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Frolova N, Gorbach D, Ihling C, Bilova T, Orlova A, Lukasheva E, Fedoseeva K, Dodueva I, Lutova LA, Frolov A. Proteome and Metabolome Alterations in Radish ( Raphanus sativus L.) Seedlings Induced by Inoculation with Agrobacterium tumefaciens. Biomolecules 2025; 15:290. [PMID: 40001593 PMCID: PMC11852571 DOI: 10.3390/biom15020290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2024] [Revised: 02/07/2025] [Accepted: 02/11/2025] [Indexed: 02/27/2025] Open
Abstract
Infection of higher plants with agrobacteria (Agrobacterium tumefaciens) represents one of the most comprehensively characterized examples of plant-microbial interactions. Incorporation of the bacterial transfer DNA (T-DNA) in the plant genome results in highly efficient expression of the bacterial auxin, cytokinin and opine biosynthesis genes, as well as the host genes of hormone-mediated signaling. These transcriptional events trigger enhanced proliferation of plant cells and formation of crown gall tumors. Because of this, infection of plant tissues with A. tumefaciens provides a convenient model to address the dynamics of cell metabolism accompanying plant development. To date, both early and late plant responses to agrobacterial infection are well-characterized at the level of the transcriptome, whereas only little information on the accompanying changes in plant metabolism is available. Therefore, here we employ an integrated proteomics and metabolomics approach to address the metabolic shifts and molecular events accompanying plant responses to inoculation with the A. tumefaciens culture. Based on the acquired proteomics dataset complemented with the results of the metabolite profiling experiment, we succeeded in characterizing the metabolic shifts associated with agrobacterial infection. The observed dynamics of the seedling proteome and metabolome clearly indicated rearrangement of the energy metabolism on the 10th day after inoculation (d.a.i.). Specifically, redirection of the energy metabolism from the oxidative to the anaerobic pathway was observed. This might be a part of the plant's adaptation response to tumor-induced hypoxic stress, which most likely involved activation of sugar signaling.
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Affiliation(s)
- Nadezhda Frolova
- Laboratory of Analytical Biochemistry and Biotechnology, K.A. Timiryazev Institute of Plant Physiology Russian Academy of Science, 127276 Moscow, Russia; (N.F.); (D.G.); (T.B.); (A.O.)
| | - Daria Gorbach
- Laboratory of Analytical Biochemistry and Biotechnology, K.A. Timiryazev Institute of Plant Physiology Russian Academy of Science, 127276 Moscow, Russia; (N.F.); (D.G.); (T.B.); (A.O.)
| | - Christian Ihling
- Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, 06099 Halle (Saale), Germany;
| | - Tatiana Bilova
- Laboratory of Analytical Biochemistry and Biotechnology, K.A. Timiryazev Institute of Plant Physiology Russian Academy of Science, 127276 Moscow, Russia; (N.F.); (D.G.); (T.B.); (A.O.)
- Department of Plant Physiology and Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Anastasia Orlova
- Laboratory of Analytical Biochemistry and Biotechnology, K.A. Timiryazev Institute of Plant Physiology Russian Academy of Science, 127276 Moscow, Russia; (N.F.); (D.G.); (T.B.); (A.O.)
| | - Elena Lukasheva
- Department of Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia;
| | - Ksenia Fedoseeva
- Resource Center “Molecular and Cell Technologies”, St. Petersburg State University, 199034 St. Petersburg, Russia;
| | - Irina Dodueva
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (I.D.); (L.A.L.)
| | - Lyudmila A. Lutova
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (I.D.); (L.A.L.)
| | - Andrej Frolov
- Laboratory of Analytical Biochemistry and Biotechnology, K.A. Timiryazev Institute of Plant Physiology Russian Academy of Science, 127276 Moscow, Russia; (N.F.); (D.G.); (T.B.); (A.O.)
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Meng G, Yong M, Zhang Z, Zhang Y, Wang Y, Xiong A, Su X. Exogenous gibberellin suppressed taproot secondary thickening by inhibiting the formation and maintenance of vascular cambium in radish ( Raphanus sativus L.). FRONTIERS IN PLANT SCIENCE 2024; 15:1395999. [PMID: 39328795 PMCID: PMC11424454 DOI: 10.3389/fpls.2024.1395999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 08/26/2024] [Indexed: 09/28/2024]
Abstract
Introduction The thickening of radish taproots is primarily determined by secondary growth driven by the vascular cambium and is a highly intricate process regulated by plant hormones, transcription factors, and many metabolic pathways. Gibberellin (GA), a plant hormone associated with cell elongation, is essential in secondary growth. However, the mechanism through which exogenous GA3 regulates secondary taproot growth in radishes remains unclear. Methods Integrated morphological, anatomical, hormonal, and transcriptomic analyses of taproots in radishes treated with GA3 and its biosynthesis inhibitor paclobutrazol (PBZ) were performed to explore their effects on taproot secondary growth and key regulatory pathways. Results GA3 significantly hindered taproot thickening by inhibiting the formation and maintenance of the vascular cambium, and PBZ promoted root development by increasing root length rather than root diameter. Transcriptome analysis revealed 2,014, 948, and 1,831 differentially expressed genes identified from the control vs. GA3, control vs. PBZ, and GA3 vs. PBZ comparisons, respectively. Kyoto Encyclopedia of Genes and Genome pathway enrichment analysis revealed that differentially expressed genes were primarily involved in the biosyntheses of secondary metabolites and metabolic pathways. GA3 significantly increased the levels of endogenous indole-acetic acid and the expression of auxin synthesis and signal transduction genes. Discussion Exogenous GA3 significantly inhibited the expression of genes involved in the maintenance and differentiation of vascular cambium, including WOX14, ER/ERL1, and XCP2. Exogenous GA3 affects root thickening in radishes primarily by regulating hormone signal transduction pathways, vascular cambium activity, and substance and energy metabolisms. Our findings provide insights into the mechanisms underlying taproot thickening in radishes and provide a valuable gene database for future studies.
