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Ren Z, Qin L, Chen L, Xu H, Liu H, Guo H, Li J, Yang C, Hu H, Wu R, Zhou Y, Xue K, Liu B, Wang X. Spatial Lipidomics of EPSPS and PAT Transgenic and Non-Transgenic Soybean Seeds Using Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37318082 DOI: 10.1021/acs.jafc.3c01377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Herbicide-resistant soybeans are among the most widely planted transgenic crops. The in situ evaluation of spatial lipidomics in transgenic and non-transgenic soybeans is important for directly assessing the unintended effects of exogenous gene introduction. In this study, matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI)-based non-targeted analytical strategies were used for the first time for in situ detection and imaging of endogenous lipid distributions in transgenic (EPSPS and PAT genes) herbicide-resistant soybean (Glycine max Merrill) (S4003.14) and non-transgenic soybean (JACK) seeds. Statistical analysis revealed significant differences in lipids between S4003.14 and JACK seeds. The variable importance of projection analysis further revealed that 18 identified lipids, including six phosphatidylcholines (PCs), four phosphatidylethanolamines (PEs), five triacylglycerols (TAGs), and three cytidine diphosphate-diacylglycerols (CDP-DAGs), had the strongest differential expression between S4003.14 and JACK seeds. Among those, the upregulated expressions of PC(P-36:1), PC(36:2), PC(P-36:0), PC(37:5), PE(40:2), TAG(52:1), TAG(55:5), and CDP-DAG(37:2) and the downregulated expressions of PC (36:1), TAG(43:0), and three PEs (i.e., PE(P-38:1), PE(P-38:0), and PE(P-40:3)) were successfully found in the S4003.14 seeds, compared to these lipids detected in the JACK seeds. Meanwhile, the lipids of PC (44:8), CDP-DAG(38:0), and CDP-DAG(42:0) were uniquely detected in the S4003.14 soybean seeds, and TAG(45:2) and TAG(57:10) were detected as the unique lipids in the JACK seeds. The heterogeneous distribution of these lipids in the soybean seeds was also clearly visualized using MALDI-MSI. MSI results showed that lipid expression was significantly up/downregulated in S4003.14 seeds, compared to that in JACK seeds. This study improves our understanding of the unintended effects of herbicide-resistant EPSPS and PAT gene transfers on spatial lipidomes in soybean seeds and enables the continued progression of MALDI-MSI as an emerging, reliable, and rapid molecular imaging tool for evaluating unintended effects in transgenic plants.
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Affiliation(s)
- Zhentao Ren
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Liang Qin
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Lulu Chen
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Hualei Xu
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Haiqiang Liu
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Hua Guo
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Jinrong Li
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Chenyu Yang
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Hao Hu
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Ran Wu
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Yijun Zhou
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Kun Xue
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Biao Liu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Xiaodong Wang
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
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Medison MB, Pan R, Peng Y, Medison RG, Shalmani A, Yang X, Zhang W. Identification of HQT gene family and their potential function in CGA synthesis and abiotic stresses tolerance in vegetable sweet potato. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:361-376. [PMID: 37033766 PMCID: PMC10073390 DOI: 10.1007/s12298-023-01299-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 03/14/2023] [Accepted: 03/17/2023] [Indexed: 06/19/2023]
Abstract
Hydroxycinnamate-CoA quinate hydroxycinnamoyl transferase (HQT) enzyme affect plant secondary metabolism and are crucial for growth and development. To date, limited research on the genome-wide analysis of HQT family genes and their regulatory roles in chlorogenic acid (CGA) accumulation in leafy vegetable sweet potato is available. Here, a total of 58 HQT family genes in the sweet potato genome (named IbHQT) were identified and analyzed. We studied the chromosomal distribution, phylogenetic relationship, motifs distribution, collinearity, and cis-acting element analysis of HQT family genes. This study used two sweet potato varieties, high CGA content Fushu 7-6-14-7 (HC), and low CGA content Fushu 7-6 (LC). Based on the phylogenetic analysis, clade A was unique among the identified four clades as it contained HQT genes from various species. The chromosomal location and collinearity analysis revealed that tandem gene duplication may promote the IbHQT gene expansion and expression. The expression patterns and profile analysis showed changes in gene expression levels at different developmental stages and under cold, drought, and salt stress conditions. The expression analysis verified by qRT-PCR revealed that IbHQT genes were highly expressed in the HC variety leaves than in the LC variety. Furthermore, cloning and gene function analysis unveiled that IbHQT family genes are involved in the biosynthesis and accumulation of CGA in sweet-potato. This study expands our understanding of the regulatory role of HQT genes in sweet-potato and lays a foundation for further functional characterization and genetic breeding by engineering targeted HQT candidate genes in various sweet-potato varieties and other species. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01299-4.
