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Wei Y, Wang M, Wang M, Yu D, Wei X. Elevated CO 2 concentration enhance carbon and nitrogen metabolism and biomass accumulation of Ormosiahosiei. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 212:108725. [PMID: 38772164 DOI: 10.1016/j.plaphy.2024.108725] [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: 10/05/2023] [Revised: 04/28/2024] [Accepted: 05/10/2024] [Indexed: 05/23/2024]
Abstract
Elevated CO2 concentrations may inhibit photosynthesis due to nitrogen deficiency, but legumes may be able to overcome this limitation and continue to grow. Our study confirms this conjecture well. First, we placed the two-year-old potted saplings of Ormosia hosiei (O. hosiei) (a leguminous tree species) in the open-top chamber (OTC) with three CO2 concentrations of 400 (CK), 600 (E1), and 800 μmol·mol-1 (E2) to simulate the elevated CO2 concentration environment. After 146 days, the light saturation point (LSP), light compensation point (LCP), apparent quantum efficiency (AQE), and dark respiration rate (Rd) of O. hosiei were increased under increasing CO2 concentration and obtain the maximum ribulose diphosphate (RuBP) carboxylation rate (Vc max) and RuBP regenerated photosynthetic electron transfer rate (Jmax) were also significantly increased under E2 treatment (P < 0.05). This results in a significant increase of the maximum assimilation rate (Amax) under elevated CO2 concentrations. Sucrose phosphate synthase (SPS) activity in sucrose metabolism increased in the leaves, more soluble sugars, starches, and sucrose was produced, but sucrose content only in leaves increased at E2, and more carbon flows to the roots. The activity of the NH4+ assimilating enzymes glutamine synthetase (GS), glutamate synthetase (GOGAT), and glutamate dehydrogenase (GDH) in the leaves of O. hosiei increases under elevated CO2 concentrations to promote nitrogen synthesis that reduces the content of ammonium nitrogen and increases the content of nitrate nitrogen. In addition, under E1 conditions, sucrose synthase (SS), direction of synthesis activity was highest and sucrose invertase (INV) activity was lowest, this means that the balance of C and N metabolism is maintained. While under E2 conditions SS activity decreased and INV activity increased, this increased C/N and nitrogen use efficiency. So, the elevated CO2 concentration promotes the accumulation of O. hosiei biomass, especially in the aboveground part, but did not have a significant effect on the accumulation of root biomass. This means that O. hosiei is able to cope under the elevated CO2 concentration without showing photosynthetic adaptation during the experimental period.
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Affiliation(s)
- Yi Wei
- College of Forestry, Guizhou University, Guiyang, China
| | - Mingbin Wang
- College of Forestry, Guizhou University, Guiyang, China
| | - Man Wang
- College of Forestry, Guizhou University, Guiyang, China
| | - Dalong Yu
- College of Forestry, Guizhou University, Guiyang, China
| | - Xiaoli Wei
- College of Forestry, Guizhou University, Guiyang, China; Institute for Forest Resources and the Environment of Guizhou, Guizhou University, Guiyang, China.
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Hou G, Wu G, Jiang H, Bai X, Chen Y. RNA-Seq Reveals That Multiple Pathways Are Involved in Tuber Expansion in Tiger Nuts ( Cyperus esculentus L.). Int J Mol Sci 2024; 25:5100. [PMID: 38791140 PMCID: PMC11121407 DOI: 10.3390/ijms25105100] [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: 04/16/2024] [Revised: 05/03/2024] [Accepted: 05/03/2024] [Indexed: 05/26/2024] Open
Abstract
The tiger nut (Cyperus esculentus L.) is a usable tuber and edible oil plant. The size of the tubers is a key trait that determines the yield and the mechanical harvesting of tiger nut tubers. However, little is known about the anatomical and molecular mechanisms of tuber expansion in tiger nut plants. This study conducted anatomical and comprehensive transcriptomics analyses of tiger nut tubers at the following days after sowing: 40 d (S1); 50 d (S2); 60 d (S3); 70 d (S4); 90 d (S5); and 110 d (S6). The results showed that, at the initiation stage of a tiger nut tuber (S1), the primary thickening meristem (PTM) surrounded the periphery of the stele and was initially responsible for the proliferation of parenchyma cells of the cortex (before S1) and then the stele (S2-S3). The increase in cell size of the parenchyma cells occurred mainly from S1 to S3 in the cortex and from S3 to S4 in the stele. A total of 12,472 differentially expressed genes (DEGs) were expressed to a greater extent in the S1-S3 phase than in S4-S6 phase. DEGs related to tuber expansion were involved in cell wall modification, vesicle transport, cell membrane components, cell division, the regulation of plant hormone levels, signal transduction, and metabolism. DEGs involved in the biosynthesis and the signaling of indole-3-acetic acid (IAA) and jasmonic acid (JA) were expressed highly in S1-S3. The endogenous changes in IAA and JAs during tuber development showed that the highest concentrations were found at S1 and S1-S3, respectively. In addition, several DEGs were related to brassinosteroid (BR) signaling and the G-protein, MAPK, and ubiquitin-proteasome pathways, suggesting that these signaling pathways have roles in the tuber expansion of tiger nut. Finally, we come to the conclusion that the cortex development preceding stele development in tiger nut tubers. The auxin signaling pathway promotes the division of cortical cells, while the jasmonic acid pathway, brassinosteroid signaling, G-protein pathway, MAPK pathway, and ubiquitin protein pathway regulate cell division and the expansion of the tuber cortex and stele. This finding will facilitate searches for genes that influence tuber expansion and the regulatory networks in developing tubers.
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Affiliation(s)
- Guangshan Hou
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (G.H.); (G.W.); (H.J.)
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guojiang Wu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (G.H.); (G.W.); (H.J.)
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Huawu Jiang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (G.H.); (G.W.); (H.J.)
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Xue Bai
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun 666303, China;
| | - Yaping Chen
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (G.H.); (G.W.); (H.J.)