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Affiliation(s)
- Ge Meng
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Mingli Yong
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Ziyue Zhang
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yuqing Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yahui Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Aisheng Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xiaojun Su
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- College of Life Sciences, Jiangsu University, Zhenjiang, China
- College of Horticulture, Anhui Agricultural University, Hefei, China
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Li C, Mao B, Wang K, Xu L, Fan L, Wang Y, Li Y, Ma Y, Wang L, Liu L. RsERF40 contributes to cold stress tolerance and cell expansion of taproot in radish ( Raphanus sativus L.). HORTICULTURE RESEARCH 2023; 10:uhad013. [PMID: 36968181 PMCID: PMC10031735 DOI: 10.1093/hr/uhad013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 01/25/2023] [Indexed: 06/18/2023]
Abstract
The growth and development of taproots are inhibited by cold stress in radish (Raphanus sativus L.). Ethylene-responsive element binding factors (ERF) are key participators in the cold stress response and growth regulation of plants. However, the function of ERF genes in cold tolerance and root development in radish remains elusive. Here, we showed that the secondary growth of radish taproots was inhibited by cold stress. Comparative transcriptome analysis demonstrated that the RsERF40 gene is an important regulator of the cold stress response and root growth regulation. The cold tolerance of transgenic Arabidopsis plants overexpressing the RsERF40 gene was significantly improved. Overexpressing RsERF40 in the cold-sensitive radish genotype and silencing RsERF40 in the cold-tolerant radish genotype indicated that RsERF40 was beneficial for alleviating oxidative damage under cold stress in radish. Transgenic Arabidopsis seedlings showed an increase in the elongation and radial growth of dark-grown roots. RT-qPCR analysis showed that the expression of the cold-related genes (CORs) RsCOR78 and RsCOR413PM1 and the cell wall strengthening-related genes RsCESA6 and RsEXPB3 was upregulated in transgenic Arabidopsis seedlings. Yeast one-hybrid (Y1H) and dual-luciferase reporter assays (DLA) revealed that RsERF40 directly regulates RsCOR78, RsCOR413PM1, RsCESA6 and RsEXPB3 expression, illustrating that RsERF40 enhances cold tolerance and taproot growth by modulating osmotic adjustment and cell wall mechanical strength in radish. In this study, the RsERF40-regulon was firstly found to be a new cold response pathway independent of the CBF-COR pathway conferring cold stress tolerance with increasing radish taproot growth. These results provided novel insight into the molecular mechanism underlying cold stress response and would facilitate the genetic improvement of cold tolerance in radish and other root vegetable crops.
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Affiliation(s)
- Cui Li
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and utilization, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Baozhen Mao
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and utilization, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Kai Wang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and utilization, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Liang Xu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and utilization, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Lianxue Fan
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and utilization, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yan Wang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and utilization, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ying Li
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and utilization, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yinbo Ma
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Lun Wang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
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Kong Y, Wang G, Tang H, Yang J, Yang Y, Wang J, Li G, Li Y, Yuan J. Multi-omics analysis provides insight into the phytotoxicity of chicken manure and cornstalk on seed germination. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 861:160611. [PMID: 36460104 DOI: 10.1016/j.scitotenv.2022.160611] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/21/2022] [Accepted: 11/27/2022] [Indexed: 06/17/2023]
Abstract
To minimize environmental risks and the phytotoxic influence of organic materials on crop growth, it is necessary to test their phytotoxicity and maturity when they were used in farmland. However, the stress response of seed germination to chicken manure and cornstalks is not clear. This study used multi-omics analysis to investigate the inhibition mechanism of seed germination by chicken manure and cornstalk. Chicken manure caused destructive inhibition of seed germination with higher phytotoxicity (GI = 0). Cornstalk also had a low GI (8.81 %), while it mainly inhibited radicle growth (RL = 9.39 %) rather than seed germination (GR = 93.33 %). The response of radish seed germination to chicken manure and cornstalk phytotoxic stresses was accompanied by metabolic adjustments of storage substance accumulation, antioxidant enzyme activity change, phytohormone induction, and expression of specific proteins and gene regulation. Combined transcriptomic and proteomic analysis revealed that differential expression of 13,090 (5944 upregulated/7146 downregulated) and 3850 (2389 upregulated/1461 downregulated) genes (DEGs), and 1041 (82 upregulated/932 downregulated) and 575 (111 upregulated/464 downregulated) proteins (DEPs) at chicken manure and cornstalk treatment, respectively. Most down-regulated genes and proteins were involved in phenylpropanoid biosynthesis under chicken manure stress, which caused irreversible inhibition of seed germination. Down-regulation of phytohormone signal transduction-related genes under cornstalk stress resulted in inhibition of radicle growth, but the inhibitory stress was restorable. These findings provide new insight into the phytotoxicity of livestock manure and cornstalk on seed germination.
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Affiliation(s)
- Yilin Kong
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, China
| | - Guoying Wang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, China
| | - Huan Tang
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Jia Yang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, China
| | - Yan Yang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, China
| | - Jiani Wang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, China
| | - Guoxue Li
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Suzhou 215128, China
| | - Yun Li
- College of Resources and Environmental Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Jing Yuan
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Suzhou 215128, China.
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Dong J, Wang Y, Xu L, Li B, Wang K, Ying J, He Q, Liu L. RsCLE22a regulates taproot growth through an auxin signaling-related pathway in radish (Raphanus sativus L.). JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:233-250. [PMID: 36239471 DOI: 10.1093/jxb/erac406] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
CLAVATA3/EMBRYO SURROUNDING REGION-related (CLE) peptides are a class of small molecules involved in plant growth and development. Although radish (Raphanus sativus) is an important root vegetable crop worldwide, the functions of CLE peptides in its taproot formation remain elusive. Here, a total of 48 RsCLE genes were identified from the radish genome. RNA in situ hybridization showed that RsCLE22a gene was highly expressed in the vascular cambium. Overexpression of RsCLE22a inhibited root growth by impairing stem cell proliferation in Arabidopsis, and radish plants with exogenous supplementation of RsCLE22 peptide (CLE22p) showed a similar phenotype. The vascular cambial activity was increased in RsCLE22a-silenced plants. Transcriptome analysis revealed that CLE22p altered the expression of several genes involved in meristem development and hormone signal transduction in radish. Immunolocalization results showed that CLE22p increased auxin accumulation in vascular cambium. Yeast one-hybrid and dual-luciferase assays showed that the WUSCHEL-RELATED HOMEOBOX 4 (RsWOX4) binds to RsCLE22a promoter and activates its transcription. The expression level of RsWOX4 was related to vascular cambial activity and was regulated by auxin. Furthermore, a RsCLE22a-RsWOX4 module is proposed to regulate taproot vascular cambium activity through an auxin signaling-related pathway in radish. These findings provide novel insights into the regulation of root growth in a horticultural crop.