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Affiliation(s)
- Milca Banda Medison
- Research Center of Crop Stresses Resistance Technologies/ Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, 434025 China
| | - Rui Pan
- Research Center of Crop Stresses Resistance Technologies/ Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, 434025 China
| | - Ying Peng
- Research Center of Crop Stresses Resistance Technologies/ Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, 434025 China
| | - Rudoviko Galileya Medison
- Research Center of Crop Stresses Resistance Technologies/ Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, 434025 China
| | - Abdullah Shalmani
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, 712100 China
| | - XinSun Yang
- Institute of Food Crops/Hubei Engineering and Technology Research Centre of Sweet Potato/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Hubei Academy of Agricultural Sciences, Wuhan, 430064 China
| | - Wenying Zhang
- Research Center of Crop Stresses Resistance Technologies/ Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, 434025 China
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Peng Y, Pan R, Liu Y, Medison MB, Shalmani A, Yang X, Zhang W. LncRNA-mediated ceRNA regulatory network provides new insight into chlorogenic acid synthesis in sweet potato. PHYSIOLOGIA PLANTARUM 2022; 174:e13826. [PMID: 36377281 DOI: 10.1111/ppl.13826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 06/16/2023]
Abstract
Sweet potato (Ipomoea batatas L.) is considered a highly nutritional and economical crop due to its high contents of bioactive substances, such as anthocyanin and chlorogenic acid (CGA), especially in leaves and stems. The roles of noncoding RNAs (ncRNA), including long noncoding RNA (lncRNA) and microRNA (miRNA), in CGA synthesis, are still unknown. In this study, the differentially expressed (DE) mRNAs, miRNAs, and lncRNAs in two leafy vegetable genotypes "FS7-6-14-7" (high CGA content) and "FS7-6" (low CGA content) were identified. The cis-regulation between lncRNA and mRNA was analyzed. Then, the CGA synthesis-related modules MEBlue and MEYellow were identified to detect trans-regulation mRNA-lncRNA pairs. The GO and KEGG annotations suggested that mRNA in these two modules was significantly enriched in the secondary metabolite synthesis biosynthesis category. A competing endogenous RNAs (ceRNA) network, including 8730 miRNA-mRNA and 444 miRNA-lncRNA pairs, was constructed by DEmiRNA target prediction. Then, a CGA synthesis-related ceRNA network was obtained with lncRNA and mRNA from MEBlue and MEYellow. Finally, one relational pair, MSTRG.47662.1/mes-miR398/itb04g00990, was selected for functional validation. Overexpression of lncRNA MSTRG.47662.1 and mRNA itb04g00990 increased CGA content in both tobacco and sweet potato callus, while overexpression of miRNA mes-miR398 decreased CGA content. Meanwhile, regression analysis of the expression patterns demonstrated that MSTRG.47662.1, acting as a ceRNA, promoted itb04g00990 expression by competitively binding mes-miR398 in CGA synthesis in sweet potato. Our results provide insights into how ncRNA-mediated ceRNA regulatory networks likely contribute to CGA synthesis in leafy sweet potato.
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Affiliation(s)
- Ying Peng
- Research Center of Crop Stresses Resistance Technologies/Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, China
| | - Rui Pan
- Research Center of Crop Stresses Resistance Technologies/Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, China
| | - Yi Liu
- Research Center of Crop Stresses Resistance Technologies/Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, China
- Institute of Food Crops/Hubei Engineering and Technology Research Centre of Sweet Potato/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Milca Banda Medison
- Research Center of Crop Stresses Resistance Technologies/Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, China
| | - Abdullah Shalmani
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Xinsun Yang
- Institute of Food Crops/Hubei Engineering and Technology Research Centre of Sweet Potato/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Wenying Zhang
- Research Center of Crop Stresses Resistance Technologies/Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, China
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Moyo B, Tavengwa NT, Madala NE. Diverse chemical modifications of the chlorogenic acid composition of Viscum combreticola Engl.: A premise for the state of readiness against excessive sunlight exposure. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2022; 233:112501. [PMID: 35751972 DOI: 10.1016/j.jphotobiol.2022.112501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 06/08/2022] [Accepted: 06/11/2022] [Indexed: 12/11/2022]
Abstract
