundant epigenetic modifications, which plays important roles in flower development, sex differentiation, and regulation of flowering time. Its pattern is affected by cytosine-5 DNA methyltransferase (C5-MTase) and DNA demethylase (dMTase). At present, there are no reports on C5-MTase and dMTase genes in heterodichogamous Cyclocarya paliurus. RESULTS In this study, 6 CpC5-MTase and 3 CpdMTase genes were identified in diploid (2n = 2 × = 32) C. paliurus, while 20 CpC5-MTase and 13 CpdMTase genes were identified in autotetraploid (2n = 4 × = 64). 80% of identified genes maintained relatively fixed positions on chromosomes during polyploidization. In addition, we found that some DRM subfamily members didn't contain the UBA domain. The transcript abundance of CpC5-MTase and CpdMTase in male and female flowers of two morphs (protandry and protogyny) from diploidy was analyzed. Results showed that all genes were significantly up-regulated at the stage of floral bud break (S2), but significantly down-regulated at the stage of flower maturation (S4). At S2, some CpC5-MTase genes showed higher expression levels in PG-M than in PG-F, whereas some CpdMTase genes showed higher expression levels in PA-M than in PA-F. In addition, these genes were significantly associated with gibberellin synthesis-related genes (e.g. DELLA and GID1), suggesting that DNA methylation may play a role in the asynchronous floral development process through gibberellin signal. CONCLUSIONS These results broaden our understanding of the CpC5-MTase and CpdMTase genes in diploid and autotetraploid C. paliurus, and provide a novel insight into regulatory mechanisms of DNA methylation in heterodichogamy.
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Affiliation(s)
- Qian Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Yinquan Qu
- Fishery College, Zhejiang Ocean University, Zhoushan, 316022, Zhejiang, China
| | - Yanhao Yu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Xia Mao
- Jiangsu Vocational College of Agriculture and Forestry, Zhenjiang, 212400, Jiangsu, China
| | - Xiangxiang Fu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.
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Wang Q, Chen B, Chen X, Mao X, Fu X. Squalene epoxidase (SE) gene related to triterpenoid biosynthesis assists to select elite genotypes in medicinal plant: Cyclocarya paliurus (Batal.) Iljinskaja. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 199:107726. [PMID: 37167758 DOI: 10.1016/j.plaphy.2023.107726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/15/2023] [Accepted: 04/27/2023] [Indexed: 05/13/2023]
Abstract
Triterpenoids, known for their anti-inflammatory, anticancer, and hypoglycemic properties, are the major bioactive components in Cyclocarya paliurus (Batal.) Iljinskaja. Selecting elite individuals with high triterpenoids content is the basis of C. paliurus industry for medicinal use. In this study, seasonal variation patterns of total triterpenoids and five triterpene monomers accumulation for three groups with different total triterpenoid contents (TTC; H: 59.74-64.03 mg g-1; M: 47.66-57.08 mg g-1, and L: 35.26-42.22 mg g-1) were surveyed. Seasonal expression dynamics of 6 key genes relevant to triterpenoids biosynthesis, including HMGR, DXR, SQS, SE, LUS, and β-AS, were described by quantitative real-time PCR (qRT-PCR) for three groups. The expression levels of HMGR, SE, LUS, and β-AS genes in group H were higher than in groups M and L. In addition, Pearson correlation analysis showed that they were significantly positively correlated with triterpene accumulation, and the expression level of SE gene not only was significantly correlated with downstream genes, but also exhibited a linear relationship with TTC, especially in September. These results suggest that SE gene could serve as an effective make for screening elite individuals with high TTC from the germplasm of C. paliurus for medicinal use. Further testing on randomly selected individuals in next September proved the feasibility and reliability of SE gene in assisted selection. Also, we successfully cloned the full-length cDNA of SE. Thus, our work provides an efficient way to attain superior genotypes to develop medicinal industry of C. paliurus in practice.