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Affiliation(s)
- Junhui Dong
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yan Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Liang Xu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Bingshuang Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Kai Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiali Ying
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Qing He
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Liwang Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
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Transcriptomic Analysis of Distal Parts of Roots Reveals Potentially Important Mechanisms Contributing to Limited Flooding Tolerance of Canola ( Brassica napus) Plants. Int J Mol Sci 2022; 23:ijms232415469. [PMID: 36555110 PMCID: PMC9779561 DOI: 10.3390/ijms232415469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 11/29/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Since most of the root metabolic activities as well as root elongation and the uptake of water and mineral nutrients take place in the distal parts of roots, we aimed to gain insight into the physiological and transcriptional changes induced by root hypoxia in the distal parts of roots in canola (Brassica napus) plants, which are relatively sensitive to flooding conditions. Plants were subject to three days of root hypoxia via lowering oxygen content in hydroponic medium, and various physiological and anatomical features were examined to characterize plant responses. Untargeted transcriptomic profiling approaches were also applied to investigate changes in gene expression that took place in the distal root tissues in response to hypoxia. Plants responded to three days of root hypoxia by reducing growth and gas exchange rates. These changes were accompanied by decreases in leaf water potential (Ψleaf) and root hydraulic conductivity (Lpr). Increased deposition of lignin and suberin was also observed in the root tissues of hypoxic plants. The transcriptomic data demonstrated that the effect of hypoxia on plant water relations involved downregulation of most BnPIPs in the root tissues with the exception of BnPIP1;3 and BnPIP2;7, which were upregulated. Since some members of the PIP1 subfamily of aquaporins are known to transport oxygen, the increase in BnPIP1;3 may represent an important hypoxia tolerance strategy in plants. The results also demonstrated substantial rearrangements of different signaling pathways and transcription factors (TFs), which resulted in alterations of genes involved in the regulation of Lpr, TCA (tricarboxylic acid) cycle-related enzymes, antioxidant enzymes, and cell wall modifications. An integration of these data enabled us to draft a comprehensive model of the molecular pathways involved in the responses of distal parts of roots in B. napus. The model highlights systematic transcriptomic reprogramming aimed at explaining the relative sensitivity of Brassica napus to root hypoxia.
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Xiao Z, Fan N, Wang X, Ji H, Yue L, He F, Wang Z. Earthworms Drive the Effect of La 2O 3 Nanoparticles on Radish Taproot Metabolite Profiles and Rhizosphere Microbial Communities. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:17385-17395. [PMID: 36351052 DOI: 10.1021/acs.est.2c05828] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
To promote the sustainable and safe application of nanotechnology employing engineered nanoparticles (NPs) in agroecosystems, it is crucial to pay more attention to the NP-mediated biological response process and environmental impact assessment simultaneously. Herein, 50 mg kg-1 La2O3 NPs were added to soils without and with earthworms for cherry radish growth for 50 days to investigate the response changes of metabolites in radish above- and below-ground organs and rhizosphere bacterial communities. We found that La2O3 NP exposure, especially with earthworms, notably increased the La bioavailability and uptake by taproots and eventually increased radish leaf sucrose content and plant biomass. The La2O3 NP exposure significantly altered metabolite profiles in taproot flesh and peel tissues, and particularly La2O3 NP exposure combined with earthworms was more conducive to La2O3 NPs to promote radish taproot peel to synthesize more secondary antioxidant metabolites. Moreover, compared with the control, the La2O3 NP exposure resulted in weaker and fewer correlations between rhizosphere bacteria and taproot metabolites, but this was recovered somewhat after the inoculation of earthworms. Altogether, our results provide novel insights into the soil-fauna-driven biological and biochemical impact of La2O3 NP exposure on edible root crops and the long-term environmental risks to the rhizosphere microbiota in agroecosystems.
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Affiliation(s)
- Zhenggao Xiao
- Institute of Environmental Processes and Pollution Control, School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Ningke Fan
- Institute of Environmental Processes and Pollution Control, School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Xie Wang
- Institute of Agricultural Resources and Environment, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Haihua Ji
- Institute of Environmental Processes and Pollution Control, School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Le Yue
- Institute of Environmental Processes and Pollution Control, School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Feng He
- Institute of Environmental Processes and Pollution Control, School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Zhenyu Wang
- Institute of Environmental Processes and Pollution Control, School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China
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Zheng W, Shi J, Zhu ZY, Jin P, Chen JH, Zhang L, Zhang E, Lin T, Zhu ZJ, Zang YX, Wu JG. Transcriptomic analysis of succulent stem development of Chinese kale ( Brassica oleracea var. alboglabra Bailey) and its synthetic allotetraploid via RNA sequencing. FRONTIERS IN PLANT SCIENCE 2022; 13:1004590. [PMID: 36340371 PMCID: PMC9630916 DOI: 10.3389/fpls.2022.1004590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Chinese kale (Brassica oleracea var. alboglabra Bailey, CC) is a succulent stem vegetable in the Brassica family. Its allotetraploid (AACC) vegetable germplasm, which was synthesized via distant hybridization with the colloquially named 'yellow turnip' (B. rapa L. ssp. rapifera Matzg., AA), has a swelling stem similar to CC. To address the molecular mechanism of stem development for CC and AACC, RNA sequencing (RNA-seq) was used to investigate transcriptional regulation of their stem development at three key stages including 28 days, 42 days and the bolting stage (BS) after sowing. As a result, 32,642, 32,665, 33,816, 32,147, 32,293 and 32,275 genes were identified in six corresponding cDNA libraries. Among them, 25,459 genes were co-expressed, while 7,183, 7,206, 8,357, 6,688, 6,834 and 6,814 genes were specifically expressed. Additionally, a total of 29,222 differentially expressed genes (DEGs) were found for functional enrichment as well as many genes involved in plant hormones including gibberellin (GA), abscisic acid (ABA), cytokinin (CTK) and auxin (AUX). Based on gene expression consistency between CC and AACC, the gene families including DELLA, GID, PYR/PYL, PP2C, A-ARR and AUX/IAA might be related to stem development. Among these, eight genes including Bo00834s040, Bo5g093140, Bo6g086770, Bo9g070200, Bo7g116570, Bo3g054410, Bo7g093470 and Bo5g136600 may play important roles in stem development based on their remarkable expression levels as confirmed by qRT-PCR. These findings provide a new theoretical basis for understanding the molecular mechanism of stem development in Brassica vegetable stem breeding.
