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Khan T. An insight into in silico strategies used for exploration of medicinal utility and toxicology of nanomaterials. Comput Biol Chem 2025; 117:108435. [PMID: 40158237 DOI: 10.1016/j.compbiolchem.2025.108435] [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: 12/04/2024] [Revised: 03/12/2025] [Accepted: 03/17/2025] [Indexed: 04/02/2025]
Abstract
Nanomaterials (NMs) and the exploration of their comprehensive uses is an emerging research area of interest. They have improved physicochemical and biological properties and diverse functionality owing to their unique shape and size and therefore they are being explored for their enormous uses, particularly as medicinal and therapeutic agents. Nanoparticles (NPs) including metal and metal oxide-based NPs have received substantial consideration because of their biological applications. Computer-aided drug design (CADD) involving different strategies like homology modelling, molecular docking, virtual screening (VS), quantitative structure-activity relationship (QSAR) etc. and virtual screening hold significant importance in CADD used for lead identification and target identification. Despite holding importance, there are very few computational studies undertaken so far to explore their binding to the target proteins and macromolecules. Although the structural properties of nanomaterials are well documented, it is worthwhile to know how they interact with the target proteins making it a pragmatic issue for comprehension. This review discusses some important computational strategies like molecular docking and simulation, Nano-QSAR, quantum chemical calculations based on Density functional Theory (DFT) and computational nanotoxicology. Nano-QSAR modelling, based on semiempirical calculations and computational simulation can be useful for biomedical applications, whereas the DFT calculations make it possible to know about the behaviour of the material by calculations based on quantum mechanics, without the requirement of higher-order material properties. Other than the beneficial interactions, it is also important to know the hazardous consequences of engineered nanostructures and NPs can penetrate more deeply into the human body, and computational nanotoxicology has emerged as a potential strategy to predict the delirious effects of NMs. Although computational tools are helpful, yet more studies like in vitro assays are still required to get the complete picture, which is essential in the development of potent and safe drug entities.
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Affiliation(s)
- Tahmeena Khan
- Department of Chemistry, Integral University, Lucknow, U.P 226026, India.
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Lu X, Wang Y, Pan M, Chen S, Li R, Geng M, Chen Y, Liu J, Guo J, Yao Y. Mutation of MeMinD increased amyloplast size with a changed starch granule morphologenesis and structures in cassava storage roots. Carbohydr Polym 2025; 348:122884. [PMID: 39567162 DOI: 10.1016/j.carbpol.2024.122884] [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: 07/15/2024] [Revised: 10/11/2024] [Accepted: 10/15/2024] [Indexed: 11/22/2024]
Abstract
Amyloplasts are the sites of starch synthesis and accumulation. Little is known about amyloplast division and its effects on the size, structure, and physicochemical properties of starch granules. In this study, we created mutants of plastid division-related gene MeMinD by CRISPR/Cas9 technology, leading to the disruption of normal division of amyloplasts in cassava storage roots. The memind mutants exhibited significantly enlarged amyloplasts with an increased number of starch granules, and broader range of granule sizes. The loss of MeMinD function led to transcriptional reprogramming of gene expressions related to starch-synthesizing enzymes, affecting the fine structure of starch. Starch in memind mutant storage roots showed a significantly decreased proportion of shorter amylopectin chains and an increased proportion of medium and long chains, which ultimately led to a significant increase in apparent amylose content (AAC) in memind mutants compared to that in WT. The changes in starch granule size and structure resulted in a significant increase in onset temperature (To), peak temperature (Tp), and conclusion temperature (Tc) of the gelatinization process, extending the time to reach peak temperature. These data suggest that regulating amyloplast division affects starch accumulation in cassava, presenting an effective strategy for developing novel cassava starch.
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Affiliation(s)
- Xiaohua Lu
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Sanya Research Institute, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Yajie Wang
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Sanya Research Institute, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Mu Pan
- School of Life and Health Sciences, Hainan University, Haikou 570228, 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, Haikou 571101, China
| | - Ruimei Li
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Sanya Research Institute, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Mengting Geng
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Yinhua Chen
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Jiao Liu
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Sanya Research Institute, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.
| | - Jianchun Guo
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Sanya Research Institute, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.
| | - Yuan Yao
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Sanya Research Institute, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.
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Adegbaju MS, Ajose T, Adegbaju IE, Omosebi T, Ajenifujah-Solebo SO, Falana OY, Shittu OB, Adetunji CO, Akinbo O. Genetic engineering and genome editing technologies as catalyst for Africa's food security: the case of plant biotechnology in Nigeria. Front Genome Ed 2024; 6:1398813. [PMID: 39045572 PMCID: PMC11263695 DOI: 10.3389/fgeed.2024.1398813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 05/15/2024] [Indexed: 07/25/2024] Open
Abstract
Many African countries are unable to meet the food demands of their growing population and the situation is worsened by climate change and disease outbreaks. This issue of food insecurity may lead to a crisis of epic proportion if effective measures are not in place to make more food available. Thus, deploying biotechnology towards the improvement of existing crop varieties for tolerance or resistance to both biotic and abiotic stresses is crucial to increasing crop production. In order to optimize crop production, several African countries have implemented strategies to make the most of this innovative technology. For example, Nigerian government has implemented the National Biotechnology Policy to facilitate capacity building, research, bioresource development and commercialization of biotechnology products for over two decades. Several government ministries, research centers, universities, and agencies have worked together to implement the policy, resulting in the release of some genetically modified crops to farmers for cultivation and Commercialization, which is a significant accomplishment. However, the transgenic crops were only brought to Nigeria for confined field trials; the manufacturing of the transgenic crops took place outside the country. This may have contributed to the suspicion of pressure groups and embolden proponents of biotechnology as an alien technology. Likewise, this may also be the underlying issue preventing the adoption of biotechnology products in other African countries. It is therefore necessary that African universities develop capacity in various aspects of biotechnology, to continuously train indigenous scientists who can generate innovative ideas tailored towards solving problems that are peculiar to respective country. Therefore, this study intends to establish the role of genetic engineering and genome editing towards the achievement of food security in Africa while using Nigeria as a case study. In our opinion, biotechnology approaches will not only complement conventional breeding methods in the pursuit of crop improvements, but it remains a viable and sustainable means of tackling specific issues hindering optimal crop production. Furthermore, we suggest that financial institutions should offer low-interest loans to new businesses. In order to promote the growth of biotechnology products, especially through the creation of jobs and revenues through molecular farming.