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Affiliation(s)
- Qian Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Biqin Chen
- Administration of Agriculture and Rural Affairs of Hongze District, Huai'an City, Huai'an, 223199, China
| | - Xiaoling Chen
- School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Xia Mao
- Jiangsu Vocational College of Agriculture and Forestry, Zhenjiang, Jiangsu, 212400, China
| | - Xiangxiang Fu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.
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Zhang Z, Fang J, Zhang L, Jin H, Fang S. Genome-wide identification of bHLH transcription factors and their response to salt stress in Cyclocarya paliurus. FRONTIERS IN PLANT SCIENCE 2023; 14:1117246. [PMID: 36968403 PMCID: PMC10035414 DOI: 10.3389/fpls.2023.1117246] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
As a highly valued and multiple function tree species, the leaves of Cyclocarya paliurus are enriched in diverse bioactive substances with healthy function. To meet the requirement for its leaf production and medical use, the land with salt stress would be a potential resource for developing C. paliurus plantations due to the limitation of land resources in China. The basic helix-loop-helix (bHLH) transcription factor protein family, the second largest protein family in plants, has been found to play essential roles in the response to multiple abiotic stresses, especially salt stress. However, the bHLH gene family in C.paliurus has not been investigated. In this study, 159 CpbHLH genes were successfully identified from the whole-genome sequence data, and were classified into 26 subfamilies. Meanwhile, the 159 members were also analyzed from the aspects of protein sequences alignment, evolution, motif prediction, promoter cis-acting elements analysis and DNA binding ability. Based on transcriptome profiling under a hydroponic experiment with four salt concentrations (0%, 0.15%, 0.3%, and 0.45% NaCl), 9 significantly up- or down-regulated genes were screened, while 3 genes associated with salt response were selected in term of the GO annotation results. Totally 12 candidate genes were selected in response to salt stress. Moreover, based on expression analysis of the 12 candidate genes sampled from a pot experiment with three salt concentrations (0%, 0.2% and 0.4% NaCl), CpbHLH36/68/146 were further verified to be involved in the regulation of salt tolerance genes, which is also confirmed by protein interaction network analysis. This study was the first analysis of the transcription factor family at the genome-wide level of C. paliurus, and our findings would not only provide insight into the function of the CpbHLH gene family members involved in salt stress but also drive progress in genetic improvement for the salt tolerance of C. paliurus.
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Affiliation(s)
- Zijie Zhang
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Jie Fang
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Lei Zhang
- College of Forestry, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing, China
| | - Huiyin Jin
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Shengzuo Fang
- College of Forestry, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing, China
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Jin H, Yang Z, Luo J, Li C, Chen J, Lim KJ, Wang Z. Comprehensive identification and analysis of circRNAs during hickory ( Carya cathayensis Sarg.) flower bud differentiation. FRONTIERS IN PLANT SCIENCE 2023; 13:1000489. [PMID: 36684801 PMCID: PMC9846342 DOI: 10.3389/fpls.2022.1000489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Flower bud differentiation represents a crucial transition from vegetative growth to reproductive development. Carya cathayensis (hickory) is an important economic species in China, with a long juvenile period that hinders its commercial development. In recent years, circular RNAs (circRNAs) have been widely studied and identified as sponges for miRNA regulation of mRNA expression. However, little is known regarding the role of circRNAs in flower buds. In this study, we sequenced circRNAs at three developmental stages (undifferentiated, differentiating, and fully differentiated) in both female and male buds. A total of 6,931 circRNAs were identified in the three developmental stages and 4,449 and 2,209 circRNAs were differentially expressed in female and male buds, respectively. Gene ontology demonstrated that many circRNA host genes participated in various processes, for example, cellular and intracellular pH regulation. Function annotation identified 46 differentially expressed circRNAs involved in flowering regulation, with 28 circRNAs found only in female buds, 4 found only in male buds, and 11 found in both female and male buds. A circRNA-miRNA-mRNA network was predicted based on 13 flowering-related circRNAs and their seven putative interacting miRNAs to describe the regulatory mechanism. Our preliminary results demonstrated a potential involvement of circRNA in bud differentiation. They provided a preliminary theoretical basis for how circRNA might participate in flower development in hickory, perhaps in woody plants.
