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Qu L, Huang X, Su X, Zhu G, Zheng L, Lin J, Wang J, Xue H. Potato: from functional genomics to genetic improvement. MOLECULAR HORTICULTURE 2024; 4:34. [PMID: 39160633 PMCID: PMC11331666 DOI: 10.1186/s43897-024-00105-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 07/17/2024] [Indexed: 08/21/2024]
Abstract
Potato is the most widely grown non-grain crop and ranks as the third most significant global food crop following rice and wheat. Despite its long history of cultivation over vast areas, slow breeding progress and environmental stress have led to a scarcity of high-yielding potato varieties. Enhancing the quality and yield of potato tubers remains the ultimate objective of potato breeding. However, conventional breeding has faced challenges due to tetrasomic inheritance, high genomic heterozygosity, and inbreeding depression. Recent advancements in molecular biology and functional genomic studies of potato have provided valuable insights into the regulatory network of physiological processes and facilitated trait improvement. In this review, we present a summary of identified factors and genes governing potato growth and development, along with progress in potato genomics and the adoption of new breeding technologies for improvement. Additionally, we explore the opportunities and challenges in potato improvement, offering insights into future avenues for potato research.
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Affiliation(s)
- Li Qu
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xueqing Huang
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xin Su
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Guoqing Zhu
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lingli Zheng
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jing Lin
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiawen Wang
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hongwei Xue
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China.
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Apriyanto A, Compart J, Fettke J. Transcriptomic analysis of mesocarp tissue during fruit development of the oil palm revealed specific isozymes related to starch metabolism that control oil yield. FRONTIERS IN PLANT SCIENCE 2023; 14:1220237. [PMID: 37554560 PMCID: PMC10405827 DOI: 10.3389/fpls.2023.1220237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 07/05/2023] [Indexed: 08/10/2023]
Abstract
The oil palm (Elaeis guineensis Jacq.) produces a large amount of oil from the fruit. However, increasing the oil production in this fruit is still challenging. A recent study has shown that starch metabolism is essential for oil synthesis in fruit-producing species. Therefore, the transcriptomic analysis by RNA-seq was performed to observe gene expression alteration related to starch metabolism genes throughout the maturity stages of oil palm fruit with different oil yields. Gene expression profiles were examined with three different oil yields group (low, medium, and high) at six fruit development phases (4, 8, 12, 16, 20, and 22 weeks after pollination). We successfully identified and analyzed differentially expressed genes in oil palm mesocarps during development. The results showed that the transcriptome profile for each developmental phase was unique. Sucrose flux to the mesocarp tissue, rapid starch turnover, and high glycolytic activity have been identified as critical factors for oil production in oil palms. For starch metabolism and the glycolytic pathway, we identified specific gene expressions of enzyme isoforms (isozymes) that correlated with oil production, which may determine the oil content. This study provides valuable information for creating new high-oil-yielding palm varieties via breeding programs or genome editing approaches.
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Affiliation(s)
- Ardha Apriyanto
- Biopolymer Analytics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
- Research and Development, PT. Astra Agro Lestari Tbk, Jakarta Timur, Indonesia
| | - Julia Compart
- Biopolymer Analytics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
| | - Joerg Fettke
- Biopolymer Analytics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
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3
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Chincholikar P, Singh KR, Natarajan A, Kerry RG, Singh J, Malviya J, Singh RP. Green nanobiopolymers for ecological applications: a step towards a sustainable environment. RSC Adv 2023; 13:12411-12429. [PMID: 37091622 PMCID: PMC10116188 DOI: 10.1039/d2ra07707h] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 04/15/2023] [Indexed: 04/25/2023] Open
Abstract
To minimize the usage of non-renewable resources and to maintain a sustainable environment, the exploitation of green nanobiopolymers should be enhanced. Biopolymers are generally developed from various microorganisms and plants in the specified condition. This review article discusses the current advances and trends of biopolymers, particularly in the arena of nanotechnology. In addition, discussion on various synthesis steps and structural characterization of green polymer materials like cellulose, chitin, and lignin is also encompassed. This article aims to coordinate the most recent outputs and possible future utilization of nanobiopolymers to the ecosystem with negligible effects by promoting the utilities of polymeric materials like polycaprolactones, starch, and nanocellulose. Additionally, strategic modification of cellulose into nanocellulose via rearrangement of the polymeric compound to serve various industrial and medical purposes has also been highlighted in the review. Specifically, the process of nanoencapsulation and its advancements in terms of nutritional aspects was also presented. The potential utility of green nanobiopolymers is one of the best cost-effective alternatives concerning circular economy and thereby helps to maintain sustainability.
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Affiliation(s)
- Preeti Chincholikar
- Department of Chemistry, IES College of Technology Bhopal Madhya Pradesh India
| | - Kshitij Rb Singh
- Department of Chemistry, Banaras Hindu University Varanasi Uttar Pradesh India
| | - Arunadevi Natarajan
- Department of Chemistry, PSGR Krishnammal College for Women Coimbatore Tamil Nadu India
| | - Rout George Kerry
- Department of Biotechnology, Utkal University Bhubaneswar Odisha India
| | - Jay Singh
- Department of Chemistry, Banaras Hindu University Varanasi Uttar Pradesh India
| | - Jitendra Malviya
- Department of Life Sciences & Biological Sciences, IES University Bhopal Madhya Pradesh India
| | - Ravindra Pratap Singh
- Department of Biotechnology, Indira Gandhi National Tribal University Amarkantak Madhya Pradesh India
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4
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Iqbal A, Bocian J, Hameed A, Orczyk W, Nadolska-Orczyk A. Cis-Regulation by NACs: A Promising Frontier in Wheat Crop Improvement. Int J Mol Sci 2022; 23:ijms232315431. [PMID: 36499751 PMCID: PMC9736367 DOI: 10.3390/ijms232315431] [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: 11/09/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Crop traits are controlled by multiple genes; however, the complex spatio-temporal transcriptional behavior of genes cannot be fully understood without comprehending the role of transcription factors (TFs) and the underlying mechanisms of the binding interactions of their cis-regulatory elements. NAC belongs to one of the largest families of plant-specific TFs and has been associated with the regulation of many traits. This review provides insight into the cis-regulation of genes by wheat NACs (TaNACs) for the improvement in yield-related traits, including phytohormonal homeostasis, leaf senescence, seed traits improvement, root modulation, and biotic and abiotic stresses in wheat and other cereals. We also discussed the current potential, knowledge gaps, and prospects of TaNACs.
