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Yan Y, Li M, Ding Z, Yang J, Xie Z, Ye X, Tie W, Tao X, Chen G, Huo K, Ma J, Ye J, Hu W. The regulation mechanism of ethephon-mediated delaying of postharvest physiological deterioration in cassava storage roots based on quantitative acetylproteomes analysis. Food Chem 2024; 458:140252. [PMID: 38964113 DOI: 10.1016/j.foodchem.2024.140252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 06/05/2024] [Accepted: 06/25/2024] [Indexed: 07/06/2024]
Abstract
Ethylene plays diverse roles in post-harvest processes of horticultural crops. However, its impact and regulation mechanism on the postharvest physiological deterioration (PPD) of cassava storage roots is unknown. In this study, a notable delay in PPD of cassava storage roots was observed when ethephon was utilized as an ethylene source. Physiological analyses and quantitative acetylproteomes were employed to investigate the regulation mechanism regulating cassava PPD under ethephon treatment. Ethephon was found to enhance the reactive oxygen species (ROS) scavenging system, resulting in a significant decrease in H2O2 and malondialdehyde (MDA) content. The comprehensive acetylome analysis identified 12,095 acetylation sites on 4403 proteins. Subsequent analysis demonstrated that ethephon can regulate the acetylation levels of antioxidant enzymes and members of the energy metabolism pathways. In summary, ethephon could enhance the antioxidant properties and regulate energy metabolism pathways, leading to the delayed PPD of cassava.
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Affiliation(s)
- Yan Yan
- National Key Laboratory for Tropical Crop Breeding, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572025, China
| | - Meiying Li
- National Key Laboratory for Tropical Crop Breeding, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572025, China
| | - Zehong Ding
- National Key Laboratory for Tropical Crop Breeding, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572025, China
| | - Jinghao Yang
- National Key Laboratory for Tropical Crop Breeding, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Zhengnan Xie
- National Key Laboratory for Tropical Crop Breeding, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Xiaoxue Ye
- National Key Laboratory for Tropical Crop Breeding, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572025, China
| | - Weiwei Tie
- National Key Laboratory for Tropical Crop Breeding, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572025, China
| | - Xiangru Tao
- National Key Laboratory for Tropical Crop Breeding, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Ganlu Chen
- National Key Laboratory for Tropical Crop Breeding, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Kaisen Huo
- Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572025, China
| | - Jianxiang Ma
- Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572025, China
| | - Jianqiu Ye
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Wei Hu
- National Key Laboratory for Tropical Crop Breeding, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572025, China; Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China.
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2
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Li R, Rosado-Souza L, Sampathkumar A, Fernie AR. The relationship between cell wall and postharvest physiological deterioration of fresh produce. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108568. [PMID: 38581806 DOI: 10.1016/j.plaphy.2024.108568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/08/2024] [Accepted: 03/25/2024] [Indexed: 04/08/2024]
Abstract
Postharvest physiological deterioration (PPD) reduces the availability and economic value of fresh produces, resulting in the waste of agricultural products and becoming a worldwide problem. Therefore, many studies have been carried out at the anatomical structural, physiological and biochemical levels and molecular levels of PPD of fresh produces to seek ways to manage the postharvest quality of fresh produce. The cell wall is the outermost structure of a plant cell and as such represents the first barrier to prevent external microorganisms and other injuries. Many studies on postharvest quality of crop storage organs relate to changes in plant cell wall-related components. Indeed, these studies evidence the non-negligible role of the plant cell wall in postharvest storage ability. However, the relationship between cell wall metabolism and postharvest deterioration of fresh produces has not been well summarized. In this review, we summarize the structural changes of cell walls in different types of PPD, metabolic changes, and the possible molecular mechanism regulating cell wall metabolism in PPD of fresh produce. This review provides a basis for further research on delaying the occurrence of PPD of fresh produce.
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Affiliation(s)
- Ruimei Li
- National Key Laboratory for Tropical Crop Breeding, Sanya Research Institute/Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Sanya, China; Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Laise Rosado-Souza
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Arun Sampathkumar
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
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3
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Wang C, Chen Y, Chen S, Min Y, Tang Y, Ma X, Li H, Li J, Liu Z. Spraying chitosan on cassava roots reduces postharvest deterioration by promoting wound healing and inducing disease resistance. Carbohydr Polym 2023; 318:121133. [PMID: 37479443 DOI: 10.1016/j.carbpol.2023.121133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/28/2023] [Accepted: 06/16/2023] [Indexed: 07/23/2023]
Abstract
Postharvest damage makes cassava roots vulnerable to pathogen infections and decay, which significantly hinders the development of the cassava industry. The objective of this study was to assess the antibacterial properties of chitosan in vitro, as well as its effect on wound healing and resistance in cassava roots. The findings demonstrated that the bacteriostatic effect of chitosan became increasingly prominent as the concentration of chitosan enhanced. Chitosan at a concentration of 0.5 mg/mL was revealed to significantly inhibit the germination of P. palmivora spores and damage to their structure. Moreover, chitosan activated the transcription of crucial genes and enzyme activities associated with the phenylpropane metabolism pathway in cassava roots, thus promoting rapid lignin accumulation and resulting in the early formation of a fracture layer. Chitosan was also found to enhance cassava root resistance by promoting the expression of pathogenesis-related proteins and the accumulation of flavonoids and total phenols. After 48 h of inoculation, cassava roots treated with chitosan exhibited a 51.4 % and 53.4 % decrease in lesion area for SC9 and SC6 varieties, respectively. The findings of this study offer a novel approach for managing postharvest deterioration of cassava roots.
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Affiliation(s)
- Congcong Wang
- School of Life Sciences, Hainan University, Haikou 570228, China
| | - Yinhua Chen
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou 570228, Hainan, China
| | - Songbi Chen
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Ministry of Agriculture for Germplasm Resources Conservation and Utilization of Cassava, Hainan, China
| | - Yi Min
- School of Life Sciences, Hainan University, Haikou 570228, China
| | - Yanqiong Tang
- School of Life Sciences, Hainan University, Haikou 570228, China
| | - Xiang Ma
- School of Life Sciences, Hainan University, Haikou 570228, China
| | - Hong Li
- School of Life Sciences, Hainan University, Haikou 570228, China
| | - Juanjuan Li
- School of Life Sciences, Hainan University, Haikou 570228, China
| | - Zhu Liu
- School of Life Sciences, Hainan University, Haikou 570228, China.
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4
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Lamm CE, Rabbi IY, Medeiros DB, Rosado-Souza L, Pommerrenig B, Dahmani I, Rüscher D, Hofmann J, van Doorn AM, Schlereth A, Neuhaus HE, Fernie AR, Sonnewald U, Zierer W. Efficient sugar utilization and transition from oxidative to substrate-level phosphorylation in high starch storage roots of African cassava genotypes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:38-57. [PMID: 37329210 DOI: 10.1111/tpj.16357] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/19/2023] [Accepted: 06/14/2023] [Indexed: 06/18/2023]
Abstract
Cassava's storage roots represent one of the most important sources of nutritional carbohydrates worldwide. Particularly, smallholder farmers in sub-Saharan Africa depend on this crop plant, where resilient and yield-improved varieties are of vital importance to support steadily increasing populations. Aided by a growing understanding of the plant's metabolism and physiology, targeted improvement concepts already led to visible gains in recent years. To expand our knowledge and to contribute to these successes, we investigated storage roots of eight cassava genotypes with differential dry matter content from three successive field trials for their proteomic and metabolic profiles. At large, the metabolic focus in storage roots transitioned from cellular growth processes toward carbohydrate and nitrogen storage with increasing dry matter content. This is reflected in higher abundance of proteins related to nucleotide synthesis, protein turnover, and vacuolar energization in low starch genotypes, while proteins involved in sugar conversion and glycolysis were more prevalent in high dry matter genotypes. This shift in metabolic orientation was underlined by a clear transition from oxidative- to substrate-level phosphorylation in high dry matter genotypes. Our analyses highlight metabolic patterns that are consistently and quantitatively associated with high dry matter accumulation in cassava storage roots, providing fundamental understanding of cassava's metabolism as well as a data resource for targeted genetic improvement.
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Affiliation(s)
- Christian E Lamm
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Division of Biochemistry, Erlangen, Germany
| | - Ismail Y Rabbi
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | | | - Laise Rosado-Souza
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | - Ismail Dahmani
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - David Rüscher
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Division of Biochemistry, Erlangen, Germany
| | - Jörg Hofmann
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Division of Biochemistry, Erlangen, Germany
| | - Anna M van Doorn
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Armin Schlereth
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Uwe Sonnewald
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Division of Biochemistry, Erlangen, Germany
| | - Wolfgang Zierer
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Division of Biochemistry, Erlangen, Germany
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5
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Wahengbam ED, Devi CP, Sharma SK, Roy SS, Maibam A, Dasgupta M, Luikham S, Chongtham T, Ningombam A, Bhupenchandra I, Singh LK, Devi YP, Thokchom S, Khaba CI, Singh NB, Rajashekar Y, Das S, Mohanty S, Sahoo MR. Reactive oxygen species turnover, phenolics metabolism, and some key gene expressions modulate postharvest physiological deterioration in cassava tubers. Front Microbiol 2023; 14:1148464. [PMID: 36925477 PMCID: PMC10011484 DOI: 10.3389/fmicb.2023.1148464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 02/13/2023] [Indexed: 03/08/2023] Open
Abstract
Rapid postharvest physiological deterioration (PPD) in cassava (Manihot esculenta Crantz) tuber is a significant concern during storage. The freshly harvested tubers start spoiling within 24 to 72 h. Accumulation of H2O2 is one of the earliest biochemical events that occurred during PPD, which was detected using the 3,3 diaminobenzidine (DAB) in two contrast cassava genotypes, MNP Local A (29-57 μg g-1) and Sree Prakash (64-141 μg g-1). Accumulating the fluorescence hydroxycoumarin compounds emitted by the cassava tubers observed under an ultraviolet (UV) lamp showed significant variations at 0, 3, 6, 9, 12, and 15 days of storage. The total phenolics and carotenoids significantly and negatively correlated with PPD progression; however, the anthocyanin and flavonoids positively correlated with the PPD-anchored ROS accumulation. The primary compound, Phthalic acid, di(2-propylpentyl) ester, was identified in both the cassava tubers, Sree Prakash (57.21 and 35.21%), and MNP Local A (75.58 and 60.21%) at 0, and 72 h of PPD, respectively. The expression of PPD-associated genes APX-2, APX-3, PAL, and AP was higher at 6-12 days of PPD, which signified the synthesis of ROS turnover and phenylpropanoid biosynthesis. A significant, strong, and positive correlation was established between the secondary metabolites and PPD signaling gene expression, which was inversely correlated with hydroxycoumarin and H2O2 accumulation. MNP Local A tubers exhibited longer storage life of 15 days with a low PPD score, higher metabolites synthesis, and gene expression. The PPD-resistant lines may be used to augment cassava breeding strategies for large-scale commercial and industrial use.
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Affiliation(s)
| | | | | | - Subhra Saikat Roy
- ICAR Research Complex for North Eastern Hill Region, Imphal, Manipur, India
| | - Albert Maibam
- ICAR Research Complex for North Eastern Hill Region, Imphal, Manipur, India
| | - Madhumita Dasgupta
- ICAR Research Complex for North Eastern Hill Region, Imphal, Manipur, India
| | - Star Luikham
- ICAR Research Complex for North Eastern Hill Region, Imphal, Manipur, India
| | - Tania Chongtham
- ICAR Research Complex for North Eastern Hill Region, Imphal, Manipur, India
| | - Arati Ningombam
- ICAR Research Complex for North Eastern Hill Region, Imphal, Manipur, India
| | - Ingudam Bhupenchandra
- Farm Science Centre, ICAR Research Complex for North Eastern Hill Region, Imphal, Manipur, India
| | - Laishram Kanta Singh
- Farm Science Centre, ICAR Research Complex for North Eastern Hill Region, Imphal, Manipur, India
| | - Yumnam Prabhabati Devi
- Farm Science Centre, ICAR Research Complex for North Eastern Hill Region, Imphal, Manipur, India
| | | | | | | | - Yallappa Rajashekar
- Institute of Bioresources and Sustainable Development, Imphal, Manipur, India
| | - Sudripta Das
- Institute of Bioresources and Sustainable Development, Imphal, Manipur, India
| | - Sansuta Mohanty
- Central Horticultural Experiment Station, ICAR–Indian Institute of Horticultural Research, Bhubaneswar, Odisha, India
| | - Manas Ranjan Sahoo
- ICAR Research Complex for North Eastern Hill Region, Imphal, Manipur, India
- Central Horticultural Experiment Station, ICAR–Indian Institute of Horticultural Research, Bhubaneswar, Odisha, India
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Zainuddin IM, Lecart B, Sudarmonowati E, Vanderschuren H. A method for rapid and homogenous initiation of post-harvest physiological deterioration in cassava storage roots identifies Indonesian cultivars with improved shelf-life performance. PLANT METHODS 2023; 19:4. [PMID: 36653871 PMCID: PMC9847153 DOI: 10.1186/s13007-022-00977-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Cassava is the most cultivated and consumed root crop in the world. One of the major constraints to the cassava value chain is the short shelf life of cassava storage roots which is primarily due to the so-called post-harvest physiological deterioration (PPD). The identification of natural sources of PPD tolerance represents a key approach to mitigating PPD losses by generating farmer- and industry-preferred cassava cultivars with prolonged shelf life. In the present study, a PPD assessment method was developed to screen for PPD tolerance in the cassava germplasm. The proposed PPD assessment method displayed a reduced rate of microbial infection and allowed a rapid and homogenous development of typical PPD symptoms in the cassava storage roots. We successfully used the PPD assessment method in combination with an image-based PPD scoring method to identify and characterize PPD tolerance in 28 cassava cultivars from the Indonesian cassava germplasm. Our analysis showed a significant and positive correlation between PPD score and dry matter content (r = 0.589-0.664, p-value < 0.001). Analysis of additional root parameters showed a significant and positive correlation between PPD scores at 2 days post-harvest (dph) and root length (r = 0.388, p-value < 0.05). Our analysis identified at least 4 cultivars displaying a significantly delayed onset of PPD symptoms as compared to the other selected cultivars. The availability of cassava cultivars contrasting for tolerance to PPD will be particularly instrumental to understanding the molecular mechanisms associated with delayed PPD in cassava roots.
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Affiliation(s)
- Ima M Zainuddin
- Department of Biology, Plant Biotechnology, Eidgenössische Technische Hochschule (ETH) Zurich, Universitätstrasse 2, 8092, Zurich, Switzerland.