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Affiliation(s)
- Muyiwa Seyi Adegbaju
- Department of Crop, Soil and Pest Management, Federal University of Technology Akure, Akure, Ondo, Nigeria
| | - Titilayo Ajose
- Fruits and Spices Department, National Horticultural Institute, Ibadan, Oyo, Nigeria
| | | | - Temitayo Omosebi
- Department of Agricultural Technology, Federal College of Forestry, Jos, Nigeria
| | | | - Olaitan Yetunde Falana
- Department of Genetics, Genomic and Bioinformatics, National Biotechnology Research and Development Agency, Abuja, Nigeria
| | - Olufunke Bolatito Shittu
- Department of Microbiology, College of Biosciences, Federal University of Agriculture, Abeokuta, Nigeria
| | | | - Olalekan Akinbo
- African Union Development Agency-NEPAD, Office of Science, Technology and Innovation, Midrand, South Africa
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Lu XH, Wang YJ, Zhen XH, Yu H, Pan M, Fu DQ, Li RM, Liu J, Luo HY, Hu XW, Yao Y, Guo JC. Functional Characterization of the MeSSIII-1 Gene and Its Promoter from Cassava. Int J Mol Sci 2024; 25:4711. [PMID: 38731930 PMCID: PMC11083483 DOI: 10.3390/ijms25094711] [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: 03/22/2024] [Revised: 04/21/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024] Open
Abstract
Soluble starch synthases (SSs) play important roles in the synthesis of cassava starch. However, the expression characteristics of the cassava SSs genes have not been elucidated. In this study, the MeSSIII-1 gene and its promoter, from SC8 cassava cultivars, were respectively isolated by PCR amplification. MeSSIII-1 protein was localized to the chloroplasts. qRT-PCR analysis revealed that the MeSSIII-1 gene was expressed in almost all tissues tested, and the expression in mature leaves was 18.9 times more than that in tuber roots. MeSSIII-1 expression was induced by methyljasmonate (MeJA), abscisic acid (ABA), and ethylene (ET) hormones in cassava. MeSSIII-1 expression patterns were further confirmed in proMeSSIII-1 transgenic cassava. The promoter deletion analysis showed that the -264 bp to -1 bp MeSSIII-1 promoter has basal activity. The range from -1228 bp to -987 bp and -488 bp to -264 bp significantly enhance promoter activity. The regions from -987 bp to -747 bp and -747 bp to -488 bp have repressive activity. These findings will provide an important reference for research on the potential function and transcriptional regulation mechanisms of the MeSSIII-1 gene and for further in-depth exploration of the regulatory network of its internal functional elements.
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Affiliation(s)
- Xiao-Hua Lu
- National Key Laboratory for Tropical Crop Breeding, School of Life and Health Sciences, Hainan University, Haikou 570228, China; (X.-H.L.); (X.-H.Z.); (M.P.); (X.-W.H.)
| | - Ya-Jie Wang
- National Key Laboratory for Tropical Crop Breeding, Sanya Research Institute, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (Y.-J.W.); (H.Y.); (R.-M.L.); (J.L.)
| | - Xing-Hou Zhen
- National Key Laboratory for Tropical Crop Breeding, School of Life and Health Sciences, Hainan University, Haikou 570228, China; (X.-H.L.); (X.-H.Z.); (M.P.); (X.-W.H.)
| | - Hui Yu
- National Key Laboratory for Tropical Crop Breeding, Sanya Research Institute, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (Y.-J.W.); (H.Y.); (R.-M.L.); (J.L.)
| | - Mu Pan
- National Key Laboratory for Tropical Crop Breeding, School of Life and Health Sciences, Hainan University, Haikou 570228, China; (X.-H.L.); (X.-H.Z.); (M.P.); (X.-W.H.)
| | - Dong-Qing Fu
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China;
| | - Rui-Mei Li
- National Key Laboratory for Tropical Crop Breeding, Sanya Research Institute, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (Y.-J.W.); (H.Y.); (R.-M.L.); (J.L.)
| | - Jiao Liu
- National Key Laboratory for Tropical Crop Breeding, Sanya Research Institute, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (Y.-J.W.); (H.Y.); (R.-M.L.); (J.L.)
| | - Hai-Yan Luo
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China;
| | - Xin-Wen Hu
- National Key Laboratory for Tropical Crop Breeding, School of Life and Health Sciences, Hainan University, Haikou 570228, China; (X.-H.L.); (X.-H.Z.); (M.P.); (X.-W.H.)
| | - Yuan Yao
- National Key Laboratory for Tropical Crop Breeding, Sanya Research Institute, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (Y.-J.W.); (H.Y.); (R.-M.L.); (J.L.)
| | - Jian-Chun Guo
- National Key Laboratory for Tropical Crop Breeding, Sanya Research Institute, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (Y.-J.W.); (H.Y.); (R.-M.L.); (J.L.)