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
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Li X, Zhao Y, He S, Meng J, Lu Y, Shi H, Liu C, Hao B, Tang Q, Zhang S, Zhang G, Luo Y, Yang S, Yang J, Fan W. Integrated metabolome and transcriptome analyses reveal the molecular mechanism underlying dynamic metabolic processes during taproot development of Panax notoginseng. BMC PLANT BIOLOGY 2024; 24:170. [PMID: 38443797 PMCID: PMC10913227 DOI: 10.1186/s12870-024-04861-8] [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: 05/12/2023] [Accepted: 02/23/2024] [Indexed: 03/07/2024]
Abstract
BACKGROUND Panax notoginseng (Burk) F. H. Chen is one of the most famous Chinese traditional medicinal plants. The taproot is the main organ producing triterpenoid saponins, and its development is directly linked to the quality and yield of the harvested P. notoginseng. However, the mechanisms underlying the dynamic metabolic changes occurring during taproot development of P. notoginseng are unknown. RESULTS We carried out metabolomic and transcriptomic analyses to investigate metabolites and gene expression during the development of P. notoginseng taproots. The differentially accumulated metabolites included amino acids and derivatives, nucleotides and derivatives, and lipids in 1-year-old taproots, flavonoids and terpenoids in 2- and 3-year-old taproots, and phenolic acids in 3-year-old taproots. The differentially expressed genes (DEGs) are related to phenylpropanoid biosynthesis, metabolic pathway and biosynthesis of secondary metabolites at all three developmental stages. Integrative analysis revealed that the phenylpropanoid biosynthesis pathway was involved in not only the development of but also metabolic changes in P. notoginseng taproots. Moreover, significant accumulation of triterpenoid saponins in 2- and 3-year-old taproots was highly correlated with the up-regulated expression of cytochrome P450s and uridine diphosphate-dependent glycosyltransferases genes. Additionally, a gene encoding RNase-like major storage protein was identified to play a dual role in the development of P. notoginseng taproots and their triterpenoid saponins synthesis. CONCLUSIONS These results elucidate the molecular mechanism underlying the accumulation of and change relationship between primary and secondary metabolites in P. notoginseng taproots, and provide a basis for the quality control and genetic improvement of P. notoginseng.
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Affiliation(s)
- Xuejiao Li
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, China
| | - Yan Zhao
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, China
| | - Shuilian He
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, China
| | - Jing Meng
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, China
| | - Yingchun Lu
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Huineng Shi
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Chunlan Liu
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Bing Hao
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Qingyan Tang
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Shuangyan Zhang
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Guanghui Zhang
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Yu Luo
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| | - Shengchao Yang
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Jianli Yang
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, China.
| | - Wei Fan
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China.
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, China.
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Zhao X, Wang L, Zhou Y, Wang Q, Wang F, Li Y. Integrating Full-Length and Second-Generation Transcriptomics to Reveal Differentially Expressed Genes Associated with the Development of Corydalis yanhusuo Tuber. Life (Basel) 2023; 13:2207. [PMID: 38004347 PMCID: PMC10672666 DOI: 10.3390/life13112207] [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: 09/19/2023] [Revised: 11/05/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Corydalis yanhusuo is a medicinal herb in China that has been widely used to treat various kinds of pain. The tuber is the main organ of C. yanhusuo used for medicinal purposes, but changes in related genes during the development of the tuber have rarely been reported. To identify the differentially expressed genes during tuber development, C. yanhusuo full-length transcriptomic sequencing was performed using single-molecule real-time technology, and tubers at three development stages were selected for comparative transcriptome analysis. A total of 90,496 full-length non-chimeric transcripts were obtained, and 19,341 transcripts were annotated in at least one public database. A total of 9221 differentially expressed genes were identified during the swelling process of C. yanhusuo tuber. A Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis revealed that differentially expressed genes associated with a "starch and sucrose metabolism pathway", "phenylpropanoid biosynthesis pathway", "isoquinoline alkaloid biosynthesis pathway", "zeatin biosynthesis pathway", and "brassinosteroid biosynthesis pathway" were predominantly enriched. In addition, the genes involved in cell wall metabolism were potentially associated with tuber swelling. These processes regulated and were involved in C. yanhusuo tuber development. The results provide a foundation for further research on tuber formation in medicinal plants.
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Affiliation(s)
| | | | | | | | | | - Yan Li
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi’an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), Xi’an 710061, China (L.W.); (Y.Z.); (Q.W.); (F.W.)
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Xufeng X, Yuanfeng H, Ming Z, Shucheng S, Haonan Z, Weifeng Z, Fei G, Caijun W, Shuying F. Transcriptome profiling reveals the genes involved in tuberous root expansion in Pueraria (Pueraria montana var. thomsonii). BMC PLANT BIOLOGY 2023; 23:338. [PMID: 37365513 DOI: 10.1186/s12870-023-04303-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/20/2023] [Indexed: 06/28/2023]
Abstract
BACKGROUND Pueraria is a dry root commonly used in Traditional Chinese Medicine or as food and fodder, and tuberous root expansion is an important agronomic characteristic that influences its yield. However, no specific genes regulating tuberous root expansion in Pueraria have been identified. Therefore, we aimed to explore the expansion mechanism of Pueraria at six developmental stages (P1-P6), by profiling the tuberous roots of an annual local variety "Gange No.1" harvested at 105, 135, 165, 195, 225, and 255 days after transplanting. RESULTS Observations of the tuberous root phenotype and cell microstructural morphology revealed that the P3 stage was a critical boundary point in the expansion process, which was preceded by a thickening diameter and yield gain rapidly of the tuberous roots, and followed by longitudinal elongation at both ends. A total of 17,441 differentially expressed genes (DEGs) were identified by comparing the P1 stage (unexpanded) against the P2-P6 stages (expanded) using transcriptome sequencing; 386 differential genes were shared across the six developmental stages. KEGG pathway enrichment analysis showed that the DEGs shared by P1 and P2-P6 stages were mainly involved in pathways related to the "cell wall and cell cycle", "plant hormone signal transduction", "sucrose and starch metabolism", and "transcription factor (TF)". The finding is consistent with the physiological data collected on changes in sugar, starch, and hormone contents. In addition, TFs including bHLHs, AP2s, ERFs, MYBs, WRKYs, and bZIPs were involved in cell differentiation, division, and expansion, which may relate to tuberous root expansion. The combination of KEGG and trend analyses revealed six essential candidate genes involved in tuberous root expansion; of them, CDC48, ARF, and EXP genes were significantly upregulated during tuberous root expansion while INV, EXT, and XTH genes were significantly downregulated. CONCLUSION Our findings provide new insights into the complex mechanisms of tuberous root expansion in Pueraria and candidate target genes, which can aid in increasing Pueraria yield.