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Uitdewilligen JGAML, Wolters AMA, van Eck HJ, Visser RGF. Allelic variation for alpha-Glucan Water Dikinase is associated with starch phosphate content in tetraploid potato. PLANT MOLECULAR BIOLOGY 2022; 108:469-480. [PMID: 34994920 PMCID: PMC8894227 DOI: 10.1007/s11103-021-01236-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 12/13/2021] [Indexed: 06/14/2023]
Abstract
Association analysis resulted in the identification of specific StGWD alleles causing either an increase or decrease in starch phosphate content which was verified in diploid and tetraploid potato mapping populations. Potatoes are grown for various purposes like French fries, table potatoes, crisps and for their starch. One of the most important aspects of potato starch is that it contains a high amount of phosphate ester groups which are considered to be important for providing improved functionalization after derivatization processes. Little is known about the variation in phosphate content as such in different potato varieties and thus we studied the genetic diversity for this trait. From other studies it was clear that the phosphate content is controlled by a quantitative trait locus (QTL) underlying the candidate gene α-Glucan Water Dikinase (StGWD) on chromosome 5. We performed direct amplicon sequencing of this gene by Sanger sequencing. Sequences of two StGWD amplicons from a global collection of 398 commercial cultivars and progenitor lines were used to identify 16 different haplotypes. By assigning tag SNPs to these haplotypes, each of the four alleles present in a cultivar could be deduced and linked to a phosphate content. A high value for intra-individual heterozygosity was observed (Ho = 0.765). The average number of different haplotypes per individual (Ai) was 3.1. Pedigree analysis confirmed that the haplotypes are identical-by-descent (IBD) and offered insight in the breeding history of elite potato germplasm. Haplotypes originating from introgression of wild potato accessions carrying resistance genes could be traced. Furthermore, association analysis resulted in the identification of specific StGWD alleles causing either an increase or decrease in starch phosphate content varying from 12 nmol PO4/mg starch to 38 nmol PO4/mg starch. These allele effects were verified in diploid and tetraploid mapping populations and offer possibilities to breed and select for this trait.
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Affiliation(s)
- J. G. A. M. L. Uitdewilligen
- Plant Breeding, Wageningen University & Research, PO Box 386, 6700 AJ Wageningen, The Netherlands
- The Graduate School for Experimental Plant Sciences, Wageningen, The Netherlands
- Present Address: Limgroup BV, Born, The Netherlands
| | - A. M. A. Wolters
- Plant Breeding, Wageningen University & Research, PO Box 386, 6700 AJ Wageningen, The Netherlands
| | - H. J. van Eck
- Plant Breeding, Wageningen University & Research, PO Box 386, 6700 AJ Wageningen, The Netherlands
- Centre for BioSystems Genomics, Wageningen, The Netherlands
| | - R. G. F. Visser
- Plant Breeding, Wageningen University & Research, PO Box 386, 6700 AJ Wageningen, The Netherlands
- Centre for BioSystems Genomics, Wageningen, The Netherlands
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6
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Yang Y, Xu C, Shen Z, Yan C. Crop Quality Improvement Through Genome Editing Strategy. Front Genome Ed 2022; 3:819687. [PMID: 35174353 PMCID: PMC8841430 DOI: 10.3389/fgeed.2021.819687] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 12/30/2021] [Indexed: 11/13/2022] Open
Abstract
Good quality of crops has always been the most concerning aspect for breeders and consumers. However, crop quality is a complex trait affected by both the genetic systems and environmental factors, thus, it is difficult to improve through traditional breeding strategies. Recently, the CRISPR/Cas9 genome editing system, enabling efficiently targeted modification, has revolutionized the field of quality improvement in most crops. In this review, we briefly review the various genome editing ability of the CRISPR/Cas9 system, such as gene knockout, knock-in or replacement, base editing, prime editing, and gene expression regulation. In addition, we highlight the advances in crop quality improvement applying the CRISPR/Cas9 system in four main aspects: macronutrients, micronutrients, anti-nutritional factors and others. Finally, the potential challenges and future perspectives of genome editing in crop quality improvement is also discussed.
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Affiliation(s)
- Yihao Yang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou, China
- Department of Crop Genetics and Breeding, Agricultural College of Yangzhou University, Yangzhou, China
| | - Chenda Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou, China
| | - Ziyan Shen
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou, China
| | - Changjie Yan
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou, China
- Department of Crop Genetics and Breeding, Agricultural College of Yangzhou University, Yangzhou, China
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7
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Motto M, Sahay S. Energy plants (crops): potential natural and future designer plants. HANDBOOK OF BIOFUELS 2022:73-114. [DOI: 10.1016/b978-0-12-822810-4.00004-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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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: 17] [Impact Index Per Article: 5.7] [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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Zhong X, Feng X, Li Y, Guzmán C, Lin N, Xu Q, Zhang Y, Tang H, Qi P, Deng M, Ma J, Wang J, Chen G, Lan X, Wei Y, Zheng Y, Jiang Q. Genome-wide identification of bZIP transcription factor genes related to starch synthesis in barley ( Hordeum vulgare L.). Genome 2021; 64:1067-1080. [PMID: 34058097 DOI: 10.1139/gen-2020-0195] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The basic leucine zipper (bZIP) family of genes encode transcription factors that play key roles in plant growth and development. In this study, a total of 92 HvbZIP genes were identified and compared with previous studies using recently released barley genome data. Two novel genes were characterized in this study, and some misannotated and duplicated genes from previous studies have been corrected. Phylogenetic analysis results showed that 92 HvbZIP genes were classified into 10 groups and three unknown groups. The gene structure and motif distribution of the three unknown groups implied that the genes of the three groups may be functionally different. Expression profiling indicated that the HvbZIP genes exhibited different patterns of spatial and temporal expression. Using qRT-PCR, more than 10 HvbZIP genes were identified with expression patterns similar to those of starch synthase genes in barley. Yeast one-hybrid analysis revealed that two of the HvbZIP genes exhibited in vitro binding activity to the promoter of HvAGP-S. The two HvbZIP genes may be candidate genes for further study to explore the mechanism by which they regulate the synthesis of barley starch.