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Affiliation(s)
- Wen Zheng
- College of Horticulture Science, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Zhejiang A&F University, Hangzhou, China
| | - Jiang Shi
- Institute of Crop Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Zhi-Yu Zhu
- College of Modern Agriculture, Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, Zhejiang A&F University, Hangzhou, China
| | - Ping Jin
- College of Horticulture Science, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Zhejiang A&F University, Hangzhou, China
| | - Jia-Hong Chen
- Department of Health and Agriculture, Hangzhou Wanxiang Polytechnic, Hangzhou, China
| | - Liang Zhang
- College of Horticulture Science, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Zhejiang A&F University, Hangzhou, China
| | - E. Zhang
- College of Horticulture Science, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Zhejiang A&F University, Hangzhou, China
| | - Tao Lin
- College of Horticulture Science, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Zhejiang A&F University, Hangzhou, China
| | - Zhu-Jun Zhu
- College of Horticulture Science, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Zhejiang A&F University, Hangzhou, China
| | - Yun-Xiang Zang
- College of Horticulture Science, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Zhejiang A&F University, Hangzhou, China
| | - Jian-Guo Wu
- College of Horticulture Science, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Zhejiang A&F University, Hangzhou, 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: 0.3] [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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10
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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: 10] [Impact Index Per Article: 3.3] [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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11
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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: 3.0] [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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12
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Kanjevac M, Jakovljević D, Todorović M, Stanković M, Ćurčić S, Bojović B. Improvement of Germination and Early Growth of Radish ( Raphanus sativus L.) through Modulation of Seed Metabolic Processes. PLANTS (BASEL, SWITZERLAND) 2022; 11:757. [PMID: 35336639 PMCID: PMC8949023 DOI: 10.3390/plants11060757] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/09/2022] [Accepted: 03/10/2022] [Indexed: 06/14/2023]
Abstract
Radish (Raphanus sativus L.) is a vegetable cultivated worldwide because of its large succulent hypocotyls. The priming method initiates metabolic processes at early stages and regulates the metabolic events in seed necessary for germination. This research was conducted to examine the influence of various priming treatments on physiological performance (germination, growth, lipid peroxidation, primary and secondary metabolism) and antioxidant activity of radish seedlings. On the basis of germination and growth characteristics, vigor index, and relative water content in leaves, it was confirmed that priming treatments with 0.01% ascorbic acid (AA) and 1% KNO3 improves the initial stages of radish development. Furthermore, the efficiency of AA as a priming agent was confirmed through the reduction of malondialdehyde (MDA) level compared to unprimed seedlings. On the other hand, hormopriming with indole-3-acetic acid (IAA) significantly increased the concentration of photosynthetic pigments and total soluble leaf proteins compared to non-primed seedlings. The highest content of total phenolic compounds, including flavonoids, were obtained after hormopriming with 1 mM IAA and halopriming with 1% MgSO4. On the basis of the percentage of inhibition of DPPH radicals, it was confirmed that treatments with IAA and AA can improve the antioxidant activity of radish seedlings. This study provides useful information regarding the possibilities of pregerminative metabolic modulation through the seed priming for the biochemical and physiological improvement of radish, and this topic should be further investigated in order to determine the potential use of AA and IAA as suitable priming agents in radish commercial production.
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Affiliation(s)
- Milica Kanjevac
- Department of Biology and Ecology, Faculty of Science, University of Kragujevac, 34000 Kragujevac, Serbia
| | - Dragana Jakovljević
- Department of Biology and Ecology, Faculty of Science, University of Kragujevac, 34000 Kragujevac, Serbia
| | - Marija Todorović
- Department of Biology and Ecology, Faculty of Science, University of Kragujevac, 34000 Kragujevac, Serbia
| | - Milan Stanković
- Department of Biology and Ecology, Faculty of Science, University of Kragujevac, 34000 Kragujevac, Serbia
| | - Svetlana Ćurčić
- Department of Natural Sciences, Faculty of Education, University of Kragujevac, 35000 Jagodina, Serbia
| | - Biljana Bojović
- Department of Biology and Ecology, Faculty of Science, University of Kragujevac, 34000 Kragujevac, Serbia
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13
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Henschel JM, Brito FAL, Pimenta TM, Picoli EAT, Zsögön A, Ribeiro DM. Irradiance-regulated biomass allocation in Raphanus sativus plants depends on gibberellin biosynthesis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 168:43-52. [PMID: 34619597 DOI: 10.1016/j.plaphy.2021.09.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 09/21/2021] [Accepted: 09/30/2021] [Indexed: 06/13/2023]
Abstract
Gibberellin has been proposed to increase leaf elongation in radish (Raphanus sativus L.) plants, which is associated with decreased tuber growth. Since light intensity can control growth through interaction with gibberellin, investigation of the effect of gibberellin levels on the growth of radish plants would be a step forward towards unraveling factors that underlie biomass accumulation and allocation in response to irradiance levels. Here, we report that the gibberellin biosynthesis inhibitor paclobutrazol (PAC) decreased petiole elongation, but not lamina growth of radish plants grown under full sunlight. However, shading promoted an increase in shoot elongation, while in plants treated with PAC the petiole and leaf lamina fail to elongate. Plants treated with PAC allocated proportionally more biomass to their tubers and less to shoot compared to control under shade. Moreover, PAC decreased the abundance of transcripts encoding cell wall expansion proteins in leaf lamina and petiole of plants grown under shade, which was positively correlated with sugar consumption by the tuber, thereby increasing the mass fraction and concentrations of minerals for tuber. Thus, allocation of biomass during the growth of radish plants and nutritional quality of tubers depend on gibberellin and light intensity.
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Affiliation(s)
- Juliane M Henschel
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Fred A L Brito
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Thaline M Pimenta
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Edgard A T Picoli
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Agustín Zsögön
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Dimas M Ribeiro
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil.
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14
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Ji G, Xu Z, Fan X, Zhou Q, Yu Q, Liu X, Liao S, Feng B, Wang T. Identification of a major and stable QTL on chromosome 5A confers spike length in wheat ( Triticum aestivum L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:56. [PMID: 37309397 PMCID: PMC10236030 DOI: 10.1007/s11032-021-01249-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 08/29/2021] [Indexed: 06/14/2023]
Abstract
Spike length (SL) is the key determinant of plant architecture and yield potential. In this study, 193 recombinant inbred lines (RILs) derived from a cross between 13F10 and Chuanmai 42 (CM42) were evaluated for spike length in six environments. Sixty RILs consisting of 30 high and 30 low SLs were genotyped using the bulked segregant analysis exome sequencing (BSE-Seq) analysis for preliminary quantitative trait locus (QTL) mapping. A 6.69 Mb (518.43-525.12 Mb) region on chromosome 5AL was found to have a significant effect on the SL trait. Fifteen competitive allele-specific PCR (KASP) markers were successfully converted from the single nucleotide polymorphisms (SNPs) in the SL target region. Combined with four novel simple sequence repeat (SSR) markers, a genetic linkage map spanning 21.159 cM was constructed. The mapping result confirmed the identity of a major and stable QTL named QSl.cib-5A in the targeted region that explained 7.88-26.60% of the phenotypic variation in SL. QSl.cib-5A was narrowed to a region of 4.84 cM interval corresponding to a 4.67 Mb (516.60-521.27 Mb) physical region in the Chinese Spring RefSeq v2.0 containing 17 high-confidence genes with 25 transcripts. In addition, this QTL exhibited pleiotropic effects on spikelet density (SD), with the phenotypic variances proportion ranging from 11.34 to 19.92%. This study provides a foundational step for cloning the QSl.cib-5A, which is involved in the regulation of spike morphology in common wheat. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01249-6.