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Affiliation(s)
- Xiao Xufeng
- College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Hu Yuanfeng
- College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Zhang Ming
- Department of Biological Engineering, Jiangxi Biotech Vocational College, Nanchang, 330200, China
| | - Si Shucheng
- College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Zhou Haonan
- College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Zhu Weifeng
- College of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang, 330004, China
| | - Ge Fei
- College of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang, 330004, China
| | - Wu Caijun
- College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Fan Shuying
- College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China.
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Integrative Analysis of the Transcriptome and Metabolome Reveals the Developmental Mechanisms and Metabolite Biosynthesis of the Tuberous Roots of Tetrastigma hemsleyanum. Molecules 2023; 28:molecules28062603. [PMID: 36985574 PMCID: PMC10054749 DOI: 10.3390/molecules28062603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 03/08/2023] [Accepted: 03/11/2023] [Indexed: 03/18/2023] Open
Abstract
The tuberous root of Tetrastigma hemsleyanum Diels et Gilg (T. hemsleyanum) is a traditional Chinese medicine with a wide range of clinical applications. However, the scarcity of its wild resources, its low yield, and the variable quality that results from its artificial cultivation leads to expensive market prices that are not conducive to the further industrial development of T. hemsleyanum. In this study, transcriptomic and non-targeted metabolomic analyses were integrated to explore the underlying molecular mechanisms and metabolite biosynthesis that occur during its root development. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that differentially expressed genes (DEGs) were predominantly enriched for processes associated with flavonoid and phenylpropanoid biosynthesis, starch and sucrose metabolism, and plant hormone signal transduction. Genes related to lignin were downregulated in tuberous roots (TRs), resulting in a decrease in lignification and the downregulation of metabolites related to flavonoids and phenylpropanoid biosynthesis. In addition, the expression levels of starch- and sucrose-related genes were upregulated in TRs. The root development of SYQ is also related to IAA, GA, ABA, and JA signaling pathways. Collectively, this study lays the foundation for analyzing the root development and quality-modulating mechanisms employed by T. hemsleyanum; this will be beneficial in conducting molecular-assisted breeding and controlling its secondary metabolite production.
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Huang Y, Li Y, Liu Z, Chen W, Wang Y, Wang X, Liu Y, Zheng Y. Combined analysis of the transcriptome and metabolome provides insights into the fleshy stem expansion mechanism in stem lettuce. FRONTIERS IN PLANT SCIENCE 2022; 13:1101199. [PMID: 36589074 PMCID: PMC9798005 DOI: 10.3389/fpls.2022.1101199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
As a stem variety of lettuce, the fleshy stem is the main product organ of stem lettuce. The molecular mechanism of fleshy stem expansion in stem lettuce is a complex biological process. In the study, the material accumulation, gene expression, and morphogenesis during fleshy stem expansion process were analyzed by the comparative analysis of metabolome, transcriptome and the anatomical studies. The anatomical studies showed that the occurrence and activity of vascular cambium mainly led to the development of fleshy stems; and the volume of pith cells gradually increased and arranged tightly during the expansion process. A total of 822 differential metabolites and 9,383 differentially expressed genes (DEGs) were identified by the metabolomics and transcriptomics analyses, respectively. These changes significantly enriched in sugar synthesis, glycolysis, and plant hormone anabolism. The expression profiles of genes in the sugar metabolic pathway gradually increased in fleshy stem expansion process. But the sucrose content was the highest in the early stage of fleshy stem expansion, other sugars such as fructose and glucose content increased during fleshy stem expansion process. Plant hormones, including IAA, GA, CTK, and JA, depicted important roles at different stem expansion stages. A total of 1,805 DEGs were identified as transcription factors, such as MYB, bHLH, and bZIP, indicating that these transcription factor families might regulate the fleshy stems expansion in lettuce. In addition, the expression patterns identified by qRT-PCR were consistent with the expression abundance identified by the transcriptome data. The important genes and metabolites identified in the lettuce fleshy stem expansion process will provide important information for the further molecular mechanism study of lettuce fleshy stem growth and development.
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Affiliation(s)
- Ying Huang
- College of Agriculture and Forestry Sciences, Linyi University, Linyi, China
| | - Yanwen Li
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Zhenning Liu
- College of Agriculture and Forestry Sciences, Linyi University, Linyi, China
| | - Wanqin Chen
- College of Hydraulic and Environmental Engineering, China Three Gorges University, Yichang, China
| | - Yalin Wang
- College of Hydraulic and Environmental Engineering, China Three Gorges University, Yichang, China
| | - Xiaohua Wang
- College of Agriculture and Forestry Sciences, Linyi University, Linyi, China
| | - Yihua Liu
- College of Agriculture and Forestry Sciences, Linyi University, Linyi, China
| | - Yangxia Zheng
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
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Nuruzzaman M, Sato M, Okamoto S, Hoque M, Shea DJ, Fujimoto R, Shimizu M, Fukai E, Okazaki K. Comparative transcriptome analysis during tuberous stem formation in Kohlrabi (B. oleracea var. gongylodes) at early growth periods (seedling stages). PHYSIOLOGIA PLANTARUM 2022; 174:e13770. [PMID: 36018597 DOI: 10.1111/ppl.13770] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 08/18/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
Tuberous stem of kohlrabi is an important agronomic trait, however, the molecular basis of tuberization is poorly understood. To elucidate the tuberization mechanism, we conducted a comparative transcriptomic analysis between kohlrabi and broccoli at 10 and 20 days after germination (DAG) as tuberous stem initiated between these time points. A total of 5580 and 2866 differentially expressed transcripts (DETs) were identified between genotypes (kohlrabi vs. broccoli) and growth stages (10 DAG vs. 20 DAG), respectively, and most of the DETs were down-regulated in kohlrabi. Gene ontology (GO) and KEGG pathway enrichment analyses showed that the DETs between genotypes are involved in cell wall loosening and expansion, cell cycle and division, carbohydrate metabolism, hormone transport, hormone signal transduction and in several transcription factors. The DETs identified in those categories may directly/indirectly relate to the initiation and development of tuberous stem in kohlrabi. In addition, the expression pattern of the hormone synthesis related DETs coincided with the endogenous IAA, IAAsp, GA, ABA, and tZ profiles in kohlrabi and broccoli seedlings, that were revealed in our phytohormone analysis. This is the first report on comparative transcriptome analysis for tuberous stem formation in kohlrabi at early growth periods. The resulting data could provide significant insights into the molecular mechanism underlying tuberous stem development in kohlrabi as well as in other tuberous organ forming crops.