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Affiliation(s)
- Xiaojuan Zhong
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Xiuqin Feng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Yulong Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Carlos Guzmán
- Departamento de Genética, Escuela Técnica Superior de Ingeniería Agronómica y de Montes, Edificio Gregor Mendel, Campus de Rabanales, Universidad de Córdoba, Cordoba, 14071, Spain
| | - Na Lin
- College of Sichuan Tea, Yibin University, Yibin, Sichuan 644000, China
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Yazhou Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Mei Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Xiujin Lan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
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10
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Wu Y, Ren Z, Gao C, Sun M, Li S, Min R, Wu J, Li D, Wang X, Wei Y, Xia Y. Change in Sucrose Cleavage Pattern and Rapid Starch Accumulation Govern Lily Shoot-to-Bulblet Transition in vitro. FRONTIERS IN PLANT SCIENCE 2021; 11:564713. [PMID: 33519832 PMCID: PMC7840508 DOI: 10.3389/fpls.2020.564713] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 11/30/2020] [Indexed: 05/11/2023]
Abstract
In bulb crops, bulbing is a key progress in micropropagation and is the feature that most distinguishes bulbous crops from other plants. Generally, bulbing involves a shoot-to-bulblet transition; however, the underlying mechanism remains elusive. We explored this process by tracking the shoot-to-bulblet transition under different culture conditions. Rapid starch accumulation occurred at 15 days after transplanting (DAT) in the bulblet-inducing treatments as confirmed via histological observations and the significant elevation of starch synthesis related-gene transcription, including LohAGPS, LohAGPL, LohGBSS, LohSS, and LohSBE. However, for shoots that did not transition to bulblets and maintained the shoot status, much higher soluble sugars were detected. Interestingly, we observed a clear shift from invertase-catalyzed to sucrose synthase-catalyzed sucrose cleavage pattern based on the differential expression of LohCWIN and LohSuSy during the key transition stage (prior to and after bulbing at 0-15 DAT). Shoots that transitioned into bulblets showed significantly higher LohSuSy expression, especially LohSuSy4 expression, than shoots that did not transition. A symplastic phloem unloading pathway at the bulblet emergence stage (15 DAT) was verified via the 6(5)-carboxyfluorescein diacetate fluorescent tracer. We propose that starch is the fundamental compound in the shoot-to-bulblet transition and that starch synthesis is likely triggered by the switch from apoplastic to symplastic sucrose unloading, which may be related to sucrose depletion. Furthermore, this study is the first to provide a complete inventory of the genes involved in starch metabolism based on our transcriptome data. Two of these genes, LohAGPS1.2b and LohSSIIId, were verified by rapid amplification of cDNA ends cloning, and these data will provide additional support for Lilium research since whole genome is currently lacking.
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Affiliation(s)
- Yun Wu
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Department of Landscape Architecture, School of Civil Engineering and Architecture, Zhejiang Sci-Tech University, Hangzhou, China
| | - Ziming Ren
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Cong Gao
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Minyi Sun
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Shiqi Li
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Ruihan Min
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Jian Wu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing, China
| | - Danqing Li
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Xiuyun Wang
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yanping Wei
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yiping Xia
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
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11
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Verma A, Prakash G, Ranjan R, Tyagi AK, Agarwal P. Silencing of an Ubiquitin Ligase Increases Grain Width and Weight in indica Rice. Front Genet 2021; 11:600378. [PMID: 33510769 PMCID: PMC7835794 DOI: 10.3389/fgene.2020.600378] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 11/27/2020] [Indexed: 11/18/2022] Open
Abstract
Many quantitative trait loci (QTLs) have been identified by molecular genetic studies which control grain size by regulating grain width, length, and/or thickness. Grain width 2 (GW2) is one such QTL that codes for a RING-type E3 ubiquitin ligase and increases grain size by regulating grain width through ubiquitin-mediated degradation of unknown substrates. A natural variation (single-nucleotide polymorphism at the 346th position) in the functional domain-coding region of OsGW2 in japonica rice genotypes has been shown to cause an increase in grain width/weight in rice. However, this variation is absent in indica rice genotypes. In this study, we report that reduced expression of OsGW2 can alter grain size, even though natural sequence variation is not responsible for increased grain size in indica rice genotypes. OsGW2 shows high expression in seed development stages and the protein localizes to the nucleus and cytoplasm. Downregulation of OsGW2 by RNAi technology results in wider and heavier grains. Microscopic observation of grain morphology suggests that OsGW2 determines grain size by influencing both cell expansion and cell proliferation in spikelet hull. Using transcriptome analysis, upregulated genes related to grain size regulation have been identified among 1,426 differentially expressed genes in an OsGW2_RNAi transgenic line. These results reveal that OsGW2 is a negative regulator of grain size in indica rice and affects both cell number and cell size in spikelet hull.
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Affiliation(s)
- Ankit Verma
- National Institute of Plant Genome Research, New Delhi, India
| | - Geeta Prakash
- National Institute of Plant Genome Research, New Delhi, India.,Department of Botany, Gargi College, University of Delhi, New Delhi, India
| | - Rajeev Ranjan
- National Institute of Plant Genome Research, New Delhi, India.,Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research, New Delhi, India.,Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | - Pinky Agarwal
- National Institute of Plant Genome Research, New Delhi, India
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12
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Ding J, Karim H, Li Y, Harwood W, Guzmán C, Lin N, Xu Q, Zhang Y, Tang H, Jiang Y, Qi P, Deng M, Ma J, Wang J, Chen G, Lan X, Wei Y, Zheng Y, Jiang Q. Re-examination of the APETALA2/Ethylene-Responsive Factor Gene Family in Barley ( Hordeum vulgare L.) Indicates a Role in the Regulation of Starch Synthesis. FRONTIERS IN PLANT SCIENCE 2021; 12:791584. [PMID: 34925430 PMCID: PMC8672199 DOI: 10.3389/fpls.2021.791584] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/11/2021] [Indexed: 05/07/2023]
Abstract
The APETALA2/Ethylene-Responsive factor (AP2/ERF) gene family is a large plant-specific transcription factor family, which plays important roles in regulating plant growth and development. A role in starch synthesis is among the multiple functions of this family of transcription factors. Barley (Hordeum vulgare L.) is one of the most important cereals for starch production. However, there are limited data on the contribution of AP2 transcription factors in barley. In this study, we used the recently published barley genome database (Morex) to identify 185 genes of the HvAP2/ERF family. Compared with previous work, we identified 64 new genes in the HvAP2/ERF gene family and corrected some previously misannotated and duplicated genes. After phylogenetic analysis, HvAP2/ERF genes were classified into four subfamilies and 18 subgroups. Expression profiling showed different patterns of spatial and temporal expression for HvAP2/ERF genes. Most of the 12 HvAP2/ERF genes analyzed using quantitative reverse transcription-polymerase chain reaction had similar expression patterns when compared with those of starch synthase genes in barley, except for HvAP2-18 and HvERF-73. HvAP2-18 is homologous to OsRSR1, which negatively regulates the synthesis of rice starch. Luciferase reporter gene, and yeast one-hybrid assays showed that HvAP2-18 bound the promoter of AGP-S and SBE1 in vitro. Thus, HvAP2-18 might be an interesting candidate gene to further explore the mechanisms involved in the regulation of starch synthesis in barley.
