1
|
Qiao Q, Gao Y, Liu Q. Metabolic and molecular mechanisms of spine color formation in Chinese red chestnut. FRONTIERS IN PLANT SCIENCE 2024; 15:1377899. [PMID: 38835869 PMCID: PMC11148441 DOI: 10.3389/fpls.2024.1377899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 04/11/2024] [Indexed: 06/06/2024]
Abstract
The spines of Chinese red chestnut are red and the depth of their color gradually increases with maturity. To identify the anthocyanin types and synthesis pathways in red chestnut and to identify the key genes regulating the anthocyanin biosynthesis pathway, we obtained and analyzed the transcriptome and anthocyanin metabolism of red chestnut and its control variety with green spines at 3 different periods. GO and KEGG analyses revealed that photosynthesis was more highly enriched in green spines compared with red spines, while processes related to defense and metabolism regulation were more highly enriched in red spines. The analysis showed that the change in spine color promoted photoprotection in red chestnut, especially at the early growth stage, which resulted in the accumulation of differentially expressed genes involved in the defense metabolic pathway. The metabolome results revealed 6 anthocyanins in red spines. Moreover, red spines exhibited high levels of cyanidin, peonidin and pelargonidin and low levels of delphinidin, petunidin and malvidin. Compared with those in the control group, the levels of cyanidin, peonidin, pelargonidin and malvidin in red spines were significantly increased, indicating that the cyanidin and pelargonidin pathways were enriched in the synthesis of anthocyanins in red spines, whereas the delphinidin pathways were inhibited and mostly transformed into malvidin. During the process of flower pigment synthesis, the expression of the CHS, CHI, F3H, CYP75A, CYP75B1, DFR and ANS genes clearly increased, that of CYP73A decreased obviously, and that of PAL, 4CL and LAR both increased and decreased. Notably, the findings revealed that the synthesized anthocyanin can be converted into anthocyanidin or epicatechin. In red spines, the upregulation of BZ1 gene expression increases the corresponding anthocyanidin content, and the upregulation of the ANR gene also promotes the conversion of anthocyanin to epicatechin. The transcription factors involved in color formation included 4 WRKYs.
Collapse
Affiliation(s)
- Qian Qiao
- Shandong Key Laboratory of Fruit Biotechnology Breeding, Shandong Institute of Pomology, Taian, Shandong, China
| | - Yun Gao
- College of Plant Protection, Shandong Agricultural University, Taian, Shandong, China
| | - Qingzhong Liu
- Shandong Key Laboratory of Fruit Biotechnology Breeding, Shandong Institute of Pomology, Taian, Shandong, China
| |
Collapse
|
2
|
Lin Y, Zhang N, Lin Y, Gao Y, Li H, Zhou C, Meng W, Qin W. Transcriptomic and metabolomic correlation analysis: effect of initial SO 2 addition on higher alcohol synthesis in Saccharomyces cerevisiae and identification of key regulatory genes. Front Microbiol 2024; 15:1394880. [PMID: 38803372 PMCID: PMC11128613 DOI: 10.3389/fmicb.2024.1394880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 04/17/2024] [Indexed: 05/29/2024] Open
Abstract
Introduction Higher alcohols are volatile compounds produced during alcoholic fermentation that affect the quality and safety of the final product. This study used a correlation analysis of transcriptomics and metabolomics to study the impact of the initial addition of SO2 (30, 60, and 90 mg/L) on the synthesis of higher alcohols in Saccharomyces cerevisiae EC1118a and to identify key genes and metabolic pathways involved in their metabolism. Methods Transcriptomics and metabolomics correlation analyses were performed and differentially expressed genes (DEGs) and differential metabolites were identified. Single-gene knockouts for targeting genes of important pathways were generated to study the roles of key genes involved in the regulation of higher alcohol production. Results We found that, as the SO2 concentration increased, the production of total higher alcohols showed an overall trend of first increasing and then decreasing. Multi-omics correlation analysis revealed that the addition of SO2 affected carbon metabolism (ko01200), pyruvate metabolism (ko00620), glycolysis/gluconeogenesis (ko00010), the pentose phosphate pathway (ko00030), and other metabolic pathways, thereby changing the precursor substances. The availability of SO2 indirectly affects the formation of higher alcohols. In addition, excessive SO2 affected the growth of the strain, leading to the emergence of a lag phase. We screened the ten most likely genes and constructed recombinant strains to evaluate the impact of each gene on the formation of higher alcohols. The results showed that ADH4, SER33, and GDH2 are important genes of alcohol metabolism in S. cerevisiae. The isoamyl alcohol content of the EC1118a-ADH4 strain decreased by 21.003%; The isobutanol content of the EC1118a-SER33 strain was reduced by 71.346%; and the 2-phenylethanol content of EC1118a-GDH2 strain was reduced by 25.198%. Conclusion This study lays a theoretical foundation for investigating the mechanism of initial addition of SO2 in the synthesis of higher alcohols in S. cerevisiae, uncovering DEGs and key metabolic pathways related to the synthesis of higher alcohols, and provides guidance for regulating these mechanisms.
Collapse
Affiliation(s)
- Yuan Lin
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Na Zhang
- College of Biology and Brewing Engineering, Taishan University, Taian, China
| | - Yonghong Lin
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Yinhao Gao
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Hongxing Li
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Cuixia Zhou
- College of Biology and Brewing Engineering, Taishan University, Taian, China
| | - Wu Meng
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Weishuai Qin
- College of Biology and Brewing Engineering, Taishan University, Taian, China
| |
Collapse
|
3
|
Huang X, Zhu Y, Su W, Song S, Chen R. Widely-targeted metabolomics and transcriptomics identify metabolites associated with flowering regulation of Choy Sum. Sci Rep 2024; 14:10682. [PMID: 38724517 PMCID: PMC11081954 DOI: 10.1038/s41598-024-60801-4] [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: 01/20/2024] [Accepted: 04/26/2024] [Indexed: 05/12/2024] Open
Abstract
Choy Sum, a stalk vegetable highly valued in East and Southeast Asia, is characterized by its rich flavor and nutritional profile. Metabolite accumulation is a key factor in Choy Sum stalk development; however, no research has focused on metabolic changes during the development of Choy Sum, especially in shoot tip metabolites, and their effects on growth and flowering. Therefore, in the present study, we used a widely targeted metabolomic approach to analyze metabolites in Choy Sum stalks at the seedling (S1), bolting (S3), and flowering (S5) stages. In total, we identified 493 metabolites in 31 chemical categories across all three developmental stages. We found that the levels of most carbohydrates and amino acids increased during stalk development and peaked at S5. Moreover, the accumulation of amino acids and their metabolites was closely related to G6P, whereas the expression of flowering genes was closely related to the content of T6P, which may promote flowering by upregulating the expressions of BcSOC1, BcAP1, and BcSPL5. The results of this study contribute to our understanding of the relationship between the accumulation of stem tip substances during development and flowering and of the regulatory mechanisms of stalk development in Choy Sum and other related species.
Collapse
Affiliation(s)
- Xinmin Huang
- Guangdong Provincial Engineering Technology Research Center for Protected Horticulture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- College of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000, Guangdong, People's Republic of China
| | - Yunna Zhu
- Guangdong Provincial Engineering Technology Research Center for Protected Horticulture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Wei Su
- Guangdong Provincial Engineering Technology Research Center for Protected Horticulture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Shiwei Song
- Guangdong Provincial Engineering Technology Research Center for Protected Horticulture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China.
| | - Riyuan Chen
- Guangdong Provincial Engineering Technology Research Center for Protected Horticulture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China.
| |
Collapse
|
4
|
Zeng S, Yu L, He P, Feng H, Wang J, Zhang H, Song Y, Liu R, Li Y. Integrated transcriptome and metabolome analysis reveals the regulation of phlorizin synthesis in Lithocarpus polystachyus under nitrogen fertilization. BMC PLANT BIOLOGY 2024; 24:366. [PMID: 38711037 DOI: 10.1186/s12870-024-05090-9] [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: 04/17/2023] [Accepted: 05/01/2024] [Indexed: 05/08/2024]
Abstract
BACKGROUND Nitrogen (N) is essential for plant growth and development. In Lithocarpus polystachyus Rehd., a species known for its medicinal and food value, phlorizin is the major bioactive compound with pharmacological activity. Research has revealed a positive correlation between plant nitrogen (N) content and phlorizin synthesis in this species. However, no study has analyzed the effect of N fertilization on phlorizin content and elucidated the molecular mechanisms underlying phlorizin synthesis in L. polystachyus. RESULTS A comparison of the L. polystachyus plants grown without (0 mg/plant) and with N fertilization (25, 75, 125, 175, 225, and 275 mg/plant) revealed that 75 mg N/plant fertilization resulted in the greatest seedling height, ground diameter, crown width, and total phlorizin content. Subsequent analysis of the leaves using ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) detected 150 metabolites, including 42 flavonoids, that were differentially accumulated between the plants grown without and with 75 mg/plant N fertilization. Transcriptomic analysis of the L. polystachyus plants via RNA sequencing revealed 162 genes involved in flavonoid biosynthesis, among which 53 significantly differed between the N-treated and untreated plants. Fertilization (75 mg N/plant) specifically upregulated the expression of the genes phenylalanine ammonia-lyase (PAL), 4-coumarate-CoA ligase (4CL), and phlorizin synthase (PGT1) but downregulated the expression of trans-cinnamate 4-monooxygenase (C4H), shikimate O-hydroxycinnamoyltransferase (HCT), and chalcone isomerase (CHI), which are related to phlorizin synthesis. Finally, an integrated analysis of the transcriptome and metabolome revealed that the increase in phlorizin after N fertilization was consistent with the upregulation of phlorizin biosynthetic genes. Quantitative real-time PCR (qRT‒PCR) was used to validate the RNA sequencing data. Thus, our results indicated that N fertilization increased phlorizin metabolism in L. polystachyus by regulating the expression levels of the PAL, PGT1, 5-O-(4-coumaroyl)-D-quinate 3'-monooxygenase (C3'H), C4H, and HCT genes. CONCLUSIONS Our results demonstrated that the addition of 75 mg/plant N to L. polystachyus significantly promoted the accumulation of flavonoids, including phlorizin, and the expression of flavonoid synthesis-related genes. Under these conditions, the genes PAL, 4CL, and PGT1 were positively correlated with phlorizin accumulation, while C4H, CHI, and HCT were negatively correlated with phlorizin accumulation. Therefore, we speculate that PAL, 4CL, and PGT1 participate in the phlorizin pathway under an optimal N environment, regulating phlorizin biosynthesis. These findings provide a basis for improving plant bioactive constituents and serve as a reference for further pharmacological studies.
Collapse
Affiliation(s)
- Suping Zeng
- Experimental Center of Subtropical Forestry, Chinese Academy of Forestry, Xinyu, 336600, China
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Longhua Yu
- Experimental Center of Subtropical Forestry, Chinese Academy of Forestry, Xinyu, 336600, China
| | - Ping He
- Experimental Center of Subtropical Forestry, Chinese Academy of Forestry, Xinyu, 336600, China
| | - Hui Feng
- Xinyu University, School of Public Health and Health, Xinyu, 338004, China
| | - Jia Wang
- Experimental Center of Subtropical Forestry, Chinese Academy of Forestry, Xinyu, 336600, China
| | - Huacong Zhang
- Experimental Center of Subtropical Forestry, Chinese Academy of Forestry, Xinyu, 336600, China
| | - Yunxia Song
- Experimental Center of Subtropical Forestry, Chinese Academy of Forestry, Xinyu, 336600, China
| | - Ren Liu
- Experimental Center of Subtropical Forestry, Chinese Academy of Forestry, Xinyu, 336600, China
| | - Yueqiao Li
- Experimental Center of Subtropical Forestry, Chinese Academy of Forestry, Xinyu, 336600, China.
| |
Collapse
|
5
|
Jiang L, Yang X, Gao X, Yang H, Ma S, Huang S, Zhu J, Zhou H, Li X, Gu X, Zhou H, Liang Z, Yang A, Huang Y, Xiao M. Multiomics Analyses Reveal the Dual Role of Flavonoids in Pigmentation and Abiotic Stress Tolerance of Soybean Seeds. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:3231-3243. [PMID: 38303105 DOI: 10.1021/acs.jafc.3c08202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
The color of the seed coat has great diversity and is regarded as a biomarker of metabolic variations. Here we isolated a soybean variant (BLK) from a population of recombinant inbred lines with a black seed coat, while its sibling plants have yellow seed coats (YL). The BLK and YL plants showed no obvious differences in vegetative growth and seed weight. However, the BLK seeds had higher anthocyanins and flavonoids level and showed tolerance to various abiotic stresses including herbicide, oxidation, salt, and alkalinity during germination. Integrated metabolomic and transcriptomic analyses revealed that the upregulation of biosynthetic genes probably contributed to the overaccumulation of flavonoids in BLK seeds. The transient expression of those biosynthetic genes in soybean root hairs increased the levels of total flavonoids or anthocyanins. Our study revealed the molecular basis of flavonoid accumulation in soybean seeds, leveraging genetic engineering for both nutritious and stress-tolerant soybean germplasm.
Collapse
Affiliation(s)
- Ling Jiang
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, People's Republic of China
- Yuelushan Laboratory, Changsha 410128, People's Republic of China
| | - Xiaofeng Yang
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, People's Republic of China
| | - Xiewang Gao
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, People's Republic of China
- School of Life Sciences, Chinese University of Hong Kong, Hong Kong 999077, People's Republic of China
| | - Hui Yang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, People's Republic of China
| | - Shumei Ma
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life Science, Hunan University of Science and Technology, Xiangtan 411201, People's Republic of China
| | - Shan Huang
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, People's Republic of China
| | - Jianyu Zhu
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, People's Republic of China
| | - Hong Zhou
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, People's Republic of China
| | - Xiaohong Li
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, People's Republic of China
| | - Xiaoyan Gu
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, People's Republic of China
| | - Hongming Zhou
- College of Agronomy, Hunan Agricultural University, Changsha 410128, People's Republic of China
| | - Zeya Liang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, People's Republic of China
| | - Antong Yang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, People's Republic of China
| | - Yong Huang
- Yuelushan Laboratory, Changsha 410128, People's Republic of China
- Key Laboratory of Hunan Province on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha 410128, People's Republic of China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Mu Xiao
- Yuelushan Laboratory, Changsha 410128, People's Republic of China
- College of Agronomy, Hunan Agricultural University, Changsha 410128, People's Republic of China
- Key Laboratory of Hunan Province on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha 410128, People's Republic of China
| |
Collapse
|
6
|
Sui D, Wang B, El-Kassaby YA, Wang L. Integration of Physiological, Transcriptomic, and Metabolomic Analyses Reveal Molecular Mechanisms of Salt Stress in Maclura tricuspidata. PLANTS (BASEL, SWITZERLAND) 2024; 13:397. [PMID: 38337930 PMCID: PMC10857159 DOI: 10.3390/plants13030397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 01/21/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024]
Abstract
Salt stress is a universal abiotic stress that severely affects plant growth and development. Understanding the mechanisms of Maclura tricuspidate's adaptation to salt stress is crucial for developing salt-tolerant plant varieties. This article discusses the integration of physiology, transcriptome, and metabolome to investigate the mechanism of salt adaptation in M. tricuspidata under salt stress conditions. Overall, the antioxidant enzyme system (SOD and POD) of M. tricuspidata exhibited higher activities compared with the control, while the content of soluble sugar and concentrations of chlorophyll a and b were maintained during salt stress. KEGG analysis revealed that deferentially expressed genes were primarily involved in plant hormone signal transduction, phenylpropanoid and flavonoid biosynthesis, alkaloids, and MAPK signaling pathways. Differential metabolites were enriched in amino acid metabolism, the biosynthesis of plant hormones, butanoate, and 2-oxocarboxylic acid metabolism. Interestingly, glycine, serine, and threonine metabolism were found to be important both in the metabolome and transcriptome-metabolome correlation analyses, suggesting their essential role in enhancing the salt tolerance of M. tricuspidata. Collectively, our study not only revealed the molecular mechanism of salt tolerance in M. tricuspidata, but also provided a new perspective for future salt-tolerant breeding and improvement in salt land for this species.