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Affiliation(s)
- Md Nuruzzaman
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Masato Sato
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Satoru Okamoto
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Mozammel Hoque
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
- Faculty of Agriculture, Sylhet Agricultural University (SAU), Sylhet, Bangladesh
| | - Daniel J Shea
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Ryo Fujimoto
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | | | - Eigo Fukai
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Keiichi Okazaki
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
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Cai Z, Cai Z, Huang J, Wang A, Ntambiyukuri A, Chen B, Zheng G, Li H, Huang Y, Zhan J, Xiao D, He L. Transcriptomic analysis of tuberous root in two sweet potato varieties reveals the important genes and regulatory pathways in tuberous root development. BMC Genomics 2022; 23:473. [PMID: 35761189 PMCID: PMC9235109 DOI: 10.1186/s12864-022-08670-x] [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: 01/20/2022] [Accepted: 05/30/2022] [Indexed: 11/16/2022] Open
Abstract
Background Tuberous root formation and development is a complex process in sweet potato, which is regulated by multiple genes and environmental factors. However, the regulatory mechanism of tuberous root development is unclear. Results In this study, the transcriptome of fibrous roots (R0) and tuberous roots in three developmental stages (Rl, R2, R3) were analyzed in two sweet potato varieties, GJS-8 and XGH. A total of 22,914 and 24,446 differentially expressed genes (DEGs) were identified in GJS-8 and XGH respectively, 15,920 differential genes were shared by GJS-8 and XGH. KEGG pathway enrichment analysis showed that the DEGs shared by GJS-8 and XGH were mainly involved in “plant hormone signal transduction” “starch and sucrose metabolism” and “MAPK signal transduction”. Trihelix transcription factor (Tai6.25300) was found to be closely related to tuberous root enlargement by the comprehensive analysis of these DEGs and weighted gene co-expression network analysis (WGCNA). Conclusion A hypothetical model of genetic regulatory network for tuberous root development of sweet potato is proposed, which emphasizes that some specific signal transduction pathways like “plant hormone signal transduction” “Ca2+signal” “MAPK signal transduction” and metabolic processes including “starch and sucrose metabolism” and “cell cycle and cell wall metabolism” are related to tuberous root development in sweet potato. These results provide new insights into the molecular mechanism of tuberous root development in sweet potato. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08670-x.
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Affiliation(s)
- Zhaoqin Cai
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, People's Republic of China.,Guangxi South Subtropical Agricultural Science Research Institute, Chongzuo, 532406, People's Republic of China
| | - Zhipeng Cai
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, People's Republic of China
| | - Jingli Huang
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, People's Republic of China
| | - Aiqin Wang
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, People's Republic of China.,Guangxi Colleges and Universities Key Laboratory of Crop Cultivation and Tillage, Nanning, 530004, People's Republic of China
| | - Aaron Ntambiyukuri
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, People's Republic of China
| | - Bimei Chen
- Hepu Institute of Agricultural Sciences, Beihai, 536101, People's Republic of China
| | - Ganghui Zheng
- Hepu Institute of Agricultural Sciences, Beihai, 536101, People's Republic of China
| | - Huifeng Li
- Maize Research Institute of Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Yongmei Huang
- Maize Research Institute of Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Jie Zhan
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, People's Republic of China.,Guangxi Colleges and Universities Key Laboratory of Crop Cultivation and Tillage, Nanning, 530004, People's Republic of China
| | - Dong Xiao
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, People's Republic of China. .,Guangxi Colleges and Universities Key Laboratory of Crop Cultivation and Tillage, Nanning, 530004, People's Republic of China.
| | - Longfei He
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, People's Republic of China. .,Guangxi Colleges and Universities Key Laboratory of Crop Cultivation and Tillage, Nanning, 530004, People's Republic of China.
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10
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Jiang Z, Gao H, Liu R, Xia M, Lu Y, Wang J, Chen X, Zhang Y, Li D, Tong Y, Liu P, Liu Y, Luo Y, Gao J, Yin Y, Huang L, Gao W. Key Glycosyltransferase Genes of Panax notoginseng: Identification and Engineering Yeast Construction of Rare Ginsenosides. ACS Synth Biol 2022; 11:2394-2404. [PMID: 35687875 DOI: 10.1021/acssynbio.2c00094] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Panax notoginseng is one of the most famous valuable medical plants in China, and its broad application in clinical treatment has an inseparable relationship with the active molecules, ginsenosides. Ginsenosides are glycoside compounds that have varied structures for the diverse sugar chain. Although extensive work has been done, there are still unknown steps in the biosynthetic pathway of ginsenosides. Here, we screened candidate glycosyltransferase genes based on the previous genome and transcriptome data of P. notoginseng and cloned the full length of 27 UGT genes successfully. Among them, we found that PnUGT33 could catalyze different ginsenoside substrates to produce higher polarity rare ginsenosides by extending the sugar chain. We further analyzed the enzymatic kinetics and predicted the catalytic mechanism of PnUGT33 by simulating molecular docking. After that, we reconstructed the biosynthetic pathway of rare ginsenoside Rg3 and gypenoside LXXV in yeast. By combining the Golden Gate method and overexpressing the UDPG biosynthetic genes, we further improved the yield of engineering yeast strain. Finally, the shake-flask culture yield of Rg3 reached 51 mg/L and the fed-batch fermentation yield of gypenoside LXXV reached 94.5 mg/L, which was the first and highest record.