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Affiliation(s)
- Jinjin Ding
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Hassan Karim
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yulong Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wendy Harwood
- John Innes Center, Norwich Research Park, Norwich, United Kingdom
| | - Carlos Guzmán
- Departamento de Genética, Escuela Técnica Superior de Ingeniería Agronómica y de Montes, Edificio Gregor Mendel, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - Na Lin
- College of Sichuan Tea, Yibin University, Yibin, China
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yazhou Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yunfeng Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Mei Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiujin Lan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- *Correspondence: Qiantao Jiang,
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13
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Preiser AL, Banerjee A, Weise SE, Renna L, Brandizzi F, Sharkey TD. Phosphoglucoisomerase Is an Important Regulatory Enzyme in Partitioning Carbon out of the Calvin-Benson Cycle. FRONTIERS IN PLANT SCIENCE 2020; 11:580726. [PMID: 33362810 PMCID: PMC7758399 DOI: 10.3389/fpls.2020.580726] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 11/18/2020] [Indexed: 05/04/2023]
Abstract
Phosphoglucoisomerase (PGI) isomerizes fructose 6-phosphate (F6P) and glucose 6-phosphate (G6P) in starch and sucrose biosynthesis. Both plastidic and cytosolic isoforms are found in plant leaves. Using recombinant enzymes and isolated chloroplasts, we have characterized the plastidic and cytosolic isoforms of PGI. We have found that the Arabidopsis plastidic PGI K m for G6P is three-fold greater compared to that for F6P and that erythrose 4-phosphate is a key regulator of PGI activity. Additionally, the K m of spinach plastidic PGI can be dynamically regulated in the dark compared to the light and increases by 200% in the dark. We also found that targeting Arabidopsis cytosolic PGI into plastids of Nicotiana tabacum disrupts starch accumulation and degradation. Our results, in combination with the observation that plastidic PGI is not in equilibrium, indicates that PGI is an important regulatory enzyme that restricts flow and acts as a one-way valve preventing backflow of G6P into the Calvin-Benson cycle. We propose the PGI may be manipulated to improve flow of carbon to desired targets of biotechnology.
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Affiliation(s)
- Alyssa L. Preiser
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Aparajita Banerjee
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Sean E. Weise
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
| | - Luciana Renna
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
| | - Federica Brandizzi
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
| | - Thomas D. Sharkey
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
- Plant Resilience Institute, Michigan State University, East Lansing, MI, United States
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14
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eQTL mapping of the 12S globulin cruciferin gene PGCRURSE5 as a novel candidate associated with starch content in potato tubers. Sci Rep 2020; 10:17168. [PMID: 33051578 PMCID: PMC7553954 DOI: 10.1038/s41598-020-74285-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 09/30/2020] [Indexed: 11/09/2022] Open
Abstract
Tuber starch content (TSC) is a very important trait in potato (Solanum tuberosum L.). This study is the first to use expression quantitative trait loci (eQTL) mapping of transcript-derived markers for TSC in potato. Thirty-four differentially expressed genes were selected by comparing the RNA-seq data of contrasting bulked segregants. For the 11 candidate genes, we determined their relative expression levels across the segregating diploid potato population using RT-qPCR. We detected 36 eQTL as candidate genes distributed on all twelve potato chromosomes, and nine of them overlapped with QTL for TSC. Peaks for two eQTL, eAGPaseS-a and ePGRCRURSE5, were close to the corresponding loci of the large subunit of ADP-glucose pyrophosphorylase (AGPaseS-a) and the 12S globulin cruciferin gene (PGCRURSE5), respectively. The eQTL peaks for AGPaseS-a and PGRCRURSE5 explained 41.0 and 28.3% of the phenotypic variation at the transcript level. We showed the association of the DNA markers for AGPaseS-a and PGRCRURSE5 with QTL for TSC, and significant correlation between the expression level of PGRCRURSE5 and TSC. We did not observe a significant correlation between the expression level of AGPaseS-a and TSC. We concluded that the cruciferin gene PGRCRURSE5 is a novel candidate involved in the regulation of starch content in potato tubers.
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15
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Liu Y, Hou J, Wang X, Li T, Majeed U, Hao C, Zhang X. The NAC transcription factor NAC019-A1 is a negative regulator of starch synthesis in wheat developing endosperm. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5794-5807. [PMID: 32803271 DOI: 10.1093/jxb/eraa333] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 07/29/2020] [Indexed: 05/20/2023]
Abstract
Starch is a major component of wheat (Triticum aestivum L.) endosperm and is an important part of the human diet. The functions of many starch synthesis genes have been elucidated. However, little is known about their regulatory mechanisms in wheat. Here, we identified a novel NAC transcription factor, TaNAC019-A1 (TraesCS3A02G077900), that negatively regulates starch synthesis in wheat and rice (Oryza sativa L.) endosperms. TaNAC019-A1 was highly expressed in the endosperm of developing grains and encoded a nucleus-localized transcriptional repressor. Overexpression of TaNAC019-A1 in rice and wheat led to significantly reduced starch content, kernel weight, and kernel width. The TaNAC019-A1-overexpression wheat lines had smaller A-type starch granules and fewer B-type starch granules than wild-type. Moreover, TaNAC019-A1 could directly bind to the 'ACGCAG' motif in the promoter regions of ADP-glucose pyrophosphorylase small subunit 1 (TaAGPS1-A1, TraesCS7A02G287400) and TaAGPS1-B1 (TraesCS7B02G183300) and repress their expression, thereby inhibiting starch synthesis in wheat endosperm. One haplotype of TaNAC019-B1 (TaNAC019-B1-Hap2, TraesCS3B02G092800) was positively associated with thousand-kernel weight and underwent positive selection during the Chinese wheat breeding process. Our data demonstrate that TaNAC019-A1 is a negative regulator of starch synthesis in wheat endosperm and provide novel insight into wheat yield improvement.
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Affiliation(s)
- Yunchuan Liu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jian Hou
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaolu Wang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tian Li
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Uzma Majeed
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chenyang Hao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xueyong Zhang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
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16
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Malinova I, Kössler S, Orawetz T, Matthes U, Orzechowski S, Koch A, Fettke J. Identification of Two Arabidopsis thaliana Plasma Membrane Transporters Able to Transport Glucose 1-Phosphate. PLANT & CELL PHYSIOLOGY 2020; 61:381-392. [PMID: 31722406 DOI: 10.1093/pcp/pcz206] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 10/25/2019] [Indexed: 06/10/2023]
Abstract
Primary carbohydrate metabolism in plants includes several sugar and sugar-derivative transport processes. Over recent years, evidences have shown that in starch-related transport processes, in addition to glucose 6-phosphate, maltose, glucose and triose-phosphates, glucose 1-phosphate also plays a role and thereby increases the possible fluxes of sugar metabolites in planta. In this study, we report the characterization of two highly similar transporters, At1g34020 and At4g09810, in Arabidopsis thaliana, which allow the import of glucose 1-phosphate through the plasma membrane. Both transporters were expressed in yeast and were biochemically analyzed to reveal an antiport of glucose 1-phosphate/phosphate. Furthermore, we showed that the apoplast of Arabidopsis leaves contained glucose 1-phosphate and that the corresponding mutant of these transporters had higher glucose 1-phosphate amounts in the apoplast and alterations in starch and starch-related metabolism.