Collapse
Affiliation(s)
- Dezong Sui
- Jiangsu Academy of Forestry, Nanjing 211153, China; (D.S.); (B.W.)
| | - Baosong Wang
- Jiangsu Academy of Forestry, Nanjing 211153, China; (D.S.); (B.W.)
| | - Yousry A. El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC V6T IZ4, Canada;
| | - Lei Wang
- Jiangsu Academy of Forestry, Nanjing 211153, China; (D.S.); (B.W.)
| |
Collapse
|
7
|
Bao Y, He M, Zhang C, Jiang S, Zhao L, Ye Z, Sun Q, Xia Z, Zou M. Advancing understanding of Ficus carica: a comprehensive genomic analysis reveals evolutionary patterns and metabolic pathway insights. FRONTIERS IN PLANT SCIENCE 2023; 14:1298417. [PMID: 38155853 PMCID: PMC10754049 DOI: 10.3389/fpls.2023.1298417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 11/20/2023] [Indexed: 12/30/2023]
Abstract
Ficus carica L. (dioecious), the most significant commercial species in the genus Ficus, which has been cultivated for more than 11,000 years and was one of the first species to be domesticated. Herein, we reported the most comprehensive F. carica genome currently. The contig N50 of the Orphan fig was 9.78 Mb, and genome size was 366.34 Mb with 13 chromosomes. Based on the high-quality genome, we discovered that F. carica diverged from Ficus microcarpa ~34 MYA, and a WGD event took place about 2─3 MYA. Throughout the evolutionary history of F. carica, chromosomes 2, 8, and 10 had experienced chromosome recombination, while chromosome 3 saw a fusion and fission. It is worth proposing that the chromosome 9 experienced both inversion and translocation, which facilitated the emergence of the F. carica as a new species. And the selections of F. carica for the genes of recombination chromosomal fragment are compatible with their goal of domestication. In addition, we found that the F. carica has the FhAG2 gene, but there are structural deletions and positional jumps. This gene is thought to replace the one needed for female common type F. carica to be pollinated. Subsequently, we conducted genomic, transcriptomic, and metabolomic analysis to demonstrate significant differences in the expression of CHS among different varieties of F. carica. The CHS playing an important role in the anthocyanin metabolism pathway of F. carica. Moreover, the CHS gene of F. carica has a different evolutionary trend compared to other Ficus species. These high-quality genome assembly, transcriptomic, and metabolomic resources further enrich F. carica genomics and provide insights for studying the chromosomes evolution, sexual system, and color characteristics of Ficus.
Collapse
Affiliation(s)
- Yuting Bao
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Miaohua He
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Chenji Zhang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
- College of Agriculture, China Agricultural University, Beijing, China
| | - Sirong Jiang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Long Zhao
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, Qinghai, China
| | - Zhengwen Ye
- Forestry and Fruit Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Qian Sun
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
- College of Life Science and Technology, Guangxi University, Guangxi, China
| | - Zhiqiang Xia
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Meiling Zou
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| |
Collapse
|
8
|
Lv R, Gou X, Li N, Zhang Z, Wang C, Wang R, Wang B, Yang C, Gong L, Zhang H, Liu B. Chromosome translocation affects multiple phenotypes, causes genome-wide dysregulation of gene expression, and remodels metabolome in hexaploid wheat. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1564-1582. [PMID: 37265000 DOI: 10.1111/tpj.16338] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/17/2023] [Accepted: 05/30/2023] [Indexed: 06/03/2023]
Abstract
Chromosomal rearrangements (CRs) may occur in newly formed polyploids due to compromised meiotic fidelity. Moreover, CRs can be more readily tolerated in polyploids allowing their longer-term retention and hence potential spreading/fixation within a lineage. The direct functional consequences of CRs in plant polyploids remain unexplored. Here, we identified a heterozygous individual from a synthetic allohexaploid wheat in which the terminal parts of the long-arms of chromosomes 2D (approximately 193 Mb) and 4A (approximately 167 Mb) were reciprocally translocated. Five homogeneous translocation lines including both unbalanced and balanced types were developed by selfing fertilization of the founder mutant (RT [2DL; 4AL]-ter/1, reciprocal translocation). We investigated impacts of these translocations on phenotype, genome-wide gene expression and metabolome. We find that, compared with sibling wild-type, CRs in the form of both unbalanced and balanced translocations induced substantial changes of gene expression primarily via trans-regulation in the nascent allopolyploid wheat. The CRs also manifested clear phenotypic and metabolic consequences. In particular, the genetically balanced, stable reciprocal translocations lines showed immediate enhanced reproductive fitness relative to wild type. Our results underscore the profound impact of CRs on gene expression in nascent allopolyploids with wide-ranging phenotypic and metabolic consequences, suggesting CRs are an important source of genetic variation that can be exploited for crop breeding.
Collapse
Affiliation(s)
- Ruili Lv
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Xiaowan Gou
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
- School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Zhibin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Changyi Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Ruisi Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Bin Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Chunwu Yang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Huakun Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| |
Collapse
|
9
|
Liu Y, Li Y, Liu Z, Wang L, Bi Z, Sun C, Yao P, Zhang J, Bai J, Zeng Y. Integrated transcriptomic and metabolomic analysis revealed altitude-related regulatory mechanisms on flavonoid accumulation in potato tubers. Food Res Int 2023; 170:112997. [PMID: 37316022 DOI: 10.1016/j.foodres.2023.112997] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/14/2023] [Accepted: 05/16/2023] [Indexed: 06/16/2023]
Abstract
Not least because it is adaptable to a variety of geographies and climates, potato (Solanum tuberosum L.) is grown across much of the world. Pigmented potato tubers have been found to contain large quantities of flavonoids, which have various functional roles and act as antioxidants in the human diet. However, the effect of altitude on the biosynthesis and accumulation of flavonoids in potato tubers is poorly characterized. Here we carried out an integrated metabolomic and transcriptomic study in order to evaluate how cultivation at low (800 m), moderate (1800 m), and high (3600 m) altitude affects flavonoid biosynthesis in pigmented potato tubers. Both red and purple potato tubers grown at a high altitude contained the highest flavonoid content, and the most highly pigmented flesh, followed by those grown at a low altitude. Co-expression network analysis revealed three modules containing genes which were positively correlated with altitude-responsive flavonoid accumulation. The anthocyanin repressors StMYBATV and StMYB3 exhibited a significant positive relationship with altitude-responsive flavonoid accumulation. The repressive function of StMYB3 was further verified in tobacco flowers and potato tubers. The results presented here add to the growing body of knowledge regarding the response of flavonoid biosynthesis to environmental conditions, and should aid in efforts to develop novel varieties of pigmented potatoes for use across different geographies.
Collapse
Affiliation(s)
- Yuhui Liu
- State Key Laboratory of Aridland Crop Science/Agronomy College, Gansu Agricultural University, Lanzhou 730070, China.
| | - Yuanming Li
- State Key Laboratory of Aridland Crop Science/Agronomy College, Gansu Agricultural University, Lanzhou 730070, China
| | - Zhen Liu
- State Key Laboratory of Aridland Crop Science/Agronomy College, Gansu Agricultural University, Lanzhou 730070, China
| | - Lei Wang
- Potato Research Center, Hebei North University, Zhangjiakou 075000, China
| | - Zhenzhen Bi
- State Key Laboratory of Aridland Crop Science/Agronomy College, Gansu Agricultural University, Lanzhou 730070, China
| | - Chao Sun
- State Key Laboratory of Aridland Crop Science/Agronomy College, Gansu Agricultural University, Lanzhou 730070, China
| | - Panfeng Yao
- State Key Laboratory of Aridland Crop Science/Agronomy College, Gansu Agricultural University, Lanzhou 730070, China
| | - Junlian Zhang
- State Key Laboratory of Aridland Crop Science/Agronomy College, Gansu Agricultural University, Lanzhou 730070, China
| | - Jiangping Bai
- State Key Laboratory of Aridland Crop Science/Agronomy College, Gansu Agricultural University, Lanzhou 730070, China
| | - Yuting Zeng
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lasa 850000, China
| |
Collapse
|
10
|
Xin J, Che T, Huang X, Yan H, Jiang S. A comprehensive view of metabolic responses to CYP98 perturbation in ancestral plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107793. [PMID: 37276808 DOI: 10.1016/j.plaphy.2023.107793] [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: 01/10/2023] [Revised: 05/20/2023] [Accepted: 05/22/2023] [Indexed: 06/07/2023]
Abstract
Cytochrome P450 monooxygenase 98 (CYP98) is a critical rate-limiting enzyme of the phenylpropanoid pathway. One of the end-product of the phenylpropanoid pathway is a lignin monomer, although the occurrence of lignin in bryophytes is controversial. Here we investigated the functions of PpCYP98 in Physcomitrium patens by transcriptome and metabolome analyses. We identified 5266 differentially expressed genes (DEGs) and 68 differentially abundant secondary metabolites between wild-type and ΔPpCYP98 gametophores. Of the identified metabolites, 23 phenolic acids were identified, with only one showing upregulation. Among the phenolic acids, 4-coumaroyl tartaric acid and chlorogenic acid showed significant decreases. Declines were also observed in coniferylaldehyde and coniferin, precursor substances and downstream products of the lignin monomer coniferyl alcohol, respectively. Thus, the pre-lignin synthesis pathway already exists in bryophytes, and PpCYP98 plays vital roles in this pathway. Besides, most flavonoids show significant reductions, including eriodyctiol, dihydroquecetin, and dihydromyricetin, whereas naringenin chalone and dihydrokaempferol were increased after PpCYP98 knockout. Therefore, the synthesis of flavonoids shares the core pathway with phenylpropanoids and mainly starts from caffeoyl-CoA, that is the compound of divergence between the two pathways in moss. PpCYP98 showed systemic effects on metabolisms, including carbohydrate, fatty acid, and hormonal signaling transductions, suggesting that PpCYP98 might indirectly regulate carbon influx allocation. Our results demonstrated roles of PpCYP98 were essential for the development of the early landing plant.
Collapse
Affiliation(s)
- Jiankang Xin
- School of Life Sciences, Guizhou Normal University, Guiyang, 550001, China.
| | - Tianmin Che
- School of Life Sciences, Guizhou Normal University, Guiyang, 550001, China.
| | - Xiaolong Huang
- School of Life Sciences, Guizhou Normal University, Guiyang, 550001, China; Key Laboratory of Plant Physiology and Development Regulation, Guizhou Normal University, Guiyang, 550001, China; Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Normal University, Guiyang, 550001, China.
| | - Huiqing Yan
- School of Life Sciences, Guizhou Normal University, Guiyang, 550001, China.
| | - Shan Jiang
- School of Life Sciences, Guizhou Normal University, Guiyang, 550001, China; College of International Education, Guizhou Normal University, Guiyang, 550001, China.
| |
Collapse
|
11
|
Gao P, Qi Y, Li L, Yang S, Liu J, Wei H, Huang F, Yu L. Amorphophallus muelleri activates ferulic acid and phenylpropane biosynthesis pathways to defend against Fusarium solani infection. FRONTIERS IN PLANT SCIENCE 2023; 14:1207970. [PMID: 37476174 PMCID: PMC10354422 DOI: 10.3389/fpls.2023.1207970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 06/19/2023] [Indexed: 07/22/2023]
Abstract
Amorphophallus sp. is an economically important crop for rural revitalization in southwest China. However, Fusarium solani often infects Amorphophallus sp. corms during storage, damaging the corm quality and affecting leaf elongation and flowering in the subsequent crop. In this study, the mechanism of resistance to F. solani was investigated in the leaf bud and flower bud corms of Amorphophallus muelleri through transcriptome and metabolome analyses. A total of 42.52 Gb clean reads and 1,525 metabolites were detected in a total of 12 samples including 3 samples each of disease-free leaf bud corms (LC), leaf bud corms inoculated with F. solani for three days (LD), disease-free flower bud corms (FC), and flower bud corms inoculated with F. solani for three days (FD). Transcriptome, metabolome, and conjoint analyses showed that 'MAPK signal transduction', 'plant-pathogen interaction', 'plant hormone signal transduction', and other secondary metabolite biosynthesis pathways, including 'phenylpropane biosynthesis', 'arachidonic acid metabolism', 'stilbene, diarylheptane and gingerolin biosynthesis', and 'isoquinoline alkaloids biosynthesis', among others, were involved in the defense response of A. muelleri to F. solani. Ultimately, the expression of six genes of interest (AmCDPK20, AmRBOH, AmWRKY33, Am4CL, Am POD and AmCYP73A1) was validated by real-time fluorescence quantitative polymerase chain reaction, and the results indicated that these genes were involved in the response of A. muelleri to F. solani. Ferulic acid inhibited the growth of F. solani, reducing the harm caused by F. solani to A. muelleri corms to a certain extent. Overall, this study lays a strong foundation for further investigation of the interaction between A. muelleri and F. solani, and provides a list of genes for the future breeding of F. solani-resistant A. muelleri cultivars.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Lei Yu
- *Correspondence: Feiyan Huang, ; Lei Yu,
| |
Collapse
|
12
|
Ma X, Lu L, Yao F, Fang M, Wang P, Meng J, Shao K, Sun X, Zhang Y. High-quality genome assembly and multi-omics analysis of pigment synthesis pathway in Auricularia cornea. Front Microbiol 2023; 14:1211795. [PMID: 37396365 PMCID: PMC10308021 DOI: 10.3389/fmicb.2023.1211795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 05/22/2023] [Indexed: 07/04/2023] Open
Abstract
Owing to its great market potential for food and health care, white Auricularia cornea, a rare edible fungus, has received increased attention in recent years. This study presents a high-quality genome assembly of A. cornea and multi-omics analysis of its pigment synthesis pathway. Continuous Long Reads libraries, combined with Hi-C-assisted assembly were used to assemble of white A. cornea. Based on this data, we analyzed the transcriptome and metabolome of purple and white strains during the mycelium, primordium, and fruiting body stages. Finally, we obtained the genome of A.cornea assembled from 13 clusters. Comparative and evolutionary analysis suggests that A.cornea is more closely related to Auricularia subglabra than to Auricularia heimuer. The divergence of white/purple A.cornea occurred approximately 40,000 years ago, and there were numerous inversions and translocations between homologous regions of the two genomes. Purple strain synthesized pigment via the shikimate pathway. The pigment in the fruiting body of A. cornea was γ-glutaminyl-3,4-dihydroxy-benzoate. During pigment synthesis, α-D-glucose-1P, citrate, 2-Oxoglutarate, and glutamate were four important intermediate metabolites, whereas polyphenol oxidase and other 20 enzyme genes were the key enzymes. This study sheds light on the genetic blueprint and evolutionary history of the white A.cornea genome, revealing the mechanism of pigment synthesis in A.cornea. It has important theoretical and practical implications for understanding the evolution of basidiomycetes, molecular breeding of white A.cornea, and deciphering the genetic regulations of edible fungi. Additionally, it provides valuable insights for the study of phenotypic traits in other edible fungi.
Collapse
Affiliation(s)
- Xiaoxu Ma
- Lab of Genetic Breeding of Edible Fungi, Horticultural, College of Horticulture, Jilin Agricultural University, Changchun, China
- Guizhou Academy of Agricultural Sciences, Guizhou Key Laboratory of Edible Fungi Breeding, Guiyang, China
| | - Lixin Lu
- Lab of Genetic Breeding of Edible Fungi, Horticultural, College of Horticulture, Jilin Agricultural University, Changchun, China
| | - Fangjie Yao
- Lab of Genetic Breeding of Edible Fungi, Horticultural, College of Horticulture, Jilin Agricultural University, Changchun, China
- Country Engineering Research Centre of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Ming Fang
- Lab of Genetic Breeding of Edible Fungi, Horticultural, College of Horticulture, Jilin Agricultural University, Changchun, China
| | - Peng Wang
- Economic Plants Research Insitute, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Jingjing Meng
- Lab of Genetic Breeding of Edible Fungi, Horticultural, College of Horticulture, Jilin Agricultural University, Changchun, China
| | - Kaisheng Shao
- Guizhou Academy of Agricultural Sciences, Guizhou Key Laboratory of Edible Fungi Breeding, Guiyang, China
| | - Xu Sun
- Guizhou Academy of Agricultural Sciences, Guizhou Key Laboratory of Edible Fungi Breeding, Guiyang, China
| | - Youmin Zhang
- Lab of Genetic Breeding of Edible Fungi, Horticultural, College of Horticulture, Jilin Agricultural University, Changchun, China
| |
Collapse
|
13
|
Chen M, Chang C, Li H, Huang L, Zhou Z, Zhu J, Liu D. Metabolome analysis reveals flavonoid changes during the leaf color transition in Populus × euramericana 'Zhonghuahongye'. FRONTIERS IN PLANT SCIENCE 2023; 14:1162893. [PMID: 37223816 PMCID: PMC10200940 DOI: 10.3389/fpls.2023.1162893] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 04/19/2023] [Indexed: 05/25/2023]
Abstract
Introduction To investigate the mechanism of leaf color change at different stages in Populus × euramericana 'Zhonghuahongye' ('Zhonghong' poplar). Methods Leaf color phenotypes were determined and a metabolomic analysis was performed on leaves at three stages (R1, R2 and R3). Results The a*, C* and chromatic light values of the leaves decreased by 108.91%, 52.08% and 113.34%, while the brightness L values and chromatic b* values gradually increased by 36.01% and 13.94%, respectively. In the differential metabolite assay, 81 differentially expressed metabolites were detected in the R1 vs. R3 comparison, 45 were detected in the R1 vs. R2 comparison, and 75 were detected in the R2 vs. R3 comparison. Ten metabolites showed significant differences in all comparisons, which were mostly flavonoid metabolites. The metabolites that were upregulated in the three periods were cyanidin 3,5-O-diglucoside, delphinidin, and gallocatechin, with flavonoid metabolites accounting for the largest proportion and malvidin 3- O-galactoside as the primary downregulated metabolite. The color shift of red leaves from a bright purplish red to a brownish green was associated with the downregulation of malvidin 3-O-glucoside, cyanidin, naringenin, and dihydromyricetin. Discussion Here, we analyzed the expression of flavonoid metabolites in the leaves of 'Zhonghong' poplar at three stages and identified key metabolites closely related to leaf color change, providing an important genetic basis for the genetic improvement of this cultivar.