- Department of Biosystems, KU Leuven, Willem de Croylaan 42, Box 2455, 3001, Louvain, Belgium.
- Institut Teknologi Bandung (ITB), Jl. Ganesha 10, Bandung, 40132, Indonesia.
- Research Center for Genetics Engineering, National Research and Innovation Agency (BRIN), Jl. Raya Bogor Km. 46, Cibinong, 16911, Indonesia.
| | - Brieuc Lecart
- Plant Genetics, Gembloux Agro-Bio Tech, University of Liège, Passage Des Déportés 2, 5030, Gembloux, Belgium
| | - Enny Sudarmonowati
- Research Center for Genetics Engineering, National Research and Innovation Agency (BRIN), Jl. Raya Bogor Km. 46, Cibinong, 16911, Indonesia
| | - Hervé Vanderschuren
- Department of Biology, Plant Biotechnology, Eidgenössische Technische Hochschule (ETH) Zurich, Universitätstrasse 2, 8092, Zurich, Switzerland.
- Department of Biosystems, KU Leuven, Willem de Croylaan 42, Box 2455, 3001, Louvain, Belgium.
- Plant Genetics, Gembloux Agro-Bio Tech, University of Liège, Passage Des Déportés 2, 5030, Gembloux, Belgium.
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7
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Li R, Yuan S, Zhou Y, Wang S, Zhou Q, Ding Z, Wang Y, Yao Y, Liu J, Guo J. Comparative Transcriptome Profiling of Cassava Tuberous Roots in Response to Postharvest Physiological Deterioration. Int J Mol Sci 2022; 24:ijms24010246. [PMID: 36613690 PMCID: PMC9820078 DOI: 10.3390/ijms24010246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/15/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
Cassava is one of the most versatile tuberous-root crops on Earth. However, the postharvest storage properties of cassava tuberous root mean that it is perishable through a process known as postharvest physiological deterioration (PPD), which seriously affects its starch quality. Therefore, a comprehensive understanding of the transcriptional regulatory activity of cassava against the PPD response is necessary in order to extract key molecular mechanisms related to PPD tolerance. In this study, we found that RYG1 tuberous roots showed delayed PPD compared to those of SC8. In addition, RYG1 roots maintained a more stable cell wall structure after storage than those of SC8. The transcriptome changes in tuberous roots were analyzed for both RYG1 and SC8 after 21 days of storage (SR and SS) compared to fresh (FR and FS) by the RNA-Seq method. The total number of differentially expressed genes (DEGs) in the various comparisons of these four samples ranged from 68 to 3847. Of these, a total of 2008 co-DEGs in SR vs. SS were shared by either SR vs. FR or SS vs. FS. GO and KEGG enrichment analysis revealed that upregulated co-DEGs in SR vs. SS were mainly enriched in photosynthesis, protein processing, hormone and cutin, suberine and wax biosynthesis. By contrast, the downregulated co-DEGs were mainly related to cell wall organization, starch and sucrose metabolism, galactose metabolism, phenylpropanoid biosynthesis, diterpenoid biosynthesis, cysteine and methionine metabolism and flavonoid biosynthesis. The protein-protein interaction (PPI) networks of the co-DEGs showed a complex interaction of genes in different pathways, and 16 hub genes were characterized to have a degree in excess of 15, among which eight genes were associated with photosynthesis. These results provide new information for the study of cassava resistance to PPD and lay a foundation for the further molecular breeding of storage-tolerant cassava varieties.
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Affiliation(s)
- Ruimei Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China
- College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Shuai Yuan
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China
- College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Yangjiao Zhou
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China
- College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Shijia Wang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China
- College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Qin Zhou
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China
- College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Zhongping Ding
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China
- College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Yajie Wang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China
- College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Yuan Yao
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China
- College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Jiao Liu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China
- College of Tropical Crops, Hainan University, Haikou 570228, China
- Correspondence: (J.L.); (J.G.); Tel.: +86-898-6698-6031 (J.L.); +86-898-6696-2953 (J.G.)
| | - Jianchun Guo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China
- College of Tropical Crops, Hainan University, Haikou 570228, China
- Correspondence: (J.L.); (J.G.); Tel.: +86-898-6698-6031 (J.L.); +86-898-6696-2953 (J.G.)
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8
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Zierer W, Anjanappa RB, Lamm CE, Chang SH, Gruissem W, Sonnewald U. A promoter toolbox for tissue-specific expression supporting translational research in cassava ( Manihot esculenta). FRONTIERS IN PLANT SCIENCE 2022; 13:1042379. [PMID: 36605961 PMCID: PMC9807883 DOI: 10.3389/fpls.2022.1042379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 11/18/2022] [Indexed: 06/17/2023]
Abstract
There is an urgent need to stimulate agricultural output in many tropical and subtropical countries of the world to combat hunger and malnutrition. The starchy crop cassava (Manihot esculenta), growing even under sub-optimal conditions, is a key staple food in these regions, providing millions of people with food. Cassava biotechnology is an important technique benefiting agricultural progress, but successful implementation of many biotechnological concepts depends on the availability of the right spatiotemporal expression tools. Yet, well-characterized cassava promoters are scarce in the public domain. In this study, we investigate the promoter activity and tissue specificity of 24 different promoter elements in stably transformed cassava plants. We show that many of the investigated promoters, especially from other species, have surprisingly low activity and/or tissue specificity, but feature several promoter sequences that can drive tissue-specific expression in either autotrophic-, transport- or storage tissues. We especially highlight pAtCAB1, pMePsbR, and pSlRBCS2 as strong and specific source promoters, pAtSUC2, pMeSWEET1-like, and pMeSUS1 as valuable tools for phloem and phloem parenchyma expression, and pStB33, pMeGPT, pStGBSS1, as well as pStPatatin Class I, as strong and specific promoters for heterotrophic storage tissues. We hope that the provided information and sequences prove valuable to the cassava community by contributing to the successful implementation of biotechnological concepts aimed at the improvement of cassava nutritional value and productivity.
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Affiliation(s)
- Wolfgang Zierer
- Biochemistry, Department of Biology, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Ravi Bodampalli Anjanappa
- Plant Biotechnology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Christian Erwin Lamm
- Biochemistry, Department of Biology, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Shu-Heng Chang
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Wilhelm Gruissem
- Plant Biotechnology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Uwe Sonnewald
- Biochemistry, Department of Biology, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
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9
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Yan Y, Zhao S, Ye X, Tian L, Shang S, Tie W, Zeng L, Zeng L, Yang J, Li M, Wang Y, Xie Z, Hu W. Abscisic Acid Signaling in the Regulation of Postharvest Physiological Deterioration of Sliced Cassava Tuberous Roots. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:12830-12840. [PMID: 36183268 DOI: 10.1021/acs.jafc.2c05483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Phytohormone abscisic acid (ABA) influences the shelf life of fruit, vegetables, and tubers after harvest. However, little is known about the core signaling module involved in ABA's control of the postharvest physiological process. Exogenous ABA alleviated postharvest physiological deterioration (PPD) symptoms of sliced cassava tuberous roots, increased endogenous ABA levels, and reduced endogenous H2O2 content. The specific ABA signaling module during the PPD process was identified as MePYL6-MePP2C16-MeSnRK2.1-MebZIP5/34. MebZIP5/MebZIP34 directly binds to and activates the promoters of MeGRX6/MeMDAR1 through ABRE elements. Exogenous ABA significantly induced the expression of genes involved in this module, glutaredoxin content, and monodehydroascorbate reductase activity. We presented a hypothesis suggesting that MePYL6-MePP2C16-MeSnRK2.1-MebZIP5/34-MeGRX6/MeMDAR1 is involved in ABA-induced antioxidative capacity, thus alleviating PPD symptoms in cassava tuberous roots. The identification of the specific signaling module involved in ABA's control of PPD provides a basis and potential targets for extending the shelf life of cassava tuberous roots.
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Affiliation(s)
- Yan Yan
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, China
| | - Sihan Zhao
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, China
- School of Horticulture, School of Life Sciences, Hainan University, Haikou570228, China
| | - Xiaoxue Ye
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, China
- Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya572025, China
| | - Libo Tian
- School of Horticulture, School of Life Sciences, Hainan University, Haikou570228, China
| | - Sang Shang
- School of Horticulture, School of Life Sciences, Hainan University, Haikou570228, China
| | - Weiwei Tie
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, China
- Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya572025, China
| | - Liwang Zeng
- Institute of Scientific and Technical Information, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, China
| | - Liming Zeng
- Institute of Scientific and Technical Information, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, China
| | - Jinghao Yang
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, China
| | - Meiying Li
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, China
| | - Yu Wang
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, China
- Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya572025, China
| | - Zhengnan Xie
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, China
- Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya572025, China
| | - Wei Hu
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, China
- Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya572025, China
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10
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Abstract
Vanderschuren and Agusti introduce plant storage roots.
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Affiliation(s)
- Hervé Vanderschuren
- Tropical Crop Improvement Laboratory, Biosystems Department, KU Leuven, Belgium; Plant Genetics and Rhizosphere Processes Laboratory, TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech, Gembloux, Belgium.
| | - Javier Agusti
- IBMCP, Departament de Producció Vegetal, Universitat Politècnica de València, Valencia, Spain.
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11
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Lyons JB, Bredeson JV, Mansfeld BN, Bauchet GJ, Berry J, Boyher A, Mueller LA, Rokhsar DS, Bart RS. Current status and impending progress for cassava structural genomics. PLANT MOLECULAR BIOLOGY 2022; 109:177-191. [PMID: 33604743 PMCID: PMC9162999 DOI: 10.1007/s11103-020-01104-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 12/08/2020] [Indexed: 05/26/2023]
Abstract
We demystify recent advances in genome assemblies for the heterozygous staple crop cassava (Manihot esculenta), and highlight key cassava genomic resources. Cassava, Manihot esculenta Crantz, is a crop of societal and agricultural importance in tropical regions around the world. Genomics provides a platform for accelerated improvement of cassava's nutritional and agronomic traits, as well as for illuminating aspects of cassava's history including its path towards domestication. The highly heterozygous nature of the cassava genome is widely recognized. However, the full extent and context of this heterozygosity has been difficult to reveal because of technological limitations within genome sequencing. Only recently, with several new long-read sequencing technologies coming online, has the genomics community been able to tackle some similarly difficult genomes. In light of these recent advances, we provide this review to document the current status of the cassava genome and genomic resources and provide a perspective on what to look forward to in the coming years.
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Affiliation(s)
- Jessica B. Lyons
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720 USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720 USA
| | - Jessen V. Bredeson
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720 USA
| | - Ben N. Mansfeld
- Donald Danforth Plant Science Center (DDPSC), St. Louis, MO 63132 USA
| | | | - Jeffrey Berry
- Donald Danforth Plant Science Center (DDPSC), St. Louis, MO 63132 USA
| | - Adam Boyher
- Donald Danforth Plant Science Center (DDPSC), St. Louis, MO 63132 USA
| | | | - Daniel S. Rokhsar
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720 USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720 USA
- DOE Joint Genome Institute, Walnut Creek, CA USA
- Chan-Zuckerberg BioHub, 499 Illinois, San Francisco, CA 94158 USA
| | - Rebecca S. Bart
- Donald Danforth Plant Science Center (DDPSC), St. Louis, MO 63132 USA
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12
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Beyene G, Chauhan RD, Gehan J, Siritunga D, Taylor N. Cassava shrunken-2 homolog MeAPL3 determines storage root starch and dry matter content and modulates storage root postharvest physiological deterioration. PLANT MOLECULAR BIOLOGY 2022; 109:283-299. [PMID: 32270429 PMCID: PMC9163024 DOI: 10.1007/s11103-020-00995-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/05/2020] [Indexed: 05/05/2023]
Abstract
Among the five cassava isoforms (MeAPL1-MeAPL5), MeAPL3 is responsible for determining storage root starch content. Degree of storage root postharvest physiological deterioration (PPD) is directly correlated with starch content. AGPase is heterotetramer composed of two small and two large subunits each coded by small gene families in higher plants. Studies in cassava (Manihot esculenta) identified and characterized five isoforms of Manihot esculenta ADP-glucose pyrophosphorylase large subunit (MeAPL1-MeAPL5) and employed virus induced gene silencing (VIGS) to show that MeAPL3 is the key isoform responsible for starch and dry matter accumulation in cassava storage roots. Silencing of MeAPL3 in cassava through stable transgenic lines resulted in plants displaying significant reduction in storage root starch and dry matter content (DMC) and induced a distinct phenotype associated with increased petiole/stem angle, resulting in a droopy leaf phenotype. Plants with reduced starch and DMC also displayed significantly reduced or no postharvest physiological deterioration (PPD) compared to controls and lines with high DMC and starch content. This provides strong evidence for direct relationships between starch/dry matter content and its role in PPD and canopy architecture traits in cassava.
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Affiliation(s)
- Getu Beyene
- Donald Danforth Plant Science Center, St. Louis, MO, USA.
| | | | - Jackson Gehan
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Dimuth Siritunga
- Department of Biology, University of Puerto Rico, Mayaguez, Puerto Rico
| | - Nigel Taylor
- Donald Danforth Plant Science Center, St. Louis, MO, USA
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13
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Wu X, Xu J, Ma Q, Ahmed S, Lu X, Ling E, Zhang P. Lysozyme inhibits postharvest physiological deterioration of cassava. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:621-624. [PMID: 35195347 DOI: 10.1111/jipb.13219] [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: 10/20/2021] [Accepted: 12/29/2021] [Indexed: 05/24/2023]
Abstract
After harvest, cassava (Manihot esculenta Crantz) storage roots undergo rapid postharvest physiological deterioration, producing blue-brown discoloration in the vasculature due to the production of polyphenolics (mainly quinones and coumarins) by enzymes such as polyphenol oxidase (PPO). Here, we report the application of hen egg-white lysozyme (HEWL), a natural PPO inhibitor, in transgenic cassava to repress the symptoms of postharvest physiological deterioration. The HEWL-expressing transgenic plants had lower levels of the two main cassava coumarins tested, scopoletin and scopolin, compared with wild type. HEWL-expressing cassava also showed increased tolerance of oxidative stress. Overall, the lysozyme-PPO system proved to be functional in plants for repressing PPO-mediated commercial product browning.