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Affiliation(s)
- Irina Malinova
- Group of Biopolymer Analytics, University of Potsdam, Potsdam-Golm 14476, Germany
| | - Stella Kössler
- Group of Biopolymer Analytics, University of Potsdam, Potsdam-Golm 14476, Germany
| | - Tom Orawetz
- Group of Biopolymer Analytics, University of Potsdam, Potsdam-Golm 14476, Germany
| | - Ulrike Matthes
- Group of Biopolymer Analytics, University of Potsdam, Potsdam-Golm 14476, Germany
| | - Slawomir Orzechowski
- Department of Biochemistry, Warsaw University of Life Sciences-SGGW, Warsaw 02-776, Poland
| | - Anke Koch
- Plant Physiology, University of Potsdam, Potsdam-Golm 14476, Germany
| | - Joerg Fettke
- Group of Biopolymer Analytics, University of Potsdam, Potsdam-Golm 14476, Germany
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17
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Jaymand M. Chemically Modified Natural Polymer-Based Theranostic Nanomedicines: Are They the Golden Gate toward a de Novo Clinical Approach against Cancer? ACS Biomater Sci Eng 2019; 6:134-166. [DOI: 10.1021/acsbiomaterials.9b00802] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Mehdi Jaymand
- Nano Drug Delivery Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah 6715847141, Iran
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18
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Zhang Y, He P, Ma X, Yang Z, Pang C, Yu J, Wang G, Friml J, Xiao G. Auxin-mediated statolith production for root gravitropism. THE NEW PHYTOLOGIST 2019; 224:761-774. [PMID: 31111487 DOI: 10.1111/nph.15932] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 05/11/2019] [Indexed: 05/11/2023]
Abstract
Root gravitropism is one of the most important processes allowing plant adaptation to the land environment. Auxin plays a central role in mediating root gravitropism, but how auxin contributes to gravitational perception and the subsequent response are still unclear. Here, we showed that the local auxin maximum/gradient within the root apex, which is generated by the PIN directional auxin transporters, regulates the expression of three key starch granule synthesis genes, SS4, PGM and ADG1, which in turn influence the accumulation of starch granules that serve as a statolith perceiving gravity. Moreover, using the cvxIAA-ccvTIR1 system, we also showed that TIR1-mediated auxin signaling is required for starch granule formation and gravitropic response within root tips. In addition, axr3 mutants showed reduced auxin-mediated starch granule accumulation and disruption of gravitropism within the root apex. Our results indicate that auxin-mediated statolith production relies on the TIR1/AFB-AXR3-mediated auxin signaling pathway. In summary, we propose a dual role for auxin in gravitropism: the regulation of both gravity perception and response.
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Affiliation(s)
- Yuzhou Zhang
- Key Laboratory of the Ministry of Education for Medicinal Plant Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in the Northwest of China, College of Life Sciences, Shaanxi Normal University, No. 620, West Chang'an Avenue, Chang'an District, Xi'an, 710119, China
- Institute of Science and Technology (IST) Austria, 3400, Klosterneuburg, Austria
| | - Peng He
- Key Laboratory of the Ministry of Education for Medicinal Plant Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in the Northwest of China, College of Life Sciences, Shaanxi Normal University, No. 620, West Chang'an Avenue, Chang'an District, Xi'an, 710119, China
| | - Xiongfeng Ma
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, No.100 Science Avenue, Zhengzhou, 450001, China
- Cotton Research Institute, Chinese Academy of Agricultural Sciences, No. 38 Yellow River Avenue, Anyang, 455000, China
| | - Zuoren Yang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, No.100 Science Avenue, Zhengzhou, 450001, China
- Cotton Research Institute, Chinese Academy of Agricultural Sciences, No. 38 Yellow River Avenue, Anyang, 455000, China
| | - Chaoyou Pang
- Cotton Research Institute, Chinese Academy of Agricultural Sciences, No. 38 Yellow River Avenue, Anyang, 455000, China
| | - Jianing Yu
- Key Laboratory of the Ministry of Education for Medicinal Plant Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in the Northwest of China, College of Life Sciences, Shaanxi Normal University, No. 620, West Chang'an Avenue, Chang'an District, Xi'an, 710119, China
| | - Guodong Wang
- Key Laboratory of the Ministry of Education for Medicinal Plant Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in the Northwest of China, College of Life Sciences, Shaanxi Normal University, No. 620, West Chang'an Avenue, Chang'an District, Xi'an, 710119, China
| | - Jiří Friml
- Institute of Science and Technology (IST) Austria, 3400, Klosterneuburg, Austria
| | - Guanghui Xiao
- Key Laboratory of the Ministry of Education for Medicinal Plant Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in the Northwest of China, College of Life Sciences, Shaanxi Normal University, No. 620, West Chang'an Avenue, Chang'an District, Xi'an, 710119, China
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Veillet F, Chauvin L, Kermarrec MP, Sevestre F, Merrer M, Terret Z, Szydlowski N, Devaux P, Gallois JL, Chauvin JE. The Solanum tuberosum GBSSI gene: a target for assessing gene and base editing in tetraploid potato. PLANT CELL REPORTS 2019; 38:1065-1080. [PMID: 31101972 DOI: 10.1007/s00299-019-02426-w] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/08/2019] [Accepted: 05/08/2019] [Indexed: 05/20/2023]
Abstract
The StGBSSI gene was successfully and precisely edited in the tetraploid potato using gene and base-editing strategies, leading to plants with impaired amylose biosynthesis. Genome editing has recently become a method of choice for basic research and functional genomics, and holds great potential for molecular plant-breeding applications. The powerful CRISPR-Cas9 system that typically produces double-strand DNA breaks is mainly used to generate knockout mutants. Recently, the development of base editors has broadened the scope of genome editing, allowing precise and efficient nucleotide substitutions. In this study, we produced mutants in two cultivated elite cultivars of the tetraploid potato (Solanum tuberosum) using stable or transient expression of the CRISPR-Cas9 components to knock out the amylose-producing StGBSSI gene. We set up a rapid, highly sensitive and cost-effective screening strategy based on high-resolution melting analysis followed by direct Sanger sequencing and trace chromatogram analysis. Most mutations consisted of small indels, but unwanted insertions of plasmid DNA were also observed. We successfully created tetra-allelic mutants with impaired amylose biosynthesis, confirming the loss of function of the StGBSSI protein. The second main objective of this work was to demonstrate the proof of concept of CRISPR-Cas9 base editing in the tetraploid potato by targeting two loci encoding catalytic motifs of the StGBSSI enzyme. Using a cytidine base editor (CBE), we efficiently and precisely induced DNA substitutions in the KTGGL-encoding locus, leading to discrete variation in the amino acid sequence and generating a loss-of-function allele. The successful application of base editing in the tetraploid potato opens up new avenues for genome engineering in this species.