Collapse
Affiliation(s)
- Mengjiao Chen
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, Henan, China
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, Guangdong, China
| | - Cuifang Chang
- College of Forestry, Henan Agricultural University, Zhengzhou, Henan, China
| | - Hui Li
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, Henan, China
| | - Lin Huang
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, Henan, China
| | - Zongshun Zhou
- China Experimental Centre of Subtropical Forestry, Chinese Academy of Forestry, Xinyu, Jiangxi, China
| | - Jingle Zhu
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, Henan, China
| | - Dan Liu
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, Shandong, China
| |
Collapse
|
14
|
Xu R, Luo M, Xu J, Wang M, Huang B, Miao Y, Liu D. Integrative Analysis of Metabolomic and Transcriptomic Data Reveals the Mechanism of Color Formation in Corms of Pinellia ternata. Int J Mol Sci 2023; 24:ijms24097990. [PMID: 37175702 PMCID: PMC10178707 DOI: 10.3390/ijms24097990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/24/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
Pinellia ternata (Thunb.) Breit. (P. ternata) is a very important plant that is commonly used in traditional Chinese medicine. Its corms can be used as medicine and function to alleviate cough, headache, and phlegm. The epidermis of P. ternata corms is often light yellow to yellow in color; however, within the range of P. ternata found in JingZhou City in Hubei Province, China, there is a form of P. ternata in which the epidermis of the corm is red. We found that the total flavonoid content of red P. ternata corms is significantly higher than that of yellow P. ternata corms. The objective of this study was to understand the molecular mechanisms behind the difference in epidermal color between the two forms of P. ternata. The results showed that a high content of anthocyanidin was responsible for the red epidermal color in P. ternata, and 15 metabolites, including cyanidin-3-O-rutinoside-5-O-glucoside, cyanidin-3-O-glucoside, and cyanidin-3-O-rutinoside, were screened as potential color markers in P. ternata through metabolomic analysis. Based on an analysis of the transcriptome, seven genes, including PtCHS1, PtCHS2, PtCHI1, PtDFR5, PtANS, PtUPD-GT2, and PtUPD-GT3, were found to have important effects on the biosynthesis of anthocyanins in the P. ternata corm epidermis. Furthermore, two transcription factors (TFs), bHLH1 and bHLH2, may have regulatory functions in the biosynthesis of anthocyanins in red P. ternata corms. Using an integrative analysis of the metabolomic and transcriptomic data, we identified five genes, PtCHI, PtDFR2, PtUPD-GT1, PtUPD-GT2, and PtUPD-GT3, that may play important roles in the presence of the red epidermis color in P. ternata corms.
Collapse
Affiliation(s)
- Rong Xu
- Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Ming Luo
- Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Jiawei Xu
- Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Mingxing Wang
- Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Bisheng Huang
- Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Yuhuan Miao
- Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Dahui Liu
- Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, Hubei University of Chinese Medicine, Wuhan 430065, China
| |
Collapse
|
15
|
Cao W, Sun W, Chen S, Jia X, Wang J, Lai S. Comprehensive analysis of microRNA and metabolic profiles in bovine seminal plasma of different semen quality. Front Vet Sci 2023; 10:1088148. [PMID: 37056229 PMCID: PMC10086235 DOI: 10.3389/fvets.2023.1088148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 03/09/2023] [Indexed: 03/30/2023] Open
Abstract
BackgroundSeminal plasma plays a pivotal role in modulating sperm viability and function. However, the underlying mechanisms have not been fully elucidated.MethodIn this study, the bull semen production records of core breeding farms and bull stations in the past 10 years were analyzed.ResultsWe found that the semen of 5-year-old bulls collected for the first time is of the best quality (p < 0.05). Despite the bull semen collected under the above conditions, low-quality sperm is still obtained from part of bulls due to individual differences. Interestingly, seminal plasma from normal semen is capable of improving low-quality semen motility. To identify the potential key factors in seminal plasma, the differences in miRNA and metabolite profiles between normal and low-quality seminal plasma were analyzed. We found that 59 miRNAs were differently expressed, including 38 up-regulated and 21 down-regulated miRNAs. Three hundred and ninety-one and 327 significantly different metabolites were identified from the positive and negative ion models, respectively. These multiple miRNAs and metabolites collectively contribute to the motility of sperm, subsequently, affect semen quality.DiscussionTogether, these results not only revealed the critical factors of seminal plasma improving sperm quality but also provided potential miRNA- or metabolite-based biomarkers to identify the high semen quality.
Collapse
Affiliation(s)
- Wei Cao
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, Chengdu, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- College of Animal Science and Technology, Sichuan Province General Station of Animal Husbandry, Chengdu, China
| | - Wenqiang Sun
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, Chengdu, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Shiyi Chen
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, Chengdu, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xianbo Jia
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, Chengdu, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Jie Wang
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, Chengdu, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Songjia Lai
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, Chengdu, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- *Correspondence: Songjia Lai
| |
Collapse
|
16
|
Luo Y, Deng M, Zhang X, Zhang D, Cai W, Long Y, Xiong X, Li Y. Integrative Transcriptomic and Metabolomic Analysis Reveals the Molecular Mechanism of Red Maple ( Acer rubrum L.) Leaf Coloring. Metabolites 2023; 13:metabo13040464. [PMID: 37110123 PMCID: PMC10143518 DOI: 10.3390/metabo13040464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/09/2023] [Accepted: 03/20/2023] [Indexed: 04/29/2023] Open
Abstract
This study employed a combination of ultraviolet spectrophotometry, LC-ESI-MS/MS system, and RNA-sequencing technology; the extracts and isolation of total RNA from the red and yellow leaf strains of red maple (Acer rubrum L.) at different developmental stages were subjected to an intercomparison of the dynamic content of chlorophyll and total anthocyanin, flavonoid metabolite fingerprinting, and gene expression. The metabonomic results indicated that one hundred and ninety-two flavonoids were identified, which could be classified into eight categories in the red maple leaves. Among them, 39% and 19% were flavones and flavonols, respectively. The metabolomic analysis identified 23, 32, 24, 24, 38, and 41 DAMs in the AR1018r vs. AR1031r comparison, the AR1018r vs. AR1119r comparison, the AR1031r vs. AR1119r comparison, the AR1018y vs. AR1031y comparison, the AR1018y vs. AR1119y comparison, and the AR1031y vs. AR1119y comparison, respectively. In total, 6003 and 8888 DEGs were identified in AR1018r vs. AR1031r comparison and in the AR1018y vs. AR1031y comparison, respectively. The GO and KEGG analyses showed that the DEGs were mainly involved in plant hormone signal transduction, flavonoid biosynthesis, and other metabolite metabolic processes. The comprehensive analysis revealed that caffeoyl-CoA 3-O-methyltransferase (Cluster-28704.45358 and Cluster-28704.50421) was up-regulated in the red strain but down-regulated in the yellow strain, while Peonidin 3-O-glucoside chloride and Pelargonidin 3-O-beta-D-glucoside were up-regulated in both the red and yellow strains. By successfully integrating the analyses on the behavior of pigment accumulation, dynamics of flavonoids, and differentially expressed genes with omics tools, the regulation mechanisms underlying leaf coloring in red maple at the transcriptomic and metabolomic levels were demonstrated, and the results provide valuable information for further research on gene function in red maple.
Collapse
Affiliation(s)
- Yuanyuan Luo
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
- College of Oriental Science & Technology, Hunan Agricultural University, Changsha 410128, China
| | - Min Deng
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Xia Zhang
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha 410128, China
- Hunan Mid-Subtropical Quality Plant Breeding and Utilization Engineering Technology Research Center, Changsha 410128, China
| | - Damao Zhang
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha 410128, China
- Hunan Mid-Subtropical Quality Plant Breeding and Utilization Engineering Technology Research Center, Changsha 410128, China
| | - Wenqi Cai
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha 410128, China
- Hunan Mid-Subtropical Quality Plant Breeding and Utilization Engineering Technology Research Center, Changsha 410128, China
| | - Yuelin Long
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
- College of Landscape Architecture and Art Design, Hunan Agricultural University, Changsha 410128, China
| | - Xingyao Xiong
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Yanlin Li
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha 410128, China
- Hunan Mid-Subtropical Quality Plant Breeding and Utilization Engineering Technology Research Center, Changsha 410128, China
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Kunpeng Institute of Modern Agriculture, Foshan 528200, China
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| |
Collapse
|
17
|
Peng XQ, Ai YJ, Pu YT, Wang XJ, Li YH, Wang Z, Zhuang WB, Yu BJ, Zhu ZQ. Transcriptome and metabolome analyses reveal molecular mechanisms of anthocyanin-related leaf color variation in poplar ( Populus deltoides) cultivars. FRONTIERS IN PLANT SCIENCE 2023; 14:1103468. [PMID: 36909390 PMCID: PMC9998943 DOI: 10.3389/fpls.2023.1103468] [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: 11/20/2022] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Colored-leaf plants are increasingly popular for their aesthetic, ecological, and social value, which are important materials for research on the regulation of plant pigments. However, anthocyanin components and the molecular mechanisms of anthocyanin biosynthesis in colored-leaf poplar remain unclear. Consequently, an integrative analysis of transcriptome and metabolome is performed to identify the key metabolic pathways and key genes, which could contribute to the molecular mechanism of anthocyanin biosynthesis in the colored-leaf cultivars poplar. METHODS In this study, integrated metabolite and transcriptome analysis was performed to explore the anthocyanin composition and the specific regulatory network of anthocyanin biosynthesis in the purple leaves of the cultivars 'Quanhong' (QHP) and 'Zhongshanyuan' (ZSY). Correlation analysis between RNA-seq data and metabolite profiles were also performed to explore the candidate genes associated with anthocyanin biosynthesis. R2R3-MYB and bHLH TFs with differential expression levels were used to perform a correlation analysis with differentially accumulated anthocyanins. RESULTS AND DISCUSSION A total of 39 anthocyanin compounds were detected by LC-MS/MS analysis. Twelve cyanidins, seven pelargonidins, five delphinidins, and five procyanidins were identified as the major anthocyanin compounds, which were differentially accumulated in purple leaves of QHP and ZSY. The major genes associated with anthocyanin biosynthesis, including structural genes and transcription factors, were differentially expressed in purple leaves of QHP and ZSY through RNA-sequencing (RNA-seq) data analysis, which was consistent with quantitative real-time PCR analysis results. Correlation analysis between RNA-seq data and metabolite profiles showed that the expression patterns of certain differentially expressed genes in the anthocyanin biosynthesis pathway were strongly correlated with the differential accumulation of anthocyanins. One R2R3-MYB subfamily member in the SG5 subgroup, Podel.04G021100, showed a similar expression pattern to some structural genes. This gene was strongly correlated with 16 anthocyanin compounds, indicating that Podel.04G021100 might be involved in the regulation of anthocyanin biosynthesis. These results contribute to a systematic and comprehensive understanding of anthocyanin accumulation and to the molecular mechanisms of anthocyanin biosynthesis in QHP and ZSY.
Collapse
Affiliation(s)
- Xu Qian Peng
- College of Tea Science, Guizhou University, Guiyang, China
| | - Yu Jie Ai
- College of Tea Science, Guizhou University, Guiyang, China
| | - Yu Ting Pu
- College of Tea Science, Guizhou University, Guiyang, China
| | - Xiao Jing Wang
- College of Tea Science, Guizhou University, Guiyang, China
| | - Yu Hang Li
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, China
| | - Zhong Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, China
| | - Wei Bing Zhuang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, China
- Laboratory of Plant Stress Biology, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
- Laizhou, Ornamental Research Center, Hongshun Plum Planting Technology Co., Ltd, Yantai, China
| | - Bing Jun Yu
- Laboratory of Plant Stress Biology, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Zhi Qi Zhu
- Laizhou, Ornamental Research Center, Hongshun Plum Planting Technology Co., Ltd, Yantai, China
| |
Collapse
|
18
|
Ji N, Wang Q, Li S, Wen J, Wang L, Ding X, Zhao S, Feng H. Metabolic profile and transcriptome reveal the mystery of petal blotch formation in rose. BMC PLANT BIOLOGY 2023; 23:46. [PMID: 36670355 PMCID: PMC9854060 DOI: 10.1186/s12870-023-04057-6] [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: 09/20/2022] [Accepted: 01/11/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Petal blotch is a unique ornamental trait in angiosperm families, and blotch in rose petal is rare and has great esthetic value. However, the cause of the formation of petal blotch in rose is still unclear. The influence of key enzyme genes and regulatory genes in the pigment synthesis pathways needs to be explored and clarified. RESULTS In this study, the rose cultivar 'Sunset Babylon Eyes' with rose-red to dark red blotch at the base of petal was selected as the experimental material. The HPLC-DAD and UPLC-TQ-MS analyses indicated that only cyanidin 3,5-O-diglucoside (Cy3G5G) contributed to the blotch pigmentation of 'Sunset Babylon Eyes', and the amounts of Cy3G5G varied at different developmental stages. Only flavonols but no flavone were found in blotch and non-blotch parts. As a consequence, kaempferol and its derivatives as well as quercetin and its derivatives may act as background colors during flower developmental stages. Despite of the differences in composition, the total content of carotenoids in blotch and non-blotch parts were similar, and carotenoids may just make the petals show a brighter color. Transcriptomic data, quantitative real-time PCR and promoter sequence analyses indicated that RC7G0058400 (F3'H), RC6G0470600 (DFR) and RC7G0212200 (ANS) may be the key enzyme genes for the early formation and color deepening of blotch at later stages. As for two transcription factor, RC7G0019000 (MYB) and RC1G0363600 (WRKY) may bind to the promoters of critical enzyme genes, or RC1G0363600 (WRKY) may bind to the promoter of RC7G0019000 (MYB) to activate the anthocyanin accumulation in blotch parts of 'Sunset Babylon Eyes'. CONCLUSIONS Our findings provide a theoretical basis for the understanding of the chemical and molecular mechanism for the formation of petal blotch in rose.
Collapse
Affiliation(s)
- Naizhe Ji
- Beijing Key Lab of Greening Plants Breeding, Beijing Academy of Forestry and Landscape Architecture, Beijing, China
| | - Qianyu Wang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shanshan Li
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jiaxin Wen
- College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Liangsheng Wang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaohao Ding
- College of Food Science, Fuyang Normal University, Fuyang, China
| | - Shiwei Zhao
- Beijing Key Lab of Greening Plants Breeding, Beijing Academy of Forestry and Landscape Architecture, Beijing, China.
| | - Hui Feng
- Beijing Key Lab of Greening Plants Breeding, Beijing Academy of Forestry and Landscape Architecture, Beijing, China.
| |
Collapse
|
19
|
Colzi I, Gonnelli C, Vergata C, Golia G, Coppi A, Castellani MB, Giovino A, Buti M, Sabato T, Capuana M, Aprile A, De Bellis L, Cicatelli A, Guarino F, Castiglione S, Ioannou AG, Fotopoulos V, Martinelli F. Transgenerational effects of chromium stress at the phenotypic and molecular level in Arabidopsis thaliana. JOURNAL OF HAZARDOUS MATERIALS 2023; 442:130092. [PMID: 36303345 DOI: 10.1016/j.jhazmat.2022.130092] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/22/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
In this study, we describe the results obtained in a study of the transgenerational phenotypic effects of chromium (Cr) stress on the model plant species Arabidopsis thaliana. The F1 generation derived from parents grown under chronic and medium chronic stress showed significantly higher levels of the maximal effective concentration (EC50) compared with F1 plants generated from unstressed parents. Moreover, F1 plants from Cr-stressed parents showed a higher germination rate when grown in the presence of Cr. F1 plants derived from parents cultivated under chronic Cr stress displayed reduced hydrogen peroxide levels under Cr stress compared to controls. At lower Cr stress levels, F1 plants were observed to activate promptly more genes involved in Cr stress responses than F0 plants, implying a memory effect linked to transgenerational priming. At higher Cr levels, and at later stages, F1 plants modulated significantly fewer genes than F0 plants, implying a memory effect leading to Cr stress adaptation. Several bHLH transcription factors were induced by Cr stress in F1 but not in F0 plants, including bHLH100, ORG2 and ORG3. F1 plants optimized gene expression towards pathways linked to iron starvation response. A model of the transcriptional regulation of transgenerational memory to Cr stress is presented here, and could be applied for other heavy metal stresses.