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Affiliation(s)
- Guangsi Ji
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Zhibin Xu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
| | - Xiaoli Fan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
| | - Qiang Zhou
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
| | - Qin Yu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Xiaofeng Liu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Simin Liao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Bo Feng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
| | - Tao Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
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15
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Kang L, Qian L, Zheng M, Chen L, Chen H, Yang L, You L, Yang B, Yan M, Gu Y, Wang T, Schiessl SV, An H, Blischak P, Liu X, Lu H, Zhang D, Rao Y, Jia D, Zhou D, Xiao H, Wang Y, Xiong X, Mason AS, Chris Pires J, Snowdon RJ, Hua W, Liu Z. Genomic insights into the origin, domestication and diversification of Brassica juncea. Nat Genet 2021; 53:1392-1402. [PMID: 34493868 PMCID: PMC8423626 DOI: 10.1038/s41588-021-00922-y] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 07/23/2021] [Indexed: 02/07/2023]
Abstract
Despite early domestication around 3000 BC, the evolutionary history of the ancient allotetraploid species Brassica juncea (L.) Czern & Coss remains uncertain. Here, we report a chromosome-scale de novo assembly of a yellow-seeded B. juncea genome by integrating long-read and short-read sequencing, optical mapping and Hi-C technologies. Nuclear and organelle phylogenies of 480 accessions worldwide supported that B. juncea is most likely a single origin in West Asia, 8,000-14,000 years ago, via natural interspecific hybridization. Subsequently, new crop types evolved through spontaneous gene mutations and introgressions along three independent routes of eastward expansion. Selective sweeps, genome-wide trait associations and tissue-specific RNA-sequencing analysis shed light on the domestication history of flowering time and seed weight, and on human selection for morphological diversification in this versatile species. Our data provide a comprehensive insight into the origin and domestication and a foundation for genomics-based breeding of B. juncea.
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Affiliation(s)
- Lei Kang
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Lunwen Qian
- College of Agronomy, Hunan Agricultural University, Changsha, China
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, China
| | - Ming Zheng
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Liyang Chen
- Novogene Bioinformatics Institute, Beijing, China
| | - Hao Chen
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Liu Yang
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Liang You
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Bin Yang
- College of Agronomy, Hunan Agricultural University, Changsha, China
- Guizhou Institute of Oil Crops, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Mingli Yan
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life Science, Hunan University of Science and Technology, Xiangtan, China
| | - Yuanguo Gu
- Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Tianyi Wang
- Novogene Bioinformatics Institute, Beijing, China
| | | | - Hong An
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - Paul Blischak
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Xianjun Liu
- College of Life Sciences, Resources and Environment Sciences, Yichun University, Yichun, China
| | - Hongfeng Lu
- Novogene Bioinformatics Institute, Beijing, China
| | - Dawei Zhang
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life Science, Hunan University of Science and Technology, Xiangtan, China
| | - Yong Rao
- Guizhou Institute of Oil Crops, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Donghai Jia
- Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Dinggang Zhou
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life Science, Hunan University of Science and Technology, Xiangtan, China
| | - Huagui Xiao
- Guizhou Institute of Oil Crops, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Yonggang Wang
- Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Xinghua Xiong
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Annaliese S Mason
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
- Plant Breeding Department, University of Bonn, Bonn, Germany
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - Rod J Snowdon
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Wei Hua
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China.
| | - Zhongsong Liu
- College of Agronomy, Hunan Agricultural University, Changsha, China.
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16
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Xie Y, Ying J, Tang M, Wang Y, Xu L, Liu M, Liu L. Genome-wide identification of AUX/IAA in radish and functional characterization of RsIAA33 gene during taproot thickening. Gene 2021; 795:145782. [PMID: 34146634 DOI: 10.1016/j.gene.2021.145782] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 05/17/2021] [Accepted: 06/14/2021] [Indexed: 11/27/2022]
Abstract
Auxin/indole-3-acetic acid (Aux/IAA) genes encode short lived nuclear proteins that cooperated with auxin or auxin response factor (ARF), which are involved in plant growth and developmental processes. However, it's still ambiguous how the Aux/IAA genes regulate the process governing taproot thickening in radish. Herein, 65 Aux/IAA genes were identified from the radish genome. Gene duplication analysis showed that two pairs of tandem duplication and 17 (27%) segmental duplication events were identified among Aux/IAA family genes in radish. Transcriptomic analysis revealed that most of Aux/IAA genes (52/65) exhibited differential expression pattern in different root tissues, and six root-specific genes were highly expressed in root cortex, cambium, xylem, and root tip in radish. RT-qPCR analysis showed that the expression level of RsIAA33 was the highest at cortex splitting stage (CSS), and early expanding stage (ES). Furthermore, amiRNA-mediated gene silencing of RsIAA33 indicated that it could inhibit the reproductive growth, thus promoting taproot thickening and development. These results would provide valuable information for elucidating the molecular function of Aux/IAA genes involved in taproot thickening in radish.
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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; Hebei Key Laboratory of Horticultural Germplasm Excavation and Innovative Utilization, 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
| | - 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
| | - 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
| | - 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.
| | - Meiyan Liu
- Hebei Key Laboratory of Horticultural Germplasm Excavation and Innovative Utilization, College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao 066004, 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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17
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Xiao Z, Yue L, Wang C, Chen F, Ding Y, Liu Y, Cao X, Chen Z, Rasmann S, Wang Z. Downregulation of the photosynthetic machinery and carbon storage signaling pathways mediate La 2O 3 nanoparticle toxicity on radish taproot formation. JOURNAL OF HAZARDOUS MATERIALS 2021; 411:124971. [PMID: 33429308 DOI: 10.1016/j.jhazmat.2020.124971] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/18/2020] [Accepted: 12/23/2020] [Indexed: 06/12/2023]
Abstract
The molecular and physiological mechanisms of how rare earth oxide nanoparticles (NPs) alter radish (Raphanus sativus L.) taproot formation and cracking were investigated in the present study. We compared plants that received suspensions of 10, 50, 100, 300 mg L-1 of La2O3 NPs, 300 m L-1 La2O3 bulk-particles (BPs), 0.8 m L-1 La3+, or only water for six days during their tuber formation period. 100 and 300 mg L-1 La2O3 NPs exposure decreased storage root biomass by 38% and 60%, respectively, and they both induced visible root cracking. Physiological analyses showed that La2O3 NPs exposure (>100 mg L-1) significantly inhibited leaf net photosynthetic rate, cell wall pectin synthesis of both storage root epidermis and xylem parenchyma tissues, but increased the contents of cellulose and hemicellulose 1 in root epidermis cell walls. Moreover, transcriptome analysis further found that La2O3 NPs changed root cell wall structure by down-regulating core genes involved in cell wall pectin and IAA biosynthesis, which coincided with the observed La2O3 NPs-induced root cracking. Our results revealed the molecular mechanisms related to cell wall carbohydrate metabolism in response to NPs stress, providing a step forward for understanding the causes of NPs phytotoxicity on edible plant taproot formation and cracking.