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Affiliation(s)
- Florian Veillet
- INRA, Agrocampus Ouest, Université Rennes 1, UMR 1349 IGEPP, Domaine de Kéraïber, 29260, Ploudaniel, France.
| | - Laura Chauvin
- INRA, Agrocampus Ouest, Université Rennes 1, UMR 1349 IGEPP, Domaine de Kéraïber, 29260, Ploudaniel, France
| | - Marie-Paule Kermarrec
- INRA, Agrocampus Ouest, Université Rennes 1, UMR 1349 IGEPP, Domaine de Kéraïber, 29260, Ploudaniel, France
| | - François Sevestre
- Unité de Glycobiologie Structurale et Fonctionnelle, Univ. Lille, CNRS, UMR8576, UGSF, Lille, France
- Univ. Lille, CNRS, USR 3290, MSAP, Miniaturisation pour la Synthèse, l'Analyse et la Protéomique, Lille, France
| | - Mathilde Merrer
- INRA, Agrocampus Ouest, Université Rennes 1, UMR 1349 IGEPP, Domaine de Kéraïber, 29260, Ploudaniel, France
| | - Zoé Terret
- GAFL, INRA, Montfavet, France
- SYNGENTA SEEDS SAS, 346 Route des Pasquiers, 84260, Sarrians, France
| | - Nicolas Szydlowski
- Unité de Glycobiologie Structurale et Fonctionnelle, Univ. Lille, CNRS, UMR8576, UGSF, Lille, France
- Univ. Lille, CNRS, USR 3290, MSAP, Miniaturisation pour la Synthèse, l'Analyse et la Protéomique, Lille, France
| | - Pierre Devaux
- Germicopa Breeding, Kerguivarc'h, 29520, Chateauneuf Du Faou, France
| | | | - Jean-Eric Chauvin
- INRA, Agrocampus Ouest, Université Rennes 1, UMR 1349 IGEPP, Domaine de Kéraïber, 29260, Ploudaniel, France
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Rapid Visco Analyser (RVA) as a Tool for Measuring Starch-Related Physiochemical Properties in Cereals: a Review. FOOD ANAL METHOD 2019. [DOI: 10.1007/s12161-019-01581-w] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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21
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Zhang X, Xie S, Han J, Zhou Y, Liu C, Zhou Z, Wang F, Cheng Z, Zhang J, Hu Y, Hao Z, Li M, Zhang D, Yong H, Huang Y, Weng J, Li X. Integrated transcriptome, small RNA, and degradome analysis reveals the complex network regulating starch biosynthesis in maize. BMC Genomics 2019; 20:574. [PMID: 31296166 PMCID: PMC6625009 DOI: 10.1186/s12864-019-5945-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 06/30/2019] [Indexed: 12/18/2022] Open
Abstract
Background Starch biosynthesis in endosperm is a key process influencing grain yield and quality in maize. Although a number of starch biosynthetic genes have been well characterized, the mechanisms by which the expression of these genes is regulated, especially in regard to microRNAs (miRNAs), remain largely unclear. Results Sequence data for small RNAs, degradome, and transcriptome of maize endosperm at 15 and 25 d after pollination (DAP) from inbred lines Mo17 and Ji419, which exhibit distinct starch content and starch granule structure, revealed the mediation of starch biosynthetic pathways by miRNAs. Transcriptome analysis of these two lines indicated that 33 of 40 starch biosynthetic genes were differentially expressed, of which 12 were up-regulated in Ji419 at 15 DAP, one was up-regulated in Ji419 at 25 DAP, 14 were up-regulated in Ji419 at both 15 and 25 DAP, one was down-regulated in Ji419 at 15 DAP, two were down-regulated in Ji419 at 25 DAP, and three were up-regulated in Ji419 at 15 DAP and down-regulated in Ji419 at 25 DAP, compared with Mo17. Through combined analyses of small RNA and degradome sequences, 22 differentially expressed miRNAs were identified, including 14 known and eight previously unknown miRNAs that could target 35 genes. Furthermore, a complex co-expression regulatory network was constructed, in which 19 miRNAs could modulate starch biosynthesis in endosperm by tuning the expression of 19 target genes. Moreover, the potential operation of four miRNA-mediated pathways involving transcription factors, miR169a-NF-YA1-GBSSI/SSIIIa and miR169o-GATA9-SSIIIa/SBEIIb, was validated via analyses of expression pattern, transient transformation assays, and transactivation assays. Conclusion Our results suggest that miRNAs play a critical role in starch biosynthesis in endosperm, and that miRNA-mediated networks could modulate starch biosynthesis in this tissue. These results have provided important insights into the molecular mechanism of starch biosynthesis in developing maize endosperm. Electronic supplementary material The online version of this article (10.1186/s12864-019-5945-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaocong Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sidi Xie
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jienan Han
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yu Zhou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Agronomy, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Chang Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Agronomy, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Zhiqiang Zhou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Feifei Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zixiang Cheng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junjie Zhang
- College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan, China
| | - Yufeng Hu
- College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhuanfang Hao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mingshun Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Degui Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongjun Yong
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yubi Huang
- College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jianfeng Weng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Xinhai Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.
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Genetic Modification for Wheat Improvement: From Transgenesis to Genome Editing. BIOMED RESEARCH INTERNATIONAL 2019; 2019:6216304. [PMID: 30956982 PMCID: PMC6431451 DOI: 10.1155/2019/6216304] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 02/08/2019] [Accepted: 02/21/2019] [Indexed: 12/12/2022]
Abstract
To feed the growing human population, global wheat yields should increase to approximately 5 tonnes per ha from the current 3.3 tonnes by 2050. To reach this goal, existing breeding practices must be complemented with new techniques built upon recent gains from wheat genome sequencing, and the accumulated knowledge of genetic determinants underlying the agricultural traits responsible for crop yield and quality. In this review we primarily focus on the tools and techniques available for accessing gene functions which lead to clear phenotypes in wheat. We provide a view of the development of wheat transformation techniques from a historical perspective, and summarize how techniques have been adapted to obtain gain-of-function phenotypes by gene overexpression, loss-of-function phenotypes by expressing antisense RNAs (RNA interference or RNAi), and most recently the manipulation of gene structure and expression using site-specific nucleases, such as CRISPR/Cas9, for genome editing. The review summarizes recent successes in the application of wheat genetic manipulation to increase yield, improve nutritional and health-promoting qualities in wheat, and enhance the crop's resistance to various biotic and abiotic stresses.
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23
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Lloyd JR, Kossmann J. Starch Trek: The Search for Yield. FRONTIERS IN PLANT SCIENCE 2019; 9:1930. [PMID: 30719029 PMCID: PMC6348371 DOI: 10.3389/fpls.2018.01930] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 12/12/2018] [Indexed: 05/27/2023]
Abstract
Starch is a plant storage polyglucan that accumulates in plastids. It is composed of two polymers, amylose and amylopectin, with different structures and plays several roles in helping to determine plant yield. In leaves, it acts as a buffer for night time carbon starvation. Genetically altered plants that cannot synthesize or degrade starch efficiently often grow poorly. There have been a number of successful approaches to manipulate leaf starch metabolism that has resulted in increased growth and yield. Its degradation is also a source of sugars that can help alleviate abiotic stress. In edible parts of plants, starch often makes up the majority of the dry weight constituting much of the calorific value of food and feed. Increasing starch in these organs can increase this as well as increasing yield. Enzymes involved in starch metabolism are well known, and there has been much research analyzing their functions in starch synthesis and degradation, as well as genetic and posttranslational regulatory mechanisms affecting them. In this mini review, we examine work on this topic and discuss future directions that could be used to manipulate this metabolite for improved yield.