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Affiliation(s)
- Xiaoyun Wu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, The Chinese Academy of Science, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jia Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, The Chinese Academy of Science, Shanghai, 200032, China
| | - Qiuxiang Ma
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, The Chinese Academy of Science, Shanghai, 200032, China
| | - Sulaiman Ahmed
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, The Chinese Academy of Science, Shanghai, 200032, China
| | - Xinlu Lu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, The Chinese Academy of Science, Shanghai, 200032, China
| | - Erjun Ling
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, The Chinese Academy of Science, Shanghai, 200032, China
| | - Peng Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, The Chinese Academy of Science, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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14
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Mehta D, Scandola S, Uhrig RG. BoxCar and Library-Free Data-Independent Acquisition Substantially Improve the Depth, Range, and Completeness of Label-Free Quantitative Proteomics. Anal Chem 2022; 94:793-802. [DOI: 10.1021/acs.analchem.1c03338] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Devang Mehta
- Department of Biological Sciences, University of Alberta, Edmonton T6G 2E9, Alberta, Canada
| | - Sabine Scandola
- Department of Biological Sciences, University of Alberta, Edmonton T6G 2E9, Alberta, Canada
| | - R. Glen Uhrig
- Department of Biological Sciences, University of Alberta, Edmonton T6G 2E9, Alberta, Canada
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15
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Ramulifho E, Rey MEC. Proteome Mapping of South African Cassava Mosaic Virus-Infected Susceptible and Tolerant Landraces of Cassava. Proteomes 2021; 9:41. [PMID: 34842800 PMCID: PMC8628908 DOI: 10.3390/proteomes9040041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 11/25/2022] Open
Abstract
The production of cassava is threatened by the geminivirus South African cassava mosaic virus (SACMV), which causes cassava mosaic disease. Cassava landrace TME3 shows tolerance to SACMV, while T200 is highly susceptible. This study aimed to identify the leaf proteome involved in anti-viral defence. Liquid chromatography mass spectrometry (LC-MS) identified 2682 (54 differentially expressed) and 2817 (206 differentially expressed) proteins in both landraces at systemic infection (32 days post infection) and symptom recovery (67 days post infection), respectively. Differences in the number of differentially expressed proteins (DEPs) between the two landraces were observed. Gene ontology analysis showed that defence-associated pathways such as the chloroplast, proteasome, and ribosome were overrepresented at 67 days post infection (dpi) in SACMV-tolerant TME3. At 67 dpi, a high percentage (56%) of over-expressed proteins were localized in the chloroplast in TME3 compared to T200 (31% under-expressed), proposing that chloroplast proteins play a role in tolerance in TME3. Ribosomal_L7Ae domain-containing protein (Manes.12G139100) was over-expressed uniquely in TME3 at 67 dpi and interacts with the ribosomal protein Sac52 (RPL10). RPL10 is a known key player in the NIK1-mediated effector triggered immunity (ETI) response to geminivirus infection, indicating a possible role for Sac52 in SACMV recovery in TME3. In conclusion, differential protein expression responses in TME3 and T200 may be key to unravel tolerance to CMD.
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Affiliation(s)
- Elelwani Ramulifho
- Plant Biotechnology Laboratory, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2001, South Africa;
- Germplasm Development, Agricultural Research Council-Small Grain Institute, Bethlehem 9700, South Africa
| | - Marie Emma Christine Rey
- Plant Biotechnology Laboratory, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2001, South Africa;
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16
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Wu MX, Zou Y, Yu YH, Chen BX, Zheng QW, Ye ZW, Wei T, Ye SQ, Guo LQ, Lin JF. Comparative transcriptome and proteome provide new insights into the regulatory mechanisms of the postharvest deterioration of Pleurotus tuoliensis fruitbodies during storage. Food Res Int 2021; 147:110540. [PMID: 34399517 DOI: 10.1016/j.foodres.2021.110540] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 06/05/2021] [Accepted: 06/14/2021] [Indexed: 10/21/2022]
Abstract
The Pleurotus tuoliensis (Pt), a precious edible mushroom with high economic value, is widely popular for its rich nutrition and meaty texture. However, rapid postharvest deterioration depreciates the commercial value of Pt and severely restricts its marketing. By RNA-Seq transcriptomic and TMT-MS MS proteomic, we study the regulatory mechanisms of the postharvest storage of Pt fruitbodies at 25 ℃ for 0, 38, and 76 h (these three-time points recorded as groups A, B, and C, respectively). 2,008 DEGs (Differentially expressed genes) were identified, and all DEGs shared 265 factors with all DEPs (Differentially expressed proteins). Jointly, the DEGs and DEPs of two-omics showed that the category of the metabolic process contained the most DEGs and DEPs in the biological process by GO (Gene Ontology) classification. The top 17 KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways with the highest sum of DEG and DEP numbers in groups B/A (38 h vs. 0 h) and C/A (76 h vs. 0 h) and pathways closely related to energy metabolism were selected for analysis and discussion. Actively expression of CAZymes (Carbohydrate active enzymes), represented by laccase, chitinase, and β-glucanase, directly leads to the softening of fruitbodies. The transcription factor Rlm1 of 1,3-β-glucan synthase attracted attention with a significant down-regulation of gene levels in the C/A group. Laccase also contributes, together with phenylalanine ammonia-lyase (PAL), to the discoloration reaction in the first 76 h of the fruitbodies. Significant expression of several crucial enzymes for EMP (Glycolysis), Fatty acid degradation, and Valine, leucine and isoleucine degradation at the gene or protein level supply substantial amounts of acetyl-CoA to the TCA cycle. Citrate synthase (CS), isocitrate dehydrogenase (ICDH), and three mitochondrial respiratory complexes intensify respiration and produce high levels of ROS (Reactive oxygen species) by significant up-regulation. In the ROS scavenging system, only Mn-SOD was significantly up-regulated at the gene level and was probably interacted with Hsp60 (Heat shock protein 60), which was significantly up-regulated at the protein level, to play a dominant role in antioxidation. Three types of stresses - cell wall stress, starvation, and oxidative stress - were suffered by Pt fruitbodies postharvest, resulting in cell cycle arrest and gene expression disorder.
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Affiliation(s)
- Mu-Xiu Wu
- College of Food Science, South China Agricultural University, Guangzhou 510642, China; Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou 510642, China
| | - Yuan Zou
- College of Food Science, South China Agricultural University, Guangzhou 510642, China; Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou 510642, China
| | - Ying-Hao Yu
- College of Food Science, South China Agricultural University, Guangzhou 510642, China; Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou 510642, China
| | - Bai-Xiong Chen
- College of Food Science, South China Agricultural University, Guangzhou 510642, China; Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou 510642, China
| | - Qian-Wang Zheng
- College of Food Science, South China Agricultural University, Guangzhou 510642, China; Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou 510642, China
| | - Zhi-Wei Ye
- College of Food Science, South China Agricultural University, Guangzhou 510642, China; Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou 510642, China
| | - Tao Wei
- College of Food Science, South China Agricultural University, Guangzhou 510642, China; Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou 510642, China
| | - Si-Qiang Ye
- College of Food Science, South China Agricultural University, Guangzhou 510642, China; Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou 510642, China
| | - Li-Qiong Guo
- College of Food Science, South China Agricultural University, Guangzhou 510642, China; Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou 510642, China.
| | - Jun-Fang Lin
- College of Food Science, South China Agricultural University, Guangzhou 510642, China; Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou 510642, China.
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17
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Li C, Dong G, Bian M, Liu X, Gong J, Hao J, Wang W, Li K, Ou W, Xia T. Brewing rich 2-phenylethanol beer from cassava and its producing metabolisms in yeast. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2021; 101:4050-4058. [PMID: 33349937 DOI: 10.1002/jsfa.11040] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 12/08/2020] [Accepted: 11/25/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND Cassava is rich in nutrition and has high edible value, but the development of the cassava industry is limited by the traditional low added value processing and utilization mode. In this study, cassava tuber was used as beer adjunct to develop a complete set of fermentation technology for manufacturing cassava beer. RESULTS The activities of transaminase, phenylpyruvate decarboxylase and dehydrogenase in 2-phenylethanol Ehrlich biosynthesis pathway of Saccharomyces cerevisiae were higher in cassava beer than that of malt beer. Aminotransferase ARO9 gene and phenylpyruvate decarboxylase ARO10 gene were up-regulated in the late stage of fermentation, which indicated that they were the main regulated genes of 2-phenylethanol Ehrlich pathway with phenylalanine as substrate in cassava beer preparation. CONCLUSIONS Compared with traditional wheat beer, cassava beer was similar in the content of nutrition elements, diacetyl, total acid, alcohol and carbon dioxide, but has the characteristics of fresh fragrance and better taste. The hydrocyanic acid contained in cassava root tubes was catabolized during fermentation and compliant with the safety standard of beverage. Further study found that the content of 2-phenylethanol in cassava beer increased significantly, which gave cassava beer a unique elegant and delicate rose flavor. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Can Li
- School of Bioengineering, Qilu University of Technology, Jinan, China
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Jinan, China
| | - Geyu Dong
- School of Bioengineering, Qilu University of Technology, Jinan, China
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Jinan, China
| | - Meng Bian
- School of Bioengineering, Qilu University of Technology, Jinan, China
| | - Xinli Liu
- School of Bioengineering, Qilu University of Technology, Jinan, China
| | - Jing Gong
- TsingTao Brewery (Jinan) Co. LTD, Jinan, China
| | - Jingxin Hao
- TsingTao Brewery (Jinan) Co. LTD, Jinan, China
| | - Wenquan Wang
- College of Tropical Crops, Hainan University, Haiko, China
| | - Kaimian Li
- Tropical Crops Genetics Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haiko, China
| | - Wenjun Ou
- Tropical Crops Genetics Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haiko, China
| | - Tao Xia
- School of Bioengineering, Qilu University of Technology, Jinan, China
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Jinan, China
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18
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Rüscher D, Corral JM, Carluccio AV, Klemens PAW, Gisel A, Stavolone L, Neuhaus HE, Ludewig F, Sonnewald U, Zierer W. Auxin signaling and vascular cambium formation enable storage metabolism in cassava tuberous roots. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:3688-3703. [PMID: 33712830 PMCID: PMC8096603 DOI: 10.1093/jxb/erab106] [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] [Received: 11/10/2020] [Accepted: 03/04/2021] [Indexed: 05/10/2023]
Abstract
Cassava storage roots are among the most important root crops worldwide, and represent one of the most consumed staple foods in sub-Saharan Africa. The vegetatively propagated tropical shrub can form many starchy tuberous roots from its stem. These storage roots are formed through the activation of secondary root growth processes. However, the underlying genetic regulation of storage root development is largely unknown. Here we report distinct structural and transcriptional changes occurring during the early phases of storage root development. A pronounced increase in auxin-related transcripts and the transcriptional activation of secondary growth factors, as well as a decrease in gibberellin-related transcripts were observed during the early stages of secondary root growth. This was accompanied by increased cell wall biosynthesis, most notably increased during the initial xylem expansion within the root vasculature. Starch storage metabolism was activated only after the formation of the vascular cambium. The formation of non-lignified xylem parenchyma cells and the activation of starch storage metabolism coincided with increased expression of the KNOX/BEL genes KNAT1, PENNYWISE, and POUND-FOOLISH, indicating their importance for proper xylem parenchyma function.
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Affiliation(s)
- David Rüscher
- Friedrich-Alexander-University Erlangen-Nuremberg, Department of Biology, Division of Biochemistry, Staudtstrasse 5, Erlangen, Germany
| | - José María Corral
- Friedrich-Alexander-University Erlangen-Nuremberg, Department of Biology, Division of Biochemistry, Staudtstrasse 5, Erlangen, Germany
| | - Anna Vittoria Carluccio
- International Institute for Tropical Agriculture, Ibadan, Oyo State, Nigeria
- Institute for Sustainable Plant Protection, CNR, Bari, Italy
| | - Patrick A W Klemens
- Technical University Kaiserslautern, Department of Biology, Division of Plant Physiology, Erwin-Schrödinger-Str. 22, Kaiserslautern, Germany
| | - Andreas Gisel
- International Institute for Tropical Agriculture, Ibadan, Oyo State, Nigeria
- Institute for Biomedical Technologies, CNR, Bari, Italy
| | - Livia Stavolone
- International Institute for Tropical Agriculture, Ibadan, Oyo State, Nigeria
- Institute for Sustainable Plant Protection, CNR, Bari, Italy
| | - H Ekkehard Neuhaus
- Technical University Kaiserslautern, Department of Biology, Division of Plant Physiology, Erwin-Schrödinger-Str. 22, Kaiserslautern, Germany
| | - Frank Ludewig
- Friedrich-Alexander-University Erlangen-Nuremberg, Department of Biology, Division of Biochemistry, Staudtstrasse 5, Erlangen, Germany
- Present address: KWS Saat SE, Grimsehlstraße 31, D-37574 Einbeck, Germany
| | - Uwe Sonnewald
- Friedrich-Alexander-University Erlangen-Nuremberg, Department of Biology, Division of Biochemistry, Staudtstrasse 5, Erlangen, Germany
| | - Wolfgang Zierer
- Friedrich-Alexander-University Erlangen-Nuremberg, Department of Biology, Division of Biochemistry, Staudtstrasse 5, Erlangen, Germany
- Correspondence:
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Rüscher D, Corral JM, Carluccio AV, Klemens PAW, Gisel A, Stavolone L, Neuhaus HE, Ludewig F, Sonnewald U, Zierer W. Auxin signaling and vascular cambium formation enable storage metabolism in cassava tuberous roots. JOURNAL OF EXPERIMENTAL BOTANY 2021. [PMID: 33712830 DOI: 10.5061/dryad.0cfxpnw0t] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Cassava storage roots are among the most important root crops worldwide, and represent one of the most consumed staple foods in sub-Saharan Africa. The vegetatively propagated tropical shrub can form many starchy tuberous roots from its stem. These storage roots are formed through the activation of secondary root growth processes. However, the underlying genetic regulation of storage root development is largely unknown. Here we report distinct structural and transcriptional changes occurring during the early phases of storage root development. A pronounced increase in auxin-related transcripts and the transcriptional activation of secondary growth factors, as well as a decrease in gibberellin-related transcripts were observed during the early stages of secondary root growth. This was accompanied by increased cell wall biosynthesis, most notably increased during the initial xylem expansion within the root vasculature. Starch storage metabolism was activated only after the formation of the vascular cambium. The formation of non-lignified xylem parenchyma cells and the activation of starch storage metabolism coincided with increased expression of the KNOX/BEL genes KNAT1, PENNYWISE, and POUND-FOOLISH, indicating their importance for proper xylem parenchyma function.