Collapse
Affiliation(s)
- Ilaria Colzi
- Department of Biology, University of Florence, Italy.
| | | | | | | | - Andrea Coppi
- Department of Biology, University of Florence, Italy.
| | | | - Antonio Giovino
- CREA Consiglio per la ricerca in Agricoltura e l'analisi dell'economia agraria, Centro di Ricerca Difesa e Certificazione, Bagheria, Italy.
| | - Matteo Buti
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Italy.
| | | | - Maurizio Capuana
- Institute of Biosciences and Bioresources, National Research Council, Italy.
| | - Alessio Aprile
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy.
| | - Luigi De Bellis
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy.
| | - Angela Cicatelli
- Department of Chemistry and Biology, University of Salerno, Italy.
| | | | | | - Andreas G Ioannou
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, 3603 Lemesos, Cyprus.
| | - Vasileios Fotopoulos
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, 3603 Lemesos, Cyprus.
| | | |
Collapse
|
20
|
Xiao J, Xu X, Li M, Wu X, Guo H. Regulatory network characterization of anthocyanin metabolites in purple sweetpotato via joint transcriptomics and metabolomics. FRONTIERS IN PLANT SCIENCE 2023; 14:1030236. [PMID: 36844045 PMCID: PMC9951203 DOI: 10.3389/fpls.2023.1030236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 01/25/2023] [Indexed: 05/14/2023]
Abstract
INTRODUCTION Sweet potato is an important staple food crop in the world and contains abundant secondary metabolites in its underground tuberous roots. The large accumulation of several categories of secondary metabolites result in colorful pigmentation of the roots. Anthocyanin, is a typical flavonoid compound present in purple sweet potatoes and it contributes to the antioxidant activity. METHODS In this study, we developed joint omics research via by combing the transcriptomic and metabolomic analysis to explore the molecular mechanisms underlying the anthocyanin biosynthesis in purple sweet potato. Four experimental materials with different pigmentation phenotypes, 1143-1 (white root flesh), HS (orange root flesh), Dianziganshu No.88 (DZ88, purple root flesh), and Dianziganshu No.54 (DZ54, dark purple root flesh) were comparably studied. RESULTS AND DISCUSSION We identified 38 differentially accumulated pigment metabolites and 1214 differentially expressed genes from a total of 418 metabolites and 50893 genes detected. There were 14 kinds of anthocyanin detected in DZ88 and DZ54, with glycosylated cyanidin and peonidin as the major components. The significantly enhanced expression levels of multiple structural genes involved in the central anthocyanin metabolic network, such as chalcone isomerase (CHI), flavanone 3-hydroxylase (F3H), dihydroflavonol 4-reductase (DFR), anthocyanidin synthase/leucocyanidin oxygenase (ANS), and glutathione S-transferase (GST) were manifested to be the primary reason why the purple sweet potatoes had a much higher accumulation of anthocyanin. Moreover, the competition or redistribution of the intermediate substrates (i.e. dihydrokaempferol and dihydroquercetin) between the downstream production of anthocyanin products and the flavonoid derivatization (i.e. quercetin and kaempferol) under the regulation of the flavonol synthesis (FLS) gene, might play a crucial role in the metabolite flux repartitioning, which further led to the discrepant pigmentary performances in the purple and non-purple materials. Furthermore, the substantial production of chlorogenic acid, another prominent high-value antioxidant, in DZ88 and DZ54 seemed to be an interrelated but independent pathway differentiated from the anthocyanin biosynthesis. Collectively, these data from the transcriptomic and metabolomic analysis of four kinds of sweet potatoes provide insight to understand the molecular mechanisms of the coloring mechanism in purple sweet potatoes.
Collapse
|
21
|
Li Y, Li H, Wang S, Li J, Bacha SAS, Xu G, Li J. Metabolomic and transcriptomic analyses of the flavonoid biosynthetic pathway in blueberry ( Vaccinium spp.). FRONTIERS IN PLANT SCIENCE 2023; 14:1082245. [PMID: 37152168 PMCID: PMC10157174 DOI: 10.3389/fpls.2023.1082245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 03/29/2023] [Indexed: 05/09/2023]
Abstract
As a highly economic small fruit crop, blueberry is enjoyed by most people in terms of color, taste, and rich nutrition. To better understand its coloring mechanism on the process of ripening, an integrative analysis of the metabolome and transcriptome profiles was performed in three blueberry varieties at three developmental stages. In this study, 41 flavonoid metabolites closely related to the coloring in blueberry samples were analyzed. It turned out that the most differential metabolites in the ripening processes were delphinidin-3-O-arabinoside (dpara), peonidin-3-O-glucoside (pnglu), and delphinidin-3-O-galactoside (dpgal), while the most differential metabolites among different varieties were flavonols. Furthermore, to obtain more accurate and comprehensive transcripts of blueberry during the developmental stages, PacBio and Illumina sequencing technology were combined to obtain the transcriptome of the blueberry variety Misty, for the very first time. Finally, by applying the gene coexpression network analysis, the darkviolet and bisque4 modules related to flavonoid synthesis were determined, and the key genes related to two flavonoid 3', 5'-hydroxylase (F3'5'H) genes in the darkviolet module and one bHLH transcription factor in the bisque4 module were predicted. It is believed that our findings could provide valuable information for the future study on the molecular mechanism of flavonoid metabolites and flavonoid synthesis pathways in blueberries.
Collapse
Affiliation(s)
- Yinping Li
- Laboratory of Quality and Safety Risk Assessment for Fruit, Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
| | - Haifei Li
- Laboratory of Quality and Safety Risk Assessment for Fruit, Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
| | - Shiyao Wang
- Department of Applied Biosciences, Toyo University, Ora-gun, Japan
| | - Jing Li
- Laboratory of Quality and Safety Risk Assessment for Fruit, Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
| | - Syed Asim Shah Bacha
- Laboratory of Quality and Safety Risk Assessment for Fruit, Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
| | - Guofeng Xu
- Laboratory of Quality and Safety Risk Assessment for Fruit, Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
- *Correspondence: Guofeng Xu, ; Jing Li,
| | - Jing Li
- Laboratory of Quality and Safety Risk Assessment for Fruit, Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
- *Correspondence: Guofeng Xu, ; Jing Li,
| |
Collapse
|
22
|
Liu Y, Li Y, Liu Z, Wang L, Lin-Wang K, Zhu J, Bi Z, Sun C, Zhang J, Bai J. Integrative analysis of metabolome and transcriptome reveals a dynamic regulatory network of potato tuber pigmentation. iScience 2022; 26:105903. [PMID: 36818280 PMCID: PMC9932491 DOI: 10.1016/j.isci.2022.105903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 11/12/2022] [Accepted: 12/26/2022] [Indexed: 12/30/2022] Open
Abstract
Potatoes consist of flavonoids that provide health benefits for human consumers. To learn more about how potato tuber flavonoid accumulation and flesh pigmentation are controlled, we analyzed the transcriptomic and metabolomic profile of potato tubers from three colored potato clones at three developmental phases using an integrated approach. From the 72 flavonoids identified in pigmented flesh, differential abundance was noted for anthocyanins, flavonols, and flavones. Weighted gene co-expression network analysis further allowed modules and candidate genes that positively or negatively regulate flavonoid biosynthesis to be identified. Furthermore, an R2R3-MYB repressor StMYB3 and an R3-MYB repressor StMYBATV involved in the modulation of anthocyanin biosynthesis during tuber development were identified. Both StMYB3 and StMYBATV could interact with the cofactor StbHLH1 and repress anthocyanin biosynthesis. Our results indicate a feedback regulatory mechanism of a coordinated MYB activator-repressor network on fine-tuning of potato tuber pigmentation during tuber development.
Collapse
Affiliation(s)
- Yuhui Liu
- State Key Laboratory of Aridland Crop Science/Agronomy College, Gansu Agricultural University, Lanzhou 730070, China
| | - Yuanming Li
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Zhen Liu
- State Key Laboratory of Aridland Crop Science/Agronomy College, Gansu Agricultural University, Lanzhou 730070, China
| | - Lei Wang
- Potato Research Center, Hebei North University, Zhangjiakou 075000, China
| | - Kui Lin-Wang
- The New Zealand Institute for Plant and Food Research Limited, Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
| | - Jinyong Zhu
- State Key Laboratory of Aridland Crop Science/Agronomy College, Gansu Agricultural University, Lanzhou 730070, China
| | - Zhenzhen Bi
- State Key Laboratory of Aridland Crop Science/Agronomy College, Gansu Agricultural University, Lanzhou 730070, China
| | - Chao Sun
- State Key Laboratory of Aridland Crop Science/Agronomy College, Gansu Agricultural University, Lanzhou 730070, China
| | - Junlian Zhang
- State Key Laboratory of Aridland Crop Science/Agronomy College, Gansu Agricultural University, Lanzhou 730070, China,College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Jiangping Bai
- State Key Laboratory of Aridland Crop Science/Agronomy College, Gansu Agricultural University, Lanzhou 730070, China,Corresponding author
| |
Collapse
|
23
|
Zhang J, Li S, An H, Zhang X, Zhou B. Integrated transcriptome and metabolome analysis reveals the anthocyanin biosynthesis mechanisms in blueberry ( Vaccinium corymbosum L.) leaves under different light qualities. FRONTIERS IN PLANT SCIENCE 2022; 13:1073332. [PMID: 36570935 PMCID: PMC9772006 DOI: 10.3389/fpls.2022.1073332] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/21/2022] [Indexed: 05/27/2023]
Abstract
INTRODUCTION Blueberry (Vaccinium corymbosum L.) is a popular fruit with an abundance of anthocyanins in its leaves and fruits. Light is one of the pivotal environmental elements that affects plant growth and development, but the regulatory mechanism between light quality and anthocyanin formation is poorly understood. METHODS An integrated transcriptome and metabolome analysis was performed to investigate the effects of white (control), blue (B), red (R), and red/blue (60R/40B) light on blueberry growth and reveal the potential pathway controlling anthocyanin biosynthesis in blueberry leaves. RESULTS The anthocyanin content was significantly improved by the blue and red/blue light when compared with white light, whereas there was a significant reduction in the photosynthesis under the blue light, showing an inverse trend to that of anthocyanin accumulation. Transcriptomic analysis resulted in the assembly of 134,709 unigenes. Of these, 22 were differentially expressed genes (DEGs) that participate in the anthocyanin biosynthesis pathway, with the majority being significantly up-regulated under the blue light. Most of the photosynthesis-related genes that were down-regulated were expressed during anthocyanin accumulation. Targeted metabolome profiling identified 44 metabolites associated with anthocyanin biosynthesis. The contents of most of these metabolites were higher under blue light than the other light conditions, which was consistent with the transcriptome results. The integrated transcriptome and metabolome analysis suggested that, under blue light, leucoanthocyanidin dioxygenase (LDOX), O-methyltransferase (OMT), and UDP-glucose flavonoid glucosyltransferase (UFGT) were the most significantly expressed, and they promoted the synthesis of cyanidin (Cy), malvidin (Mv), and pelargonidin (Pg) anthocyanidins, respectively. The expression levels of dihydroflavonol 4-reductase (DFR) and OMT, as well as the accumulation of delphinidin (Dp), peonidin (Pn), and petunidin (Pt), were significantly increased by the red/blue light. DISCUSSION The blue and red/blue lights promoted anthocyanin biosynthesis via inducing the expression of key structural genes and accumulation of metabolites involved in anthocyanin synthesis pathway. Moreover, there was a possible feedback regulating correlation between anthocyanin biosynthesis and photosynthesis under different light qualities in blueberry leaves. This study would provide a theoretical basis for elucidating the underlying regulatory mechanism of anthocyanin biosynthesis of V. corymbosum.
Collapse
Affiliation(s)
- Jiaying Zhang
- Forestry and Pomology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Key Lab of Protected Horticultural Technology, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Shuigen Li
- Forestry and Pomology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Key Lab of Protected Horticultural Technology, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Haishan An
- Forestry and Pomology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Key Lab of Protected Horticultural Technology, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Xueying Zhang
- Forestry and Pomology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Key Lab of Protected Horticultural Technology, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Boqiang Zhou
- Forestry and Pomology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Key Lab of Protected Horticultural Technology, Shanghai Academy of Agricultural Sciences, Shanghai, China
| |
Collapse
|
24
|
Biosynthetic regulatory network of flavonoid metabolites in stems and leaves of Salvia miltiorrhiza. Sci Rep 2022; 12:18212. [PMID: 36307498 PMCID: PMC9616839 DOI: 10.1038/s41598-022-21517-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 09/28/2022] [Indexed: 12/31/2022] Open
Abstract
Flavonoid secondary metabolites can treat and prevent many diseases, but systematic studies on regulation of the biosynthesis of such metabolites in aboveground parts of Salvia miltiorrhiza are lacking. In this study, metabonomic and transcriptomic analyses of different S. miltiorrhiza phenotypes were conducted to explore pathways of synthesis, catalysis, accumulation, and transport of the main flavonoid secondary metabolites regulating pigment accumulation. Tissue localization and quantitative analysis of flavonoid secondary metabolites were conducted by laser scanning confocal microscopy (LSCM). A total 3090 differentially expressed genes were obtained from 114,431 full-length unigenes in purple and green phenotypes, and 108 functional genes were involved in flavonoid biosynthesis. Five key phenylpropane structural genes (PAL, 4CL, ANS, 3AT, HCT) were highly differentially expressed, and four transcription factor genes (MYB, WRKY, bHLH, bZiP) were identified. In addition, six GST genes, nine ABC transporters, 22 MATE genes, and three SNARE genes were detected with key roles in flavonoid transport. According to LSCM, flavonoids were mainly distributed in epidermis, cortex, and collenchyma. Thus, comprehensive and systematic analyses were used to determine biosynthesis, accumulation, and transport of flavonoids in stems and leaves of different S. miltiorrhiza phenotypes. The findings will provide a reference for flavonoid production and cultivar selection.
Collapse
|
25
|
Wang L, Li L, Zhao W, Fan L, Meng H, Zhang G, Wu W, Shi J, Wu G. Integrated metabolomic and transcriptomic analysis of the anthocyanin and proanthocyanidin regulatory networks in red walnut natural hybrid progeny leaves. PeerJ 2022; 10:e14262. [PMID: 36285329 PMCID: PMC9588303 DOI: 10.7717/peerj.14262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/27/2022] [Indexed: 01/24/2023] Open
Abstract
Background Walnuts are among the most important dry fruit crops worldwide, typically exhibiting green leaves and yellow-brown or gray-yellow seed coats. A specific walnut accession with red leaves and seed coats, 'RW-1', was selected for study because of its high anthocyanin and proanthocyanidin (PA) contents. Anthocyanins and PAs are important secondary metabolites and play key roles in plant responses to biotic and abiotic stresses. However, few studies have focused on the molecular mechanism of anthocyanin biosynthesis in walnuts. Methods In this study, we determined the anthocyanin and PA components and their contents in different color leaves of 'RW-1' natural hybrid progenies at various developmental stages. Integrated transcriptome and metabolome analyses were used to identify the differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs). We also performed conjoint analyses on DEGs and DAMs to ascertain the degree pathways, and explore the regulation of anthocyanin and PA biosynthesis. Results The results of widely targeted metabolome profiling and anthocyanin detection revealed 395 substances, including four PAs and 26 anthocyanins, in red (SR) and green leaves (SG) of 'RW-1' natural hybrid progenies. From the research, the contents of all anthocyanin components in SR were higher than that in SG. Among them, the contents of delphinidin 3-O-galactoside, cyanidin 3-O-galactoside, delphinidin 3-O-arabinoside and cyanidin 3-O-glucoside were significantly higher than others, and they were considered as the main types of anthocyanins. However, nine anthocyanins were detected only in SR. For PAs, the content of procyanidin C1 was higher in SR compared with SG, while procyanidin B1 and procyanidin B3 were higher in SR-1 and SR-3 but downregulated in SR-2 compared with the controls. Furthermore, transcriptome analysis revealed that the expressions of structural genes (C4H, F3H, F3'5'H, UFGT, LAR and ANR), three MYBs predicted as the activators of anthocyanin and PA biosynthesis, two MYBs predicted as the repressors of anthocyanin biosynthesis, and five WD40s in the anthocyanin and PA biosynthetic pathways were significantly higher in the SR walnuts. Gene-metabolite correlation analyses revealed a core set of 31 genes that were strongly correlated with four anthocyanins and one PA metabolites. The alteration of gene coding sequence altered the binding or regulation of regulatory factors to structural genes in different color leaves, resulting in the effective increase of anthocyanins and PAs accumulation in red walnut. Conclusions This study provides valuable information on anthocyanin and PA metabolites and candidate genes for anthocyanin and PA biosynthesis, yielding new insights into anthocyanin and PA biosynthesis in walnuts.