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Affiliation(s)
- Zhenggao Xiao
- Institute of Environmental Processes and Pollution Control, and School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Le Yue
- Institute of Environmental Processes and Pollution Control, and School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Chuanxi Wang
- Institute of Environmental Processes and Pollution Control, and School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Feiran Chen
- Institute of Environmental Processes and Pollution Control, and School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Ying Ding
- Institute of Environmental Processes and Pollution Control, and School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Yinglin Liu
- Institute of Environmental Processes and Pollution Control, and School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Xuesong Cao
- Institute of Environmental Processes and Pollution Control, and School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Zhe Chen
- Institute of Tropical Fruit Trees, Hainan Academy of Agricultural Science, Haikou 571100, China
| | - Sergio Rasmann
- Institute of Biology, University of Neuchâtel, Rue-Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Zhenyu Wang
- Institute of Environmental Processes and Pollution Control, and School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China.
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Zhang HP, Su Y, Yu Q, Qin GH. Quantitative proteomic analysis of pear (Pyrus pyrifolia cv. "Hosui") flesh provides novel insights about development and quality characteristics of fruit. PLANTA 2021; 253:69. [PMID: 33599839 DOI: 10.1007/s00425-021-03585-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
A total of 6763 proteins were identified in the developing pear flesh, which were further screened for differentially expressed proteins related to fruit quality and ATP-binding cassette transporters. To obtain further details on changes in protein levels during fruit ripening and to identify and evaluate changes in various metabolic pathways that affect fruit quality, a proteomic method using tandem mass tags was implemented at three developmental stages in Pyrus pyrifolia cv. "Hosui" that identified 6763 proteins. Subcellular localization and Gene Ontology enrichment analysis revealed major functions of all identified proteins. Kyoto Encyclopedia of Genes and Genomes pathway analysis suggested that all metabolic processes are reflected in the up- and downregulation of differentially expressed proteins during fruit development, which play predominant roles in cell division, cell expansion, and fruit ripening. Among the examined differentially expressed proteins, 160 related to fruit quality, and 14 ATP-binding cassette transporters related to fruit development were identified and analyzed. The quantitative data were validated by parallel reaction monitoring, which confirmed the reliability of the experimental results.
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Affiliation(s)
- Hu Ping Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Ying Su
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qing Yu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Gai Hua Qin
- Key Laboratory of Horticultural Crop Genetic Improvement and Eco-Physiology of Anhui Province, Institute of Horticulture Research, Anhui Academy of Agricultural Sciences, Hefei, 230031, China.
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19
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Wu Y, Zhang S, Zhang H, Li F, Li G, Fan C, Sun R, Zhang S. QTL Mapping and Candidate Gene Identification of Swollen Root Formation in Turnip. Int J Mol Sci 2021; 22:ijms22020653. [PMID: 33440867 PMCID: PMC7826719 DOI: 10.3390/ijms22020653] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/29/2020] [Accepted: 01/07/2021] [Indexed: 12/17/2022] Open
Abstract
The swollen root is an important agronomic trait and is a determinant of yield for turnips, which are cultivated as both vegetables and fodder. However, the genetic mechanism of swollen root formation is poorly understood. In this study, we analyzed the F2 and BC1P2 populations derived from a cross between “10601” (European turnip with swollen root, Brassica rapa ssp. rapifera, AA, 2n = 2× = 20) and “10603” (Chinese cabbage with normal root, Brassica rapa ssp. pekinensis, AA, 2n = 2× = 20), and suggested that the swollen root is a quantitative trait. Two major quantitative trait loci (QTLs), FR1.1 (Fleshy root 1.1) and FR7.1 (Fleshy root 7.1), were identified by QTL-seq analysis and further confirmed by QTL mapping in F2 and BC1P2 populations. The QTL FR1.1 with a likelihood of odd (LOD) of 7.01 explained 17.2% of the total phenotypic variations for root diameter and the QTL FR7.1 explained 23.0% (LOD = 9.38) and 31.0% (LOD = 13.27) of the total phenotypic variations in root diameter and root weight, respectively. After a recombinant screening, the major QTL FR7.1 was further narrowed down to a 220 kb region containing 47 putative genes. A candidate gene, Bra003652, which is a homolog of AT1G78240 that plays an essential role in cell adhesion and disorganized tumor-like formation in Arabidopsis thaliana, was identified in this region. In addition, expression and parental allele analysis supported that Bra003652 was a possible candidate gene of QTL FR7.1 for swollen root formation in turnip. Our research may provide new insight into the molecular mechanism of swollen root formation in root crops.
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Affiliation(s)
- Yudi Wu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (S.Z.); (H.Z.); (F.L.); (G.L.)
| | - Shifan Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (S.Z.); (H.Z.); (F.L.); (G.L.)
| | - Hui Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (S.Z.); (H.Z.); (F.L.); (G.L.)
| | - Fei Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (S.Z.); (H.Z.); (F.L.); (G.L.)
| | - Guoliang Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (S.Z.); (H.Z.); (F.L.); (G.L.)
| | - Chuchuan Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence: (C.F.); (R.S.); (S.Z.); Tel.: +86-027-87286873 (C.F.); +86-010-82109548 (R.S.); +86-010-82109548 (S.Z.)
| | - Rifei Sun
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (S.Z.); (H.Z.); (F.L.); (G.L.)
- Correspondence: (C.F.); (R.S.); (S.Z.); Tel.: +86-027-87286873 (C.F.); +86-010-82109548 (R.S.); +86-010-82109548 (S.Z.)
| | - Shujiang Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (S.Z.); (H.Z.); (F.L.); (G.L.)
- Correspondence: (C.F.); (R.S.); (S.Z.); Tel.: +86-027-87286873 (C.F.); +86-010-82109548 (R.S.); +86-010-82109548 (S.Z.)