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Affiliation(s)
- David Rüscher
- Friedrich-Alexander-University Erlangen-Nuremberg, Department of Biology, Division of Biochemistry, Staudtstrasse 5, Erlangen, Germany
| | - José María Corral
- Friedrich-Alexander-University Erlangen-Nuremberg, Department of Biology, Division of Biochemistry, Staudtstrasse 5, Erlangen, Germany
| | - Anna Vittoria Carluccio
- International Institute for Tropical Agriculture, Ibadan, Oyo State, Nigeria
- Institute for Sustainable Plant Protection, CNR, Bari, Italy
| | - Patrick A W Klemens
- Technical University Kaiserslautern, Department of Biology, Division of Plant Physiology, Erwin-Schrödinger-Str. 22, Kaiserslautern, Germany
| | - Andreas Gisel
- International Institute for Tropical Agriculture, Ibadan, Oyo State, Nigeria
- Institute for Biomedical Technologies, CNR, Bari, Italy
| | - Livia Stavolone
- International Institute for Tropical Agriculture, Ibadan, Oyo State, Nigeria
- Institute for Sustainable Plant Protection, CNR, Bari, Italy
| | - H Ekkehard Neuhaus
- Technical University Kaiserslautern, Department of Biology, Division of Plant Physiology, Erwin-Schrödinger-Str. 22, Kaiserslautern, Germany
| | - Frank Ludewig
- Friedrich-Alexander-University Erlangen-Nuremberg, Department of Biology, Division of Biochemistry, Staudtstrasse 5, Erlangen, Germany
| | - Uwe Sonnewald
- Friedrich-Alexander-University Erlangen-Nuremberg, Department of Biology, Division of Biochemistry, Staudtstrasse 5, Erlangen, Germany
| | - Wolfgang Zierer
- Friedrich-Alexander-University Erlangen-Nuremberg, Department of Biology, Division of Biochemistry, Staudtstrasse 5, Erlangen, Germany
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Transcriptome integrated metabolic modeling of carbon assimilation underlying storage root development in cassava. Sci Rep 2021; 11:8758. [PMID: 33888810 PMCID: PMC8062692 DOI: 10.1038/s41598-021-88129-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 04/08/2021] [Indexed: 02/02/2023] Open
Abstract
The existing genome-scale metabolic model of carbon metabolism in cassava storage roots, rMeCBM, has proven particularly resourceful in exploring the metabolic basis for the phenotypic differences between high and low-yield cassava cultivars. However, experimental validation of predicted metabolic fluxes by carbon labeling is quite challenging. Here, we incorporated gene expression data of developing storage roots into the basic flux-balance model to minimize infeasible metabolic fluxes, denoted as rMeCBMx, thereby improving the plausibility of the simulation and predictive power. Three different conceptual algorithms, GIMME, E-Flux, and HPCOF were evaluated. The rMeCBMx-HPCOF model outperformed others in predicting carbon fluxes in the metabolism of storage roots and, in particular, was highly consistent with transcriptome of high-yield cultivars. The flux prediction was improved through the oxidative pentose phosphate pathway in cytosol, as has been reported in various studies on root metabolism, but hardly captured by simple FBA models. Moreover, the presence of fluxes through cytosolic glycolysis and alanine biosynthesis pathways were predicted with high consistency with gene expression levels. This study sheds light on the importance of prediction power in the modeling of complex plant metabolism. Integration of multi-omics data would further help mitigate the ill-posed problem of constraint-based modeling, allowing more realistic simulation.
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Abstract
Virus-induced gene silencing (VIGS) is an efficient, low-cost, and rapid functional validation tool for candidate genes in planta. The VIGS approach is particularly suitable to perform reverse genetics studies in crop species. Here we present a detailed method to perform VIGS in cassava, from target gene fragment to agroinoculation and VIGS quantitation.
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Zheng Y, Zhao Y, Xue S, Wang W, Wang Y, Cao Z, Yang H, Li S. Feeding Value Assessment of Substituting Cassava ( Manihot esculenta) Residue for Concentrate of Dairy Cows Using an In Vitro Gas Test. Animals (Basel) 2021; 11:ani11020307. [PMID: 33530353 PMCID: PMC7912291 DOI: 10.3390/ani11020307] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/14/2021] [Accepted: 01/22/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Cassava (Manihot esculenta) residue is a by-product of cassava processing. Although it contains residual nutrients, it is highly perishable. Decayed cassava residue pollutes the environment and leads to major losses in feed. If cassava residue could be utilized as a dairy cow feedstuff, these problems could be solved. Our study showed that cassava residue is a good alternative to concentrate in the feed of Holstein cows. Furthermore, our data demonstrate the efficacy of the application of cassava residue as a feed for dairy cows and could help solve the shortage of feed resources in China. Abstract The feeding value of replacing concentrate with cassava (Manihot esculenta) residue in the feed of Holstein cows was confirmed using an in vitro gas test. The treatments consisted of 0% (control, CON), 5%, 10%, 15%, 20%, 25%, and 30% inclusion of cassava residue in fermentation culture medium composed of buffer solution (50 mL) and filtrated rumen fluid (25 mL). The parameters analyzed included the kinetics of gas production and fermentation indexes. Forty-eight hours later, there were no significant differences on in vitro dry matter disappearance (IVDMD), pH, and microbial crude protein (MCP) content among treatments (p > 0.05). However, the “cumulative gas production at 48 h” (GP48), the “asymptotic gas production” (A), and the “maximum gas production rate” (RmaxG) all increased linearly or quadratically (p < 0.01). The GP48 was significantly higher in the 25% treatment compared to the other treatments, except for the 30% (p < 0.01). The A was significantly larger in the 25% treatment compared to the other treatments, except for the 20% and 30% (p < 0.01). The RmaxG was distinctly larger in the 25% treatment compared to other treatments (p < 0.01); moreover, the “time at which RmaxG is reached” (TRmaxG) and the “time at which the maximum rate of substrate degradation is reached” (TRmaxS) were significantly higher in the 25% treatment than the CON, 20%, and 30% treatments (p < 0.01). Additionally, the content of ammonia-N (NH3-N) in all treatments showed linearly and quadratically decreases (p < 0.01), whereas total volatile fatty acid (VFA), iso-butyrate, butyrate, and iso-valerate contents changed quadratically (p = 0.02, p = 0.05, p = 0.01, and p = 0.02, respectively); all of these values peaked in the 25% treatment. In summary, the 25% treatment was associated with more in vitro gas and VFA production, indicating that this cassava residue inclusion level may be used to replace concentrate in the feed of Holstein cows. However, these results need to be verified in vivo.
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Affiliation(s)
| | | | | | | | | | | | | | - Shengli Li
- Correspondence: ; Tel.: +86-010-6273-1254
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23
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Elegba W, McCallum E, Gruissem W, Vanderschuren H. Efficient Genetic Transformation and Regeneration of a Farmer-Preferred Cassava Cultivar From Ghana. FRONTIERS IN PLANT SCIENCE 2021; 12:668042. [PMID: 34140963 PMCID: PMC8204248 DOI: 10.3389/fpls.2021.668042] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/22/2021] [Indexed: 05/04/2023]
Abstract
Cassava is an important staple crop that provides food and income for about 700 million Africans. Cassava productivity in Africa is limited by viral diseases, mainly cassava mosaic disease (CMD) and cassava brown streak disease (CBSD). Genetic barriers such as high heterozygosity, allopolyploidy, poor seed set, and irregular flowering constrain the development of virus-resistant cassava varieties via conventional breeding. Genetic transformation represents a valuable tool to circumvent several challenges associated with the development of virus resistance and other valuable agronomic traits in cassava. The implementation of genetic transformation in many local African cultivars is limited either by the difficulty to produce friable embryogenic callus (FEC), low transformation, and/or regeneration efficiencies. Here, we report the successful induction of organized embryogenic structures (OES) in 11 farmer-preferred cultivars locally grown in Ghana. The production of high quality FEC from one local cultivar, ADI 001, facilitated its genetic transformation with high shoot regeneration and selection efficiency, comparable to the model cassava cultivar 60444. We show that using flow cytometry for analysis of nuclear ploidy in FEC tissues prior to genetic transformation ensures the selection of genetically uniform FEC tissue for transformation. The high percentage of single insertion events in transgenic lines indicates the suitability of the ADI 001 cultivar for the introduction of virus resistance and other useful agronomic traits into the farmer-preferred cassava germplasm in Ghana and Africa.
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Affiliation(s)
- Wilfred Elegba
- Plant Biotechnology, Institute of Molecular Plant Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
- Biotechnology and Nuclear Agriculture Research Institute, GAEC, Legon, Ghana
- *Correspondence: Wilfred Elegba, ;
| | - Emily McCallum
- Plant Biotechnology, Institute of Molecular Plant Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Wilhelm Gruissem
- Plant Biotechnology, Institute of Molecular Plant Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
- Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Hervé Vanderschuren
- Plant Biotechnology, Institute of Molecular Plant Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, Leuven, Belgium
- Plant Genetics, TERRA Research and Teaching Centre, Gembloux Agro BioTech, University of Liège, Gembloux, Belgium
- Hervé Vanderschuren,
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Zeng J, Wu C, Wang C, Liao F, Mo J, Ding Z, Tie W, Yan Y, Hu W. Genomic analyses of heat stress transcription factors (HSFs) in simulated drought stress response and storage root deterioration after harvest in cassava. Mol Biol Rep 2020; 47:5997-6007. [PMID: 32710389 DOI: 10.1007/s11033-020-05673-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/17/2020] [Indexed: 12/11/2022]
Abstract
Heat shock factors (HSFs) play crucial roles in various plant stress responses. However, the current knowledge about HSFs in cassava, an important crop, is still insufficient. In this research, we identified 32 cassava HSF genes (MeHSFs) and clustered them into three groups (A, B, C) based on phylogenetic analysis and structural characteristics. Conserved motif analyses showed that MeHSFs display domains characteristic to HSF transcription factors. Gene structure analyses suggested that 29 MeHSFs contained only two exons. All identified 32 cassava MeHSFs were distributed on 13 chromosomes. Their expression profiles revealed that the different MeHSFs were expressed differentially in different tissues, most high expression genes belonged to group A. The similar MeHSFs were up-regulated after treatment with both PEG and abscisic acid (ABA), which implied that these MeHSFs may participate in resistance to simulated drought stress associated with the ABA signaling pathway. In addition, several MeHSFs were induced during postharvest physiological deterioration (PPD) in cassava. Our results provided basic but important knowledge for future gene function analysis of MeHSFs toward efforts in improving tolerance to abiotic stress and PPD in cassava.
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Affiliation(s)
- Jian Zeng
- Henry Fok College of Biology and Agriculture, Shaoguan University, Shaoguan, China.,Shaoguan Engineering Research Center for Aromatic Plants, Shaoguan, China
| | - Chunlai Wu
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Cheng Wang
- Yue Bei People's Hospital, Shaoguan, China
| | - Fengfeng Liao
- Henry Fok College of Biology and Agriculture, Shaoguan University, Shaoguan, China
| | - Jiajia Mo
- Henry Fok College of Biology and Agriculture, Shaoguan University, Shaoguan, China
| | - Zehong Ding
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.,Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Weiwei Tie
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.,Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yan Yan
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.,Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Wei Hu
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China. .,Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
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Thanasomboon R, Kalapanulak S, Netrphan S, Saithong T. Exploring dynamic protein-protein interactions in cassava through the integrative interactome network. Sci Rep 2020; 10:6510. [PMID: 32300157 PMCID: PMC7162878 DOI: 10.1038/s41598-020-63536-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 04/01/2020] [Indexed: 01/01/2023] Open
Abstract
Protein-protein interactions (PPIs) play an essential role in cellular regulatory processes. Despite, in-depth studies to uncover the mystery of PPI-mediated regulations are still lacking. Here, an integrative interactome network (MePPI-Ux) was obtained by incorporating expression data into the improved genome-scale interactome network of cassava (MePPI-U). The MePPI-U, constructed by both interolog- and domain-based approaches, contained 3,638,916 interactions and 24,590 proteins (59% of proteins in the cassava AM560 genome version 6). After incorporating expression data as information of state, the MePPI-U rewired to represent condition-dependent PPIs (MePPI-Ux), enabling us to envisage dynamic PPIs (DPINs) that occur at specific conditions. The MePPI-Ux was exploited to demonstrate timely PPIs of cassava under various conditions, namely drought stress, brown streak virus (CBSV) infection, and starch biosynthesis in leaf/root tissues. MePPI-Uxdrought and MePPI-UxCBSV suggested involved PPIs in response to stress. MePPI-UxSB,leaf and MePPI-UxSB,root suggested the involvement of interactions among transcription factor proteins in modulating how leaf or root starch is synthesized. These findings deepened our knowledge of the regulatory roles of PPIs in cassava and would undeniably assist targeted breeding efforts to improve starch quality and quantity.
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Affiliation(s)
- Ratana Thanasomboon
- Biological Engineering Program, Faculty of Engineering, King Mongkut's University of Technology Thonburi, Bangkok, 10140, Thailand.,Center for Agricultural Systems Biology, Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi (Bang Khun Thian), Bangkok, 10150, Thailand
| | - Saowalak Kalapanulak
- Center for Agricultural Systems Biology, Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi (Bang Khun Thian), Bangkok, 10150, Thailand.,Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (Bang Khun Thian), Bangkok, 10150, Thailand
| | - Supatcharee Netrphan
- National Center for Genetic Engineering and Biotechnology, Pathum Thani, 12120, Thailand
| | - Treenut Saithong
- Center for Agricultural Systems Biology, Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi (Bang Khun Thian), Bangkok, 10150, Thailand. .,Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (Bang Khun Thian), Bangkok, 10150, Thailand.
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26
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Shan Z, Luo X, Wu M, Wei L, Fan Z, Zhu Y. Genome-wide identification and expression of GRAS gene family members in cassava. BMC PLANT BIOLOGY 2020; 20:46. [PMID: 31996133 PMCID: PMC6990482 DOI: 10.1186/s12870-020-2242-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 01/08/2020] [Indexed: 05/28/2023]
Abstract
BACKGROUND Cassava is highly tolerant to stressful conditions, especially drought stress conditions; however, the mechanisms underlying this tolerance are poorly understood. The GRAS gene family is a large family of transcription factors that are involved in regulating the growth, development, and stress responses of plants. Currently, GRAS transcription factors have not been systematically studied in cassava, which is the sixth most important crop in the world. RESULTS Seventy-seven MeGRAS genes were identified from the cassava genome database. Phylogenetic analysis revealed that the MeGRAS proteins could be divided into 14 subfamilies. The gene structure and motif compositions of the proteins were considerably conserved within the same subfamily. Duplication events, particularly segmental duplication, were identified as the main driving force for GRAS gene expansion in cassava. Global expression analysis revealed that MeGRAS genes exhibited similar or distinct expression profiles within different tissues among different varieties. Moreover, qRT-PCR analysis revealed the expression patterns of MeGRAS genes in response to abiotic stress (drought, salt, cold, and H2O2), and the results suggest that these genes may have multiple functions. CONCLUSION This study is the first to provide comprehensive information on GRAS gene family members in cassava. The data will increase our understanding of both the molecular basis and the effects of GRAS genes. In addition, the results will contribute further to identifying the responses to various environmental conditions and provide insights into the potential functions of GRAS genes.