Collapse
Affiliation(s)
- Lei Wang
- Henan Agricultural University, Zhengzhou, China
| | - Lin Li
- Henan Agricultural University, Zhengzhou, China
| | - Wei Zhao
- Henan Agricultural University, Zhengzhou, China
| | - Lu Fan
- Henan Agricultural University, Zhengzhou, China
| | - Haijun Meng
- Henan Agricultural University, Zhengzhou, China
| | | | - Wenjiang Wu
- Henan Agricultural University, Zhengzhou, China
| | - Jiangli Shi
- Henan Agricultural University, Zhengzhou, China
| | - Guoliang Wu
- Henan Agricultural University, Zhengzhou, China
| |
Collapse
|
26
|
Zhang W, Tang Y, Han Y, Huang L, Zhou W, Zhou C, Hu Y, Lu R, Wang F, Shi W, Liu G. Immunotoxicity of pentachlorophenol to a marine bivalve species and potential toxification mechanisms underpinning. JOURNAL OF HAZARDOUS MATERIALS 2022; 439:129681. [PMID: 36104908 DOI: 10.1016/j.jhazmat.2022.129681] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 07/06/2022] [Accepted: 07/24/2022] [Indexed: 06/15/2023]
Abstract
The ubiquitous presence of pentachlorophenol (PCP) in ocean environments threatens marine organisms. However, its effects on immunity of marine invertebrates at environmentally realistic levels are still largely unknown. In this study, the immunotoxicity of PCP to a representative bivalve species was evaluated. In addition, its impacts on metabolism, energy supply, detoxification, and oxidative stress status were also analysed by physiological examination as well as comparative transcriptomic and metabolomic analyses to reveal potential mechanisms underpinning. Results illustrated that the immunity of blood clams was evidently hampered upon PCP exposure. Additionally, significant alterations in energy metabolism were detected in PCP-exposed clams. Meanwhile, the expressions of key detoxification genes and the in vivo contents (or activity) of key detoxification enzymes were markedly altered. Exposure to PCP also triggered significant elevations in intracellular ROS and MDA whereas evident suppression of haemocyte viability. The abovementioned findings were further supported by transcriptomic and metabolomic analyses. Our results suggest that PCP may hamper the immunity of the blood clam by (i) constraining the cellular energy supply through disrupting metabolism; and (ii) damaging haemocytes through inducing oxidative stress. Considering the high similarity of immunity among species, many marine invertebrates may be threatened by PCP, which deserves more attention.
Collapse
Affiliation(s)
- Weixia Zhang
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yu Tang
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yu Han
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lin Huang
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Weishang Zhou
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Chaosheng Zhou
- Zhejiang Mariculture Research Institute, Wenzhou 325005, China
| | - Yuan Hu
- Zhejiang Mariculture Research Institute, Wenzhou 325005, China
| | - Rongmao Lu
- Zhejiang Mariculture Research Institute, Wenzhou 325005, China
| | - Fang Wang
- Zhejiang Mariculture Research Institute, Wenzhou 325005, China
| | - Wei Shi
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Guangxu Liu
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China.
| |
Collapse
|
27
|
Wang F, Xia Z, Zou M, Zhao L, Jiang S, Zhou Y, Zhang C, Ma Y, Bao Y, Sun H, Wang W, Wang J. The autotetraploid potato genome provides insights into highly heterozygous species. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1996-2005. [PMID: 35767385 PMCID: PMC9491450 DOI: 10.1111/pbi.13883] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 05/24/2022] [Accepted: 06/21/2022] [Indexed: 05/19/2023]
Abstract
Potato (Solanum tuberosum L.) originated in the Andes and evolved its vegetative propagation strategy through short day-dependent tuber development. Herein, we present a high-quality, chromosome-scale reference genome sequence of a tetraploid potato cultivar. The total length of this genome assembly was 2.67 Gb, with scaffold N50 and contig N50 sizes of 46.24 and 2.19 Mb, respectively. In total, 1.69 Gb repetitive sequences were obtained through de novo annotation, and long terminal repeats were the main transposable elements. A total of 126 070 protein-coding genes were annotated, of which 125 077 (99.21%) were located on chromosomes. The 48 chromosomes were classified into four haplotypes. We annotated 31 506 homologous genes, including 5913 (18.77%) genes with four homologues, 11 103 (35.24%) with three homologues, 12 177 (38.65%) with two homologues and 2313 (7.34%) with one homologue. MLH3, MSH6/7 and RFC3, which are the genes involved in the mismatch repair pathway, were found to be significantly expanded in the tetraploid potato genome relative to the diploid potato genome. Genome-wide association analysis revealed that cytochrome P450, flavonoid synthesis, chalcone enzyme, glycosyl hydrolase and glycosyl transferase genes were significantly correlated with the flesh colours of potato tuber in 150 tetraploid potatoes. This study provides valuable insights into the highly heterozygous autotetraploid potato genome and may facilitate the development of tools for potato cultivar breeding and further studies on autotetraploid crops.
Collapse
Affiliation(s)
- Fang Wang
- Academy of Agriculture and Forestry SciencesQinghai UniversityXiningChina
- National Key Laboratory of Sanjiangyuan Ecology and Plateau Agriculture and Animal HusbandryQinghai UniversityXiningChina
- Key Laboratory of Qinghai‐Tibet Plateau Biotechnology Ministry of EducationXiningChina
- Qinghai Provincial Key Laboratory of Potato BreedingXiningChina
| | - Zhiqiang Xia
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed LaboratorySanyaChina
- College of Tropical Crops Hainan University, Hainan UniversityHaikouChina
| | - Meiling Zou
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed LaboratorySanyaChina
- College of Tropical Crops Hainan University, Hainan UniversityHaikouChina
| | - Long Zhao
- Academy of Agriculture and Forestry SciencesQinghai UniversityXiningChina
- National Key Laboratory of Sanjiangyuan Ecology and Plateau Agriculture and Animal HusbandryQinghai UniversityXiningChina
| | - Sirong Jiang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed LaboratorySanyaChina
- College of Tropical Crops Hainan University, Hainan UniversityHaikouChina
| | - Yun Zhou
- Academy of Agriculture and Forestry SciencesQinghai UniversityXiningChina
- National Key Laboratory of Sanjiangyuan Ecology and Plateau Agriculture and Animal HusbandryQinghai UniversityXiningChina
- Key Laboratory of Qinghai‐Tibet Plateau Biotechnology Ministry of EducationXiningChina
- Qinghai Provincial Key Laboratory of Potato BreedingXiningChina
| | - Chenji Zhang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed LaboratorySanyaChina
- College of Tropical Crops Hainan University, Hainan UniversityHaikouChina
| | - Yongzhen Ma
- Academy of Agriculture and Forestry SciencesQinghai UniversityXiningChina
| | - Yuting Bao
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed LaboratorySanyaChina
- College of Tropical Crops Hainan University, Hainan UniversityHaikouChina
| | - Haihong Sun
- Academy of Agriculture and Forestry SciencesQinghai UniversityXiningChina
- National Key Laboratory of Sanjiangyuan Ecology and Plateau Agriculture and Animal HusbandryQinghai UniversityXiningChina
- Key Laboratory of Qinghai‐Tibet Plateau Biotechnology Ministry of EducationXiningChina
- Qinghai Provincial Key Laboratory of Potato BreedingXiningChina
| | - Wenquan Wang
- College of Tropical Crops Hainan University, Hainan UniversityHaikouChina
| | - Jian Wang
- Academy of Agriculture and Forestry SciencesQinghai UniversityXiningChina
- National Key Laboratory of Sanjiangyuan Ecology and Plateau Agriculture and Animal HusbandryQinghai UniversityXiningChina
- Key Laboratory of Qinghai‐Tibet Plateau Biotechnology Ministry of EducationXiningChina
- Qinghai Provincial Key Laboratory of Potato BreedingXiningChina
| |
Collapse
|
28
|
Shen J, Liu J, Yuan Y, Chen L, Ma J, Li X, Li J. The mechanism of abscisic acid regulation of wild Fragaria species in response to cold stress. BMC Genomics 2022; 23:670. [PMID: 36162976 PMCID: PMC9513977 DOI: 10.1186/s12864-022-08889-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 09/12/2022] [Indexed: 11/16/2022] Open
Abstract
Background Abiotic stresses have increasingly serious effects on the growth and yield of crops. Cold stress, in particular, is an increasing problem. In this study, Fragaria daltoniana and F. vesca were determined to be cold-resistant and cold-sensitive species, respectively. Integrated transcriptomics and metabolomics methods were used to analyze the regulatory mechanism of abscisic acid (ABA) in F. daltoniana and F. vesca in their response to low temperature stress. Results F. daltoniana and F. vesca increased their ABA content under low temperature stress by upregulating the expression of the ABA biosynthetic pathway gene NCED and downregulating the expression of the ABA degradative gene CYP707A. Both types of regulation increased the accumulation of glucose and fructose, resulting in a reduction of damage under low temperature stress. Twelve transcription factors were found to be involved in the ABA regulatory pathway. The strong cold tolerance of F. daltoniana could be owing to its higher levels of ABA that accumulated compared with those in F. vesca under low temperature stress. In addition, the gene ABF2, which is related to the transduction of glucose signaling, was significantly upregulated in the leaves of F. daltoniana, while it was downregulated in the leaves of F. vesca under low temperature stress. This could contribute to the higher levels of glucose signal transduction in F. daltoniana. Thus, this could explain the higher peroxidase activity and lower damage to cell membranes in the leaves of F. daltoniana compared with F. vesca under low temperature stress, which endows the former with stronger cold tolerance. Conclusions Under low temperature stress, the differences in the accumulation of ABA and the expression trends of ABF2 and ABF4 in different species of wild strawberries may be the primary reason for their differences in cold tolerance. Our results provide an important empirical reference and technical support for breeding resistant cultivated strawberry plants. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08889-8.
Collapse
Affiliation(s)
- Jincheng Shen
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, 318000, China.,College of Life Science and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.,Department of Plant and Environmental Sciences, University of Copenhagen, 1871, Frederiksberg C, Denmark
| | - Jie Liu
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, 318000, China
| | - Yongge Yuan
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, 318000, China
| | - Luxi Chen
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, 318000, China
| | - Junxia Ma
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, 318000, China
| | - Xin Li
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, 318000, China
| | - Junmin Li
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, 318000, China.
| |
Collapse
|
29
|
Xing A, Wang X, Nazir MF, Zhang X, Wang X, Yang R, Chen B, Fu G, Wang J, Ge H, Peng Z, Jia Y, He S, Du X. Transcriptomic and metabolomic profiling of flavonoid biosynthesis provides novel insights into petals coloration in Asian cotton (Gossypium arboreum L.). BMC PLANT BIOLOGY 2022; 22:416. [PMID: 36038835 PMCID: PMC9425979 DOI: 10.1186/s12870-022-03800-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Asian cotton (Gossypium arboreum L.), as a precious germplasm resource of cotton with insect resistance and stress tolerance, possesses a broad spectrum of phenotypic variation related to pigmentation. Flower color affects insect pollination and the ornamental value of plants. Studying flower color of Asian cotton varieties improves the rate of hybridization and thus enriches the diversity of germplasm resources. Meanwhile, it also impacts the development of the horticultural industry. Unfortunately, there is a clear lack of studies concerning intricate mechanisms of cotton flower-color differentiation. Hereby, we report an integrative approach utilizing transcriptome and metabolome concerning flower color variation in three Gossypium arboreum cultivars. RESULTS A total of 215 differentially accumulated metabolites (DAMs) were identified, including 83 differentially accumulated flavonoids (DAFs). Colorless kaempferol was more abundant in white flowers, while gossypetin-fer showed specificity in white flowers. Quercetin and gossypetin were the main contributors to yellow petal formation. Pelargonidin 3-O-beta-D-glucoside and cyanidin-3-O-(6''-Malonylglucoside) showed high accumulation levels in purple petals. Quercetin and gossypetin pigments also promoted purple flower coloration. Moreover, 8178 differentially expressed genes (DEGs) were identified by RNA sequencing. The correlation results between total anthocyanins and DEGs were explored, indicating that 10 key structural genes and 29 transcription factors promoted anthocyanin biosynthesis and could be candidates for anthocyanin accumulation. Ultimately, we constructed co-expression networks of key DAFs and DEGs and demonstrated the interactions between specific metabolites and transcripts in different color flowers. CONCLUSION This study provides new insights into elucidating the regulatory mechanisms of cotton flower color and lays a potential foundation for generate cotton varieties with highly attractive flowers for pollinators.
Collapse
Affiliation(s)
- Aishuang Xing
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xiaoyang Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Mian Faisal Nazir
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xiaomeng Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xiuxiu Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Ru Yang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou Henan, 450001, China
| | - Baojun Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Guoyong Fu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Jingjing Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Hao Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhen Peng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou Henan, 450001, China
| | - Yinhua Jia
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Shoupu He
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou Henan, 450001, China.
| | - Xiongming Du
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou Henan, 450001, China.
| |
Collapse
|
30
|
Zhou Y, Lv J, Yu Z, Wang Z, Li Y, Li M, Deng Z, Xu Q, Cui F, Zhou W. Integrated metabolomics and transcriptomic analysis of the flavonoid regulatory networks in Sorghum bicolor seeds. BMC Genomics 2022; 23:619. [PMID: 36028813 PMCID: PMC9414139 DOI: 10.1186/s12864-022-08852-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 08/17/2022] [Indexed: 11/10/2022] Open
Abstract
Background The objective of this study was to reveal the flavonoid biosynthesis pathway in white (Z6), red (Z27) and black (HC4) seeds of the sweet sorghum (Sorghum bicolor) using metabolomics and transcriptomics, to identify different flavonoid metabolites, and to analyze the differentially expressed genes involved in flavonoid biosynthesis. Results We analyzed the metabolomics and transcriptomics data of sweet sorghum seeds. Six hundred and fifty-one metabolites including 171 flavonoids were identified in three samples. Integrated analysis of transcriptomics and metabolomics showed that 8 chalcone synthase genes (gene19114, gene19115, gene19116, gene19117, gene19118, gene19120, gene19122 and gene19123) involved in flavonoid biosynthesis, were identified and play central role in change of color. Six flavanone including homoeriodictyol, naringin, prunin, naringenin, hesperetin and pinocembrin were main reason for the color difference. Conclusions Our results provide valuable information on the flavonoid metabolites and the candidate genes involved in the flavonoid biosynthesis pathway in sweet sorghum seeds.
Collapse
Affiliation(s)
- Yaxing Zhou
- Agricultural College, Inner Mongolia Minzu University, No. 996 Xilamulun Street, Kerqin District, Tongliao, 028000, Inner Mongolia, People's Republic of China
| | - Jingbo Lv
- Tongliao Agriculture and Animal Husbandry Research Institute, Tongliao, 028000, Inner Mongolia, People's Republic of China
| | - Zhonghao Yu
- Agricultural College, Inner Mongolia Minzu University, No. 996 Xilamulun Street, Kerqin District, Tongliao, 028000, Inner Mongolia, People's Republic of China
| | - Zhenguo Wang
- Tongliao Agriculture and Animal Husbandry Research Institute, Tongliao, 028000, Inner Mongolia, People's Republic of China
| | - Yan Li
- Tongliao Agriculture and Animal Husbandry Research Institute, Tongliao, 028000, Inner Mongolia, People's Republic of China
| | - Mo Li
- Tongliao Agriculture and Animal Husbandry Research Institute, Tongliao, 028000, Inner Mongolia, People's Republic of China
| | - Zhilan Deng
- Tongliao Agriculture and Animal Husbandry Research Institute, Tongliao, 028000, Inner Mongolia, People's Republic of China
| | - Qingquan Xu
- Tongliao Agriculture and Animal Husbandry Research Institute, Tongliao, 028000, Inner Mongolia, People's Republic of China
| | - Fengjuan Cui
- Tongliao Agriculture and Animal Husbandry Research Institute, Tongliao, 028000, Inner Mongolia, People's Republic of China
| | - Wei Zhou
- Agricultural College, Inner Mongolia Minzu University, No. 996 Xilamulun Street, Kerqin District, Tongliao, 028000, Inner Mongolia, People's Republic of China.
| |
Collapse
|
31
|
Yuan G, Sun D, An G, Li W, Si W, Liu J, Zhu Y. Transcriptomic and Metabolomic Analysis of the Effects of Exogenous Trehalose on Salt Tolerance in Watermelon (Citrullus lanatus). Cells 2022; 11:cells11152338. [PMID: 35954182 PMCID: PMC9367363 DOI: 10.3390/cells11152338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/19/2022] [Accepted: 07/26/2022] [Indexed: 12/02/2022] Open
Abstract
Trehalose can effectively protect the biomolecular structure, maintain the balance of cell metabolism, and improve the tolerance to various abiotic stresses in plants. However, the molecular mechanism underlying the improvement in salt tolerance by exogenous trehalose in watermelon (Citrullus lanatus) seedlings is still unclear. To understand these molecular mechanisms, in this study, watermelon seedlings under salt stress were treated with various concentrations of exogenous trehalose. An amount of 20 mM exogenous trehalose significantly improved the physiological status; increased the activities of enzymes such as POD, SOD, and CAT; and increased the K+/Na+ ratio in watermelon seedlings under salt stress. RNA-seq and metabolomic analysis were performed to identify the specifically expressed genes and metabolites after trehalose treatment. Watermelon seedlings were divided into salt stress (CK2), control (CK1) and trehalose treatment (T) groups as per the treatment. Overall, 421 shared differentially expressed genes (DEGs) were identified in the two comparison groups, namely CK2–CK1 and T–CK2. Functional annotation and enrichment analysis revealed that the DEGs were mainly involved in MAPK signaling pathway for plant hormone signal transduction and phenylpropanoid biosynthesis. Furthermore, 129 shared differential expressed metabolites (DEMs) were identified in the two comparison groups using liquid chromatography–mass spectrometry, which were mainly involved in the metabolic pathway and phenylpropanoid biosynthesis. The combined transcriptomic and metabolomic analyses revealed that genes involved in phenylpropanoid biosynthesis, plant hormone signal transduction, and carbohydrate biosynthesis pathways, especially bHLH family transcription factors, played an important role in improving salt tolerance of watermelon seedlings after exogenous trehalose treatment.