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Affiliation(s)
| | - Jens Kossmann
- Department of Genetics, Institute for Plant Biotechnology, University of Stellenbosch, Stellenbosch, South Africa
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24
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Siriwat W, Kalapanulak S, Suksangpanomrung M, Saithong T. Unlocking conserved and diverged metabolic characteristics in cassava carbon assimilation via comparative genomics approach. Sci Rep 2018; 8:16593. [PMID: 30413726 PMCID: PMC6226483 DOI: 10.1038/s41598-018-34730-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 10/24/2018] [Indexed: 11/09/2022] Open
Abstract
Globally, cassava is an important source of starch, which is synthesized through carbon assimilation in cellular metabolism whereby harvested atmospheric carbon is assimilated into macromolecules. Although the carbon assimilation pathway is highly conserved across species, metabolic phenotypes could differ in composition, type, and quantity. To unravel the metabolic complexity and advantage of cassava over other starch crops, in terms of starch production, we investigated the carbon assimilation mechanisms in cassava through genome-based pathway reconstruction and comparative network analysis. First, MeRecon - the carbon assimilation pathway of cassava was reconstructed based upon six plant templates: Arabidopsis, rice, maize, castor bean, potato, and turnip. MeRecon, available at http://bml.sbi.kmutt.ac.th/MeRecon, comprises 259 reactions (199 EC numbers), 1,052 proteins (870 genes) and 259 metabolites in eight sub-metabolisms. Analysis of MeRecon and the carbon assimilation pathways of the plant templates revealed the overall topology is highly conserved, but variations at sub metabolism level were found in relation to complexity underlying each biochemical reaction, such as numbers of responsible enzymatic proteins and their evolved functions, which likely explain the distinct metabolic phenotype. Thus, this study provides insights into the network characteristics and mechanisms that regulate the synthesis of metabolic phenotypes of cassava.
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Affiliation(s)
- Wanatsanan Siriwat
- Systems Biology and Bioinformatics Research Laboratory, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bang Khun Thian, Bangkok, 10150, Thailand
| | - Saowalak Kalapanulak
- Systems Biology and Bioinformatics Research Laboratory, 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
| | | | - Treenut Saithong
- Systems Biology and Bioinformatics Research Laboratory, 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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25
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Hennessy RC, Jørgensen NOG, Scavenius C, Enghild JJ, Greve-Poulsen M, Sørensen OB, Stougaard P. A Screening Method for the Isolation of Bacteria Capable of Degrading Toxic Steroidal Glycoalkaloids Present in Potato. Front Microbiol 2018; 9:2648. [PMID: 30455676 PMCID: PMC6230958 DOI: 10.3389/fmicb.2018.02648] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 10/17/2018] [Indexed: 01/07/2023] Open
Abstract
Potato juice, a by-product of starch processing, is a potential high-value food ingredient due to its high protein content. However, conversion from feed to human protein requires the removal of the toxic antinutritional glycoalkaloids (GAs) α-chaconine and α-solanine. Detoxification by enzymatic removal could potentially provide an effective and environmentally friendly process for potato-derived food protein production. While degradation of GAs by microorganisms has been documented, there exists limited knowledge on the enzymes involved and in particular how bacteria degrade and metabolize GAs. Here we describe a series of methods for the isolation, screening, and selection of GA-degrading bacteria. Bacterial cultures from soils surrounding greened potatoes, including the potato peels, were established and select bacterial isolates were studied. Screening of bacterial crude extracts for the ability to hydrolyze GAs was performed using a combination of thin layer chromatography (TLC), high performance liquid chromatography (HPLC), and liquid chromatography mass spectrometry (LC-MS). Analysis of the 16S rRNA sequences revealed that bacteria within the genus Arthrobacter were among the most efficient GA-degrading strains.
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Affiliation(s)
- Rosanna C. Hennessy
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Niels O. G. Jørgensen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Carsten Scavenius
- Department of Molecular Biology and Genetics – Protein Science, Aarhus University, Aarhus, Denmark
| | - Jan. J. Enghild
- Department of Molecular Biology and Genetics – Protein Science, Aarhus University, Aarhus, Denmark
| | | | | | - Peter Stougaard
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
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26
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Leite DC, Kakorin S, Hertle Y, Hellweg T, da Silveira NP. Smart Starch-Poly( N-isopropylacrylamide) Hybrid Microgels: Synthesis, Structure, and Swelling Behavior. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:10943-10954. [PMID: 30132672 DOI: 10.1021/acs.langmuir.8b00706] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In this study, we present hybrid microgels made of starch nanoparticles (SNPs) and poly( N-isopropylacrylamide) [p(NIPAM)]. SNPs were formed through nanoprecipitation. Hybrid microgels were prepared by surfactant-free precipitation polymerization (SFPP) or in the presence of surfactant precipitation polymerization (PP) at different NIPAM/SNP ratios. Dynamic light scattering results of hybrid microgels synthesized by SFPP revealed changes in volume phase transition temperature according to SNP amount, where the increase in the hydrophilic content caused small shifts in the lower critical solution temperature (LCST), reaching nearly 35 °C. Colloidal stability was improved with the SNP content, leading to increased stability because of the hydroxyl groups. Small-angle X-ray scattering indicates a core-shell structure above the LCST, where SNPs chains cover a p(NIPAM) core. Swelling curves experimentally obtained were analyzed using the Flory-Rehner model, where the interaction parameter (χ) has been modeled either by a series expansion of the swelling ratio or by a Hill-like equation for a cooperative thermotropic transition.
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Affiliation(s)
- Daiani C Leite
- Institute of Chemistry , Universidade Federal do Rio Grande do Sul , Av. Bento Gonçalves 9500 , 91501-970 Porto Alegre , Brazil
| | - Sergej Kakorin
- Faculty of Chemistry , Universität Bielefeld , Universitätstrasse 25 , 33615 Bielefeld , Germany
| | - Yvonne Hertle
- Faculty of Chemistry , Universität Bielefeld , Universitätstrasse 25 , 33615 Bielefeld , Germany
| | - Thomas Hellweg
- Faculty of Chemistry , Universität Bielefeld , Universitätstrasse 25 , 33615 Bielefeld , Germany
| | - Nádya P da Silveira
- Institute of Chemistry , Universidade Federal do Rio Grande do Sul , Av. Bento Gonçalves 9500 , 91501-970 Porto Alegre , Brazil
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27
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Bull SE, Seung D, Chanez C, Mehta D, Kuon JE, Truernit E, Hochmuth A, Zurkirchen I, Zeeman SC, Gruissem W, Vanderschuren H. Accelerated ex situ breeding of GBSS- and PTST1-edited cassava for modified starch. SCIENCE ADVANCES 2018; 4:eaat6086. [PMID: 30191180 PMCID: PMC6124905 DOI: 10.1126/sciadv.aat6086] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 07/20/2018] [Indexed: 05/12/2023]
Abstract
Crop diversification required to meet demands for food security and industrial use is often challenged by breeding time and amenability of varieties to genome modification. Cassava is one such crop. Grown for its large starch-rich storage roots, it serves as a staple food and a commodity in the multibillion-dollar starch industry. Starch is composed of the glucose polymers amylopectin and amylose, with the latter strongly influencing the physicochemical properties of starch during cooking and processing. We demonstrate that CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9)-mediated targeted mutagenesis of two genes involved in amylose biosynthesis, PROTEIN TARGETING TO STARCH (PTST1) or GRANULE BOUND STARCH SYNTHASE (GBSS), can reduce or eliminate amylose content in root starch. Integration of the Arabidopsis FLOWERING LOCUS T gene in the genome-editing cassette allowed us to accelerate flowering-an event seldom seen under glasshouse conditions. Germinated seeds yielded S1, a transgene-free progeny that inherited edited genes. This attractive new plant breeding technique for modified cassava could be extended to other crops to provide a suite of novel varieties with useful traits for food and industrial applications.