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Affiliation(s)
- Zhongying Shan
- Agricultural College, Guangxi University, Nanning, 530005 China
- College of Ecology and Garden Architecture, Dezhou University, Dezhou, 253023 China
| | - Xinglu Luo
- Agricultural College, Guangxi University, Nanning, 530005 China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Nanning, 530004 China
| | - Meiyan Wu
- Agricultural College, Guangxi University, Nanning, 530005 China
| | - Limei Wei
- Agricultural College, Guangxi University, Nanning, 530005 China
| | - Zhupeng Fan
- Agricultural College, Guangxi University, Nanning, 530005 China
| | - Yanmei Zhu
- Agricultural College, Guangxi University, Nanning, 530005 China
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27
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Liu G, Li B, Wang Y, Wei B, He C, Liu D, Shi H. Novel Role of Ethanol in Delaying Postharvest Physiological Deterioration and Keeping Quality in Cassava. FOOD BIOPROCESS TECH 2019. [DOI: 10.1007/s11947-019-02330-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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28
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Wu C, Ding X, Ding Z, Tie W, Yan Y, Wang Y, Yang H, Hu W. The Class III Peroxidase (POD) Gene Family in Cassava: Identification, Phylogeny, Duplication, and Expression. Int J Mol Sci 2019; 20:ijms20112730. [PMID: 31163686 PMCID: PMC6600411 DOI: 10.3390/ijms20112730] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 05/30/2019] [Accepted: 05/31/2019] [Indexed: 01/27/2023] Open
Abstract
The class III peroxidase (POD) enzymes participate in plant development, hormone signaling, and stress responses. However, little is known about the POD family in cassava. Here, we identified 91 cassava POD genes (MePODs) and classified them into six subgroups using phylogenetic analysis. Conserved motif analysis demonstrated that all MePOD proteins have typical peroxidase domains, and gene structure analysis showed that MePOD genes have between one and nine exons. Duplication pattern analysis suggests that tandem duplication has played a role in MePOD gene expansion. Comprehensive transcriptomic analysis revealed that MePOD genes in cassava are involved in the drought response and postharvest physiological deterioration. Several MePODs underwent transcriptional changes after various stresses and related signaling treatments were applied. In sum, we characterized the POD family in cassava and uncovered the transcriptional control of POD genes in response to various stresses and postharvest physiological deterioration conditions. These results can be used to identify potential target genes for improving the stress tolerance of cassava crops.
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Affiliation(s)
- Chunlai Wu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Xupo Ding
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Zehong Ding
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Weiwei Tie
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Yan Yan
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Yu Wang
- Beijing Commerce and Trade School, Beijing 100162, China.
| | - Hai Yang
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Wei Hu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
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29
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An F, Baker MR, Qin Y, Chen S, Li QX. Relevance of Class I α-Mannosidases to Cassava Postharvest Physiological Deterioration. ACS OMEGA 2019; 4:8739-8746. [PMID: 31459963 PMCID: PMC6648743 DOI: 10.1021/acsomega.8b03558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 05/09/2019] [Indexed: 05/27/2023]
Abstract
Class I α-mannosidases (MNSs) play important roles in protein N-glycosylation. However, no data are currently available about MNSs in cassava (Manihot esculenta), of which the functions are therefore not known, particularly in relevance to postharvest physiological deterioration (PPD). A total of seven genes were identified from the cassava genome in the present study. Two (MeMNS2 and MeMNS6) of the seven genes may be pseudogenes, as indicated by sequence alignment and exon-intron organizations. Five MNSs could be classified into three subfamilies. Tissue-specific expression analysis revealed that MNS genes have distinct expression patterns in different tissues between sugar cassava and cultivated cassava varieties, indicating their functional diversity. A PPD response and defense model was proposed based on the transcription data of MNSs and genes involved in reactive oxygen species, signal transduction, and cell wall remodeling. The findings help in the understanding of PPD responses in cassava.
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Affiliation(s)
- Feifei An
- Tropical
Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural
Sciences/Key Laboratory of Ministry of Agriculture for Germplasm Resources
Conservation and Utilization of Cassava, Danzhou, Hainan 571737, China
- Department
of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii 96822, United States
| | - Margaret R. Baker
- Department
of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii 96822, United States
| | - Yuling Qin
- Tropical
Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural
Sciences/Key Laboratory of Ministry of Agriculture for Germplasm Resources
Conservation and Utilization of Cassava, Danzhou, Hainan 571737, China
| | - Songbi Chen
- Tropical
Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural
Sciences/Key Laboratory of Ministry of Agriculture for Germplasm Resources
Conservation and Utilization of Cassava, Danzhou, Hainan 571737, China
| | - Qing X. Li
- Department
of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii 96822, United States
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Zhao G, Ding LL, Yao Y, Cao Y, Pan ZH, Kong DH. Extracellular Proteome Analysis and Flavor Formation During Soy Sauce Fermentation. Front Microbiol 2018; 9:1872. [PMID: 30158911 PMCID: PMC6104182 DOI: 10.3389/fmicb.2018.01872] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 07/25/2018] [Indexed: 01/07/2023] Open
Abstract
Aspergillus oryzae is an excellent strain for soy sauce fermentation because of its complicated enzyme system, especially protease. The aim of this study was to investigate the key enzymes and flavors during soy sauce fermentation, and a comparative assessment of extracellular enzymes during various fermentation stages at the proteomic level via iTRAQ analysis is presented. Many important enzymes related to the amino acid and glucose metabolisms participated in the material decomposition under high-salt stress. Dipeptidase, dipeptidyl aminopeptidase, leucine aminopeptidase, aspartic protease pep1, and extracellular metalloproteinase played positive roles during the early stage of soybean mash fermentation, whilst leucine aminopeptidase A and extracellular metalloproteinase NpI were the dominant proteolytic enzymes during the later period of fermentation. At the same time, β-glucosidase and β-xylanase exerted great effects upon glucose metabolism throughout the fermentation process. The results show that protease and amylolytic enzymes are complementary in the formation of flavors such as alcohols, acids, esters, aldehydes, furans, and pyrazines during soy sauce fermentation.
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Affiliation(s)
- Guozhong Zhao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, International Collaborative Research Center for Health Biotechnology, College of Food Engineering and Biotechnology, Tianjin University of Science & Technology, Tianjin, China
| | - Li-Li Ding
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, International Collaborative Research Center for Health Biotechnology, College of Food Engineering and Biotechnology, Tianjin University of Science & Technology, Tianjin, China
| | - Yunping Yao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, International Collaborative Research Center for Health Biotechnology, College of Food Engineering and Biotechnology, Tianjin University of Science & Technology, Tianjin, China
| | - Yanping Cao
- Beijing Laboratory for Food Quality and Safety, Beijing Technology and Business University, Beijing, China
| | - Zhi-Hui Pan
- Guangzhou Jammy Chai Sauce Workshop Co., Ltd., Guangzhou, China
| | - De-Hua Kong
- Guangzhou Jammy Chai Sauce Workshop Co., Ltd., Guangzhou, China
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Hu W, Yan Y, Tie W, Ding Z, Wu C, Ding X, Wang W, Xia Z, Guo J, Peng M. Genome-Wide Analyses of Calcium Sensors Reveal Their Involvement in Drought Stress Response and Storage Roots Deterioration after Harvest in Cassava. Genes (Basel) 2018; 9:genes9040221. [PMID: 29671773 PMCID: PMC5924563 DOI: 10.3390/genes9040221] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 04/01/2018] [Accepted: 04/12/2018] [Indexed: 12/18/2022] Open
Abstract
Calcium (Ca2+) plays a crucial role in plant development and responses to environmental stimuli. Currently, calmodulins (CaMs), calmodulin-like proteins (CMLs), and calcineurin B-like proteins (CBLs), such as Ca2+ sensors, are not well understood in cassava (Manihotesculenta Crantz), an important tropical crop. In the present study, 8 CaMs, 48 CMLs, and 9 CBLs were genome-wide identified in cassava, which were divided into two, four, and four groups, respectively, based on evolutionary relationship, protein motif, and gene structure analyses. Transcriptomic analysis revealed the expression diversity of cassava CaMs-CMLs-CBLs in distinct tissues and in response to drought stress in different genotypes. Generally, cassava CaMs-CMLs-CBLs showed different expression profiles between cultivated varieties (Arg7 and SC124) and wild ancestor (W14) after drought treatment. In addition, numerous CaMs-CMLs-CBLs were significantly upregulated at 6 h, 12 h, and 48 h after harvest, suggesting their possible role during storage roots (SR) deterioration. Further interaction network and co-expression analyses suggested that a CBL-mediated interaction network was widely involved in SR deterioration. Taken together, this study provides new insights into CaMs-CMLs-CBLs-mediated drought adaption and SR deterioration at the transcription level in cassava, and identifies some candidates for the genetic improvement of cassava.
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Affiliation(s)
- Wei Hu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou 571101, Hainan, China.
| | - Yan Yan
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou 571101, Hainan, China.
| | - Weiwei Tie
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou 571101, Hainan, China.
| | - Zehong Ding
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou 571101, Hainan, China.
| | - Chunlai Wu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou 571101, Hainan, China.
| | - Xupo Ding
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou 571101, Hainan, China.
| | - Wenquan Wang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou 571101, Hainan, China.
| | - Zhiqiang Xia
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou 571101, Hainan, China.
| | - Jianchun Guo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou 571101, Hainan, China.
| | - Ming Peng
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou 571101, Hainan, China.
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Anjanappa RB, Mehta D, Okoniewski MJ, Szabelska‐Berȩsewicz A, Gruissem W, Vanderschuren H. Molecular insights into Cassava brown streak virus susceptibility and resistance by profiling of the early host response. MOLECULAR PLANT PATHOLOGY 2018; 19:476-489. [PMID: 28494519 PMCID: PMC6638049 DOI: 10.1111/mpp.12565] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 05/02/2017] [Accepted: 05/03/2017] [Indexed: 05/19/2023]
Abstract
Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV) are responsible for significant cassava yield losses in eastern sub-Saharan Africa. To study the possible mechanisms of plant resistance to CBSVs, we inoculated CBSV-susceptible and CBSV-resistant cassava varieties with a mixed infection of CBSVs using top-cleft grafting. Transcriptome profiling of the two cassava varieties was performed at the earliest time point of full infection (28 days after grafting) in the susceptible scions. The expression of genes encoding proteins in RNA silencing, salicylic acid pathways and callose deposition was altered in the susceptible cassava variety, but transcriptional changes were limited in the resistant variety. In total, the expression of 585 genes was altered in the resistant variety and 1292 in the susceptible variety. Transcriptional changes led to the activation of β-1,3-glucanase enzymatic activity and a reduction in callose deposition in the susceptible cassava variety. Time course analysis also showed that CBSV replication in susceptible cassava induced a strong up-regulation of RDR1, a gene previously reported to be a susceptibility factor in other potyvirus-host pathosystems. The differences in the transcriptional responses to CBSV infection indicated that susceptibility involves the restriction of callose deposition at plasmodesmata. Aniline blue staining of callose deposits also indicated that the resistant variety displays a moderate, but significant, increase in callose deposition at the plasmodesmata. Transcriptome data suggested that resistance does not involve typical antiviral defence responses (i.e. RNA silencing and salicylic acid). A meta-analysis of the current RNA-sequencing (RNA-seq) dataset and selected potyvirus-host and virus-cassava RNA-seq datasets revealed that the conservation of the host response across pathosystems is restricted to genes involved in developmental processes.
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Affiliation(s)
| | - Devang Mehta
- Department of BiologyETH Zurich8092 ZurichSwitzerland
| | - Michal J. Okoniewski
- ID Scientific IT ServicesETH Zurich8092 ZurichSwitzerland
- Functional Genomics Center Zurich8057 ZurichSwitzerland
| | - Alicja Szabelska‐Berȩsewicz
- Functional Genomics Center Zurich8057 ZurichSwitzerland
- Department of Mathematical and Statistical MethodsPoznan University of Life Sciences60‐637 PoznanPoland
| | | | - Hervé Vanderschuren
- Department of BiologyETH Zurich8092 ZurichSwitzerland
- AgroBioChem Department, Gembloux Agro‐Bio TechUniversity of Liège5030 GemblouxBelgium
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Lentz EM, Kuon JE, Alder A, Mangel N, Zainuddin IM, McCallum EJ, Anjanappa RB, Gruissem W, Vanderschuren H. Cassava geminivirus agroclones for virus-induced gene silencing in cassava leaves and roots. PLANT METHODS 2018; 14:73. [PMID: 30154909 PMCID: PMC6109987 DOI: 10.1186/s13007-018-0340-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 08/16/2018] [Indexed: 05/08/2023]
Abstract
AIM We report the construction of a Virus-Induced Gene Silencing (VIGS) vector and an agroinoculation protocol for gene silencing in cassava (Manihot esculenta Crantz) leaves and roots. The African cassava mosaic virus isolate from Nigeria (ACMV-[NOg]), which was initially cloned in a binary vector for agroinoculation assays, was modified for application as VIGS vector. The functionality of the VIGS vector was validated in Nicotiana benthamiana and subsequently applied in wild-type and transgenic cassava plants expressing the uidA gene under the control of the CaMV 35S promoter in order to facilitate the visualization of gene silencing in root tissues. VIGS vectors were targeted to the Mg2+-chelatase gene in wild type plants and both the coding and promoter sequences of the 35S::uidA transgene in transgenic plants to induce silencing. We established an efficient agro-inoculation method with the hyper-virulent Agrobacterium tumefaciens strain AGL1, which allows high virus infection rates. The method can be used as a low-cost and rapid high-throughput evaluation of gene function in cassava leaves, fibrous roots and storage roots. BACKGROUND VIGS is a powerful tool to trigger transient sequence-specific gene silencing in planta. Gene silencing in different organs of cassava plants, including leaves, fibrous and storage roots, is useful for the analysis of gene function. RESULTS We developed an African cassava mosaic virus-based VIGS vector as well as a rapid and efficient agro-inoculation protocol to inoculate cassava plants. The VIGS vector was validated by targeting endogenous genes from Nicotiana benthamiana and cassava as well as the uidA marker gene in transgenic cassava for visualization of gene silencing in cassava leaves and roots. CONCLUSIONS The African cassava mosaic virus-based VIGS vector allows efficient and cost-effective inoculation of cassava for high-throughput analysis of gene function in cassava leaves and roots.