Collapse
|
32
|
Du Z, Lin W, Zhu J, Li J. Amino acids profiling and transcriptomic data integration demonstrates the dynamic regulation of amino acids synthesis in the leaves of Cyclocarya paliurus. PeerJ 2022; 10:e13689. [PMID: 35811808 PMCID: PMC9266588 DOI: 10.7717/peerj.13689] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 06/16/2022] [Indexed: 01/17/2023] Open
Abstract
Background Cyclocarya paliurus is a tree well known for its edible and medicinal leaves. Amino acids are essential nutritional components that are present in foods and closely related to the flavor and quality of tea. However, the abundance of amino acids and the regulation of amino acid biosynthesis in the leaves of C. paliurus have not been investigated across different developmental stages. Methods A combined metabolomic and transcriptomic analysis was employed to investigate the changes in the amino acid profile over several developmental stages (S1, the smallest fully expanded leaf; S3, full leaf enlargement and full leaf thickness; and S2, an intermediate developmental stage between S1 and S3) and the molecular mechanism was elucidated. Results The results showed that leaves at the S1 stage had the highest content, while those at the S3 stage had the lowest content of amino acids; fourteen differentially expressed genes were involved in the glycolysis pathway, the tricarboxylic acid cycle and the pentose phosphate pathway, which indicated that the reduced abundance of amino acids in the leaves of C. paliurus (mature leaves) may be attributable to reduced gene expression related to carbohydrate metabolism. Four basic leucine zipper transcription factors might play important roles in the regulation of the biosynthesis of amino acids in the leaves of C. paliurus. Conclusions Leaves at the S1 stage are recommended for high quality tea production because of their high content of amino acids, while leaves at the S2 stage are recommended for generous tea production because of their high levels of sweet flavor amino acids (alanine) and essential amino acids (methionine, phenylalanine, threonine, and tryptophan).
Collapse
Affiliation(s)
- Zhaokui Du
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, Zhejiang, China
| | - Weida Lin
- Taizhou Vocational College of Science and Technology, Taizhou, Zhejiang, China
| | - Jinxing Zhu
- Suichang County Bureau of Agriculture and Rural Affairs, Suichang, Zhejiang, China
| | - Junmin Li
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, Zhejiang, China
| |
Collapse
|
33
|
Ren C, Chen C, Dong S, Wang R, Xian B, Liu T, Xi Z, Pei J, Chen J. Integrated metabolomics and transcriptome analysis on flavonoid biosynthesis in flowers of safflower ( Carthamus tinctorius L.) during colour-transition. PeerJ 2022; 10:e13591. [PMID: 35762018 PMCID: PMC9233481 DOI: 10.7717/peerj.13591] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 05/24/2022] [Indexed: 01/17/2023] Open
Abstract
Background Safflower (Carthamus tinctorius L.), well known for its flower, is widely used as a dye and traditional Chinese medicine. Flavonoids, especially flavonoid glycosides, are the main pigments and active components. However, their biosynthesis is largely unknown. Interestingly, the colour of flowers in safflower changed from yellow to red during flower development, while much of the gene and chemical bases during colour transition are unclear. Methods In this research, widely targeted metabolomics and transcriptomics were used to elucidate the changes in flavonoid biosynthesis from the gene and chemical points of view in flowers of safflower during colour transition. The screening of differential metabolites depended on fold change and variable importance in project (VIP) value. Differential expressed genes (DEGs) were screened by DESeq2 method. RT-PCR was used to analyse relative expressions of DEGs. Results A total of 212 flavonoid metabolites, including hydroxysafflor yellow A, carthamin and anthocyanins, were detected and showed a large difference. The candidate genes of glycosyltransferases and flavonoid hydroxylase that might participate in flavonoid glycoside biosynthesis were screened. Ten candidate genes were screened. Through integrated metabolomics and transcriptome analysis, a uridine diphosphate glucose glycosyltransferase gene, CtUGT9 showed a significant correlation with flavonoid glycosides in safflower. In addition, expression analysis showed that CtUGT9 was mainly expressed in the middle development of flowers and was significantly upregulated under MeJA treatment. Our results indicated that CtUGT9 might play an important role in flavonoid glycoside biosynthesis during colour-transition in safflower.
Collapse
Affiliation(s)
- Chaoxiang Ren
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu, Sichuan, China,College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Chao Chen
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu, Sichuan, China,College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Shuai Dong
- The State Bank of Chinese Drug Germplam Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Rui Wang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu, Sichuan, China,College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Bin Xian
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu, Sichuan, China,College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Tianlei Liu
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Ziqing Xi
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu, Sichuan, China,College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Jin Pei
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu, Sichuan, China,College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China,The State Bank of Chinese Drug Germplam Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Jiang Chen
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu, Sichuan, China,College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China,The State Bank of Chinese Drug Germplam Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| |
Collapse
|
34
|
Shen J, Shao W, Li J, Lu H. Integrated metabolomic and transcriptomic analysis reveals factors underlying differences in fruit quality between Fragaria nilgerrensis and Fragaria pentaphylla. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:3287-3296. [PMID: 34799861 DOI: 10.1002/jsfa.11674] [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: 05/18/2021] [Revised: 11/02/2021] [Accepted: 11/19/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Strawberries have become one of the most popular fruits because of their unique flavor and high nutritional value. Fruit quality and price are the most important criteria that determine consumer acceptability. Fragaria nilgerrensis and Fragaria pentaphylla are two wild Asian diploid strawberry species that differ in fruit color, taste, and aroma. To understand the molecular mechanisms involved in the formation of high-quality strawberry fruit, we integrated transcriptomics and metabolomics research methods to compare the metabolic and biosynthetic mechanisms of the two Fragaria species. RESULTS F. nilgerrensis fruit has higher amino acid and lipid contents and a higher sugar-to-acid ratio than F. pentaphylla fruit does, underlying their superior nutritional value, aroma, firmness, and taste. Compared with F. nilgerrensis fruit, F. pentaphylla fruit contained more flavonoids, indicating its enhanced color and health benefits. In addition, candidate structural genes that regulate the biosynthesis of flavonoids, amino acids, and glycerophospholipids in the two strawberry fruit were screened. CONCLUSIONS The differences in aroma, firmness, and taste between F. nilgerrensis fruit and F. pentaphylla fruit are probably due to differences in their amino acid and lipid contents, as well as the difference in their sugar-to-acid ratios. Eight key structural genes that may play important roles in the biosynthesis of amino acids, lipids, and flavonoids were identified. © 2021 Society of Chemical Industry.
Collapse
Affiliation(s)
- Jincheng Shen
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
- College of Life Science and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Wanlu Shao
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
- College of Life Science and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Junmin Li
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Hongfei Lu
- College of Life Science and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| |
Collapse
|
35
|
Hall RD, D'Auria JC, Silva Ferreira AC, Gibon Y, Kruszka D, Mishra P, van de Zedde R. High-throughput plant phenotyping: a role for metabolomics? TRENDS IN PLANT SCIENCE 2022; 27:549-563. [PMID: 35248492 DOI: 10.1016/j.tplants.2022.02.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 01/18/2022] [Accepted: 02/02/2022] [Indexed: 05/17/2023]
Abstract
High-throughput (HTP) plant phenotyping approaches are developing rapidly and are already helping to bridge the genotype-phenotype gap. However, technologies should be developed beyond current physico-spectral evaluations to extend our analytical capacities to the subcellular level. Metabolites define and determine many key physiological and agronomic features in plants and an ability to integrate a metabolomics approach within current HTP phenotyping platforms has huge potential for added value. While key challenges remain on several fronts, novel technological innovations are upcoming yet under-exploited in a phenotyping context. In this review, we present an overview of the state of the art and how current limitations might be overcome to enable full integration of metabolomics approaches into a generic phenotyping pipeline in the near future.
Collapse
Affiliation(s)
- Robert D Hall
- BU Bioscience, Wageningen University & Research, 6700 AA, Wageningen, The Netherlands; Laboratory of Plant Physiology, Wageningen University, 6700 AA, Wageningen, The Netherlands; Netherlands Metabolomics Centre, Einsteinweg 55, Leiden, The Netherlands.
| | - John C D'Auria
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK Gatersleben), Gatersleben, Corrensstraße 3, 06466 Seeland, Germany
| | - Antonio C Silva Ferreira
- Universidade Católica Portuguesa, CBQF-Centro de Biotecnologia e Química Fina-Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, Apartado 2511, 4202-401 Porto, Portugal; Faculty of AgriSciences, University of Stellenbosch, Matieland 7602, South Africa; Cork Supply Portugal, S.A., Rua Nova do Fial, 4535, Portugal
| | - Yves Gibon
- UMR 1332 Biologie du Fruit et Pathologie, INRAE, Univ. Bordeaux, INRAE Nouvelle Aquitaine - Bordeaux, Avenue Edouard Bourlaux, Villenave d'Ornon, France; Bordeaux Metabolome, MetaboHUB, INRAE, Univ. Bordeaux, Avenue Edouard Bourlaux, Villenave d'Ornon, France PMB-Metabolome, INRAE, Centre INRAE de Nouvelle, Aquitaine-Bordeaux, Villenave d'Ornon, France
| | - Dariusz Kruszka
- Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland
| | - Puneet Mishra
- Food and Biobased Research, Wageningen University & Research, 6708 WE, Wageningen, The Netherlands
| | - Rick van de Zedde
- Plant Sciences Group, Wageningen University & Research, 6700 AA, Wageningen, The Netherlands
| |
Collapse
|
36
|
Yu XM, Wang J, Gao R, Gong BC, Ai CX. Integrated Metabolomic-Transcriptomic Analysis Reveals Diverse Resource of Functional Ingredients From Persimmon Leaves of Different Varieties. FRONTIERS IN PLANT SCIENCE 2022; 13:904208. [PMID: 35693179 PMCID: PMC9175000 DOI: 10.3389/fpls.2022.904208] [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: 03/25/2022] [Accepted: 04/22/2022] [Indexed: 06/15/2023]
Abstract
Persimmon leaves are used for making persimmon leaf tea or as functional ingredients due to their enrichment in flavonoids, the beneficial mineral contents, and favorable flavors contributed by volatile aroma compounds. The varieties/cultivars had a significant influence on the quality and flavor of persimmon leaf tea. In this study, the integrated metabolomic-transcriptomic analysis was conducted to investigate the potential in flavonoid biosynthesis, mineral absorption, and degradation of aromatic compounds from tender leaves of "Diospyros kaki. Heishi" (HS), "Diospyros kaki Thunb. Nishimurawase" (NM), and "Diospyros kaki Thunb. Taifu" (TF), using rootstock "Diospyros Lotus Linn" (DL) as the control. The metabolomic analysis showed that 382, 391, and 368 metabolites were differentially accumulated in the comparison of DL vs. HS, DL vs. NM, and DL vs. TF, respectively, and 229 common metabolites were obtained by comparative analysis. By RNA sequencing, 182,008 unigenes with 652 bp of mean length were annotated and 2,598, 3,503, and 3,333 differentially expressed genes (DEGs) were detected from the comparison of DL vs. HS, DL vs. NM, and DL vs. TF, respectively. After the Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, 6, 6, and 3 DEGs [with | log2(fold change)| ≥ 1 simultaneously in the three comparisons] involved in flavonoid biosynthesis, mineral absorption, and degradation of aromatic compounds, respectively, were selected for quantitative reverse transcription-polymerase chain reaction (qRT-PCR) validation and the consistent trends of the relative expression level of each DEG with RNA sequencing (RNA-seq) data were observed. Based on the transcriptomic analysis and qRT-PCR validation, it was observed that the leaves of HS, NM, and TF had the greatest level of mineral absorption, flavonoid biosynthesis, and degradation of aromatic compounds, respectively. In addition, a positive correlation between the 15 DEGs and their metabolites was observed by the conjoint analysis. Thus, the tender leaves of HS, NM, and TF could be recommended for the production of persimmon leaf tea rich in mineral elements, flavonoid, and aroma compounds, respectively.
Collapse
Affiliation(s)
- Xian-Mei Yu
- Shandong Institute of Pomology, Tai’an, China
| | - Jie Wang
- Shandong Institute of Pomology, Tai’an, China
| | - Rui Gao
- Shandong Institute of Pomology, Tai’an, China
| | - Bang-Chu Gong
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, China
| | | |
Collapse
|
37
|
Xia Y, Liu J, Chen C, Mo X, Tan Q, He Y, Wang Z, Yin J, Zhou G. The Multifunctions and Future Prospects of Endophytes and Their Metabolites in Plant Disease Management. Microorganisms 2022; 10:microorganisms10051072. [PMID: 35630514 PMCID: PMC9146654 DOI: 10.3390/microorganisms10051072] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/19/2022] [Accepted: 05/21/2022] [Indexed: 01/27/2023] Open
Abstract
Endophytes represent a ubiquitous and magical world in plants. Almost all plant species studied by different researchers have been found to harbor one or more endophytes, which protect host plants from pathogen invasion and from adverse environmental conditions. They produce various metabolites that can directly inhibit the growth of pathogens and even promote the growth and development of the host plants. In this review, we focus on the biological control of plant diseases, aiming to elucidate the contribution and key roles of endophytes and their metabolites in this field with the latest research information. Metabolites synthesized by endophytes are part of plant disease management, and the application of endophyte metabolites to induce plant resistance is very promising. Furthermore, multi-omics should be more fully utilized in plant–microbe research, especially in mining novel bioactive metabolites. We believe that the utilization of endophytes and their metabolites for plant disease management is a meaningful and promising research direction that can lead to new breakthroughs in the development of more effective and ecosystem-friendly insecticides and fungicides in modern agriculture.
Collapse
Affiliation(s)
- Yandong Xia
- Key Laboratory of National Forestry and Grassland Administration on Control of Artificial Forest Diseases and Pests in South China, Hunan Provincial Key Laboratory for Control of Forest Diseases and Pests, Key Laboratory for Non-Wood Forest Cultivation and Conservation of Ministry of Education, College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China; (Y.X.); (J.L.); (X.M.); (Q.T.); (Y.H.); (Z.W.)
| | - Junang Liu
- Key Laboratory of National Forestry and Grassland Administration on Control of Artificial Forest Diseases and Pests in South China, Hunan Provincial Key Laboratory for Control of Forest Diseases and Pests, Key Laboratory for Non-Wood Forest Cultivation and Conservation of Ministry of Education, College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China; (Y.X.); (J.L.); (X.M.); (Q.T.); (Y.H.); (Z.W.)
| | - Cang Chen
- College of Life Science, Hunan Normal University, Changsha 410081, China;
| | - Xiuli Mo
- Key Laboratory of National Forestry and Grassland Administration on Control of Artificial Forest Diseases and Pests in South China, Hunan Provincial Key Laboratory for Control of Forest Diseases and Pests, Key Laboratory for Non-Wood Forest Cultivation and Conservation of Ministry of Education, College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China; (Y.X.); (J.L.); (X.M.); (Q.T.); (Y.H.); (Z.W.)
| | - Qian Tan
- Key Laboratory of National Forestry and Grassland Administration on Control of Artificial Forest Diseases and Pests in South China, Hunan Provincial Key Laboratory for Control of Forest Diseases and Pests, Key Laboratory for Non-Wood Forest Cultivation and Conservation of Ministry of Education, College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China; (Y.X.); (J.L.); (X.M.); (Q.T.); (Y.H.); (Z.W.)
| | - Yuan He
- Key Laboratory of National Forestry and Grassland Administration on Control of Artificial Forest Diseases and Pests in South China, Hunan Provincial Key Laboratory for Control of Forest Diseases and Pests, Key Laboratory for Non-Wood Forest Cultivation and Conservation of Ministry of Education, College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China; (Y.X.); (J.L.); (X.M.); (Q.T.); (Y.H.); (Z.W.)
| | - Zhikai Wang
- Key Laboratory of National Forestry and Grassland Administration on Control of Artificial Forest Diseases and Pests in South China, Hunan Provincial Key Laboratory for Control of Forest Diseases and Pests, Key Laboratory for Non-Wood Forest Cultivation and Conservation of Ministry of Education, College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China; (Y.X.); (J.L.); (X.M.); (Q.T.); (Y.H.); (Z.W.)
| | - Jia Yin
- College of Life Science, Hunan Normal University, Changsha 410081, China;
- Correspondence: (J.Y.); (G.Z.)
| | - Guoying Zhou
- Key Laboratory of National Forestry and Grassland Administration on Control of Artificial Forest Diseases and Pests in South China, Hunan Provincial Key Laboratory for Control of Forest Diseases and Pests, Key Laboratory for Non-Wood Forest Cultivation and Conservation of Ministry of Education, College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China; (Y.X.); (J.L.); (X.M.); (Q.T.); (Y.H.); (Z.W.)