Mistletoe plants that are positioned on the canopy of their hosts are more susceptible to UV radiation exposure. These aerial plants are resistant to damage by UV radiation due the presence of epidermal constituents such as the cuticle, cork layer, trichomes and antioxidant secondary metabolites. In response to the photo-oxidative stress associated with UV exposure, plants generally deploy photo-protective responsive mechanisms that involve the biosynthesis of UV absorbing phenolic compounds such as chlorogenic acids (CGAs). The hydroxycinnamic acid moieties of these CGAs are predominantly in the trans configuration, naturally. However, excessive sunlight exposure of plants containing these compounds can result in geometrical isomerisation, characterized by the formation of cis isomers. Therefore, in this study, the effect of UV light radiation on the CGA composition of Viscum combreticola Engl. (Santalacaeae) plants using an in vitro model was unravelled through UHPLC-q-TOF-MS-based metabolic profiling. Interestingly, the findings of this study revealed that this plant has a diverse chemical composition of CGAs that is characterized by epimerization, monoacylation, homodiacylation and heterodiacylation of the quinic acid (QA), thereby, contributing to the state of readiness in these plants against sunlight or UV exposure. In addition to the commonly reported cinnamoyl containing heterodiacylated CGAs, hydroxybenzoyl containing heterodiacylated CGAs were also reported in this study. Moreover, cis isomers (24 in total) of some CGAs were identified in the non-irradiated samples and the formation of these compounds has been reported to help plants in the mitigation of photo-oxidative stress. An additional 28 cis isomers of CGAs and HCA derivatives were observed in the UV-irradiated samples, hence, further increasing the complexity of the metabolome of this plant, with a total of 108 compounds identified in this study. The presence of epimers, positional and geometrical isomers of these compounds could be a biochemical strategy to maximize the chemical arsenal of this plant to withstand the photo-oxidative stress posed by UV radiation from the sunlight. Due to purported pharmacological properties associated with the identified compounds these parasitic plants can be a rich source of prospective therapeutic compounds that can be employed as drug discovery leads. Moreover, UV radiation might be essential in future to produce potent drugs since plants naturally produce these compounds in low quantities.
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Affiliation(s)
- Babra Moyo
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Private Bag X5050, Thohoyandou 0950, South Africa; Department of Food Science and Technology, Faculty of Science, Engineering and Agriculture, University of Venda, Private Bag X5050, Thohoyandou 0950, South Africa
| | - Nikita Tawanda Tavengwa
- Department of Chemistry, Faculty of Science, Engineering and Agriculture, University of Venda, Private Bag X5050, Thohoyandou 0950, South Africa
| | - Ntakadzeni Edwin Madala
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Private Bag X5050, Thohoyandou 0950, South Africa.
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Su Z, Jia H, Sun M, Cai Z, Shen Z, Zhao B, Li J, Ma R, Yu M, Yan J. Integrative analysis of the metabolome and transcriptome reveals the molecular mechanism of chlorogenic acid synthesis in peach fruit. Front Nutr 2022; 9:961626. [PMID: 35928835 PMCID: PMC9344011 DOI: 10.3389/fnut.2022.961626] [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: 06/05/2022] [Accepted: 06/30/2022] [Indexed: 01/01/2023] Open
Abstract
As the most abundant phenolic acid in peach fruit, chlorogenic acid (CGA) is an important entry point for the development of natural dietary supplements and functional foods. However, the metabolic and regulation mechanisms underlying its accumulation in peach fruits remain unclear. In this study, we evaluated the composition and content of CGAs in mature fruits of 205 peach cultivars. In peach fruits, three forms of CGA (52.57%), neochlorogenic acid (NCGA, 47.13%), and cryptochlorogenic acid (CCGA, 0.30%) were identified. During the growth and development of peach fruits, the content of CGAs generally showed a trend of rising first and then decreasing. Notably, the contents of quinic acid, shikimic acid, p-coumaroyl quinic acid, and caffeoyl shikimic acid all showed similar dynamic patterns to that of CGA, which might provide the precursor material basis for the accumulation of CGA in the later stage. Moreover, CGA, lignin, and anthocyanins might have a certain correlation and these compounds work together to maintain a dynamic balance. By the comparative transcriptome analysis, 8 structural genes (Pp4CL, PpCYP98A, and PpHCT) and 15 regulatory genes (PpMYB, PpWRKY, PpERF, PpbHLH, and PpWD40) were initially screened as candidate genes of CGA biosynthesis. Our findings preliminarily analyzed the metabolic and molecular regulation mechanisms of CGA biosynthesis in peach fruit, which provided a theoretical basis for developing high-CGA content peaches in future breeding programs.