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Affiliation(s)
- Ezequiel Matias Lentz
- Department of Biology, Plant Biotechnology, ETH Zurich-LFW, E56.1, Universitaetstrasse 2, 8092 Zurich, Switzerland
| | - Joel-Elias Kuon
- Department of Biology, Plant Biotechnology, ETH Zurich-LFW, E56.1, Universitaetstrasse 2, 8092 Zurich, Switzerland
| | - Adrian Alder
- Department of Biology, Plant Biotechnology, ETH Zurich-LFW, E56.1, Universitaetstrasse 2, 8092 Zurich, Switzerland
| | - Nathalie Mangel
- Department of Biology, Plant Biotechnology, ETH Zurich-LFW, E56.1, Universitaetstrasse 2, 8092 Zurich, Switzerland
| | - Ima M. Zainuddin
- Department of Biology, Plant Biotechnology, ETH Zurich-LFW, E56.1, Universitaetstrasse 2, 8092 Zurich, Switzerland
| | - Emily Jane McCallum
- Department of Biology, Plant Biotechnology, ETH Zurich-LFW, E56.1, Universitaetstrasse 2, 8092 Zurich, Switzerland
| | - Ravi Bodampalli Anjanappa
- Department of Biology, Plant Biotechnology, ETH Zurich-LFW, E56.1, Universitaetstrasse 2, 8092 Zurich, Switzerland
| | - Wilhelm Gruissem
- Department of Biology, Plant Biotechnology, ETH Zurich-LFW, E56.1, Universitaetstrasse 2, 8092 Zurich, Switzerland
| | - Hervé Vanderschuren
- Department of Biology, Plant Biotechnology, ETH Zurich-LFW, E56.1, Universitaetstrasse 2, 8092 Zurich, Switzerland
- Plant Genetics Lab, TERRA Research and Teaching Centre, Gembloux Agro BioTech, University of Liège, Gembloux, Belgium
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Prediction of cassava protein interactome based on interolog method. Sci Rep 2017; 7:17206. [PMID: 29222529 PMCID: PMC5722940 DOI: 10.1038/s41598-017-17633-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 11/28/2017] [Indexed: 12/20/2022] Open
Abstract
Cassava is a starchy root crop whose role in food security becomes more significant nowadays. Together with the industrial uses for versatile purposes, demand for cassava starch is continuously growing. However, in-depth study to uncover the mystery of cellular regulation, especially the interaction between proteins, is lacking. To reduce the knowledge gap in protein-protein interaction (PPI), genome-scale PPI network of cassava was constructed using interolog-based method (MePPI-In, available at http://bml.sbi.kmutt.ac.th/ppi). The network was constructed from the information of seven template plants. The MePPI-In included 90,173 interactions from 7,209 proteins. At least, 39 percent of the total predictions were found with supports from gene/protein expression data, while further co-expression analysis yielded 16 highly promising PPIs. In addition, domain-domain interaction information was employed to increase reliability of the network and guide the search for more groups of promising PPIs. Moreover, the topology and functional content of MePPI-In was similar to the networks of Arabidopsis and rice. The potential contribution of MePPI-In for various applications, such as protein-complex formation and prediction of protein function, was discussed and exemplified. The insights provided by our MePPI-In would hopefully enable us to pursue precise trait improvement in cassava.
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Li G, Wu Y, Liu G, Xiao X, Wang P, Gao T, Xu M, Han Q, Wang Y, Guo T, Kang G. Large-scale Proteomics Combined with Transgenic Experiments Demonstrates An Important Role of Jasmonic Acid in Potassium Deficiency Response in Wheat and Rice. Mol Cell Proteomics 2017; 16:1889-1905. [PMID: 28821602 PMCID: PMC5671998 DOI: 10.1074/mcp.ra117.000032] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Indexed: 12/03/2022] Open
Abstract
Potassium (K+) is the most abundant inorganic cation in plants, and molecular dissection of K+ deficiency has received considerable interest in order to minimize K+ fertilizer input and develop high quality K+-efficient crops. However, the molecular mechanism of plant responses to K+ deficiency is still poorly understood. In this study, 2-week-old bread wheat seedlings grown hydroponically in Hoagland solution were transferred to K+-free conditions for 8 d, and their root and leaf proteome profiles were assessed using the iTRAQ proteome method. Over 4000 unique proteins were identified, and 818 K+-responsive protein species showed significant differences in abundance. The differentially expressed protein species were associated with diverse functions and exhibited organ-specific differences. Most of the differentially expressed protein species related to hormone synthesis were involved in jasmonic acid (JA) synthesis and the upregulated abundance of JA synthesis-related enzymes could result in the increased JA concentrations. Abundance of allene oxide synthase (AOS), one key JA synthesis-related enzyme, was significantly increased in K+-deficient wheat seedlings, and its overexpression markedly increased concentrations of K+ and JA, altered the transcription levels of some genes encoding K+-responsive protein species, as well as enhanced the tolerance of rice plants to low K+ or K+ deficiency. Moreover, rice AOS mutant (osaos) exhibited more sensitivity to low K+ or K+ deficiency. Our findings could highlight the importance of JA in K+ deficiency, and imply a network of molecular processes underlying plant responses to K+ deficiency.
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Affiliation(s)
- Gezi Li
- From the ‡National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, 450002, China.,§Collaborative Innovation Center of Henan Food Crops, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yufang Wu
- From the ‡National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, 450002, China
| | - Guoyu Liu
- From the ‡National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, 450002, China
| | - Xianghong Xiao
- §Collaborative Innovation Center of Henan Food Crops, Henan Agricultural University, Zhengzhou, 450002, China
| | - Pengfei Wang
- From the ‡National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, 450002, China
| | - Tian Gao
- From the ‡National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, 450002, China
| | - Mengjun Xu
- §Collaborative Innovation Center of Henan Food Crops, Henan Agricultural University, Zhengzhou, 450002, China
| | - Qiaoxia Han
- ¶National Engineering Research Centre for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yonghua Wang
- From the ‡National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, 450002, China.,¶National Engineering Research Centre for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Tiancai Guo
- From the ‡National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, 450002, China.,¶National Engineering Research Centre for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Guozhang Kang
- From the ‡National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, 450002, China; .,§Collaborative Innovation Center of Henan Food Crops, Henan Agricultural University, Zhengzhou, 450002, China
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Miller MAE, O’Cualain R, Selley J, Knight D, Karim MF, Hubbard SJ, Johnson GN. Dynamic Acclimation to High Light in Arabidopsis thaliana Involves Widespread Reengineering of the Leaf Proteome. FRONTIERS IN PLANT SCIENCE 2017; 8:1239. [PMID: 28775726 PMCID: PMC5517461 DOI: 10.3389/fpls.2017.01239] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 06/30/2017] [Indexed: 05/18/2023]
Abstract
Leaves of Arabidopsis thaliana transferred from low to high light increase their capacity for photosynthesis, a process of dynamic acclimation. A mutant, gpt2, lacking a chloroplast glucose-6-phosphate/phosphate translocator, is deficient in its ability to acclimate to increased light. Here, we have used a label-free proteomics approach, to perform relative quantitation of 1993 proteins from Arabidopsis wild type and gpt2 leaves exposed to increased light. Data are available via ProteomeXchange with identifier PXD006598. Acclimation to light is shown to involve increases in electron transport and carbon metabolism but no change in the abundance of photosynthetic reaction centers. The gpt2 mutant shows a similar increase in total protein content to wild type but differences in the extent of change of certain proteins, including in the relative abundance of the cytochrome b6f complex and plastocyanin, the thylakoid ATPase and selected Benson-Calvin cycle enzymes. Changes in leaf metabolite content as plants acclimate can be explained by changes in the abundance of enzymes involved in metabolism, which were reduced in gpt2 in some cases. Plants of gpt2 invest more in stress-related proteins, suggesting that their reduced ability to acclimate photosynthetic capacity results in increased stress.
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Affiliation(s)
- Matthew A. E. Miller
- School of Earth and Environmental Sciences, University of ManchesterManchester, United Kingdom
| | - Ronan O’Cualain
- School of Biological Sciences, University of ManchesterManchester, United Kingdom
| | - Julian Selley
- School of Biological Sciences, University of ManchesterManchester, United Kingdom
| | - David Knight
- School of Biological Sciences, University of ManchesterManchester, United Kingdom
| | - Mohd F. Karim
- School of Earth and Environmental Sciences, University of ManchesterManchester, United Kingdom
| | - Simon J. Hubbard
- School of Biological Sciences, University of ManchesterManchester, United Kingdom
| | - Giles N. Johnson
- School of Earth and Environmental Sciences, University of ManchesterManchester, United Kingdom
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Li S, Cui Y, Zhou Y, Luo Z, Liu J, Zhao M. The industrial applications of cassava: current status, opportunities and prospects. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2017; 97:2282-2290. [PMID: 28233322 DOI: 10.1002/jsfa.8287] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 02/17/2017] [Accepted: 02/18/2017] [Indexed: 05/27/2023]
Abstract
Cassava (Manihot esculenta Crantz) is a drought-tolerant, staple food crop that is grown in tropical and subtropical areas. As an important raw material, cassava is a valuable food source in developing countries and is also extensively employed for producing starch, bioethanol and other bio-based products (e.g. feed, medicine, cosmetics and biopolymers). These cassava-based industries also generate large quantities of wastes/residues rich in organic matter and suspended solids, providing great potential for conversion into value-added products through biorefinery. However, the community of cassava researchers is relatively small and there is very limited information on cassava. Therefore this review summarizes current knowledge on the system biology, economic value, nutritional quality and industrial applications of cassava and its wastes in an attempt to accelerate understanding of the basic biology of cassava. The review also discusses future perspectives with respect to integrating and utilizing cassava information resources for increasing the economic and environmental sustainability of cassava industries. © 2017 Society of Chemical Industry.
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Affiliation(s)
- Shubo Li
- College of Light Industry and Food Engineering, Guangxi University, Nanning, China
| | - Yanyan Cui
- College of Light Industry and Food Engineering, Guangxi University, Nanning, China
| | - Yuan Zhou
- College of Light Industry and Food Engineering, Guangxi University, Nanning, China
| | - Zhiting Luo
- College of Light Industry and Food Engineering, Guangxi University, Nanning, China
| | - Jidong Liu
- College of Light Industry and Food Engineering, Guangxi University, Nanning, China
| | - Mouming Zhao
- College of Light Industry and Food Engineering, Guangxi University, Nanning, China
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Liu S, Zainuddin IM, Vanderschuren H, Doughty J, Beeching JR. RNAi inhibition of feruloyl CoA 6'-hydroxylase reduces scopoletin biosynthesis and post-harvest physiological deterioration in cassava (Manihot esculenta Crantz) storage roots. PLANT MOLECULAR BIOLOGY 2017; 94:185-195. [PMID: 28315989 PMCID: PMC5437147 DOI: 10.1007/s11103-017-0602-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 03/09/2017] [Indexed: 05/06/2023]
Abstract
Cassava (Manihot esculenta Crantz) is a major world crop, whose storage roots provide food for over 800 million throughout the humid tropics. Despite many advantages as a crop, the development of cassava is seriously constrained by the rapid post-harvest physiological deterioration (PPD) of its roots that occurs within 24-72 h of harvest, rendering the roots unpalatable and unmarketable. PPD limits cassava's marketing possibilities in countries that are undergoing increased development and urbanisation due to growing distances between farms and consumers. The inevitable wounding of the roots caused by harvesting triggers an oxidative burst that spreads throughout the cassava root, together with the accumulation of secondary metabolites including phenolic compounds, of which the coumarin scopoletin (7-hydroxy-6-methoxy-2H-1-benzopyran-2-one) is the most abundant. Scopoletin oxidation yields a blue-black colour, which suggests its involvement in the discoloration observed during PPD. Feruloyl CoA 6'-hydroxylase is a controlling enzyme in the biosynthesis of scopoletin. The cassava genome contains a seven membered family of feruloyl CoA 6'-hydroxylase genes, four of which are expressed in the storage root and, of these, three were capable of functionally complementing Arabidopsis T-DNA insertion mutants in this gene. A RNA interference construct, designed to a highly conserved region of these genes, was used to transform cassava, where it significantly reduced feruloyl CoA 6'-hydroxylase gene expression, scopoletin accumulation and PPD symptom development. Collectively, our results provide evidence that scopoletin plays a major functional role in the development of PPD symptoms, rather than merely paralleling symptom development in the cassava storage root.
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Affiliation(s)
- Shi Liu
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK.
| | - Ima M Zainuddin
- Department of Biology, Plant Biotechnology, Eidgenössische Technische Hochschule (ETH) Zurich, Universitätstrasse 2, 8092, Zurich, Switzerland
- Research Center for Biotechnology, Indonesian Institute of Sciences, Complex CSC-LIPI Jl. Raya Bogor Km 46, Cibinong, Bogor, West Java, 16911, Indonesia
| | - Herve Vanderschuren
- Department of Biology, Plant Biotechnology, Eidgenössische Technische Hochschule (ETH) Zurich, Universitätstrasse 2, 8092, Zurich, Switzerland
- Plant Genetics, AgroBioChem Department, Gembloux Agro-BioTech, University of Liège, 4000, Liège, Belgium
| | - James Doughty
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - John R Beeching
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
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Fudge J, Mangel N, Gruissem W, Vanderschuren H, Fitzpatrick TB. Rationalising vitamin B6 biofortification in crop plants. Curr Opin Biotechnol 2017; 44:130-137. [DOI: 10.1016/j.copbio.2016.12.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 12/17/2016] [Accepted: 12/19/2016] [Indexed: 12/31/2022]
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40
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Qin Y, Djabou ASM, An F, Li K, Li Z, Yang L, Wang X, Chen S. Proteomic analysis of injured storage roots in cassava (Manihot esculenta Crantz) under postharvest physiological deterioration. PLoS One 2017; 12:e0174238. [PMID: 28339481 PMCID: PMC5365129 DOI: 10.1371/journal.pone.0174238] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 03/06/2017] [Indexed: 11/23/2022] Open
Abstract
Postharvest physiological deterioration (PPD) is a global challenge in the improvement of cassava value chain. However, how to reduce cassava spoilage and reveal the mechanism of injured cassava storage roots in response to PPD were poorly understood. In the present study, we investigated the activities of antioxidant enzymes of cassava injured storage roots in PPD-susceptible (SC9) and PPD-tolerant (QZ1) genotypes at the time-points from 0h to 120h, and further analyzed their proteomic changes using two-dimensional electrophoresis (2-DE) in combination with MALDI-TOF-MS/MS. Ninety-nine differentially expressed proteins were identified from SC9 and QZ1 genotypes in the pairwise comparison of 24h/0h, 48h/0h, 72h/0h and 96h/0h. Of those proteins were associated with 13 biological functions, in which carbohydrate and energy metabolism related proteins were the biggest amount differential proteins in both genotypes, followed by chaperones, DNA and RNA metabolism, and defense system. We speculated that SOD in combination with CAT activities would be the first line of defense against PPD to support PPD-tolerant cassava varieties. The four hub proteins including CPN60B, LOS2, HSC70-1 and CPN20B, produced from the network of protein-protein interaction, will be the candidate key proteins linked with PPD. This study provides a new clue to improve cassava PPD-tolerant varieties and would be helpful to much better understand the molecular mechanism of PPD of cassava injured storage roots.