- Correspondence: (J.Y.); (G.Z.)
| |
Collapse
|
38
|
Zheng T, Han J, Su KX, Sun BY, Liu SM. Regulation mechanisms of flavonoids biosynthesis of Hancheng Dahongpao peels (Zanthoxylum bungeanum Maxim) at different development stages by integrated metabolomics and transcriptomics analysis. BMC PLANT BIOLOGY 2022; 22:251. [PMID: 35596133 PMCID: PMC9123719 DOI: 10.1186/s12870-022-03642-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/10/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Flavonoids have strong free radical scavenging and antioxidant capacity. The high abundance of flavonoids in Chinese prickly ash peels have many benefits to human health. In this study, 'Hancheng Dahongpao', a main cultivar, was taken as materials to investigate the flavonoids biosynthesis mechanism of Zanthoxylum bungeanum Maxim at three key development stages by integration of metabolomics and transcriptomics analysis. RESULTS A total of 19 differentially accumulated metabolites were identified, the key flavonoids compounds were kaempferol, quercetin and their glycoside derivatives, and two major anthocyanins (peonidin O-hexoside and peonidin 3-O-glucoside). 5 gene networks/modules including 15 important candidate genes were identified, which was highly correlated with flavonoids. Among these genes, ZM-163828 and ZM-184209 were strongly correlated with kaempferol and quercetin, and ZM-125833 and ZM-97481 were controlled the anthocyanins biosynthesis. Moreover, it was shown that MYB-ZM1, MYB-ZM3, MYB-ZM5, MYB-ZM6 and MYB-ZM7 coordinately controlled flavonoids accumulation through regulating the structural genes. CONCLUSIONS Generally, this study systematically revealed the flavonoids metabolic pathways and candidate genes involved in flavonoids biosynthesis and laid a foundation for the potential targets for the breeding of new valuable Chinese prickly ash cultivars.
Collapse
Affiliation(s)
- Tao Zheng
- Northwest Agriculture and Forestry University, College of Science, Yangling, 712100, China
| | - Jun Han
- Forestry and Grassland Bureau of Xunhua Salar autonomous county, Xunhua, 811100, China.
| | - Ke-Xing Su
- Northwest Agriculture and Forestry University, College of Science, Yangling, 712100, China
| | - Bing-Yin Sun
- Yangling Vocational &Technical College, Yangling, 712100, China
| | - Shu-Ming Liu
- Northwest Agriculture and Forestry University, College of Science, Yangling, 712100, China.
| |
Collapse
|
39
|
Song S, Tao Y, Gao L, Liang H, Tang D, Lin J, Wang Y, Gmitter FG, Li C. An Integrated Metabolome and Transcriptome Analysis Reveal the Regulation Mechanisms of Flavonoid Biosynthesis in a Purple Tea Plant Cultivar. FRONTIERS IN PLANT SCIENCE 2022; 13:880227. [PMID: 35665157 PMCID: PMC9161209 DOI: 10.3389/fpls.2022.880227] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 04/15/2022] [Indexed: 06/15/2023]
Abstract
Purple tea plant cultivars, enrich with flavonoids and anthocyanins, are valuable materials for manufacturing tea with unique color and flavor. Researchers found that 'Zijuan' leaves changed from purple to green mainly caused by the decreased flavonoids and anthocyanins concentrations. The mechanism of flavonoids and anthocyanin biosynthesis has been studied in many purple tea plant cultivars and the key genes which regulated the biosynthesis of flavonoid and anthocyanins in different purple tea plant cultivars were quite different. Also, the molecular regulation mechanism underlying the flavonoids and anthocyanins biosynthesis during leaves development and color changes is less-thoroughly understood. In this study, an integrative analysis of transcriptome and metabolome was performed on the purple leaves and green leaves of 'Zijuan' tea plant to reveal the regulatory networks correlated to flavonoid biosynthesis and to identify key regulatory genes. Our results indicated that the 'Zijuan' new shoots leaves were purple might be due to the copigmentation of quercetin and kaempferol derivatives. In 'Zijuan' tea plant cultivar, flavonoids metabolites concentrations in purple leaves and green leaves were significantly influenced by the genes involved in flavonoid biosynthesis, transcriptional regulation, transport, and hormone response. Transcription factors including NAC008, MYB23, and bHLH96 and transporters such as ABC transporter I might be responsible for the flavonoid and anthocyanins accumulation in purple leaves. This study provides a new insight into the metabolism and molecular mechanisms underlying flavonoid and anthocyanin biosynthesis in tea plant.
Collapse
Affiliation(s)
- SaSa Song
- College of Tea Science and Tea Culture, Zhejiang A&F University, Hangzhou, China
| | - Yu Tao
- College of Tea Science and Tea Culture, Zhejiang A&F University, Hangzhou, China
| | - LongHan Gao
- College of Tea Science and Tea Culture, Zhejiang A&F University, Hangzhou, China
| | - HuiLing Liang
- College of Tea Science and Tea Culture, Zhejiang A&F University, Hangzhou, China
| | - DeSong Tang
- College of Tea Science and Tea Culture, Zhejiang A&F University, Hangzhou, China
| | - Jie Lin
- College of Tea Science and Tea Culture, Zhejiang A&F University, Hangzhou, China
| | - YuChun Wang
- College of Tea Science and Tea Culture, Zhejiang A&F University, Hangzhou, China
| | - Frederick G. Gmitter
- Institute of Food and Agricultural Sciences, Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States
| | - ChunFang Li
- College of Tea Science and Tea Culture, Zhejiang A&F University, Hangzhou, China
| |
Collapse
|
40
|
Qiu L, Zheng T, Liu W, Zhuo X, Li P, Wang J, Cheng T, Zhang Q. Integration of Transcriptome and Metabolome Reveals the Formation Mechanism of Red Stem in Prunus mume. FRONTIERS IN PLANT SCIENCE 2022; 13:884883. [PMID: 35599903 PMCID: PMC9120947 DOI: 10.3389/fpls.2022.884883] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 03/25/2022] [Indexed: 06/15/2023]
Abstract
Prunus mume var. purpurea, commonly known as "Red Bone", is a special variety with pink or purple-red xylem. It is famous due to gorgeous petals and delightful aromas, playing important roles in urban landscaping. The regulation mechanism of color formation in P. mume var. purpurea stem development is unclear. Here, we conducted a comprehensive analysis of transcriptome and metabolome in WYY ('Wuyuyu' accession, red stem) and FLE ('Fei Lve' accession, green stem), and found a total of 256 differential metabolites. At least 14 anthocyanins were detected in WYY, wherein cyanidin 3,5-O-diglucoside and peonidin3-O-glucoside were significantly accumulated through LC-MS/MS analysis. Transcriptome data showed that the genes related to flavonoid-anthocyanin biosynthesis pathways were significantly enriched in WYY. The ratio of dihydroflavonol 4-reductase (DFR) and flavonol synthase (FLS) expression levels may affect metabolic balance in WYY, suggesting a vital role in xylem color formation. In addition, several transcription factors were up-regulated, which may be the key factors contributing to transcriptional changes in anthocyanin synthesis. Overall, the results provide a reference for further research on the molecular mechanism of xylem color regulation in P. mume and lay a theoretical foundation for cultivating new varieties.
Collapse
|
41
|
Guo X, Shakeel M, Wang D, Qu C, Yang S, Ahmad S, Song Z. Metabolome and transcriptome profiling unveil the mechanisms of light-induced anthocyanin synthesis in rabbiteye blueberry (vaccinium ashei: Reade). BMC PLANT BIOLOGY 2022; 22:223. [PMID: 35488209 PMCID: PMC9052483 DOI: 10.1186/s12870-022-03585-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 04/08/2022] [Indexed: 05/27/2023]
Abstract
BACKGROUND Blueberry is one of the most important fruit crops worldwide. Anthocyanin is an important secondary metabolites that affects the appearance and nutritive quality of blueberries. However, few studies have focused on the molecular mechanism underlying anthocyanin accumulation induced by light intensity in blueberries. RESULTS The metabolic analysis revealed that there were 134 significantly changed metabolites in the natural light compared to the control, and flavone, flavonol, and anthocyanins were the most significantly increased. Transcriptome analysis found 6 candidate genes for the anthocyanin synthesis pathway. Quantitative reverse transcription PCR (qRT-PCR) results confirmed changes in the expression levels of genes encoding metabolites involved in the flavonoid synthesis pathways. The flavonoid metabolic flux in the light intensity-treatment increased the accumulation of delphinidin-3-O-arabinoside compared to under the shading-treatment. Furthermore, we performed qRT-PCR analysis of anthocyanin biosynthesis genes and predicted that the gene of VcF3'5'H4 may be a candidate gene for anthocyanin accumulation and is highly expressed in light intensity-treated fruit. Through the co-expression analysis of transcription factors and anthocyanin synthesis pathway genes, we found that the VcbHLH004 gene may regulate VcF3'5'H4, and then we transformed VcbHLH004 heterologously into tomato to verify its function. CONCLUSION These results provide novel insights into light intensity regulation of blueberry anthocyanin accumulation and represent a valuable data set to guide future functional studies and blueberry breeding.
Collapse
Affiliation(s)
- Xiaolan Guo
- College of Forestry, Guizhou University, Guiyang, Guizhou, China
- College of Life Sciences, Huizhou College, Huizhou, Guangdong, China
| | - Muhammad Shakeel
- Department of Entomology, University of the Punjab, Lahore, Pakistan
| | - Delu Wang
- College of Forestry, Guizhou University, Guiyang, Guizhou, China.
| | - Chunpu Qu
- College of Forestry, Guizhou University, Guiyang, Guizhou, China
| | - Shimei Yang
- College of Forestry, Guizhou University, Guiyang, Guizhou, China
| | - Shahbaz Ahmad
- Department of Entomology, University of the Punjab, Lahore, Pakistan
| | - Zejun Song
- College of Forestry, Guizhou University, Guiyang, Guizhou, China
| |
Collapse
|
42
|
Fu L, Ding Z, Tie W, Yang J, Yan Y, Hu W. Integrated Metabolomic and Transcriptomic Analyses Reveal Novel Insights of Anthocyanin Biosynthesis on Color Formation in Cassava Tuberous Roots. Front Nutr 2022; 9:842693. [PMID: 35449540 PMCID: PMC9017287 DOI: 10.3389/fnut.2022.842693] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 03/03/2022] [Indexed: 11/25/2022] Open
Abstract
Yellow roots are of higher nutritional quality and better appearance than white roots in cassava, a crucial tropical and subtropical root crop. In this work, two varieties with yellow and white cassava roots were selected to explore the mechanisms of color formation by using comparative metabolome and transcriptome analyses during seven developmental stages. Compared with the white-rooted cassava, anthocyanins, catechin derivatives, coumarin derivatives, and phenolic acids accumulated at higher levels in yellow-rooted cassava. Anthocyanins were particularly enriched and displayed different accumulation patterns during tuberous root development. This was confirmed by metabolic comparisons between five yellow-rooted and five white-rooted cassava accessions. The integrative metabolomic and transcriptomic analysis further revealed a coordinate regulation of 16 metabolites and 11 co-expression genes participating in anthocyanin biosynthesis, suggesting a vital role of anthocyanin biosynthesis in yellow pigmentation in cassava tuberous roots. In addition, two transcriptional factors, i.e., MeMYB5 and MeMYB42, were also identified to co-express with these anthocyanin biosynthesis genes. These findings expand our knowledge on the role of anthocyanin biosynthesis in cassava root color formation, and offer useful information for the genetic breeding of yellow-rooted cassava in the future.
Collapse
Affiliation(s)
- Lili Fu
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Zehong Ding
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, China
| | - Weiwei Tie
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, China
| | - Jinghao Yang
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yan Yan
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Wei Hu
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, China
| |
Collapse
|
43
|
Ahn JY, Kim J, Yang JY, Lee HJ, Kim S, Cho KS, Lee SH, Kim JH, Lee TH, Hur Y, Shim D. Comparative Transcriptome Analysis between Two Potato Cultivars in Tuber Induction to Reveal Associated Genes with Anthocyanin Accumulation. Int J Mol Sci 2022; 23:ijms23073681. [PMID: 35409041 PMCID: PMC8998591 DOI: 10.3390/ijms23073681] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/22/2022] [Accepted: 03/24/2022] [Indexed: 11/29/2022] Open
Abstract
Anthocyanins are generally accumulated within a few layers, including the epidermal cells of leaves and stems in plants. Solanum tuberosum cv. ‘Jayoung’ (hereafter, JY) is known to accumulate anthocyanin both in inner tissues and skins. We discovered that anthocyanin accumulation in the inner tissues of JY was almost diminished (more than 95% was decreased) in tuber induction condition. To investigate the transcriptomic mechanism of anthocyanin accumulation in JY flesh, which can be modulated by growth condition, we performed mRNA sequencing with white-colored flesh tissue of Solanum tuberosum cv. ‘Atlantic’ (hereafter, ‘Daeseo’, DS) grown under canonical growth conditions, a JY flesh sample grown under canonical growth conditions, and a JY flesh sample grown under tuber induction conditions. We could identify 36 common DEGs (differentially expressed genes) in JY flesh from canonical growth conditions that showed JY-specifically increased or decreased expression level. These genes were enriched with flavonoid biosynthetic process terms in GO analysis, as well as gene set enrichment analysis (GSEA) analysis. Further in silico analysis on expression levels of anthocyanin biosynthetic genes including rate-limiting genes such as StCHS and StCHI followed by RT-PCR and qRT-PCR analysis showed a strong positive correlation with the observed phenotypes. Finally, we identified StWRKY44 from 36 common DEGs as a possible regulator of anthocyanin accumulation, which was further supported by network analysis. In conclusion, we identified StWRKY44 as a putative regulator of tuber-induction-dependent anthocyanin accumulation.
Collapse
Affiliation(s)
- Ju Young Ahn
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea; (J.Y.A.); (J.K.); (J.Y.Y.); (H.J.L.); (S.K.)
| | - Jaewook Kim
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea; (J.Y.A.); (J.K.); (J.Y.Y.); (H.J.L.); (S.K.)
| | - Ju Yeon Yang
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea; (J.Y.A.); (J.K.); (J.Y.Y.); (H.J.L.); (S.K.)
| | - Hyun Ju Lee
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea; (J.Y.A.); (J.K.); (J.Y.Y.); (H.J.L.); (S.K.)
| | - Soyun Kim
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea; (J.Y.A.); (J.K.); (J.Y.Y.); (H.J.L.); (S.K.)
| | - Kwang-Soo Cho
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Admin-istration, Pyeongchang 25342, Korea;
| | - Sang-Ho Lee
- Department of Biomedical Engineering, Mokwon University, Daejeon 35349, Korea;
| | - Jin-Hyun Kim
- Division of Genomics, National Institute of Agricultural Sciences, Jeonju 54874, Korea; (J.-H.K.); (T.-H.L.)
| | - Tae-Ho Lee
- Division of Genomics, National Institute of Agricultural Sciences, Jeonju 54874, Korea; (J.-H.K.); (T.-H.L.)
| | - Yoonkang Hur
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea; (J.Y.A.); (J.K.); (J.Y.Y.); (H.J.L.); (S.K.)
- Correspondence: (Y.H.); (D.S.)
| | - Donghwan Shim
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea; (J.Y.A.); (J.K.); (J.Y.Y.); (H.J.L.); (S.K.)