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Affiliation(s)
- Ziwen Su
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, China
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Haoran Jia
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Meng Sun
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, China
| | - Zhixiang Cai
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, China
| | - Zhijun Shen
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, China
| | - Bintao Zhao
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, China
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Jiyao Li
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, China
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Ruijuan Ma
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, China
| | - Mingliang Yu
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, China
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Juan Yan
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, China
- *Correspondence: Juan Yan,
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Comparative transcriptome and weighted correlation network analyses reveal candidate genes involved in chlorogenic acid biosynthesis in sweet potato. Sci Rep 2022; 12:2770. [PMID: 35177832 PMCID: PMC8854667 DOI: 10.1038/s41598-022-06794-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 02/07/2022] [Indexed: 11/16/2022] Open
Abstract
Chlorogenic acids (CGAs) are important secondary metabolites produced in sweet potato. However, the mechanisms of their biosynthesis and regulation remain unclear. To identify potential genes involved in CGA biosynthesis, analysis of the dynamic changes in CGA components and RNA sequencing were performed on young leaves (YL), mature leaves (ML), young stems (YS), mature stems (MS) and storage roots (SR). Accordingly, we found that the accumulation of six CGA components varied among the different tissues and developmental stages, with YS and YL recording the highest levels, while SR exhibited low levels. Moreover, the transcriptome analysis yielded 59,287 unigenes, 3,767 of which were related to secondary-metabolite pathways. The differentially expressed genes (DEGs) were identified based on CGA content levels by comparing the different samples, including ML vs. YL, MS vs. YS, SR vs. YL and SR vs. YS. A total of 501 common DEGs were identified, and these were mainly implicated in the secondary metabolites biosynthesis. Additionally, eight co-expressed gene modules were identified following weighted gene co-expression network analysis, while genes in darkgrey module were highly associated with CGA accumulation. Darkgrey module analysis revealed that 12 unigenes encoding crucial enzymes (PAL, 4CL, C4H, C3H and HCT/HQT) and 42 unigenes encoding transcription factors (MYB, bHLH, WD40, WRKY, ERF, MADS, GARS, bZIP and zinc finger protein) had similar expression patterns with change trends of CGAs, suggesting their potential roles in CGA metabolism. Our findings provide new insights into the biosynthesis and regulatory mechanisms of CGA pathway, and will inform future efforts to build a genetically improve sweet potato through the breeding of high CGA content varieties.
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Liu Y, Su W, Wang L, Lei J, Chai S, Zhang W, Yang X. Integrated transcriptome, small RNA and degradome sequencing approaches proffer insights into chlorogenic acid biosynthesis in leafy sweet potato. PLoS One 2021; 16:e0245266. [PMID: 33481815 PMCID: PMC7822329 DOI: 10.1371/journal.pone.0245266] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 12/26/2020] [Indexed: 12/22/2022] Open
Abstract
Leafy sweet potato is rich in total phenolics (TP) which play key roles in health protection, the chlorogenic acid (CGA) constitutes the major components of phenolic compounds in leafy sweet potato. Unfortunately, the mechanism of CGA biosynthesis in leafy sweet potato is unclear. To dissect the mechanisms of CGA biosynthesis, we performed transcriptome, small RNA (sRNA) and degradome sequencing of one low-CGA content and one high-CGA content genotype at two stages. A total of 2,333 common differentially expressed genes (DEGs) were identified, and the enriched DEGs were related to photosynthesis, starch and sucrose metabolism and phenylpropanoid biosynthesis. The functional genes, such as CCR, CCoAOMT and HCT in the CGA biosynthetic pathway were down-regulated, indicating that the way to lignin was altered, and two possible CGA biosynthetic routes were hypothesized. A total of 38 DE miRNAs were identified, and 1,799 targets were predicated for 38 DE miRNAs by using in silico approaches. The target genes were enriched in lignin and phenylpropanoid catabolic processes. Transcription factors (TFs) such as apetala2/ethylene response factor (AP2/ERF) and Squamosa promoter binding protein-like (SPL) predicated in silico were validated by degradome sequencing. Association analysis of the DE miRNAs and transcriptome datasets identified that miR156 family negatively targeted AP2/ERF and SPL. Six mRNAs and six miRNAs were validated by qRT-PCR, and the results showed that the expression levels of the mRNAs and miRNAs were consistent with the sequencing data. This study established comprehensive functional genomic resources for the CGA biosynthesis, and provided insights into the molecular mechanisms involving in this process. The results also enabled the first perceptions of the regulatory roles of mRNAs and miRNAs, and offered candidate genes for leafy sweet potato improvements.
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Affiliation(s)
- Yi Liu
- Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, China
- Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Centre of Sweet Potato/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Wuhan, China
| | - Wenjin Su
- Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Centre of Sweet Potato/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Wuhan, China
| | - Lianjun Wang
- Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Centre of Sweet Potato/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Wuhan, China
| | - Jian Lei
- Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Centre of Sweet Potato/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Wuhan, China
| | - Shasha Chai
- Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Centre of Sweet Potato/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Wuhan, China
| | - Wenying Zhang
- Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, China
| | - Xinsun Yang
- Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Centre of Sweet Potato/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Wuhan, China
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