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Affiliation(s)
- Yuling Qin
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, China
- Tropical Crops Genetic Resources Institute Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Ministry of Agriculture for Germplasm Resources Conservation and Utilization of Cassava, Danzhou, China
| | - Astride Stéphanie Mouafi Djabou
- Laboratory of plant physiology, Department of Biological Science, Higher Teachers´ Training College, University of Yaounde I, Yaounde, Cameroon
| | - Feifei An
- Tropical Crops Genetic Resources Institute Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Ministry of Agriculture for Germplasm Resources Conservation and Utilization of Cassava, Danzhou, China
| | - Kaimian Li
- Tropical Crops Genetic Resources Institute Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Ministry of Agriculture for Germplasm Resources Conservation and Utilization of Cassava, Danzhou, China
| | - Zhaogui Li
- Agricultural Bureau of Wuming County, Wuming, China
| | - Long Yang
- Subtropical Crops Research Institute, Guizhou Provincial Academy of Agricultural Sciences, Xingyi, China
| | - Xiaojing Wang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, China
| | - Songbi Chen
- Tropical Crops Genetic Resources Institute Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Ministry of Agriculture for Germplasm Resources Conservation and Utilization of Cassava, Danzhou, China
- * E-mail:
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41
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Djabou ASM, Carvalho LJCB, Li QX, Niemenak N, Chen S. Cassava postharvest physiological deterioration: a complex phenomenon involving calcium signaling, reactive oxygen species and programmed cell death. ACTA PHYSIOLOGIAE PLANTARUM 2017; 39:91. [PMID: 28316353 PMCID: PMC5336541 DOI: 10.1007/s11738-017-2382-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Revised: 01/30/2017] [Accepted: 02/11/2017] [Indexed: 05/19/2023]
Abstract
Postharvest physiological deterioration (PPD) of cassava (Manihot esculenta) storage roots is a complex physiological and biochemical process which involve many regulatory networks linked with specific proteins modulation and signaling transduction pathways. However, it is poorly understood regarding biological regulation, and the interactions among protein groups and signals to determine PPD syndrome in cassava storage roots. This review sheds some light on the possible molecular mechanisms involved in reactive oxygen species (ROS), calcium signaling transduction, and programmed cell death (PCD) in cassava PPD syndrome. A model for predicting crosstalk among calcium signaling, ROS and PCD is suggested to fine-tune PPD syndrome. This would clues to cassava molecular breeding to alleviate the PPD effects on the shelf-life.
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Affiliation(s)
- Astride S. M. Djabou
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Ministry of Agriculture for Germplasm Resources Conservation and Utilization of Cassava, Hainan, China
- Laboratory of Plant Physiology, Department of Biological Science, Higher Teachers’ Training College, University of Yaounde I, Yaounde, Cameroon
| | | | - Qing X. Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, USA
| | - Nicolas Niemenak
- Laboratory of Plant Physiology, Department of Biological Science, Higher Teachers’ Training College, University of Yaounde I, Yaounde, Cameroon
| | - Songbi Chen
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Ministry of Agriculture for Germplasm Resources Conservation and Utilization of Cassava, Hainan, China
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Wilson MC, Mutka AM, Hummel AW, Berry J, Chauhan RD, Vijayaraghavan A, Taylor NJ, Voytas DF, Chitwood DH, Bart RS. Gene expression atlas for the food security crop cassava. THE NEW PHYTOLOGIST 2017; 213:1632-1641. [PMID: 28116755 PMCID: PMC5516207 DOI: 10.1111/nph.14443] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 12/18/2016] [Indexed: 05/17/2023]
Abstract
Cassava (Manihot esculenta) feeds c. 800 million people world-wide. Although this crop displays high productivity under drought and poor soil conditions, it is susceptible to disease, postharvest deterioration and the roots contain low nutritional content. Here, we provide molecular identities for 11 cassava tissue/organ types through RNA-sequencing and develop an open access, web-based interface for further interrogation of the data. Through this dataset, we consider the physiology of cassava. Specifically, we focus on identification of the transcriptional signatures that define the massive, underground storage roots used as a food source and the favored target tissue for transgene integration and genome editing, friable embryogenic callus (FEC). Further, we identify promoters able to drive strong expression in multiple tissue/organs. The information gained from this study is of value for both conventional and biotechnological improvement programs.
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Affiliation(s)
- Mark C. Wilson
- Donald Danforth Plant Science Center975 North Warson RoadSt LouisMO63132USA
| | - Andrew M. Mutka
- Donald Danforth Plant Science Center975 North Warson RoadSt LouisMO63132USA
| | - Aaron W. Hummel
- Department of Genetics, Cell Biology & Development and Center for Genome EngineeringUniversity of MinnesotaMinneapolisMN55455USA
| | - Jeffrey Berry
- Donald Danforth Plant Science Center975 North Warson RoadSt LouisMO63132USA
| | | | | | - Nigel J. Taylor
- Donald Danforth Plant Science Center975 North Warson RoadSt LouisMO63132USA
| | - Daniel F. Voytas
- Department of Genetics, Cell Biology & Development and Center for Genome EngineeringUniversity of MinnesotaMinneapolisMN55455USA
| | - Daniel H. Chitwood
- Donald Danforth Plant Science Center975 North Warson RoadSt LouisMO63132USA
| | - Rebecca S. Bart
- Donald Danforth Plant Science Center975 North Warson RoadSt LouisMO63132USA
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43
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Ma Q, Zhang T, Zhang P, Wang ZY. Melatonin attenuates postharvest physiological deterioration of cassava storage roots. J Pineal Res 2016; 60:424-34. [PMID: 26989849 DOI: 10.1111/jpi.12325] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 03/11/2016] [Indexed: 01/06/2023]
Abstract
Melatonin reportedly increases abiotic and biotic stress tolerance in plants, but information on its in vivo effects during postharvest physiological deterioration (PPD) in cassava is limited. In this study, we investigated the effect of melatonin in regulating cassava PPD. Treatment with 500 mg/L melatonin significantly delayed cassava PPD and reduced the accumulation of hydrogen peroxide (H2O2) while increasing the activity of superoxide dismutase (SOD), catalase (CAT), and glutathione reductase (GR), but not ascorbate peroxidase (APX). Transcript analysis further showed that expression of copper/zinc SOD (MeCu/ZnSOD), MeCAT1, glutathione peroxidase (MeGPX), peroxidase 3 (MePX3), and glutathione S-transferases (MeGST) was higher in cassava roots sliced treated with 500 mg/L melatonin than in those not exposed to exogenous melatonin. These data demonstrate that melatonin delays cassava PPD by directly or indirectly maintaining homoeostasis of cellular reactive oxygen species (ROS). We also found that accumulation of endogenous melatonin and the transcript levels of melatonin biosynthesis genes changed dynamically during the PPD process. This finding suggested that endogenous melatonin acts as a signal modulator for maintaining cassava PPD progression and that manipulation of melatonin biosynthesis genes through genetic engineering might prevent cassava root deterioration.
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Affiliation(s)
- Qiuxiang Ma
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ting Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Peng Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhen-Yu Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan University, Haikou, China
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44
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Schmitz GJH, de Magalhães Andrade J, Valle TL, Labate CA, do Nascimento JRO. Comparative Proteome Analysis of the Tuberous Roots of Six Cassava (Manihot esculenta) Varieties Reveals Proteins Related to Phenotypic Traits. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:3293-3301. [PMID: 26982619 DOI: 10.1021/acs.jafc.5b05585] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Cassava (Manihot esculenta Crantz) is a staple food and an important source of starch, and the attributes of its tuberous root largely depend on the variety. The proteome of cassava has been investigated; however, to date, no study has focused on varieties that reveal the molecular basis of phenotypical characteristics. Therefore, we aimed to compare the proteome of the tuberous roots of six cassava varieties that differed in carbohydrates, carotenoids, and resistance to diseases, among other attributes. Two-dimensional gels showed 146 differential spots between the varieties, and the functional roles of some differential proteins were correlated to phenotypic characteristics of the varieties, such as the amount of carbohydrates or carotenoids and the resistance to biotic or abiotic stresses. The results obtained here highlight elements that might help to direct the improvement of new cultivars of cassava, which is an economically and socially relevant crop worldwide.
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Affiliation(s)
| | | | | | | | - João Roberto Oliveira do Nascimento
- Department of Food Science and Experimental Nutrition, FCF, University of São Paulo , São Paulo, Brazil
- Food and Nutrition Research Center (NAPAN), University of São Paulo , São Paulo, Brazil
- Food Research Center (FoRC-CEPID) , São Paulo, Brazil
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45
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Wang X, Chang L, Tong Z, Wang D, Yin Q, Wang D, Jin X, Yang Q, Wang L, Sun Y, Huang Q, Guo A, Peng M. Proteomics Profiling Reveals Carbohydrate Metabolic Enzymes and 14-3-3 Proteins Play Important Roles for Starch Accumulation during Cassava Root Tuberization. Sci Rep 2016; 6:19643. [PMID: 26791570 PMCID: PMC4726164 DOI: 10.1038/srep19643] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 12/14/2015] [Indexed: 02/07/2023] Open
Abstract
Cassava is one of the most important root crops as a reliable source of food and carbohydrates. Carbohydrate metabolism and starch accumulation in cassava storage root is a cascade process that includes large amounts of proteins and cofactors. Here, comparative proteomics were conducted in cassava root at nine developmental stages. A total of 154 identified proteins were found to be differentially expressed during starch accumulation and root tuberization. Many enzymes involved in starch and sucrose metabolism were significantly up-regulated, and functional classification of the differentially expressed proteins demonstrated that the majority were binding-related enzymes. Many proteins were took part in carbohydrate metabolism to produce energy. Among them, three 14-3-3 isoforms were induced to be clearly phosphorylated during storage root enlargement. Overexpression of a cassava 14-3-3 gene in Arabidopsis thaliana confirmed that the older leaves of these transgenic plants contained higher sugar and starch contents than the wild-type leaves. The 14-3-3 proteins and their binding enzymes may play important roles in carbohydrate metabolism and starch accumulation during cassava root tuberization. These results not only deepened our understanding of the tuberous root proteome, but also uncovered new insights into carbohydrate metabolism and starch accumulation during cassava root enlargement.
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Affiliation(s)
- Xuchu Wang
- Key Laboratory of Biology and Genetic Resources for Tropical Crops, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China.,College of Agriculture, Hainan University, Haikou, Hainan 570228, China
| | - Lili Chang
- Key Laboratory of Biology and Genetic Resources for Tropical Crops, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China.,College of Agriculture, Hainan University, Haikou, Hainan 570228, China
| | - Zheng Tong
- Key Laboratory of Biology and Genetic Resources for Tropical Crops, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China
| | - Dongyang Wang
- Key Laboratory of Biology and Genetic Resources for Tropical Crops, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China.,College of Agriculture, Hainan University, Haikou, Hainan 570228, China
| | - Qi Yin
- Key Laboratory of Biology and Genetic Resources for Tropical Crops, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China.,College of Agriculture, Hainan University, Haikou, Hainan 570228, China
| | - Dan Wang
- Key Laboratory of Biology and Genetic Resources for Tropical Crops, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China
| | - Xiang Jin
- Key Laboratory of Biology and Genetic Resources for Tropical Crops, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China
| | - Qian Yang
- Key Laboratory of Biology and Genetic Resources for Tropical Crops, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China
| | - Liming Wang
- Key Laboratory of Biology and Genetic Resources for Tropical Crops, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China
| | - Yong Sun
- Key Laboratory of Biology and Genetic Resources for Tropical Crops, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China
| | - Qixing Huang
- Key Laboratory of Biology and Genetic Resources for Tropical Crops, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China
| | - Anping Guo
- Key Laboratory of Biology and Genetic Resources for Tropical Crops, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China
| | - Ming Peng
- Key Laboratory of Biology and Genetic Resources for Tropical Crops, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China.,College of Agriculture, Hainan University, Haikou, Hainan 570228, China
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46
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Hu W, Kong H, Guo Y, Zhang Y, Ding Z, Tie W, Yan Y, Huang Q, Peng M, Shi H, Guo A. Comparative Physiological and Transcriptomic Analyses Reveal the Actions of Melatonin in the Delay of Postharvest Physiological Deterioration of Cassava. FRONTIERS IN PLANT SCIENCE 2016; 7:736. [PMID: 27303428 PMCID: PMC4882330 DOI: 10.3389/fpls.2016.00736] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Accepted: 05/12/2016] [Indexed: 05/18/2023]
Abstract
Melatonin plays important roles in various aspects of biological processes. However, it is less known on the effects and mechanism of melatonin on the postharvest physiological deterioration (PPD) process of cassava, which largely restricts the potential of cassava as a food and industrial crop. In this study, we found that exogenous application of melatonin significantly delayed PPD of cassava tuberous roots by reducing H2O2 content and improving activities of catalase and peroxidase. Moreover, 3425 differentially expressed genes by melatonin during the PPD process were identified by transcriptomic analysis. Several pathways were markedly affected by melatonin treatments, including metabolic-, ion homeostasis-, and enzyme activity-related processes. Further detailed analysis revealed that melatonin acted through activation of ROS-scavenging and ROS signal transduction pathways, including antioxidant enzymes, calcium signaling, MAPK cascades, and transcription factors at early stages. Notably, the starch degradation pathway was also activated at early stages, whereas it was repressed by melatonin at middle and late stages, thereby indicating its regulatory role in starch metabolism during PPD. Taken together, this study yields new insights into the effect and underlying mechanism of melatonin on the delay of PPD and provides a good strategy for extending shelf life and improvement of cassava tuberous roots.