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Ma Q, Feng Y, Luo S, Cheng L, Tong W, Lu X, Li Y, Zhang P. The aquaporin MePIP2;7 improves MeMGT9-mediated Mg 2 + acquisition in cassava. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:2349-2367. [PMID: 37548108 DOI: 10.1111/jipb.13552] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 08/03/2023] [Indexed: 08/08/2023]
Abstract
Aquaporins are important transmembrane water transport proteins which transport water and several neutral molecules. However, how aquaporins are involved in the synergistic transport of Mg2+ and water remains poorly understood. Here, we found that the cassava aquaporin MePIP2;7 was involved in Mg2+ transport through interaction with MeMGT9, a lower affinity magnesium transporter protein. Knockdown of MePIP2;7 in cassava led to magnesium deficiency in basal mature leaves with chlorosis and necrotic spots on their edges and starch over-accumulation. Mg2+ content was significantly decreased in leaves and roots of MePIP2;7-RNA interference (PIP-Ri) plants grown in both field and Mg2+ -free hydroponic solution. Xenopus oocyte injection analysis verified that MePIP2;7 possessed the ability to transport water only and MeMGT9 was responsible for Mg2+ efflux. More importantly, MePIP2;7 improved the transportability of Mg2+ via MeMGT9 as verified using the CM66 mutant complementation assay and Xenopus oocytes expressing system. Yeast two-hybrid, bimolecular fluorescence complementation, co-localization, and co-immunoprecipitation assays demonstrated the direct protein-protein interaction between MePIP2;7 and MeMGT9 in vivo. Mg2+ flux was significantly elevated in MePIP2;7-overexpressing lines in hydroponic solution through non-invasive micro-test technique analysis. Under Mg2+ -free condition, the retarded growth of PIP-Ri transgenic plants could be recovered with Mg2+ supplementation. Taken together, our results demonstrated the synergistic effect of the MePIP2;7 and MeMGT9 interaction in regulating water and Mg2+ absorption and transport in cassava.
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Affiliation(s)
- Qiuxiang Ma
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yancai Feng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shu Luo
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lu Cheng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Weijing Tong
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xinlu Lu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Youzhi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Peng Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
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Castellanos JF, Khan A, Fettke J. Gradual Analytics of Starch-Interacting Proteins Revealed the Involvement of Starch-Phosphorylating Enzymes during Synthesis of Storage Starch in Potato ( Solanum tuberosum L.) Tubers. Molecules 2023; 28:6219. [PMID: 37687048 PMCID: PMC10489031 DOI: 10.3390/molecules28176219] [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: 08/02/2023] [Revised: 08/10/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023] Open
Abstract
The complete mechanism behind starch regulation has not been fully characterized. However, significant progress can be achieved through proteomic approaches. In this work, we aimed to characterize the starch-interacting proteins in potato (Solanum tuberosum L. cv. Desiree) tubers under variable circumstances. Starch-interacting proteins were extracted from developing tubers of wild type and transgenic lines containing antisense inhibition of glucan phosphorylases. Further, proteins were separated by SDS-PAGE and characterized through mass spectrometry. Additionally, starch-interacting proteins were analyzed in potato tubers stored at different temperatures. Most of the proteins strongly interacting with the potato starch granules corresponded to proteins involved in starch metabolism. GWD and PWD, two dikinases associated with starch degradation, were consistently found bound to the starch granules. This indicates that their activity is not only restricted to degradation but is also essential during storage starch synthesis. We confirmed the presence of protease inhibitors interacting with the potato starch surface as previously revealed by other authors. Starch interacting protein profiles of transgenic tubers appeared differently from wild type when tubers were stored under different temperatures, indicating a differential expression in response to changing environmental conditions.
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Affiliation(s)
| | | | - Joerg Fettke
- Biopolymer Analytics, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Building 20, 14476 Potsdam-Golm, Germany; (J.F.C.); (A.K.)
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Tiozon RJN, Fettke J, Sreenivasulu N, Fernie AR. More than the main structural genes: Regulation of resistant starch formation in rice endosperm and its potential application. JOURNAL OF PLANT PHYSIOLOGY 2023; 285:153980. [PMID: 37086697 DOI: 10.1016/j.jplph.2023.153980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 03/07/2023] [Accepted: 04/03/2023] [Indexed: 05/03/2023]
Abstract
In the past decade, research on resistant starch has evoked interest due to the prevention and inhibition of chronic human diseases, such as diabetes, cancer, and obesity. Increasing the amylose content (AC) and resistant starch (RS) has been pivotal in improving the nutritional benefit of rice. However, the exact mechanism of RS formation is complex due to interconnected genetic factors regulating amylose-amylopectin variation. In this review, we discussed the regulatory factors influencing the RS formation centered on the transcription, post-transcriptional, and post-translational processes. Furthermore, we described the developments in RS and AC levels in rice compared with other high RS cereals. Briefly, we enumerated potential applications of high RS mutants in health, medical, and other industries. We contest that the information captured herein can be deployed for marker-assisted breeding and precision breeding techniques through genome editing to improve rice varieties with enhanced RS content.
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Affiliation(s)
- Rhowell Jr N Tiozon
- Consumer Driven Grain Quality and Nutrition Unit, Rice Breeding and Innovation Platform, International Rice Research Institute, Los Baños, 4030, Philippines; Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Joerg Fettke
- Biopolymer Analytics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
| | - Nese Sreenivasulu
- Consumer Driven Grain Quality and Nutrition Unit, Rice Breeding and Innovation Platform, International Rice Research Institute, Los Baños, 4030, Philippines
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
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Ma M, Zhong W, Zhang Q, Deng L, Wen J, Yi B, Tu J, Fu T, Zhao L, Shen J. Genome-wide analysis of transcriptome and histone modifications in Brassica napus hybrid. FRONTIERS IN PLANT SCIENCE 2023; 14:1123729. [PMID: 36778699 PMCID: PMC9911877 DOI: 10.3389/fpls.2023.1123729] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
Although utilization of heterosis has largely improved the yield of many crops worldwide, the underlying molecular mechanism of heterosis, particularly for allopolyploids, remains unclear. Here, we compared epigenome and transcriptome data of an elite hybrid and its parental lines in three assessed tissues (seedling, flower bud, and silique) to explore their contribution to heterosis in allopolyploid B. napus. Transcriptome analysis illustrated that a small proportion of non-additive genes in the hybrid compared with its parents, as well as parental expression level dominance, might have a significant effect on heterosis. We identified histone modification (H3K4me3 and H3K27me3) variation between the parents and hybrid, most of which resulted from the differences between parents. H3K4me3 variations were positively correlated with gene expression differences among the hybrid and its parents. Furthermore, H3K4me3 and H3K27me3 were rather stable in hybridization and were mainly inherited additively in the B. napus hybrid. Together, our data revealed that transcriptome reprogramming and histone modification remodeling in the hybrid could serve as valuable resources for better understanding heterosis in allopolyploid crops.