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Affiliation(s)
- Zhouqian Jiang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, People's Republic of China
| | - Haiyun Gao
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, People's Republic of China
| | - Rong Liu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, People's Republic of China
| | - Meng Xia
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, People's Republic of China
| | - Yun Lu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, People's Republic of China
| | - Jiadian Wang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, People's Republic of China
| | - Xiaochao Chen
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, People's Republic of China
| | - Yifeng Zhang
- Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, People's Republic of China
| | - Dan Li
- School of Pharmaceutical Sciences, Capital Medical University, Beijing 100069, People's Republic of China
| | - Yuru Tong
- School of Pharmaceutical Sciences, Capital Medical University, Beijing 100069, People's Republic of China
| | - Panting Liu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, People's Republic of China
| | - Yuan Liu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, People's Republic of China
| | - Yunfeng Luo
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, People's Republic of China
| | - Jie Gao
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, People's Republic of China
| | - Yan Yin
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, People's Republic of China
| | - Luqi Huang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, People's Republic of China
| | - Wei Gao
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, People's Republic of China.,Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, People's Republic of China
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11
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Yu MY, Hua ZY, Liao PR, Zheng H, Jin Y, Peng HS, Cui XM, Huang LQ, Yuan Y. Increasing Expression of PnGAP and PnEXPA4 Provides Insights Into the Enlargement of Panax notoginseng Root Size From Qing Dynasty to Cultivation Era. FRONTIERS IN PLANT SCIENCE 2022; 13:878796. [PMID: 35668802 PMCID: PMC9164015 DOI: 10.3389/fpls.2022.878796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/07/2022] [Indexed: 06/15/2023]
Abstract
Root size is a key trait in plant cultivation and can be influenced by the cultivation environment. However, physical evidence of root size change in a secular context is scarce due to the difficulty in preserving ancient root samples, and how they were modified during the domestication and cultivation stays unclear. About 100 ancient root samples of Panax notoginseng, preserved as tribute in the Palace Museum (A.D. 1636 to 1912, Qing dynasty), provided an opportunity to investigate the root size changes during the last 100 years of cultivation. The dry weight of ancient root samples (~120 tou samples, tou represents number of roots per 500 g dry weight) is 0.22-fold of the modern samples with the biggest size (20 tou samples). Transcriptome analysis revealed that PnGAP and PnEXPA4 were highly expressed in 20 tou samples, compared with the 120 tou samples, which might contribute to the thicker cell wall and a higher content of lignin, cellulose, and callose in 20 tou samples. A relatively lower content of dencichine and higher content of ginsenoside Rb1 in 20 tou samples are also consistent with higher expression of ginsenoside biosynthesis-related genes. PnPHL8 was filtrated through transcriptome analysis, which could specifically bind the promoters of PnGAP, PnCYP716A47, and PnGGPPS3, respectively. The results in this study represent the first physical evidence of root size changes in P. notoginseng in the last 100 years of cultivation and contribute to a comprehensive understanding of how the cultivation environment affected root size, chemical composition, and clinical application.
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Affiliation(s)
- Mu-Yao Yu
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Zhong-Yi Hua
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Pei-Ran Liao
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Han Zheng
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yan Jin
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Hua-Sheng Peng
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiu-Ming Cui
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Lu-Qi Huang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yuan Yuan
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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12
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Shi R, Xiong B, He S, Liu C, Ben-Asher J, Horowitz AR, Wang S, He X. Comparative metabolic profiling of root, leaf, fruit, and stem tissues of Panax notoginseng. INTERNATIONAL JOURNAL OF FOOD PROPERTIES 2022. [DOI: 10.1080/10942912.2022.2071294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Rui Shi
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Landscape Architecture Engineering Research Center of National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
| | - Bingjie Xiong
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Landscape Architecture Engineering Research Center of National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
| | - Shu He
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Landscape Architecture Engineering Research Center of National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
| | - Can Liu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Landscape Architecture Engineering Research Center of National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
| | - Jiftah Ben-Asher
- French Associates Institute for Agriculture and Biotechnology of Dryland, the Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Israel
| | - Abraham Rami Horowitz
- French Associates Institute for Agriculture and Biotechnology of Dryland, the Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Israel
| | - Shu Wang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Landscape Architecture Engineering Research Center of National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
| | - Xiahong He
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Landscape Architecture Engineering Research Center of National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
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13
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Chen P, Yang R, Bartels D, Dong T, Duan H. Roles of Abscisic Acid and Gibberellins in Stem/Root Tuber Development. Int J Mol Sci 2022; 23:ijms23094955. [PMID: 35563355 PMCID: PMC9102914 DOI: 10.3390/ijms23094955] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 02/06/2023] Open
Abstract
Root and tuber crops are of great importance. They not only contribute to feeding the population but also provide raw material for medicine and small-scale industries. The yield of the root and tuber crops is subject to the development of stem/root tubers, which involves the initiation, expansion, and maturation of storage organs. The formation of the storage organ is a highly intricate process, regulated by multiple phytohormones. Gibberellins (GAs) and abscisic acid (ABA), as antagonists, are essential regulators during stem/root tuber development. This review summarizes the current knowledge of the roles of GA and ABA during stem/root tuber development in various tuber crops.
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Affiliation(s)
- Peilei Chen
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; (P.C.); (R.Y.); (T.D.)
| | - Ruixue Yang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; (P.C.); (R.Y.); (T.D.)
| | - Dorothea Bartels
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), Faculty of Natural Sciences, University of Bonn, Kirschallee 1, D-53115 Bonn, Germany;
| | - Tianyu Dong
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; (P.C.); (R.Y.); (T.D.)
| | - Hongying Duan
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; (P.C.); (R.Y.); (T.D.)