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Affiliation(s)
- Wei Hu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural SciencesHaikou, China
| | - Hua Kong
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural SciencesHaikou, China
| | - Yunling Guo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural SciencesHaikou, China
| | - Yuliang Zhang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural SciencesHaikou, China
| | - Zehong Ding
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural SciencesHaikou, China
| | - Weiwei Tie
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural SciencesHaikou, China
| | - Yan Yan
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural SciencesHaikou, China
| | - Qixing Huang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural SciencesHaikou, China
| | - Ming Peng
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural SciencesHaikou, China
| | - Haitao Shi
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan UniversityHaikou, China
- *Correspondence: Haitao Shi, ; Anping Guo,
| | - Anping Guo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural SciencesHaikou, China
- *Correspondence: Haitao Shi, ; Anping Guo,
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47
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Kerchev P, De Smet B, Waszczak C, Messens J, Van Breusegem F. Redox Strategies for Crop Improvement. Antioxid Redox Signal 2015; 23:1186-205. [PMID: 26062101 DOI: 10.1089/ars.2014.6033] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
SIGNIFICANCE Recently, the agro-biotech industry has been driven by overcoming the limitations imposed by fluctuating environmental stress conditions on crop productivity. A common theme among (a)biotic stresses is the perturbation of the redox homeostasis. RECENT ADVANCES As a strategy to engineer stress-tolerant crops, many approaches have been centered on restricting the negative impact of reactive oxygen species (ROS) accumulation. CRITICAL ISSUES In this study, we discuss the scientific background of the existing redox-based strategies to improve crop performance and quality. In this respect, a special focus goes to summarizing the current patent landscape because this aspect is very often ignored, despite constituting the forefront of applied research. FUTURE DIRECTIONS The current increased understanding of ROS acting as signaling molecules has opened new avenues to exploit redox biology for crop improvement required for sustainable food security.
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Affiliation(s)
- Pavel Kerchev
- 1 Department of Plant Systems Biology , VIB, Ghent, Belgium .,2 Department of Plant Biotechnology and Bioinformatics, Ghent University , Ghent, Belgium
| | - Barbara De Smet
- 1 Department of Plant Systems Biology , VIB, Ghent, Belgium .,2 Department of Plant Biotechnology and Bioinformatics, Ghent University , Ghent, Belgium .,3 Structural Biology Research Center , VIB, Brussels, Belgium .,4 Brussels Center for Redox Biology , Brussel, Belgium .,5 Structural Biology Brussels, Vrije Universiteit Brussel , Brussel, Belgium
| | - Cezary Waszczak
- 1 Department of Plant Systems Biology , VIB, Ghent, Belgium .,2 Department of Plant Biotechnology and Bioinformatics, Ghent University , Ghent, Belgium .,3 Structural Biology Research Center , VIB, Brussels, Belgium .,4 Brussels Center for Redox Biology , Brussel, Belgium .,5 Structural Biology Brussels, Vrije Universiteit Brussel , Brussel, Belgium
| | - Joris Messens
- 3 Structural Biology Research Center , VIB, Brussels, Belgium .,4 Brussels Center for Redox Biology , Brussel, Belgium .,5 Structural Biology Brussels, Vrije Universiteit Brussel , Brussel, Belgium
| | - Frank Van Breusegem
- 1 Department of Plant Systems Biology , VIB, Ghent, Belgium .,2 Department of Plant Biotechnology and Bioinformatics, Ghent University , Ghent, Belgium
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48
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Robison FM, Heuberger AL, Brick MA, Prenni JE. Proteome Characterization of Leaves in Common Bean. Proteomes 2015; 3:236-248. [PMID: 28248269 PMCID: PMC5217379 DOI: 10.3390/proteomes3030236] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 07/30/2015] [Accepted: 08/07/2015] [Indexed: 01/12/2023] Open
Abstract
Dry edible bean (Phaseolus vulgaris L.) is a globally relevant food crop. The bean genome was recently sequenced and annotated allowing for proteomics investigations aimed at characterization of leaf phenotypes important to agriculture. The objective of this study was to utilize a shotgun proteomics approach to characterize the leaf proteome and to identify protein abundance differences between two bean lines with known variation in their physiological resistance to biotic stresses. Overall, 640 proteins were confidently identified. Among these are proteins known to be involved in a variety of molecular functions including oxidoreductase activity, binding peroxidase activity, and hydrolase activity. Twenty nine proteins were found to significantly vary in abundance (p-value < 0.05) between the two bean lines, including proteins associated with biotic stress. To our knowledge, this work represents the first large scale shotgun proteomic analysis of beans and our results lay the groundwork for future studies designed to investigate the molecular mechanisms involved in pathogen resistance.
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Affiliation(s)
- Faith M Robison
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, CO 80523, USA.
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA.
| | - Adam L Heuberger
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO 80523, USA.
| | - Mark A Brick
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA.
| | - Jessica E Prenni
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, CO 80523, USA.
- Department of Biochemistry, Colorado State University, Fort Collins, CO 80523, USA.
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49
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Ding Y, Chang J, Ma Q, Chen L, Liu S, Jin S, Han J, Xu R, Zhu A, Guo J, Luo Y, Xu J, Xu Q, Zeng Y, Deng X, Cheng Y. Network analysis of postharvest senescence process in citrus fruits revealed by transcriptomic and metabolomic profiling. PLANT PHYSIOLOGY 2015; 168:357-76. [PMID: 25802366 PMCID: PMC4424016 DOI: 10.1104/pp.114.255711] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 03/19/2015] [Indexed: 05/04/2023]
Abstract
Citrus (Citrus spp.), a nonclimacteric fruit, is one of the most important fruit crops in global fruit industry. However, the biological behavior of citrus fruit ripening and postharvest senescence remains unclear. To better understand the senescence process of citrus fruit, we analyzed data sets from commercial microarrays, gas chromatography-mass spectrometry, and liquid chromatography-mass spectrometry and validated physiological quality detection of four main varieties in the genus Citrus. Network-based approaches of data mining and modeling were used to investigate complex molecular processes in citrus. The Citrus Metabolic Pathway Network and correlation networks were constructed to explore the modules and relationships of the functional genes/metabolites. We found that the different flesh-rind transport of nutrients and water due to the anatomic structural differences among citrus varieties might be an important factor that influences fruit senescence behavior. We then modeled and verified the citrus senescence process. As fruit rind is exposed directly to the environment, which results in energy expenditure in response to biotic and abiotic stresses, nutrients are exported from flesh to rind to maintain the activity of the whole fruit. The depletion of internal substances causes abiotic stresses, which further induces phytohormone reactions, transcription factor regulation, and a series of physiological and biochemical reactions.
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Affiliation(s)
- Yuduan Ding
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) and Key Laboratory of Horticultural Crop Biology and Genetic Improvement, Central Region (Ministry of Agriculture), Wuhan 430070, China (Y.D., Q.M., S.L., S.J., J.H., R.X., A.Z., Y.L., J.X., Q.X., Y.Z., X.D., Y.C.); andAgricultural Bioinformatics Key Laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, China (J.C., L.C., J.G.)
| | - Jiwei Chang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) and Key Laboratory of Horticultural Crop Biology and Genetic Improvement, Central Region (Ministry of Agriculture), Wuhan 430070, China (Y.D., Q.M., S.L., S.J., J.H., R.X., A.Z., Y.L., J.X., Q.X., Y.Z., X.D., Y.C.); andAgricultural Bioinformatics Key Laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, China (J.C., L.C., J.G.)
| | - Qiaoli Ma
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) and Key Laboratory of Horticultural Crop Biology and Genetic Improvement, Central Region (Ministry of Agriculture), Wuhan 430070, China (Y.D., Q.M., S.L., S.J., J.H., R.X., A.Z., Y.L., J.X., Q.X., Y.Z., X.D., Y.C.); andAgricultural Bioinformatics Key Laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, China (J.C., L.C., J.G.)
| | - Lingling Chen
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) and Key Laboratory of Horticultural Crop Biology and Genetic Improvement, Central Region (Ministry of Agriculture), Wuhan 430070, China (Y.D., Q.M., S.L., S.J., J.H., R.X., A.Z., Y.L., J.X., Q.X., Y.Z., X.D., Y.C.); andAgricultural Bioinformatics Key Laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, China (J.C., L.C., J.G.)
| | - Shuzhen Liu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) and Key Laboratory of Horticultural Crop Biology and Genetic Improvement, Central Region (Ministry of Agriculture), Wuhan 430070, China (Y.D., Q.M., S.L., S.J., J.H., R.X., A.Z., Y.L., J.X., Q.X., Y.Z., X.D., Y.C.); andAgricultural Bioinformatics Key Laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, China (J.C., L.C., J.G.)
| | - Shuai Jin
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) and Key Laboratory of Horticultural Crop Biology and Genetic Improvement, Central Region (Ministry of Agriculture), Wuhan 430070, China (Y.D., Q.M., S.L., S.J., J.H., R.X., A.Z., Y.L., J.X., Q.X., Y.Z., X.D., Y.C.); andAgricultural Bioinformatics Key Laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, China (J.C., L.C., J.G.)
| | - Jingwen Han
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) and Key Laboratory of Horticultural Crop Biology and Genetic Improvement, Central Region (Ministry of Agriculture), Wuhan 430070, China (Y.D., Q.M., S.L., S.J., J.H., R.X., A.Z., Y.L., J.X., Q.X., Y.Z., X.D., Y.C.); andAgricultural Bioinformatics Key Laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, China (J.C., L.C., J.G.)
| | - Rangwei Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) and Key Laboratory of Horticultural Crop Biology and Genetic Improvement, Central Region (Ministry of Agriculture), Wuhan 430070, China (Y.D., Q.M., S.L., S.J., J.H., R.X., A.Z., Y.L., J.X., Q.X., Y.Z., X.D., Y.C.); andAgricultural Bioinformatics Key Laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, China (J.C., L.C., J.G.)
| | - Andan Zhu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) and Key Laboratory of Horticultural Crop Biology and Genetic Improvement, Central Region (Ministry of Agriculture), Wuhan 430070, China (Y.D., Q.M., S.L., S.J., J.H., R.X., A.Z., Y.L., J.X., Q.X., Y.Z., X.D., Y.C.); andAgricultural Bioinformatics Key Laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, China (J.C., L.C., J.G.)
| | - Jing Guo
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) and Key Laboratory of Horticultural Crop Biology and Genetic Improvement, Central Region (Ministry of Agriculture), Wuhan 430070, China (Y.D., Q.M., S.L., S.J., J.H., R.X., A.Z., Y.L., J.X., Q.X., Y.Z., X.D., Y.C.); andAgricultural Bioinformatics Key Laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, China (J.C., L.C., J.G.)
| | - Yi Luo
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) and Key Laboratory of Horticultural Crop Biology and Genetic Improvement, Central Region (Ministry of Agriculture), Wuhan 430070, China (Y.D., Q.M., S.L., S.J., J.H., R.X., A.Z., Y.L., J.X., Q.X., Y.Z., X.D., Y.C.); andAgricultural Bioinformatics Key Laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, China (J.C., L.C., J.G.)
| | - Juan Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) and Key Laboratory of Horticultural Crop Biology and Genetic Improvement, Central Region (Ministry of Agriculture), Wuhan 430070, China (Y.D., Q.M., S.L., S.J., J.H., R.X., A.Z., Y.L., J.X., Q.X., Y.Z., X.D., Y.C.); andAgricultural Bioinformatics Key Laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, China (J.C., L.C., J.G.)
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) and Key Laboratory of Horticultural Crop Biology and Genetic Improvement, Central Region (Ministry of Agriculture), Wuhan 430070, China (Y.D., Q.M., S.L., S.J., J.H., R.X., A.Z., Y.L., J.X., Q.X., Y.Z., X.D., Y.C.); andAgricultural Bioinformatics Key Laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, China (J.C., L.C., J.G.)
| | - YunLiu Zeng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) and Key Laboratory of Horticultural Crop Biology and Genetic Improvement, Central Region (Ministry of Agriculture), Wuhan 430070, China (Y.D., Q.M., S.L., S.J., J.H., R.X., A.Z., Y.L., J.X., Q.X., Y.Z., X.D., Y.C.); andAgricultural Bioinformatics Key Laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, China (J.C., L.C., J.G.)
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) and Key Laboratory of Horticultural Crop Biology and Genetic Improvement, Central Region (Ministry of Agriculture), Wuhan 430070, China (Y.D., Q.M., S.L., S.J., J.H., R.X., A.Z., Y.L., J.X., Q.X., Y.Z., X.D., Y.C.); andAgricultural Bioinformatics Key Laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, China (J.C., L.C., J.G.)
| | - Yunjiang Cheng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) and Key Laboratory of Horticultural Crop Biology and Genetic Improvement, Central Region (Ministry of Agriculture), Wuhan 430070, China (Y.D., Q.M., S.L., S.J., J.H., R.X., A.Z., Y.L., J.X., Q.X., Y.Z., X.D., Y.C.); andAgricultural Bioinformatics Key Laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, China (J.C., L.C., J.G.)
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Navarro C, Cruz-Oró E, Prat S. Conserved function of FLOWERING LOCUS T (FT) homologues as signals for storage organ differentiation. CURRENT OPINION IN PLANT BIOLOGY 2015; 23:45-53. [PMID: 25449726 DOI: 10.1016/j.pbi.2014.10.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 10/15/2014] [Accepted: 10/16/2014] [Indexed: 05/24/2023]
Abstract
Due to their high carbohydrate content and relative low farming demands, tuber-bearing species are an important contribution to human dietary needs in many climatic zones, and interest in these staple crops for processed food and other industrial uses is increasing. Over the past years we have seen remarkable advances in our understanding of the signalling mechanisms involved in the differentiation of these organs, partly aided by their conservation with the well-characterized photoperiodic control of flowering in Arabidopsis. Recent studies have led to the identification of members of the FT gene family as major component of the tuber-inducing signal and the characterization of circadian and photoperiodic components involved in the regulation of these genes. A relevant role of microRNAs in the control of storage organ formation has been established, and hormonal balance requirements similar to those controlling shoot branching were shown to be implicated in the activation of stolon meristem cells. Hence, the recent finding that FT controls branching through direct interaction with the TCP factors holds great promise for the identification of genes acting as FT signal integrators in the stolon.
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Affiliation(s)
- Cristina Navarro
- Dpt. Plant Molecular Genetics, Centro Nacional de Biotecnología-CSIC, Darwin 3, 28049 Madrid, Spain
| | - Eduard Cruz-Oró
- Dpt. Plant Molecular Genetics, Centro Nacional de Biotecnología-CSIC, Darwin 3, 28049 Madrid, Spain
| | - Salomé Prat
- Dpt. Plant Molecular Genetics, Centro Nacional de Biotecnología-CSIC, Darwin 3, 28049 Madrid, Spain.
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