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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] [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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Apriyanto A, Compart J, Fettke J. A review of starch, a unique biopolymer - Structure, metabolism and in planta modifications. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 318:111223. [PMID: 35351303 DOI: 10.1016/j.plantsci.2022.111223] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/02/2022] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Starch is a complex carbohydrate polymer produced by plants and especially by crops in huge amounts. It consists of amylose and amylopectin, which have α-1,4- and α-1,6-linked glucose units. Despite this simple chemistry, the entire starch metabolism is complex, containing various (iso)enzymes/proteins. However, whose interplay is still not yet fully understood. Starch is essential for humans and animals as a source of nutrition and energy. Nowadays, starch is also commonly used in non-food industrial sectors for a variety of purposes. However, native starches do not always satisfy the needs of a wide range of (industrial) applications. This review summarizes the structural properties of starch, analytical methods for starch characterization, and in planta starch modifications.
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Affiliation(s)
- Ardha Apriyanto
- Biopolymer Analytics, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Building 20, 14476 Potsdam-Golm, Germany
| | - Julia Compart
- Biopolymer Analytics, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Building 20, 14476 Potsdam-Golm, Germany
| | - Joerg Fettke
- Biopolymer Analytics, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Building 20, 14476 Potsdam-Golm, Germany.
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He S, Hao X, Wang S, Zhou W, Ma Q, Lu X, Chen L, Zhang P. Starch synthase II plays a crucial role in starch biosynthesis and the formation of multienzyme complexes in cassava storage roots. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2540-2557. [PMID: 35134892 DOI: 10.1093/jxb/erac022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 02/02/2022] [Indexed: 06/14/2023]
Abstract
Starch is a glucose polymer synthesized by green plants for energy storage and is crucial for plant growth and reproduction. The biosynthesis of starch polysaccharides is mediated by members of the large starch synthase (SS) protein superfamily. Here, we showed that in cassava storage roots, soluble starch synthase II (MeSSII) plays an important role in starch biosynthesis and the formation of protein complexes with other starch biosynthetic enzymes by directly interacting with MeSSI, MeSBEII, and MeISAII. MeSSII-RNAi cassava lines showed increased amylose content and reduced biosynthesis of the intermediate chain of amylopectin (B1 type) in their storage roots, leading to altered starch physicochemical properties. Furthermore, gel permeation chromatography analysis of starch biosynthetic enzymes between wild type and MeSSII-RNAi lines confirmed the key role of MeSSII in the organization of heteromeric starch synthetic protein complexes. The lack of MeSSII in cassava also reduced the capacity of MeSSI, MeSBEII, MeISAI, and MeISAII to bind to starch granules. These findings shed light on the key components of the starch biosynthesis machinery in root crops.
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Affiliation(s)
- Shutao He
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaomeng Hao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shanshan Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wenzhi Zhou
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Qiuxiang Ma
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xinlu Lu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Luonan Chen
- Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
- Guangdong Institute of Intelligence Science and Technology, Hengqin, Zhuhai, Guangdong, China
| | - Peng Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
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12
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Wang Z, Wei K, Xiong M, Wang J, Zhang C, Fan X, Huang L, Zhao D, Liu Q, Li Q. Glucan, Water-Dikinase 1 (GWD1), an ideal biotechnological target for potential improving yield and quality in rice. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2606-2618. [PMID: 34416068 PMCID: PMC8633486 DOI: 10.1111/pbi.13686] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 08/13/2021] [Accepted: 08/15/2021] [Indexed: 05/07/2023]
Abstract
The source-sink relationship determines the overall agronomic performance of rice. Cloning and characterizing key genes involved in the regulation of source and sink dynamics is imperative for improving rice yield. However, few source genes with potential application in rice have been identified. Glucan, Water-Dikinase 1 (GWD1) is an essential enzyme that plays a pivotal role in the first step of transitory starch degradation in source tissues. In the present study, we successfully generated gwd1 weak mutants by promoter editing using CRISPR/Cas9 system, and also leaf-dominant overexpression lines of GWD1 driven by Osl2 promoter. Analysis of the gwd1 plants indicated that promoter editing mediated down-regulation of GWD1 caused no observable effects on rice growth and development, but only mildly modified its grain transparency and seed germination. However, the transgenic pOsl2::GWD1 overexpression lines showed improvements in multiple key traits, including rice yield, grain shape, rice quality, seed germination and stress tolerance. Therefore, our study shows that GWD1 is not only involved in transitory starch degradation in source tissues, but also plays key roles in the seeds, which is a sink tissue. In conclusion, we find that GWD1 is an ideal biotechnological target with promising potential for the breeding of elite rice cultivars via genetic engineering.