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Qin J, Yue X, Fang S, Qian M, Zhou S, Shang X, Yang W. Nitrogen addition modifies the relative gene expression level and accumulation of carbon-based bioactive substances in Cyclocarya paliurus. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 188:70-80. [PMID: 35988389 DOI: 10.1016/j.plaphy.2022.07.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/18/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
In China, lots of Cyclocarya paliurus plantations have been established for tea and functional food production on nitrogen (N)-limited land. The optimum N levels require for biosynthesis and accumulation of carbon-based bioactive substances vary among plant species. This study integrated field trial with hydroponic culture to assess impact of nitrogen addition on accumulation and relative gene expression level of carbon-based secondary metabolites in C. paliurus. N addition significantly influenced not only contents of polyphenols, flavonoids and triterpenoids and relative gene expression levels of their biosynthetic pathway in C. paliurus leaves but also leaf biomass production and the bioactive substance accumulations. An intermediate N addition induced the highest contents of polyphenols, flavonoids and triterpenoids in leaves, but the optimized accumulation of these bioactive substances in the leaves was the trade-off between their contents and leaf biomass production. Correlation analysis showed that related gene expression levels were closely correlated with contents of their leaf corresponding secondary metabolites. Compared with ratios of carbon/N (C/N) and carbon/phosphorus (C/P) in the soil, ratios of C/N and C/P in the leaves were more strongly related to the contents and accumulations of polyphenols, flavonoids and triterpenoids. To obtain higher yields of targeted phytochemicals, the threshold ratios of C/N and C/P in the leaves are recommended for N and P fertilization at similar sites. Overall, our findings would provide the theoretical basis and technical support for manipulating N fertilization in C. paliurus plantations to obtain higher accumulations of targeted bioactive substances.
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Affiliation(s)
- Jian Qin
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Xiliang Yue
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Shengzuo Fang
- College of Forestry, Nanjing Forestry University, Nanjing, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China.
| | - Mengyu Qian
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Shuntao Zhou
- Anhui Green and Selenium Technology Development Company in Agriculture and Ecology, Shitai, China
| | - Xulan Shang
- College of Forestry, Nanjing Forestry University, Nanjing, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Wanxia Yang
- College of Forestry, Nanjing Forestry University, Nanjing, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
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Qu Y, Chen X, Mao X, Huang P, Fu X. Transcriptome Analysis Reveals the Role of GA 3 in Regulating the Asynchronism of Floral Bud Differentiation and Development in Heterodichogamous Cyclocarya paliurus (Batal.) Iljinskaja. Int J Mol Sci 2022; 23:ijms23126763. [PMID: 35743203 PMCID: PMC9224186 DOI: 10.3390/ijms23126763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/04/2022] [Accepted: 06/11/2022] [Indexed: 12/04/2022] Open
Abstract
Cyclocarya paliurus is an important medical plant owing to the diverse bioactive compounds in its leaves. However, the heterodichogamy with female and male functions segregation within protandry (PA) or protogyny (PG) may greatly affect seed quality and its plantations for medicinal use. To speculate on the factor playing the dominant role in regulating heterodichogamy in C. paliurus, based on phenotypic observations, our study performed a multi comparison transcriptome analysis on female and male buds (PG and PA types) using RNA-seq. For the female and male bud comparisons, a total of 6753 differentially expressed genes (DEGs) were detected. In addition, functional analysis revealed that these DEGs were significantly enriched in floral development, hormone, and GA-related pathways. As the dominant hormones responsible for floral differentiation and development, gibberellins (GAs) in floral buds from PG and PA types were quantified using HPLC-MS. Among the tested GAs, GA3 positively regulated the physiological differentiation (S0) and germination (S2) of floral buds. The dynamic changes of GA3 content and floral morphological features were consistent with the expression levels of GA-related genes. Divergences of GA3 contents at S0 triggered the asynchronism of physiological differentiation between male and female buds of intramorphs (PA-M vs. PA-F and PG-F vs. PG-M). A significant difference in GA3 content enlarged this asynchronism at S2. Thus, we speculate that GA3 plays the dominant role in the formation of heterodichogamy in C. paliurus. Meanwhile, the expression patterns of GA-related DEGs, including CPS, KO, GA20ox, GA2OX, GID1, and DELLA genes, which play central roles in regulating flower development, coincided with heterodichogamous characteristics. These results support our speculations well, which should be further confirmed.