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20
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Ma Y, Xie Y, Ha R, Cao B, Song L. Effects of Elevated CO 2 on Photosynthetic Accumulation, Sucrose Metabolism-Related Enzymes, and Genes Identification in Goji Berry ( Lycium barbarum L.). FRONTIERS IN PLANT SCIENCE 2021; 12:643555. [PMID: 33777078 PMCID: PMC7991576 DOI: 10.3389/fpls.2021.643555] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/16/2021] [Indexed: 05/14/2023]
Abstract
Goji berry (Lycium barbarum L.) exposure to elevated CO2 (eCO2) for long periods reduces their sugar and secondary metabolite contents. However, sugar accumulation in fruit depends on photosynthesis and photoassimilate partitioning. This study aimed to explore photosynthesis, sugar content, and sucrose metabolism-related enzyme activities in goji berry leaves and fruits under ambient and eCO2 levels, and identify the genes encoding L. barbarum acid invertase (LBAI), L. barbarum sucrose synthase (LBSS), L. barbarum sucrose phosphate synthase (LBSPS), and L. barbarum neutral invertase (LBNI), based on transcriptome profiling. Further, the characterization of four identified genes was analyzed including subcellular localization and expression patterns. In plants grown under eCO2 for 90 or 120 days, the expression of the above-mentioned genes changed significantly as the photosynthetic rate increased. In addition, leaf and fruit sugar contents decreased, and the activities of four sucrose metabolism-related enzymes increased in leaves, while acid and neutral invertase increased in fruits. Protein sequence analysis demonstrated that LBAI and LBNI contain a conservative structure domain belonging to the glycosyl hydrolases (Glyco_hydro) family, and both LBSS and LBSPS belonging to the sucrose synthase (Sucrose_synth) and glycosyltransferase (Glycos_transf) family. Subcellular localization analysis showed that LBAI, LBNI, and LBSS were all located in the nucleus, plasma membrane, and cytoplasm, while LBSPS was located in the plasma membrane. The expressions of LBAI, LBSPS, and LBNI were high in the stems, whereas LBSS was predominantly expressed in the fruits. Our findings provide fundamental data on photosynthesis and sugar accumulation trends in goji berries under eCO2 exposure.
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Affiliation(s)
- Yaping Ma
- School of Agriculture, Ningxia University, Yinchuan, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Yun Xie
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Rong Ha
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Bing Cao
- School of Agriculture, Ningxia University, Yinchuan, China
- *Correspondence: Bing Cao,
| | - Lihua Song
- School of Agriculture, Ningxia University, Yinchuan, China
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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: 0.2] [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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22
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Characterization of the OFP Gene Family and its Putative Involvement of Tuberous Root Shape in Radish. Int J Mol Sci 2020; 21:ijms21041293. [PMID: 32075122 PMCID: PMC7072887 DOI: 10.3390/ijms21041293] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/07/2020] [Accepted: 02/10/2020] [Indexed: 12/21/2022] Open
Abstract
The shape of the tuberous root, a very important quality trait, varies dramatically among radish cultivars. Ovate family proteins (OFPs) are plant-specific proteins that regulate multiple aspects of plant growth and development. To investigate the possible role of OFPs in radish tuberous root formation, 35 putative RsOFPs were identified from radish, and their expression patterns were detected during tuberous root development in six different radish cultivars. Phylogenetically, RsOFP2.3 clustered together with AtOFP1 and other members of this family that are known to regulate organ shape. Moreover, RsOFP2.3 expression was negatively correlated with tuberous root elongation after the cortex splitting stage, which made this gene the top candidate for the involvement of tuberous root shape. To further characterize the function of RsOFP2.3, it was ectopically expressed in Arabidopsis. RsOFP2.3 overexpression in Arabidopsis led to multiple phenotypical changes, especially the decreased length and increased width of the hypocotyl. Furthermore, RsOFP2.3 expression was induced by all the five classic plant hormones except ethylene, and it was most sensitive to exogenous gibberellic acid treatment. We also found that RsOFP2.3 was localized in the cytoplasm. Taken together, our results suggested the possible involvement for RsOFP2.3 in suppressing radish tuberous root elongation and that it encodes a functional protein which mainly inhibits the elongation of Arabidopsis aerial organs.
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23
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Li XJ, Yang JL, Hao B, Lu YC, Qian ZL, Li Y, Ye S, Tang JR, Chen M, Long GQ, Zhao Y, Zhang GH, Chen JW, Fan W, Yang SC. Comparative transcriptome and metabolome analyses provide new insights into the molecular mechanisms underlying taproot thickening in Panax notoginseng. BMC PLANT BIOLOGY 2019; 19:451. [PMID: 31655543 PMCID: PMC6815444 DOI: 10.1186/s12870-019-2067-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 10/02/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND Taproot thickening is a complex biological process that is dependent on the coordinated expression of genes controlled by both environmental and developmental factors. Panax notoginseng is an important Chinese medicinal herb that is characterized by an enlarged taproot as the main organ of saponin accumulation. However, the molecular mechanisms of taproot enlargement are poorly understood. RESULTS A total of 29,957 differentially expressed genes (DEGs) were identified during the thickening process in the taproots of P. notoginseng. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment revealed that DEGs associated with "plant hormone signal transduction," "starch and sucrose metabolism," and "phenylpropanoid biosynthesis" were predominantly enriched. Further analysis identified some critical genes (e.g., RNase-like major storage protein, DA1-related protein, and Starch branching enzyme I) and metabolites (e.g., sucrose, glucose, fructose, malate, and arginine) that potentially control taproot thickening. Several aspects including hormone crosstalk, transcriptional regulation, homeostatic regulation between sugar and starch, and cell wall metabolism, were identified as important for the thickening process in the taproot of P. notoginseng. CONCLUSION The results provide a molecular regulatory network of taproot thickening in P. notoginseng and facilitate the further characterization of the genes responsible for taproot formation in root medicinal plants or crops.