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Affiliation(s)
- Zhen Wang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding /Key Laboratory of Plant Functional Genomics of the Ministry of EducationCollege of AgricultureYangzhou UniversityYangzhouJiangsuChina
| | - Ke Wei
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding /Key Laboratory of Plant Functional Genomics of the Ministry of EducationCollege of AgricultureYangzhou UniversityYangzhouJiangsuChina
| | - Min Xiong
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding /Key Laboratory of Plant Functional Genomics of the Ministry of EducationCollege of AgricultureYangzhou UniversityYangzhouJiangsuChina
| | - Jin‐Dong Wang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding /Key Laboratory of Plant Functional Genomics of the Ministry of EducationCollege of AgricultureYangzhou UniversityYangzhouJiangsuChina
| | - Chang‐Quan Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding /Key Laboratory of Plant Functional Genomics of the Ministry of EducationCollege of AgricultureYangzhou UniversityYangzhouJiangsuChina
- Co‐Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province / Jiangsu Key Laboratory of Crop Genetics and PhysiologyYangzhou UniversityYangzhouJiangsuChina
| | - Xiao‐Lei Fan
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding /Key Laboratory of Plant Functional Genomics of the Ministry of EducationCollege of AgricultureYangzhou UniversityYangzhouJiangsuChina
- Co‐Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province / Jiangsu Key Laboratory of Crop Genetics and PhysiologyYangzhou UniversityYangzhouJiangsuChina
| | - Li‐Chun Huang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding /Key Laboratory of Plant Functional Genomics of the Ministry of EducationCollege of AgricultureYangzhou UniversityYangzhouJiangsuChina
- Co‐Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province / Jiangsu Key Laboratory of Crop Genetics and PhysiologyYangzhou UniversityYangzhouJiangsuChina
| | - Dong‐Sheng Zhao
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding /Key Laboratory of Plant Functional Genomics of the Ministry of EducationCollege of AgricultureYangzhou UniversityYangzhouJiangsuChina
- Co‐Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province / Jiangsu Key Laboratory of Crop Genetics and PhysiologyYangzhou UniversityYangzhouJiangsuChina
| | - Qiao‐Quan Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding /Key Laboratory of Plant Functional Genomics of the Ministry of EducationCollege of AgricultureYangzhou UniversityYangzhouJiangsuChina
- Co‐Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province / Jiangsu Key Laboratory of Crop Genetics and PhysiologyYangzhou UniversityYangzhouJiangsuChina
| | - Qian‐Feng Li
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding /Key Laboratory of Plant Functional Genomics of the Ministry of EducationCollege of AgricultureYangzhou UniversityYangzhouJiangsuChina
- Co‐Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province / Jiangsu Key Laboratory of Crop Genetics and PhysiologyYangzhou UniversityYangzhouJiangsuChina
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13
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Engineering Properties of Sweet Potato Starch for Industrial Applications by Biotechnological Techniques including Genome Editing. Int J Mol Sci 2021; 22:ijms22179533. [PMID: 34502441 PMCID: PMC8431112 DOI: 10.3390/ijms22179533] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/20/2021] [Accepted: 08/29/2021] [Indexed: 11/25/2022] Open
Abstract
Sweet potato (Ipomoea batatas) is one of the largest food crops in the world. Due to its abundance of starch, sweet potato is a valuable ingredient in food derivatives, dietary supplements, and industrial raw materials. In addition, due to its ability to adapt to a wide range of harsh climate and soil conditions, sweet potato is a crop that copes well with the environmental stresses caused by climate change. However, due to the complexity of the sweet potato genome and the long breeding cycle, our ability to modify sweet potato starch is limited. In this review, we cover the recent development in sweet potato breeding, understanding of starch properties, and the progress in sweet potato genomics. We describe the applicational values of sweet potato starch in food, industrial products, and biofuel, in addition to the effects of starch properties in different industrial applications. We also explore the possibility of manipulating starch properties through biotechnological means, such as the CRISPR/Cas-based genome editing. The ability to target the genome with precision provides new opportunities for reducing breeding time, increasing yield, and optimizing the starch properties of sweet potatoes.
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14
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Fan W, Zhang Y, Wu Y, Zhou W, Yang J, Yuan L, Zhang P, Wang H. The H +-pyrophosphatase IbVP1 regulates carbon flux to influence the starch metabolism and yield of sweet potato. HORTICULTURE RESEARCH 2021; 8:20. [PMID: 33518705 PMCID: PMC7847997 DOI: 10.1038/s41438-020-00454-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 11/19/2020] [Accepted: 11/28/2020] [Indexed: 05/10/2023]
Abstract
Storage roots of sweet potato are important sink organs for photoassimilates and energy, and carbohydrate metabolism in storage roots affects yield and starch production. Our previous study showed that sweet potato H+-pyrophosphatase (IbVP1) plays a vital role in mitigating iron deficiency and positively controls fibrous root growth. However, its roles in regulating starch production in storage roots have not been investigated. In this study, we found that IbVP1 overexpression in sweet potato improved the photosynthesis ability of and sucrose content in source leaves and increased both the starch content in and total yield of sink tissues. Using 13C-labeled sucrose feeding, we determined that IbVP1 overexpression promotes phloem loading and sucrose long-distance transport and enhances Pi-use efficiency. In sweet potato plants overexpressing IbVP1, the expression levels of starch biosynthesis pathway genes, especially AGPase and GBSSI, were upregulated, leading to changes in the structure, composition, and physicochemical properties of stored starch. Our study shows that the IbVP1 gene plays an important role in regulating starch metabolism in sweet potato. Application of the VP1 gene in genetic engineering of sweet potato cultivars may allow the improvement of starch production and yield under stress or nutrient-limited conditions.
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Affiliation(s)
- Weijuan Fan
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Yandi Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yinliang Wu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenzhi Zhou
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jun Yang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Ling Yuan
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA
| | - Peng Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Hongxia Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
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15
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Mathew IE, Priyadarshini R, Mahto A, Jaiswal P, Parida SK, Agarwal P. SUPER STARCHY1/ONAC025 participates in rice grain filling. PLANT DIRECT 2020; 4:e00249. [PMID: 32995698 PMCID: PMC7507516 DOI: 10.1002/pld3.249] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 06/10/2020] [Accepted: 07/10/2020] [Indexed: 05/04/2023]
Abstract
NAC transcription factors (TFs) are known for their role in development and stress. This article attempts to functionally validate the role of rice SS1/ ONAC025 (LOC_Os11g31330) during seed development. The gene is seed-specific and its promoter directs reporter expression in the developing endosperm and embryo in rice transgenic plants. Furthermore, rice transgenic plants ectopically expressing SS1/ ONAC025 have a plantlet lethal phenotype with hampered vegetative growth, but increased tillers and an altered shoot apical meristem structure. The vegetative cells of these plantlets are filled with distinct starch granules. RNAseq analysis of two independent plantlets reveals the differential expression of reproductive and photosynthetic genes. A comparison with seed development transcriptome indicates differential regulation of many seed-related genes by SS1/ ONAC025. Genes involved in starch biosynthesis, especially amylopectin and those encoding seed storage proteins, and regulating seed size are also differentially expressed. In conjunction, SS1/ ONAC025 shows highest expression in japonica rice. As a TF, SS1/ ONAC025 is a transcriptional repressor localized to endoplasmic reticulum and nucleus. The article shows that SS1/ ONAC025 is a seed-specific gene promoting grain filling in rice, and negatively affecting vegetative growth.