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Identification and Expression Analysis of R2R3-MYB Family Genes Associated with Salt Tolerance in Cyclocarya paliurus. Int J Mol Sci 2022; 23:ijms23073429. [PMID: 35408785 PMCID: PMC8998414 DOI: 10.3390/ijms23073429] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 03/14/2022] [Accepted: 03/20/2022] [Indexed: 02/05/2023] Open
Abstract
R2R3-MYB transcription factors are most abundant in the MYB superfamily, while the R2R3-MYB genes play an important role in plant growth and development, especially in response to environmental stress. Cyclocarya paliurus is a multifunction tree species, and the existing resources cannot meet the requirement for its leaf production and medical use. Therefore, lands with some environmental stresses would be potential sites for developing C. paliurus plantations. However, the function of R2R3-MYB genes in C.paliurus in response to environmental stress remains unknown. In this study, to identify the roles of R2R3-MYB genes associated with salt stress response, 153 CpaMYB genes and their corresponding protein sequences were identified from the full-length transcriptome. Based on the comparison with MYB protein sequences of Arabidopsis thaliana, 69 R2R3-MYB proteins in C. paliurus were extracted for further screening combined with conserved functional domains. Furthermore, the MYB family members were analyzed from the aspects of protein sequences alignment, evolution, motif prediction, promoter cis-acting element analysis, and gene differential expression under different salt treatments using both a pot experiment and hydroponic experiment. The results showed that the R2R3-MYB genes of C.paliurus conserved functional domains, whereas four R2R3-MYB genes that might respond to salt stress via regulating plant hormone signals were identified in this study. This work provides a basis for further functional characterization of R2R3-MYB TFs in C. paliurus.
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Chen X, Chen B, Shang X, Fang S. RNA in situ hybridization and expression of related genes regulating the accumulation of triterpenoids in Cyclocarya paliurus. TREE PHYSIOLOGY 2021; 41:2189-2197. [PMID: 33960380 DOI: 10.1093/treephys/tpab067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 04/28/2021] [Indexed: 06/12/2023]
Abstract
Cyclocarya paliurus (Batal.) Iljinskaja, a woody medicinal species in the Juglandaceae, grows extensively in subtropical areas of China. Triterpenoids in the leaves have health-promoting effects, including hypoglycemic and hypolipidemic activities. To understand triterpenoid biosynthesis, transport and accumulation in C. paliurus during the growing season, gene cloning, gene expression and RNA in situ hybridization of related genes were used, and accumulation was examined in various organs. The complete coding sequences (CDSs) of three genes, CpHMGR, CpDXR and CpSQS, were obtained from GenBank and RACE. RNA in situ hybridization signals of the three genes mainly occurred in the epidermis, palisade tissue, phloem and xylem of leaf, shoot and root, with the signals generally consistent with the accumulation of metabolites in tissues, except in the xylem. Both gene expression and triterpenoid accumulations showed seasonal variations in all organs. However, total triterpenoid content in the leaves was significantly higher than that in the shoots, with the maximum in shoots in August and in leaves in October. According to Pearson correlation analysis, triterpenoid accumulation in the leaves was significantly positively related with the relative expression of CpSQS. However, the relation between gene expression and accumulation was dependent on the role of the gene in the pathway as well as on the plant organ. The results suggested that most of the intermediates catalyzed by CpHMGR and CpDXR in young shoots and roots were used in growth and flowering in the spring, whereas subsequent triterpenoid biosynthesis in the downstream catalyzed by CpSQS mainly occurred in the leaves by using transferred and in situ intermediates as substrates. Thus, this study provides a reference to improve triterpenoid accumulation in future C. paliurus plantations.