- Correspondence: (Y.H.); (D.S.)
| |
Collapse
|
44
|
Qin W, Yang Y, Wang Y, Zhang X, Liu X. Transcriptomic and metabolomic analysis reveals the difference between large and small flower taxa of Herba Epimedii during flavonoid accumulation. Sci Rep 2022; 12:2762. [PMID: 35177764 PMCID: PMC8854644 DOI: 10.1038/s41598-022-06761-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 02/03/2022] [Indexed: 11/10/2022] Open
Abstract
Herba Epimedii, as a traditional Chinese herb, is divided into large and small flower taxa, and can invigorate sexuality and strengthen muscles and bones. Herba Epimedii is rich in flavonoids, which largely contribute to its medicinal benefits. In our previous studies, we have found that the flavonoids content was much more in small than large flower taxa. To further identify molecular mechanisms of flavonoids metabolism in Herba Epimedii, combined metabolome and transcriptomic analyses were performed to profile leaves and flowers. Association analysis revealed that the expression of genes involved in flavonoid biosynthesis showed significant differences between small and large flower taxa. Eleven flavonols significantly increased in small compared to large flower taxa. Moreover, genes encoding O-methyltransferase played crucial roles in flavonoids metabolism by an integrated analysis. Taken together, these data highlight the breeding tendency of small flower taxa to improve the quality of Herba Epimedii.
Collapse
Affiliation(s)
- Weihan Qin
- Chongqing Academy of Chinese Materia Medica, Chongqing, 400065, China
| | - Yong Yang
- Chongqing Academy of Chinese Materia Medica, Chongqing, 400065, China
| | - Yunhong Wang
- Chongqing Academy of Chinese Materia Medica, Chongqing, 400065, China
| | - Xiaomei Zhang
- Chongqing Academy of Chinese Materia Medica, Chongqing, 400065, China
| | - Xiang Liu
- Chongqing Academy of Chinese Materia Medica, Chongqing, 400065, China.
| |
Collapse
|
45
|
Qiao Q, Si F, Wu C, Wang J, Zhang A, Tao J, Zhang L, Liu Y, Feng Z. Transcriptome sequencing and flavonoid metabolism analysis in the leaves of three different cultivars of Acer truncatum. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 171:1-13. [PMID: 34968987 DOI: 10.1016/j.plaphy.2021.12.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/14/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
Young and mature leaves of three Acer truncatum varieties with different leaf colors were examined. Transcriptome sequencing and flavonoid metabolism were used to analyze the differential gene expression associated with different leaf colors and growth stages and the relationships between gene expression and flavonoid and anthocyanin contents to improve ornamental value and develop flavonoid-rich A. truncatum. Kyoto Encyclopedia of Genes and Genomes database annotation of differentially expressed genes indicated that the following genes were related to flavonoid synthesis: phenylpropanoid biosynthesis genes (PAL, C4H, 4CL and CHS), flavonoid biosynthesis genes (E2.1.1.104, CHI, FLS, F3'5'H and ANR), anthocyanin biosynthesis genes (ANS, DFR, HCT, BZ1, GT1, and UGT79B1), isoflavonoid biosynthesis genes (HIDH and CYP81E17), and their transcriptional regulator (MYB). A total of 234 types of flavonoids were detected. The types and contents of anthocyanins in the red-leaf varieties 'Hong Jingling' and 'Caidie Fanfei' were significantly higher than those in the green leaf cultivar 'Lv Baoshi', especially morning glory 3-O-glucoside, delphinidin 3-O-glucoside, and pelargonium-3-O-glucoside, which were not detected in 'Lv Baoshi'. Combined omics analysis showed that downregulated expression of C4H, CHS and F3'5'H and upregulated expression of FLS reduced the supply of raw materials for anthocyanin synthesis, and downstream ANR upregulation converted anthocyanins to procyanidins, increasing the total flavonoid content. F3'5'H expression was downregulated in the leaves of each variety with development, resulting in the accumulation of catechins and the gradual greening of the leaves. F3'5'H was significantly depleted in the young leaves of 'Hong Jingling' and 'Caidie Fanfei' compared with the young leaves of 'Lv Baoshi', while ANS and BZ1 were enriched significantly. It is concluded that F3'5'H, BZ1, and ANS are the key genes needed for breeding red A. truncatum and that ANR is the key gene needed for breeding varieties with a high flavonoids contens. These results may facilitate genetic modification or selection for further improvement of the ornamental qualities and flavonoid content of A. truncatum.
Collapse
Affiliation(s)
- Qian Qiao
- Shandong Institute of Pomology, Shandong Academy of Agricultural Sciences, Tai'an, Shandong, 271000, China; College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Fenfen Si
- College of Forestry, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Chong Wu
- Shandong Institute of Pomology, Shandong Academy of Agricultural Sciences, Tai'an, Shandong, 271000, China
| | - Jiangyong Wang
- Shandong Institute of Pomology, Shandong Academy of Agricultural Sciences, Tai'an, Shandong, 271000, China
| | - Anning Zhang
- Shandong Institute of Pomology, Shandong Academy of Agricultural Sciences, Tai'an, Shandong, 271000, China
| | - Jihan Tao
- Shandong Institute of Pomology, Shandong Academy of Agricultural Sciences, Tai'an, Shandong, 271000, China
| | - Lin Zhang
- Taishan Forestry Science Institute, Tai'an, Shandong, 271000, China
| | - Yan Liu
- College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Zhen Feng
- College of Forestry, Shandong Agricultural University, Tai'an, Shandong, 271018, China.
| |
Collapse
|
46
|
Pigmented Potatoes: A Potential Panacea for Food and Nutrition Security and Health? Foods 2022; 11:foods11020175. [PMID: 35053906 PMCID: PMC8774573 DOI: 10.3390/foods11020175] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/25/2021] [Accepted: 12/27/2021] [Indexed: 02/05/2023] Open
Abstract
Although there are over 4000 potato cultivars in the world, only a few have been commercialized due to their marketability and shelf-life. Most noncommercialized cultivars are pigmented and found in remote regions of the world. White-fleshed potatoes are well known for their energy-enhancing complex carbohydrates; however, pigmented cultivars are potentially high in health-promoting polyphenolic compounds. Therefore, we reveal the comprehensive compositions of pigmented cultivars and associated potential health benefits, including their potential role in ameliorating hunger, food, and nutrition insecurity, and their prospects. The underutilization of such resources is a direct threat to plant-biodiversity and local traditions and cultures.
Collapse
|
47
|
Yuan Z, Dong F, Pang Z, Fallah N, Zhou Y, Li Z, Hu C. Integrated Metabolomics and Transcriptome Analyses Unveil Pathways Involved in Sugar Content and Rind Color of Two Sugarcane Varieties. FRONTIERS IN PLANT SCIENCE 2022; 13:921536. [PMID: 35783968 PMCID: PMC9244704 DOI: 10.3389/fpls.2022.921536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 05/18/2022] [Indexed: 05/02/2023]
Abstract
Metabolic composition can have potential impact on several vital agronomic traits, and metabolomics, which represents the bioactive compounds in plant tissues, is widely considered as a powerful approach for linking phenotype-genotype interactions. However, metabolites related to cane traits such as sugar content, rind color, and texture differences in different sugarcane cultivars using metabolome integrated with transcriptome remain largely inconclusive. In this study, metabolome integrated with transcriptome analyses were performed to identify and quantify metabolites composition, and have better insight into the molecular mechanisms underpinning the different cane traits, namely, brix, rind color, and textures in the stems (S) and leaves (L) of sugarcane varieties FN41 and 165402. We also identified metabolites and associated genes in the phenylpropanoid and flavonoid biosynthesis pathways, starch and sucrose metabolism. A total of 512 metabolites from 11 classes, with the vast majority (122) belonging to flavonoids were identified. Moreover, the relatively high amount of D-fructose 6-p, D-glucose6-p and glucose1-p detected in FN41L may have been transported and distributed by source and sink of the cane, and a majority of them reached the stem of sugarcane FN41L, thereby promoting the high accumulation of sugar in FN41S. Observations also revealed that genes such as C4H, CHS, F3H, F3'H, DFR, and FG2 in phenylpropanoid and flavonoid biosynthesis pathways were the major factors impacting the rind color and contrasting texture of FN41 and 165204. Further analysis revealed that weighted gene co-expression network analysis (WGCNA) hub genes and six transcription factors, namely, Tify and NAC, MYB-related, C2C2-Dof, WRKY, and bHLH play a key role in phenylpropanoid biosynthesis, flavone and flavonol biosynthesis, starch and sucrose metabolism. Additionally, metabolites such as L-phenylalanine, tyrosine, sinapaldehyde, pinobanksin, kaempferin, and nictoflorin were the potential drivers of phenotypic differences. Our finding also demonstrated that genes and metabolites in the starch and sucrose metabolism had a significant effect on cane sugar content. Overall, this study provided valuable insight into the molecular mechanisms underpinning high sugar accumulation and rind color in sugarcane, which we believe is important for future sugarcane breeding programs and the selection of high biomass varieties.
Collapse
Affiliation(s)
- Zhaonian Yuan
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou, China
- Province and Ministry Co-sponsored Collaborative Innovation Center of Sugar Industry, Nanning, China
- *Correspondence: Zhaonian Yuan,
| | - Fei Dong
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ziqin Pang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Nyumah Fallah
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yongmei Zhou
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou, China
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhi Li
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chaohua Hu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou, China
| |
Collapse
|
48
|
Transcriptomics integrated with metabolomics reveals the effect of Lycium barbarum polysaccharide on apoptosis in Nile tilapia (Oreochromis niloticus). Genomics 2021; 114:229-240. [PMID: 34933073 DOI: 10.1016/j.ygeno.2021.12.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 11/17/2021] [Accepted: 12/13/2021] [Indexed: 12/22/2022]
Abstract
Lycium barbarum polysaccharide (LBP) is one of the main active ingredients in the fruit of L. barbarum L. It has been used as herbal medicine for thousands of years in China. In this study, Nile tilapia (Oreochromis niloticus) was taken as the research object. After feeding tilapia with 5 different doses of LBP (0 mg/kg, 500 mg/kg, 1000 mg/kg, 1500 mg/kg, 2000 mg/kg) for 55 d, it was found that LBP could promote the growth of tilapia, and this effect was the strongest at Group 1500 mg/kg. Apoptosis analysis in the liver and spleen showed that dietary supplementation with 1000 mg/kg LBP had the best protective effect on the spleen and liver in tilapia. Combined transcriptomics and metabolomics of the spleen in tilapia at Group 0 mg/kg and 1000 mg/kg showed that the differentially expressed genes (DEGs) such as NT5C2L1, pmm1, FasL and the differentially metabolites such as xanthine, dGMP, guanine and glutamate were mainly concentrated in signaling pathways such as Purine metabolism and FoxO signaling pathway. In conclusion, LBP regulates the metabolic waste levels of tilapia mainly through Purine metabolism and the FoxO signaling pathway, thereby inhibiting cell apoptosis, improving the utilization of nutrients, and promoting the growth of tilapia. This study not only provides a theoretical basis for the application of LBP in aquatic animals but also provides useful information for the healthy development of the aquaculture.
Collapse
|
49
|
Liu T, Zhang X. Comparative transcriptome and metabolome analysis reveal glutathione metabolic network and functional genes underlying blue and red-light mediation in maize seedling leaf. BMC PLANT BIOLOGY 2021; 21:593. [PMID: 34906076 PMCID: PMC8670197 DOI: 10.1186/s12870-021-03376-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 11/30/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Light quality severely affects biosynthesis and metabolism-associated process of glutathione. However, the role of specific light is still unclear on the glutathione metabolism. In this article, comparatively transcriptome and metabolome methods are used to fully understand the blue and red-light conditions working on the glutathione metabolism in maize seedling leaf. RESULTS There are 20 differently expressed genes and 4 differently expressed metabolites in KEGG pathway of glutathione metabolism. Among them, 12 genes belong to the glutathione S-transferase family, 3 genes belong to the ascorbate peroxidase gene family and 2 genes belong to the ribonucleoside-diphosphate reductase gene family. Three genes, G6PD, SPDS1, and GPX1 belong to the gene family of glucose 6-phosphate dehydrogenase, spermidine synthase, and glutathione peroxidase, respectively. Four differently expressed metabolites are identified. Three of them, Glutathione disulfide, Glutathione, and l-γ-Glutamyl-L-amino acid are decreased while L-Glutamate is increased. In addition, Through PPI analysis, two annotated genes gst16 and DAAT, and 3 unidentified genes 100381533, pco105094 and umc2770, identified as RPP13-like3, BCAT-like1and GMPS, were obtained. By the analysis of protein sequence and PPI network, we predict that pco105094 and umc2770 were involved in the GSSG-GSH and AsA-GSH cycle in the network of glutathione metabolism. CONCLUSIONS Compared to red light, blue light remarkably changed the transcription signal transduction and metabolism of glutathione metabolism. Differently expressed genes and metabolic mapped to the glutathione metabolism signaling pathways. In total, we obtained three unidentified genes, and two of them were predicted in current glutathione metabolism network. This result will contribute to the research of glutathione metabolism of maize.
Collapse
Affiliation(s)
- Tiedong Liu
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Xiwen Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| |
Collapse
|
50
|
He Y, Chen H, Zhao J, Yang Y, Yang B, Feng L, Zhang Y, Wei P, Hou D, Zhao J, Yu M. Transcriptome and metabolome analysis to reveal major genes of saikosaponin biosynthesis in Bupleurum chinense. BMC Genomics 2021; 22:839. [PMID: 34798822 PMCID: PMC8603497 DOI: 10.1186/s12864-021-08144-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 10/25/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Bupleurum chinense DC. is a widely used traditional Chinese medicinal plant. Saikosaponins are the major bioactive constituents of B. chinense, but relatively little is known about saikosaponin biosynthesis. In the present study, we performed an integrated analysis of metabolic composition and the expressed genes involved in saikosaponin biosynthetic pathways among four organs (the root, flower, stem, and leaf) of B. chinense to discover the genes related to the saikosaponin biosynthetic pathway. RESULTS Transcript and metabolite profiles were generated through high-throughput RNA-sequencing (RNA-seq) data analysis and liquid chromatography tandem mass spectrometry, respectively. Evaluation of saikosaponin contents and transcriptional changes showed 152 strong correlations (P < 0.05) over 3 compounds and 77 unigenes. These unigenes belonged to eight gene families: the acetoacetyl CoA transferase (AACT) (6), HMG-CoA synthase (HMGS) (2), HMG-CoA reductase (HMGR) (2), mevalonate diphosphate decarboxylase (MVD) (1), 1-deoxy-D-xylulose-5-phosphate synthase (DXS) (3), farnesyl diphosphate synthase (FPPS) (11), β-amyrin synthase (β-AS) (13) and cytochrome P450 enzymes (P450s) (39) families. CONCLUSIONS Our results investigated the diversity of the saikosaponin triterpene biosynthetic pathway in the roots, stems, leaves and flowers of B. chinese by integrated transcriptomic and metabolomic analysis, implying that manipulation of P450s genes such as Bc95697 and Bc35434 might improve saikosaponin biosynthesis. This is a good candidate for the genetic improvement of this important medicinal plant.
Collapse
Affiliation(s)
- Yilian He
- School of life science and engineering, Southwest University of Science and Technology, 59 Qinglong Road, Mianyang, 621010, Sichuan, China
| | - Hua Chen
- School of life science and engineering, Southwest University of Science and Technology, 59 Qinglong Road, Mianyang, 621010, Sichuan, China
| | - Jun Zhao
- School of life science and engineering, Southwest University of Science and Technology, 59 Qinglong Road, Mianyang, 621010, Sichuan, China
| | - Yuxia Yang
- Institute of Medicinal Plant Resources, Sichuan Academy of Traditional Chinese Medicine Sciences, 51 4th Section S. Renmin Road, Chengdu, 610041, Sichuan, China
| | - Bin Yang
- School of life science and engineering, Southwest University of Science and Technology, 59 Qinglong Road, Mianyang, 621010, Sichuan, China
| | - Liang Feng
- School of life science and engineering, Southwest University of Science and Technology, 59 Qinglong Road, Mianyang, 621010, Sichuan, China
| | - Yiguan Zhang
- Sichuan Institute for Translational Chinese Medicine, Chengdu, 610041, China
| | - Ping Wei
- Sichuan Institute for Translational Chinese Medicine, Chengdu, 610041, China
| | - Dabin Hou
- School of life science and engineering, Southwest University of Science and Technology, 59 Qinglong Road, Mianyang, 621010, Sichuan, China
| | - Junning Zhao
- Sichuan Institute for Translational Chinese Medicine, Chengdu, 610041, China.
| | - Ma Yu
- School of life science and engineering, Southwest University of Science and Technology, 59 Qinglong Road, Mianyang, 621010, Sichuan, China. .,Laboratory of Medicinal Plant Cultivation, Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China.
| |
Collapse
|