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Affiliation(s)
| | | | - Arunima Mahto
- National Institute of Plant Genome ResearchNew DelhiIndia
| | - Priya Jaiswal
- National Institute of Plant Genome ResearchNew DelhiIndia
| | | | - Pinky Agarwal
- National Institute of Plant Genome ResearchNew DelhiIndia
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16
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Adegbaju MS, Morenikeji OB, Borrego EJ, Hudson AO, Thomas BN. Differential Evolution of α-Glucan Water Dikinase (GWD) in Plants. PLANTS 2020; 9:plants9091101. [PMID: 32867090 PMCID: PMC7569903 DOI: 10.3390/plants9091101] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/13/2020] [Accepted: 08/22/2020] [Indexed: 11/16/2022]
Abstract
The alpha-glucan water dikinase (GWD) enzyme catalyzes starch phosphorylation, an integral step in transitory starch degradation. The high phosphate content in stored starch has great industrial value, due to its physio–chemical properties making it more versatile, although the phosphate content of stored starch varies depending on the botanical source. In this study, we used various computational approaches to gain insights into the evolution of the GWD protein in 48 plant species with possible roles in enzyme function and alteration of phosphate content in their stored starch. Our analyses identified deleterious mutations, particularly in the highly conserved 5 aromatic amino acid residues in the dual tandem carbohydrate binding modules (CBM-45) of GWD protein in C. zofingiensis, G. hirsutum, A. protothecoides, P. miliaceum, and C. reinhardtii. These findings will inform experimental designs for simultaneous repression of genes coding for GWD and the predicted interacting proteins to elucidate the role this enzyme plays in starch degradation. Our results reveal significant diversity in the evolution of GWD enzyme across plant species, which may be evolutionarily advantageous according to the varying needs for phosphorylated stored starch between plants and environments.
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Affiliation(s)
- Muyiwa S. Adegbaju
- Institute for Plant Biotechnology, Stellenbosch University, Stellenbosch 7600, South Africa;
| | - Olanrewaju B. Morenikeji
- Department of Biomedical Sciences, College of Health Science and Technology, Rochester Institute of Technology, Rochester, NY 14623, USA;
- Department of Biology, Hamilton College, Clinton, NY 14623, USA
| | - Eli J. Borrego
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA; (E.J.B.); (A.O.H.)
| | - André O. Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA; (E.J.B.); (A.O.H.)
| | - Bolaji N. Thomas
- Department of Biomedical Sciences, College of Health Science and Technology, Rochester Institute of Technology, Rochester, NY 14623, USA;
- Correspondence: ; Tel.: +1-(585)-475-6382; Fax: +1-(585)-475-5809
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17
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Zhou W, Zhao S, He S, Ma Q, Lu X, Hao X, Wang H, Yang J, Zhang P. Production of very-high-amylose cassava by post-transcriptional silencing of branching enzyme genes. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:832-846. [PMID: 31180179 DOI: 10.1111/jipb.12848] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 05/30/2019] [Indexed: 06/09/2023]
Abstract
High amylose starch can be produced by plants deficient in the function of branching enzymes (BEs). Here we report the production of transgenic cassava (Manihot esculenta Crantz) with starches containing up to 50% amylose due to the constitutive expression of hair-pin dsRNAs targeting the BE1 or BE2 genes. All BE1-RNAi plant lines (BE1i) and BE2-RNAi plant lines (BE2i) were grown up in the field, but with reduced total biomass production. Considerably high amylose content in the storage roots of BE2i plant lines was achieved. Storage starch granules of BE1i and BE2i plants had similar morphology as wild type (WT), however, the size of BE1i starch granules were bigger than that of WT. Comparisons of amylograms and thermograms of all three sources of storage starches revealed dramatic changes to the pasting properties and a higher melting temperature for BE2i starches. Glucan chain length distribution analysis showed a slight increase in chains of DP>36 in BE1i lines and a dramatic increase in glucan chains between DP 10-20 and DP>40 in BE2i lines. Furthermore, BE2i starches displayed a B-type X-ray diffraction pattern instead of the A-type pattern found in BE1i and WT starches. Therefore, cassava BE1 and BE2 function differently in storage root starch biosynthesis.