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Affiliation(s)
- Xiaoling Chen
- College of Forestry, Nanjing Forestry University, Longpan Road, Xuanwu district, Nanjing 210037, China
| | - Biqin Chen
- College of Forestry, Nanjing Forestry University, Longpan Road, Xuanwu district, Nanjing 210037, China
| | - Xulan Shang
- College of Forestry, Nanjing Forestry University, Longpan Road, Xuanwu district, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Longpan Road, Xuanwu district, Nanjing 210037, China
| | - Shengzuo Fang
- College of Forestry, Nanjing Forestry University, Longpan Road, Xuanwu district, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Longpan Road, Xuanwu district, Nanjing 210037, China
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Genome-Wide Identification MIKC-Type MADS-Box Gene Family and Their Roles during Development of Floral Buds in Wheel Wingnut ( Cyclocarya paliurus). Int J Mol Sci 2021; 22:ijms221810128. [PMID: 34576289 PMCID: PMC8471257 DOI: 10.3390/ijms221810128] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 11/16/2022] Open
Abstract
MADS-box transcription factors (TFs) have fundamental roles in regulating floral organ formation and flowering time in flowering plants. In order to understand the function of MIKC-type MADS-box family genes in Cyclocarya paliurus (Batal.) Iljinskaja, we first implemented a genome-wide analysis of MIKC-type MADS-box genes in C. paliurus. Here, the phylogenetic relationships, chromosome location, conserved motif, gene structure, promoter region, and gene expression profile were analyzed. The results showed that 45 MIKC-type MADS-box were divided into 14 subfamilies: BS (3), AGL12 (1), AP3-PI (3), MIKC* (3), AGL15 (3), SVP (5), AGL17 (2), AG (3), TM8 (1), AGL6 (2), SEP (5), AP1-FUL (6), SOC1 (7), and FLC (1). The 43 MIKC-type MADS-box genes were distributed unevenly in 14 chromosomes, but two members were mapped on unanchored scaffolds. Gene structures were varied in the same gene family or subfamily, but conserved motifs shared similar distributions and sequences. The element analysis in promoters’ regions revealed that MIKC-type MADS-box family genes were associated with light, phytohormone, and temperature responsiveness, which may play important roles in floral development and differentiation. The expression profile showed that most MIKC-type MADS-box genes were differentially expressed in six tissues (specifically expressed in floral buds), and the expression patterns were also visibly varied in the same subfamily. CpaF1st24796 and CpaF1st23405, belonging to AP3-PI and SEP subfamilies, exhibited the high expression levels in PA-M and PG-F, respectively, indicating their functions in presenting heterodichogamy. We further verified the MIKC-type MADS-box gene expression levels on the basis of transcriptome and qRT-PCR analysis. This study would provide a theoretical basis for classification, cloning, and regulation of flowering mechanism of MIKC-type MADS-box genes in C. paliurus.