- Correspondence:
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14
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Yang L, Wang H, Wang P, Gao M, Huang L, Cui X, Liu Y. De novo and comparative transcriptomic analysis explain morphological differences in Panax notoginseng taproots. BMC Genomics 2022; 23:86. [PMID: 35100996 PMCID: PMC8802446 DOI: 10.1186/s12864-021-08283-w] [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: 10/11/2021] [Accepted: 12/28/2021] [Indexed: 12/20/2022] Open
Abstract
Background Panax notoginseng (Burk.) F. H. Chen (PN) belonging to the genus Panax of family Araliaceae is widely used in traditional Chinese medicine to treat various diseases. PN taproot, as the most vital organ for the accumulation of bioactive components, presents a variable morphology (oval or long), even within the same environment. However, no related studies have yet explained the molecular mechanism of phenotypic differences. To investigate the cause of differences in the taproot phenotype, de novo and comparative transcriptomic analysis on PN taproot was performed. Results A total of 133,730,886 and 114,761,595 paired-end clean reads were obtained based on high-throughput sequencing from oval and long taproot samples, respectively. 121,955 unigenes with contig N50 = 1,774 bp were generated by using the de novo assembly transcriptome, 63,133 annotations were obtained with the BLAST. And then, 42 genes belong to class III peroxidase (PRX) gene family, 8 genes belong to L-Ascorbate peroxidase (APX) gene family, and 55 genes belong to a series of mitogen-activated protein kinase (MAPK) gene family were identified based on integrated annotation results. Differentially expressed genes analysis indicated substantial up-regulation of PnAPX3 and PnPRX45, which are related to reactive oxygen species metabolism, and the PnMPK3 gene, which is related to cell proliferation and plant root development, in long taproots compared with that in oval taproots. Furthermore, the determination results of real-time quantitative PCR, enzyme activity, and H2O2 content verified transcriptomic analysis results. Conclusion These results collectively demonstrate that reactive oxygen species (ROS) metabolism and the PnMPK3 gene may play vital roles in regulating the taproot phenotype of PN. This study provides further insights into the genetic mechanisms of phenotypic differences in other species of the genus Panax. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08283-w.
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Affiliation(s)
- Lifang Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650000, China
| | - Hanye Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650000, China
| | - Panpan Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650000, China
| | - Mingju Gao
- Wenshan University, Wenshan, 663000, China
| | - Luqi Huang
- National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Xiuming Cui
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650000, China.,Key Laboratory of Panax notoginseng Resources Sustainable Development and Utilization of State Administration of Traditional Chinese Medicine, Kunming, 650000, China.,Yunnan Provincial Key Laboratory of Panax notoginseng, Kunming, 650000, China.,Kunming Key Laboratory of Sustainable Development and Utilization of Famous-Region Drug, Kunming, 650000, China.,Sanqi Research Institute of Yunnan Province, Kunming, 650000, China
| | - Yuan Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650000, China. .,Key Laboratory of Panax notoginseng Resources Sustainable Development and Utilization of State Administration of Traditional Chinese Medicine, Kunming, 650000, China. .,Yunnan Provincial Key Laboratory of Panax notoginseng, Kunming, 650000, China. .,Kunming Key Laboratory of Sustainable Development and Utilization of Famous-Region Drug, Kunming, 650000, China. .,Sanqi Research Institute of Yunnan Province, Kunming, 650000, China.
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15
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Gu L, Wu Y, Li M, Wang F, Li Z, Yuan F, Zhang Z. Over-immunity mediated abnormal deposition of lignin arrests the normal enlargement of the root tubers of Rehmannia glutinosa under consecutive monoculture stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 165:36-46. [PMID: 34034159 DOI: 10.1016/j.plaphy.2021.05.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 05/05/2021] [Indexed: 06/12/2023]
Abstract
The rapid accumulation of lignin in the cell wall is one of important immune defense mechanism in response to adversity stress in plants. In this study, we found that the enlargement of the root tubers of Rehmannia glutinosa (R. glutinosa) is arrested under consecutive monoculture stress, and this process is accompanied by abnormal accumulation of lignin. Meanwhile, the function of key catalytic enzyme genes in lignin biosynthetic pathway under consecutive monoculture stress was systematically analyzed, of which roles of core genes were validated using reverse genetics. We elucidated that an abnormal deposition of lignin in R. glutinosa roots, induced by consecutive monoculture stress, and arrested the enlargement of root tubers. Additionally, by manipulating the key catalytic enzyme gene RgCCR6, we were able to alter lignin content of roots of R. glutinosa, thereby affecting tuber enlargement. We speculate that cell lignification is an important defense strategy in resistance against consecutive monoculture stress, but the overreacted defense hindered the normal enlargement of root tubers. The findings provide new insights for effectively improving yield reductions of root crops subjected to environmental stress.
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Affiliation(s)
- Li Gu
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yunfang Wu
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mingjie Li
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, China.
| | - Fengqing Wang
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Zhenfang Li
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Feiyue Yuan
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhongyi Zhang
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China.
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16
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Li J, Li W, Min Z, Zheng Q, Han J, Li P. Physiological, biochemical and transcription effects of roxithromycin before and after phototransformation in Chlorella pyrenoidosa. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2021; 238:105911. [PMID: 34298405 DOI: 10.1016/j.aquatox.2021.105911] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 06/13/2021] [Accepted: 07/07/2021] [Indexed: 06/13/2023]
Abstract
Photodegradation is an important transformation pathway for macrolide antibiotics (MCLs) in aquatic environments, but the ecotoxicity of MCLs after phototransformation has not been reported in detail. This study investigated the effects of roxithromycin (ROX) before and after phototransformation on the growth and physio-biochemical characteristics of Chlorella pyrenoidosa, and its toxicity were explored using transcriptomics analysis. The results showed that 2 mg/L ROX before phototransformation (T0 group) inhibited algae growth with inhibition rates of 53.06%, 54.17%, 47.26%, 31.27%, and 28.38% at 3, 7, 10, 14, and 21 d, respectively, and chlorophyll synthesis was also inhibited. The upregulation of antioxidative enzyme activity levels and the malondialdehyde content indicated that ROX caused oxidative damage to C. pyrenoidosa during 21 d of exposure. After phototransformation for 48 h (T48 group), ROX exhibited no significant impact on the growth and physio-biochemical characteristics of the microalgae. Compared with the control group (without ROX and its phototransformation products), 2010 and 2988 differentially expressed genes were identified in the T0 and T48 treatment groups, respectively. ROX significantly downregulated genes related to porphyrin and chlorophyll metabolism, which resulted in the inhibition of chlorophyll synthesis and algae growth. ROX also significantly downregulated genes of DNA replication, suggesting the increased DNA proliferation risks in algae. After phototransformation, ROX upregulated most of the genes associated with the porphyrin and chlorophyll metabolism pathway, which may be the reason that the chlorophyll content in T48 treatment group showed no significant difference from the control group. Almost all light-harvesting chlorophyll a/b (LHCa/b) gene family members were upregulated in both T0 and T48 treatment groups, which may compensate part of the stress of ROX and its phototransformation products.