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Affiliation(s)
- Wenzhi Zhou
- 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, the Chinese Academy of Sciences, Shanghai, 200032, China
| | - Shanshan Zhao
- 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, the Chinese Academy of Sciences, Shanghai, 200032, China
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, the Chinese Academy of Sciences, Shanghai, 201602, China
| | - Shutao He
- 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, the Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - 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, the Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xinlu Lu
- 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, the Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xiaomeng Hao
- 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, the Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hongxia Wang
- 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, the Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jun Yang
- 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, the Chinese Academy of Sciences, Shanghai, 200032, China
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, the Chinese Academy of Sciences, Shanghai, 201602, 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, the Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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18
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Li L, Deng M, Lyu C, Zhang J, Peng J, Cai C, Yang S, Lu L, Ni S, Liu F, Zheng S, Yu L, Wang X. Quantitative phosphoproteomics analysis reveals that protein modification and sugar metabolism contribute to sprouting in potato after BR treatment. Food Chem 2020; 325:126875. [PMID: 32387993 DOI: 10.1016/j.foodchem.2020.126875] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 01/02/2020] [Accepted: 04/19/2020] [Indexed: 12/12/2022]
Abstract
Brassinosteroids (BRs), a new class of steroid hormones, are involved in the regulation of plant cell elongation and seed germination. Nevertheless, the molecular mechanism of the effect of BRs on tuber sprouting remains largely unknown. In this study, quantitative phosphoproteomics was employed to investigate the protein phosphorylation changes in sprouting induced by BRs. Our results showed that BRs accelerated the conversion of starch into soluble sugar in tubers. A functional enrichment cluster analysis suggested that the "amino acid metabolism pathway" was upregulated and that "plant hormone signal transduction and protein export" were downregulated. BR treatment also changed the phosphorylation of proteins involved in the BR, ABA, starch and sugar signal transduction pathways, such as serine/threonine-protein kinase (BSK), 14-3-3, alpha-glucan water dikinase (GWD), sucrose-phosphate synthase (SPS), sucrose synthase (SS) and alkaline/neutral invertase (A/N-INV). These results shed more light on the pattern of protein phosphorylation in BR promoting potato sprouting.
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Key Words
- 1,3-DPG, PubChem CID: 683
- 2-DPG, PubChem CID: 59
- 3-DPG, PubChem CID: 724
- Amylopectin, PubChem CID: 439207
- Amylose, PubChem CID: 53477771
- Brassinosteroids
- Glucose, PubChem CID: 107526
- PGAL, PubChem CID: 729
- Phosphoproteomics
- Potato
- Sprouting
- Sucrose, PubChem CID: 5988
- α-D-Glucose, PubChem CID: 79025
- α-D-Glucose-1P, PubChem CID: 65533
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Affiliation(s)
- Liqin Li
- College of Agronomy, Sichuan Agriculture University, Chengdu 611130, China.
| | - Mengsheng Deng
- College of Agronomy, Sichuan Agriculture University, Chengdu 611130, China.
| | - Chengcheng Lyu
- College of Agronomy, Sichuan Agriculture University, Chengdu 611130, China.
| | - Jie Zhang
- College of Agronomy, Sichuan Agriculture University, Chengdu 611130, China.
| | - Jie Peng
- College of Agronomy, Sichuan Agriculture University, Chengdu 611130, China.
| | - Chengcheng Cai
- College of Agronomy, Sichuan Agriculture University, Chengdu 611130, China.
| | - Shimin Yang
- College of Agronomy, Sichuan Agriculture University, Chengdu 611130, China.
| | - Liming Lu
- College of Agronomy, Sichuan Agriculture University, Chengdu 611130, China.
| | - Su Ni
- College of Agronomy, Sichuan Agriculture University, Chengdu 611130, China.
| | - Fan Liu
- College of Agronomy, Sichuan Agriculture University, Chengdu 611130, China.
| | - Shunlin Zheng
- College of Agronomy, Sichuan Agriculture University, Chengdu 611130, China.
| | - Liping Yu
- College of Agronomy, Sichuan Agriculture University, Chengdu 611130, China.
| | - Xiyao Wang
- College of Agronomy, Sichuan Agriculture University, Chengdu 611130, China.
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19
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Mdodana NT, Jewell JF, Phiri EE, Smith ML, Oberlander K, Mahmoodi S, Kossmann J, Lloyd JR. Mutations in Glucan, Water Dikinase Affect Starch Degradation and Gametophore Development in the Moss Physcomitrella patens. Sci Rep 2019; 9:15114. [PMID: 31641159 PMCID: PMC6805951 DOI: 10.1038/s41598-019-51632-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 10/01/2019] [Indexed: 11/23/2022] Open
Abstract
The role of starch degradation in non-vascular plants is poorly understood. To expand our knowledge of this area, we have studied this process in Physcomitrella patens. This has been achieved through examination of the step known to initiate starch degradation in angiosperms, glucan phosphorylation, catalysed by glucan, water dikinase (GWD) enzymes. Phylogenetic analysis indicates that GWD isoforms can be divided into two clades, one of which contains GWD1/GWD2 and the other GWD3 isoforms. These clades split at a very early stage within plant evolution, as distinct sequences that cluster within each were identified in all major plant lineages. Of the five genes we identified within the Physcomitrella genome that encode GWD-like enzymes, two group within the GWD1/GWD2 clade and the others within the GWD3 clade. Proteins encoded by both loci in the GWD1/GWD2 clade, named PpGWDa and PpGWDb, are localised in plastids. Mutations of either PpGWDa or PpGWDb reduce starch phosphate abundance, however, a mutation at the PpGWDa locus had a much greater influence than one at PpGWDb. Only mutations affecting PpGWDa inhibited starch degradation. Mutants lacking this enzyme also failed to develop gametophores, a phenotype that could be chemically complemented using glucose supplementation within the growth medium.
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Affiliation(s)
- Ntombizanele T Mdodana
- Department of Genetics, Institute for Plant Biotechnology, University of Stellenbosch, Stellenbosch, South Africa
| | - Jonathan F Jewell
- Department of Genetics, Institute for Plant Biotechnology, University of Stellenbosch, Stellenbosch, South Africa
| | - Ethel E Phiri
- Department of Genetics, Institute for Plant Biotechnology, University of Stellenbosch, Stellenbosch, South Africa
| | - Marthinus L Smith
- Department of Genetics, Institute for Plant Biotechnology, University of Stellenbosch, Stellenbosch, South Africa
| | - Kenneth Oberlander
- Schweickerdt Herbarium, Department of Plant and Soil Sciences, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa
| | - Saire Mahmoodi
- Department of Genetics, Institute for Plant Biotechnology, University of Stellenbosch, Stellenbosch, South Africa
| | - Jens Kossmann
- Department of Genetics, Institute for Plant Biotechnology, University of Stellenbosch, Stellenbosch, South Africa
| | - James R Lloyd
- Department of Genetics, Institute for Plant Biotechnology, University of Stellenbosch, Stellenbosch, South Africa.