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Liu Q, Liaquat F, He Y, Munis MFH, Zhang C. Functional Annotation of a Full-Length Transcriptome and Identification of Genes Associated with Flower Development in Rhododendronsimsii (Ericaceae). PLANTS (BASEL, SWITZERLAND) 2021; 10:649. [PMID: 33805478 PMCID: PMC8065783 DOI: 10.3390/plants10040649] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/21/2021] [Accepted: 03/24/2021] [Indexed: 11/16/2022]
Abstract
Rhododendronsimsii is one of the top ten famous flowers in China. Due to its historical value and high aesthetic, it is widely popular among Chinese people. Various colors are important breeding objectives in Rhododendron L. The understanding of the molecular mechanism of flower color formation can provide a theoretical basis for the improvement of flower color in Rhododendron L. To generate the R.simsii transcriptome, PacBio sequencing technology has been used. A total of 833,137 full-length non-chimeric reads were obtained and 726,846 high-quality full-length transcripts were found. Moreover, 40,556 total open reading frames were obtained; of which 36,018 were complete. In gene annotation analyses, 39,411, 18,565, 16,102 and 17,450 transcriptions were allocated to GO, Nr, KEGG and COG databases, correspondingly. To identify long non-coding RNAs (lncRNAs), we utilized four computational methods associated with Protein families (Pfam), Cooperative Data Classification (CPC), Coding Assessing Potential Tool (CPAT) and Coding Non Coding Index (CNCI) databases and observed 6170, 2265, 4084 and 1240 lncRNAs, respectively. Based on the results, most genes were enriched in the flavonoid biosynthetic pathway. The eight key genes on the anthocyanin biosynthetic pathway were further selected and analyzed by qRT-PCR. The F3'H and ANS showed an upward trend in the developmental stages of R. simsii. The highest expression of F3'5'H and FLS in the petal color formation of R. simsii was observed. This research provided a huge number of full-length transcripts, which will help to proceed genetic analyses of R.simsii. native, which is a semi-deciduous shrub.
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Affiliation(s)
- Qunlu Liu
- Department of Landscape Architecture, School of Design, Shanghai Jiao Tong University, Shanghai 200240, China; (Q.L.); (Y.H.)
| | - Fiza Liaquat
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China;
| | - Yefeng He
- Department of Landscape Architecture, School of Design, Shanghai Jiao Tong University, Shanghai 200240, China; (Q.L.); (Y.H.)
| | | | - Chunying Zhang
- Shanghai Engineering Research Center of Sustainable Plant Innovation, Shanghai Botanical Garden, Shanghai 200231, China
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Nitrogen Forms Alter Triterpenoid Accumulation and Related Gene Expression in Cyclocarya paliurus (Batalin) Iljinsk. Seedlings. FORESTS 2020. [DOI: 10.3390/f11060631] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Cyclocarya paliurus (Batalin) Iljinsk. is a multiple function tree species distributed in subtropical areas, and its leaves have been used in medicine and nutraceutical foods in China. However, little information on the effects of nitrogen (N) forms and ratios on growth and secondary metabolite accumulation is available for C. paliurus. The impact of five NO3−/NH4+ ratios on biomass production, triterpenoid accumulation and related gene expression in C. paliurus seedlings was evaluated at the middle N nutrition supply. Significant differences in seedling growth, triterpenoid accumulation and relative gene expression were observed among the different NO3−/NH4+ ratio treatments. The highest triterpenoid content was achieved in a sole NO3− or NH4+ nutrition, while the mixed N nutrition with equal ratio of NO3− to NH4+ produced the highest biomass production in the seedlings. However, the highest triterpenoid accumulation was achieved at the treatment with the ratio of NO3−/NH4+ = 2.33. Therefore, the mixed N nutrition of NO3− and NH4+ was beneficial to the triterpenoid accumulation per plant. The relative expression of seven genes that are involved in triterpenoid biosynthesis were all up-regulated under the sole NH4+ or NO3− nutrition conditions, and significantly positive correlations between triterpenoid content and relative gene expression of key enzymes were detected in the leaves. Our results indicated that NO3− is the N nutrition preferred by C. paliurus, but the mixture of NO3− and NH4+ at an appropriate ratio would improve the leaf triterpenoid yield per area.
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