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Affiliation(s)
- Jiping Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Longpan Road 159, Nanjing 210037, China
| | - Wei Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Longpan Road 159, Nanjing 210037, China; National Positioning Observation Station of Hung-tse Lake Wetland Ecosystem in Jiangsu Province, Hongze, Jiangsu 223100, China.
| | - Zhongfang Min
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Longpan Road 159, Nanjing 210037, China
| | - Qinqin Zheng
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Longpan Road 159, Nanjing 210037, China
| | - Jiangang Han
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Longpan Road 159, Nanjing 210037, China; National Positioning Observation Station of Hung-tse Lake Wetland Ecosystem in Jiangsu Province, Hongze, Jiangsu 223100, China
| | - Pingping Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Longpan Road 159, Nanjing 210037, China; National Positioning Observation Station of Hung-tse Lake Wetland Ecosystem in Jiangsu Province, Hongze, Jiangsu 223100, China
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17
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The dehiscence process in Panax ginseng seeds and the stigmasterol biosynthesis pathway in terms of metabolomics. J Ginseng Res 2021; 46:225-234. [PMID: 35509817 PMCID: PMC9058826 DOI: 10.1016/j.jgr.2021.06.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 05/29/2021] [Accepted: 06/09/2021] [Indexed: 11/28/2022] Open
Abstract
Background Ginseng, officially known as Panax ginseng Meyer, has been traditionally used as a medicinal herb, particularly in Asia. Ginseng is propagated from seeds; however, seed germination is challenging, especially in its natural environment on farms. The seeds typically exhibit morphophysiological dormancy and require release from both morphological and physiological dormancy before germination. Although some studies have proposed methods for increasing seed germination rates, the underlying mechanisms of its dormancy release process remain unclear. Here, we investigated metabolic alterations during dehiscence in P. ginseng to determine their potential roles in dormancy release. Methods We compared the ginseng seed metabolome before and after dehiscence and the ginsenoside and phytosterol compositions of the seeds in both periods in the presence of related enzymes. Results After seed dehiscence, the sugar, amino acid, and squalene concentrations were significantly altered, phytosterols associated with the stigmasterol biosynthesis pathway were increased, while ginsenoside and brassinosteroid levels were not significantly altered. In addition, squalene epoxidase, cycloartenol synthase, 24-methylenesterol C-methyltransferase, and the stigmasterol biosynthesis pathway were activated. Conclusion Overall, our findings suggest that morphological activities that facilitate ginseng seed growth are the primary phenomena occurring during the dehiscence process. This study improves the understanding of P. ginseng germination processes and promotes further research of its germination and cultivation.
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18
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Bai H, Zhou D, Zhang X, Cao Y, Xiao X, Zhang Y, Yu Y. The responses of Salmonella enterica serovar Typhimurium to vanillin in apple juice through global transcriptomics. Int J Food Microbiol 2021; 347:109189. [PMID: 33838479 DOI: 10.1016/j.ijfoodmicro.2021.109189] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/09/2021] [Accepted: 03/24/2021] [Indexed: 11/29/2022]
Abstract
Salmonella enterica serovar Typhimurium can survive some extreme environment in food processing, and vanillin generally recognized as safe is bactericidal to pathogens. Thus, we need to explore the responses of S. Typhimurium to vanillin in order to apply this antimicrobial agent in food processing. In this study, we exposed S. Typhimurium to commercial apple juice with/without vanillin (3.2 mg/mL) at 45 °C for 75 min to determine the survival rate. Subsequently, the 10-min cultures were selected for transcriptomic analysis. Using high-throughput RNA sequencing, genes related to vanillin resistance and their expression changes of S. Typhimurium were identified. The survival curve showed that S. Typhimurium treated with vanillin were inactivated by 5.5 log after 75 min, while the control group only decreased by 2.3 log. Such a discrepancy showed the significant antibacterial effect of vanillin on S. Typhimurium. As a result, 265 differentially expressed genes (DEGs) were found when coping with vanillin, among which, 225 showed up-regulation and 40 DEGs were down-regulated. Treated with vanillin, S. Typhimurium significantly up-regulated genes involved in cell membrane, acid tolerance response (ATR) and oxidative stress response, cold shock cross-protection, DNA repair, virulence factors and some key regulators. Firstly, membrane-related genes, including outer membrane (bamE, mepS, ygdI, lolB), inner membrane (yaiY, yicS) and other proteins (yciC, yjcH), were significantly up-regulated because of the damaged cell membrane. Then, up-regulated proteins associated with arginine synthesis (ArgABCDIG) and inward transportation (ArtI, ArtJ, ArtP and HisP), participated in ATR to pump out the protons inside the cell in this scenario. Next, superoxide stress response triggered by vanillin was found to have a significant up-regulation as well, which was controlled by SoxRS regulon. Besides, NADH-associated (nuoA, nuoB, nuoK, nadE, fre and STM3021), thioredoxin (trxA, trxC, tpx and bcp) and glutaredoxin (grxC and grxD) DEGs led to the increase of the oxidative stress response. Cold shock proteins such as CspA and CspC showed an up-regulation, suggesting it might play a role in cross-protecting S. Typhimurium from vanillin stress. Furthermore, DEGs in DNA repair and virulence factors, including flagellar assembly, adhesins and type III secretion system were up-regulated. Some regulators like fur, rpoE and csrA played a pivotal role in response to the stress caused by vanillin. Therefore, this study sounds an alarm for the risks caused by stress tolerance of S. Typhimurium in food industry.