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20
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Dhiman N, Sharma NK, Thapa P, Sharma I, Kumar Swarnkar M, Chawla A, Shankar R, Bhattacharya A. De novo transcriptome provides insights into the growth behaviour and resveratrol and trans-stilbenes biosynthesis in Dactylorhiza hatagirea - An endangered alpine terrestrial orchid of western Himalaya. Sci Rep 2019; 9:13133. [PMID: 31511556 PMCID: PMC6739469 DOI: 10.1038/s41598-019-49446-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 08/22/2019] [Indexed: 11/18/2022] Open
Abstract
This is the first report on de novo transcriptome of Dactylorhiza hatagirea, a critically-endangered, terrestrial orchid of alpine Himalayas. The plant is acclaimed for medicinal properties but little is known about its secondary-metabolites profile or cues regulating their biosynthesis. De novo transcriptome analysis was therefore, undertaken to gain basic understanding on these aspects, while circumventing the acute limitation of plant material availability. 65,384 transcripts and finally, 37,371 unigenes were assembled de novo from a total of 236 million reads obtained from shoot, tuber and leaves of the plant. Dominance of differentially-expressing-genes (DEGs) related to cold-stress-response and plant-hormone-signal-transduction; and those involved in photosynthesis, sugar-metabolism and secondary-metabolite-synthesis provided insights into carbohydrate-partitioning in the plant during its preparation for freezing winter at natural habitat. DEGs of glucomannan, ascorbic acid, carotenoids, phylloquinone/naphthoquinones, indole alkaloids, resveratrol and stilbene biosynthesis revealed the secondary-metabolite profile of D. hatagirea. UHPLC results confirmed appreciable amounts of resveratrol and trans-stilbene in D. hatagirea tubers, for the first time. Expression analysis of 15 selected genes including those of phenylpropanoid pathway confirmed the validity of RNA-seq data. Opportunistic growth, temperature- and tissue-specific-differential-expression of secondary metabolite biosynthesis and stress tolerant genes were confirmed using clonal plants growing at 8, 15 and 25 °C.
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Affiliation(s)
- Nisha Dhiman
- Division of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, H.P., India
- Academy of Scientific and Innovative Research(AcSIR), CSIR-Institute of Himalayan Bio-Resource Technology, Palampur, 176061, Himachal Pradesh, India
| | - Nitesh Kumar Sharma
- Division of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, H.P., India
- Academy of Scientific and Innovative Research(AcSIR), CSIR-Institute of Himalayan Bio-Resource Technology, Palampur, 176061, Himachal Pradesh, India
| | - Pooja Thapa
- Division of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, H.P., India
| | - Isha Sharma
- Division of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, H.P., India
| | - Mohit Kumar Swarnkar
- Division of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, H.P., India
| | - Amit Chawla
- Division of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, H.P., India
- Academy of Scientific and Innovative Research(AcSIR), CSIR-Institute of Himalayan Bio-Resource Technology, Palampur, 176061, Himachal Pradesh, India
| | - Ravi Shankar
- Division of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, H.P., India.
- Academy of Scientific and Innovative Research(AcSIR), CSIR-Institute of Himalayan Bio-Resource Technology, Palampur, 176061, Himachal Pradesh, India.
| | - Amita Bhattacharya
- Division of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, H.P., India.
- Academy of Scientific and Innovative Research(AcSIR), CSIR-Institute of Himalayan Bio-Resource Technology, Palampur, 176061, Himachal Pradesh, India.
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Yan W, Wu X, Li Y, Liu G, Cui Z, Jiang T, Ma Q, Luo L, Zhang P. Cell Wall Invertase 3 Affects Cassava Productivity via Regulating Sugar Allocation From Source to Sink. FRONTIERS IN PLANT SCIENCE 2019; 10:541. [PMID: 31114601 PMCID: PMC6503109 DOI: 10.3389/fpls.2019.00541] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 04/09/2019] [Indexed: 05/28/2023]
Abstract
Storage roots are the main sink for photo-assimilate accumulation and reflect cassava yield and productivity. Regulation of sugar partitioning from leaves to storage roots has not been elucidated. Cell wall invertases are involved in the hydrolysis of sugar during phloem unloading of vascular plants to control plant development and sink strength but have rarely been studied in root crops like cassava. MeCWINV3 encodes a typical cell wall invertase in cassava and is mainly expressed in vascular bundles. The gene is highly expressed in leaves, especially mature leaves, in response to diurnal rhythm. When MeCWINV3 was overexpressed in cassava, sugar export from leaves to storage roots was largely inhibited and sucrose hydrolysis in leaves was accelerated, leading to increased transient starch accumulation by blocking starch degradation and reduced overall plant growth. The progress of leaf senescence was promoted in the MeCWINV3 over-expressed cassava plants with increased expression of senescence-related genes. Storage root development was also delayed because of dramatically reduced sugar allocation from leaves. As a result, the transcriptional expression of starch biosynthetic genes such as small subunit ADP-glucose pyrophosphorylase, granule-bound starch synthase I, and starch branching enzyme I was reduced in accordance with insufficient sugar supply in the storage roots of the transgenic plants. These results show that MeCWINV3 regulates sugar allocation from source to sink and maintains sugar balance in cassava, thus affecting yield of cassava storage roots.
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Affiliation(s)
- Wei Yan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
- 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
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan, China
| | - Xiaoyun Wu
- 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
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanan Li
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan, China
| | - Guanghua Liu
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan, China
| | - Zhanfei Cui
- 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
- University of Chinese Academy of Sciences, Beijing, China
| | - Tailing Jiang
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan, China
| | - 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
| | - Lijuan Luo
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 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
- University of Chinese Academy of Sciences, Beijing, China
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