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Affiliation(s)
- Xue-Jiao Li
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National& Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201 China
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, 650201 China
| | - Jian-Li Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 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& Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201 China
| | - Ying-Chun Lu
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National& Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201 China
| | - Zhi-Long Qian
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National& Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201 China
| | - Ying Li
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National& Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201 China
| | - Shuang Ye
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National& Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201 China
| | - Jun-Rong Tang
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National& Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201 China
| | - Mo Chen
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National& Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201 China
| | - Guang-Qiang Long
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National& Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201 China
| | - Yan Zhao
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National& Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201 China
| | - Guang-Hui Zhang
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National& Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201 China
| | - Jun-Wen Chen
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National& Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, 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& Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201 China
| | - Sheng-Chao Yang
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National& Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201 China
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Zhou A, Sun H, Dai S, Feng S, Zhang J, Gong S, Wang J. Identification of Transcription Factors Involved in the Regulation of Flowering in Adonis Amurensis Through Combined RNA-seq Transcriptomics and iTRAQ Proteomics. Genes (Basel) 2019; 10:genes10040305. [PMID: 31003538 PMCID: PMC6523232 DOI: 10.3390/genes10040305] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 04/07/2019] [Accepted: 04/15/2019] [Indexed: 12/20/2022] Open
Abstract
Temperature is one of the most important environmental factors affecting flowering in plants. Adonis amurensis, a perennial herbaceous flower that blooms in early spring in northeast China where the temperature can drop to −15 °C, is an ideal model for studying the molecular mechanisms of flowering at extremely low temperatures. This study first investigated global gene expression profiles at different developmental stages of flowering in A. amurensis by RNA-seq transcriptome and iTRAQ proteomics. Finally, 123 transcription factors (TFs) were detected in both the transcriptome and the proteome. Of these, 66 TFs belonging to 14 families may play a key role in multiple signaling pathways of flowering in A. amurensis. The TFs FAR1, PHD, and B3 may be involved in responses to light and temperature, while SCL, SWI/SNF, ARF, and ERF may be involved in the regulation of hormone balance. SPL may regulate the age pathway. Some members of the TCP, ZFP, MYB, WRKY, and bHLH families may be involved in the transcriptional regulation of flowering genes. The MADS-box TFs are the key regulators of flowering in A. amurensis. Our results provide a direction for understanding the molecular mechanisms of flowering in A. amurensis at low temperatures.
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Affiliation(s)
- Aimin Zhou
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China.
| | - Hongwei Sun
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China.
| | - Shengyue Dai
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China.
| | - Shuang Feng
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Harbin 150040, China.
| | - Jinzhu Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China.
| | - Shufang Gong
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China.
| | - Jingang Wang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China.
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25
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Ondrasek G, Clode PL, Kilburn MR, Guagliardo P, Romić D, Rengel Z. Zinc and Cadmium Mapping in the Apical Shoot and Hypocotyl Tissues of Radish by High-Resolution Secondary Ion Mass Spectrometry (NanoSIMS) after Short-Term Exposure to Metal Contamination. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16030373. [PMID: 30699929 PMCID: PMC6388160 DOI: 10.3390/ijerph16030373] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/19/2019] [Accepted: 01/23/2019] [Indexed: 12/19/2022]
Abstract
Zinc (as an essential phytonutrient) and cadmium (as a toxic but readily bioavailable nonessential metal for plants) share similar routes for crossing plant biomembranes, although with a substantially different potential for translocation into above-ground tissues. The in situ distribution of these metals in plant cells and tissues (particularly intensively-dividing and fast-growing areas) is poorly understood. In this study, 17-day-old radish (Raphanus sativus L.) plants grown in nutrient solution were subjected to short-term (24 h) equimolar contamination (2.2 µM of each 70Zn and Cd) to investigate their accumulation and distribution in the shoot apex (leaf primordia) and edible fleshy hypocotyl tissues. After 24-h exposure, radish hypocotyl had similar concentration (in µg/g dry weight) of 70Zn (12.1 ± 1.1) and total Cd (12.9 ± 0.8), with relatively limited translocation of both metals to shoots (concentrations lower by 2.5-fold for 70Zn and 4.8-fold for Cd) as determined by inductively-coupled plasma mass spectrometry (ICP-MS). The in situ Zn/Cd distribution maps created by high-resolution secondary ion mass spectrometry (NanoSIMS, Cameca, Gennevilliers, France) imaging corresponded well with the ICP-MS data, confirming a similar pattern and uniform distribution of 70Zn and Cd across the examined areas. Both applied techniques can be powerful tools for quantification (ICP-MS) and localisation and visualisation (NanoSIMS) of some ultra-trace isotopes in the intensively-dividing cells and fast-growing tissues of non-metalophytes even after short-term metal exposure. The results emphasise the importance of the quality of (agro)ecosystem resources (growing media, metal-contaminated soils/waters) in the public health risk, given that, even under low contamination and short-term exposure, some of the most toxic metallic ions (e.g., Cd) can relatively rapidly enter the human food chain.
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Affiliation(s)
- Gabrijel Ondrasek
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Australia.
- Faculty of Agriculture, The University of Zagreb, Svetosimunska cesta 25, 10 000 Zagreb, Croatia.
| | - Peta L Clode
- The Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Australia.
| | - Matt R Kilburn
- The Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Australia.
| | - Paul Guagliardo
- The Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Australia.
| | - Davor Romić
- Faculty of Agriculture, The University of Zagreb, Svetosimunska cesta 25, 10 000 Zagreb, Croatia.
| | - Zed Rengel
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Australia.
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Transcriptome-based gene expression profiling of diploid radish (Raphanus sativus L.) and the corresponding autotetraploid. Mol Biol Rep 2018; 46:933-945. [PMID: 30560406 DOI: 10.1007/s11033-018-4549-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 11/30/2018] [Indexed: 12/11/2022]
Abstract
Polyploidy is an important evolutionary factor in most land plant lineages which possess more than two complete sets of chromosomes. Radish (Raphanus sativus L.) is an economically annual/biennial root vegetable crop worldwide. However, the expression patterns of duplicated homologs involved in the autopolyploidization remains unclear. In present study, the autotetraploid radish plants (2n = 4x = 36) were produced with colchicine and exhibited an increase in the size of flowers, leaves, stomata and pollen grains. The differential gene expression (DGE) profiling was performed to investigate the differences in gene expression patterns between diploid and its corresponding autotetraploid by RNA-Sequencing (RNA-Seq). Totally, 483 up-regulated differentially expressed genes (DEGs) and 408 down-regulated DEGs were detected in diploid and autotetraploid radishes, which majorly involved in the pathways of hormones, photosynthesis and stress response. Moreover, the xyloglucan endotransglucosylase/hydrolase (XTH) and pectin methylesterases (PME) family members related to cell enlargement and cell wall construction were found to be enriched in GO enrichment analysis, of which XTH family members enriched in "apoplast" and "cell wall" terms, while PME family members enriched in "cell wall" term. Reverse-transcription quantitative PCR (RT-qPCR) analysis indicated that the expression profile of DEGs were consistent with results from the RNA-Seq analysis. The DEGs involved in cell wall construction and auxin metabolism were predicted to be associated with organs size increase of autotetraploid radishes in the present study. These results could provide valuable information for elucidating the molecular mechanism underlying polyploidization and facilitating further genetic improvements of important traits in radish breeding programs.
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