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Affiliation(s)
- Hong Bai
- School of Food Science and Engineering, South China University of Technology, Guangzhou City, Guangdong Province 510640, China
| | - Donggen Zhou
- Ningbo International Travel Healthcare Center, No.336 LiutingStreet, Haishu District, Ningbo City, Zhejiang Province 315012, China
| | - Xiaowei Zhang
- School of Food Science and Engineering, South China University of Technology, Guangzhou City, Guangdong Province 510640, China
| | - Yifang Cao
- School of Food Science and Engineering, South China University of Technology, Guangzhou City, Guangdong Province 510640, China
| | - Xinglong Xiao
- School of Food Science and Engineering, South China University of Technology, Guangzhou City, Guangdong Province 510640, China.
| | - Yan Zhang
- School of Food Science and Engineering, South China University of Technology, Guangzhou City, Guangdong Province 510640, China
| | - Yigang Yu
- School of Food Science and Engineering, South China University of Technology, Guangzhou City, Guangdong Province 510640, China.
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Hormonal and transcriptional analyses provides new insights into the molecular mechanisms underlying root thickening and isoflavonoid biosynthesis in Callerya speciosa (Champ. ex Benth.) Schot. Sci Rep 2021; 11:9. [PMID: 33420059 PMCID: PMC7794344 DOI: 10.1038/s41598-020-76633-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/27/2020] [Indexed: 01/26/2023] Open
Abstract
Callerya speciosa (Champ. ex Benth.) Schot is a traditional Chinese medicine characterized by tuberous roots as the main organ of isoflavonoid accumulation. Root thickening and isoflavonoid accumulation are two major factors for yield and quality of C. speciosa. However, the underlying mechanisms of root thickening and isoflavonoid biosynthesis have not yet been elucidated. Here, integrated morphological, hormonal and transcriptomic analyses of C. speciosa tuberous roots at four different ages (6, 12, 18, 30 months after germination) were performed. The growth cycle of C. speciosa could be divided into three stages: initiation, rapid-thickening and stable-thickening stage, which cued by the activity of vascular cambia. Endogenous changes in phytohormones were associated with developmental changes during root thickening. Jasmonic acid might be linked to the initial development of tuberous roots. Abscisic acid seemed to be essential for tuber maturation, whereas IAA, cis-zeatin and gibberellin 3 were considered essential for rapid thickening of tuberous roots. A total of 4337 differentially expressed genes (DEGs) were identified during root thickening, including 15 DEGs participated in isoflavonoid biosynthesis, and 153 DEGs involved in starch/sucrose metabolism, hormonal signaling, transcriptional regulation and cell wall metabolism. A hypothetical model of genetic regulation associated with root thickening and isoflavonoid biosynthesis in C. speciosa is proposed, which will help in understanding the underlying mechanisms of tuberous root formation and isoflavonoid biosynthesis.
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A rapid RNA extraction method from oil palm tissues suitable for reverse transcription quantitative real-time PCR (RT-qPCR). 3 Biotech 2020; 10:530. [PMID: 33214977 DOI: 10.1007/s13205-020-02514-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 10/27/2020] [Indexed: 10/23/2022] Open
Abstract
Cetyltrimethylammonium bromide (CTAB) is the preferred detergent in RNA extraction of oil palm tissues. However, the CTAB-based protocol is time-consuming. In this study, a combination of the CTAB-based method and silica-based purification reduced the extraction time from two days to five hours. Quality of total RNA from 27 different tissues of oil palm was shown to have an RNA integrity number (RIN) value of more than seven. The extracted RNA was evaluated by RT-qPCR using three reference oil palm genes (GRAS, CYP2, and SLU7) and three putative mesocarp-specific transcripts annotated as WRKY DNA-binding protein 70 (WRKY-70), metallothionein (MT) and pentatricopeptide repeat (PPR) genes. Tissue-specific expression profiling across complete developmental stages of mesocarp and vegetative tissues was determined in this study. Overall, the RNA extraction protocol described here is rapid, simple and yields good quality RNAs from oil palm tissues.
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21
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Xie Y, Ying J, Xu L, Wang Y, Dong J, Chen Y, Tang M, Li C, M'mbone Muleke E, Liu L. Genome-wide sRNA and mRNA transcriptomic profiling insights into dynamic regulation of taproot thickening in radish (Raphanus sativus L.). BMC PLANT BIOLOGY 2020; 20:373. [PMID: 32770962 PMCID: PMC7414755 DOI: 10.1186/s12870-020-02585-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 07/29/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND Taproot is the main edible organ and ultimately determines radish yield and quality. However, the precise molecular mechanism underlying taproot thickening awaits further investigation in radish. Here, RNA-seq was performed to identify critical genes involved in radish taproot thickening from three advanced inbred lines with different root size. RESULTS A total of 2606 differentially expressed genes (DEGs) were shared between 'NAU-DY' (large acicular) and 'NAU-YB' (medium obovate), which were significantly enriched in 'phenylpropanoid biosynthesis', 'glucosinolate biosynthesis', and 'starch and sucrose metabolism' pathway. Meanwhile, a total of 16 differentially expressed miRNAs (DEMs) were shared between 'NAU-DY' and 'NAU-YH' (small circular), whereas 12 miRNAs exhibited specific differential expression in 'NAU-DY'. Association analysis indicated that miR393a-bHLH77, miR167c-ARF8, and miR5658-APL might be key factors to biological phenomenon of taproot type variation, and a putative regulatory model of taproot thickening and development was proposed. Furthermore, several critical genes including SUS1, EXPB3, and CDC5 were characterized and profiled by RT-qPCR analysis. CONCLUSION This integrated study on the transcriptional and post-transcriptional profiles could provide new insights into comprehensive understanding of the molecular regulatory mechanism underlying taproot thickening in root vegetable crops.
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Affiliation(s)
- Yang Xie
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
- College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066004, China
| | - Jiali Ying
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Liang Xu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Yan Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Junhui Dong
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Yinglong Chen
- The UWA Institute of Agriculture, and School of Agriculture and Environment, The University of Western Australia, Perth, WA, 6009, Australia
| | - Mingjia Tang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Cui Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Everlyne M'mbone Muleke
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Liwang Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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