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Affiliation(s)
- Simon E. Bull
- Plant Biotechnology, Institute of Molecular Plant Biology, ETH Zurich, 8092 Zurich, Switzerland
- Corresponding author. (S.E.B.); (H.V.)
| | - David Seung
- Plant Biochemistry, Institute of Molecular Plant Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Christelle Chanez
- Plant Biotechnology, Institute of Molecular Plant Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Devang Mehta
- Plant Biotechnology, Institute of Molecular Plant Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Joel-Elias Kuon
- Plant Biotechnology, Institute of Molecular Plant Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Elisabeth Truernit
- Plant Biochemistry, Institute of Molecular Plant Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Anton Hochmuth
- Plant Biochemistry, Institute of Molecular Plant Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Irene Zurkirchen
- Plant Biotechnology, Institute of Molecular Plant Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Samuel C. Zeeman
- Plant Biochemistry, Institute of Molecular Plant Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Wilhelm Gruissem
- Plant Biotechnology, Institute of Molecular Plant Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Hervé Vanderschuren
- Plant Biotechnology, Institute of Molecular Plant Biology, ETH Zurich, 8092 Zurich, Switzerland
- Plant Genetics, TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium
- Corresponding author. (S.E.B.); (H.V.)
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28
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McKinley BA, Casto AL, Rooney WL, Mullet JE. Developmental dynamics of stem starch accumulation in Sorghum bicolor. PLANT DIRECT 2018; 2:e00074. [PMID: 31245742 PMCID: PMC6508807 DOI: 10.1002/pld3.74] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 06/15/2018] [Accepted: 06/19/2018] [Indexed: 05/26/2023]
Abstract
Sweet sorghums were identified that accumulate up to ~9% of their total stem dry weight as starch. Starch accumulated preferentially in stem pith parenchyma in close proximity to vascular bundles. Stem starch accumulated slowly between floral initiation and anthesis and more rapidly between anthesis and 43 days post-anthesis before declining in parallel with tiller outgrowth. Genes involved in stem starch metabolism were identified through phylogenetic approaches and RNA-seq analysis of Della stem gene expression during the starch accumulation phase of development. Genes differentially expressed in stems were identified that are involved in starch biosynthesis (i.e., AGPase SS/LS, starch synthases, starch-branching enzymes), degradation (i.e., glucan-water dikinase, β-amylase, disproportionating enzyme, alpha-glucan phosphorylase) and amyloplast sugar transport (glucose-6-P translocator). Transcripts encoding AGPase SS and LS subunits with plastid localization were differentially induced during stem starch accumulation indicating that ADP-glucose for starch biosynthesis is primarily generated in stem plastids. Cytosolic heteroglucan metabolism may play a role in stem sucrose/starch accumulation because genes encoding cytosolic forms of the disproportionating enzyme and alpha-glucan phosphorylase were induced in parallel with stem sucrose/starch accumulation. Information on the stem starch pathway obtained in this study will be useful for engineering sorghum stems with elevated starch thereby improving forage quality and the efficiency of biomass conversion to biofuels and bio-products.
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Affiliation(s)
- Brian A. McKinley
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTexas
| | - Anna L. Casto
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTexas
| | - William L. Rooney
- Department of Soil and Crop SciencesTexas A&M UniversityCollege StationTexas
| | - John E. Mullet
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTexas
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Palakawong Na Ayudthaya S, van de Weijer AHP, van Gelder AH, Stams AJM, de Vos WM, Plugge CM. Organic acid production from potato starch waste fermentation by rumen microbial communities from Dutch and Thai dairy cows. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:13. [PMID: 29416558 PMCID: PMC5784674 DOI: 10.1186/s13068-018-1012-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 01/08/2018] [Indexed: 05/28/2023]
Abstract
BACKGROUND Exploring different microbial sources for biotechnological production of organic acids is important. Dutch and Thai cow rumen samples were used as inocula to produce organic acid from starch waste in anaerobic reactors. Organic acid production profiles were determined and microbial communities were compared using 16S ribosomal ribonucleic acid gene amplicon pyrosequencing. RESULTS In both reactors, lactate was the main initial product and was associated with growth of Streptococcus spp. (86% average relative abundance). Subsequently, lactate served as a substrate for secondary fermentations. In the reactor inoculated with rumen fluid from the Dutch cow, the relative abundance of Bacillus and Streptococcus increased from the start, and lactate, acetate, formate and ethanol were produced. From day 1.33 to 2, lactate and acetate were degraded, resulting in butyrate production. Butyrate production coincided with a decrease in relative abundance of Streptococcus spp. and increased relative abundances of bacteria of other groups, including Parabacteroides, Sporanaerobacter, Helicobacteraceae, Peptostreptococcaceae and Porphyromonadaceae. In the reactor with the Thai cow inoculum, Streptococcus spp. also increased from the start. When lactate was consumed, acetate, propionate and butyrate were produced (day 3-4). After day 3, bacteria belonging to five dominant groups, Bacteroides, Pseudoramibacter_Eubacterium, Dysgonomonas, Enterobacteriaceae and Porphyromonadaceae, were detected and these showed significant positive correlations with acetate, propionate and butyrate levels. CONCLUSIONS The complexity of rumen microorganisms with high adaptation capacity makes rumen fluid a suitable source to convert organic waste into valuable products without the addition of hydrolytic enzymes. Starch waste is a source for organic acid production, especially lactate.
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Affiliation(s)
- Susakul Palakawong Na Ayudthaya
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Thailand Institute of Scientific and Technological Research, 35 Mu 3, Khlong Ha, Amphoe Khlong Luang, 12120 Pathum Thani Thailand
| | | | - Antonie H. van Gelder
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Alfons J. M. Stams
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Willem M. de Vos
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- RPU Immunology, Department of Bacteriology and Immunology, University of Helsinki, Haartmaninkatu 3, 00014 Helsinki, Finland
| | - Caroline M. Plugge
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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30
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Xie S, Zhang X, Zhou Z, Li X, Huang Y, Zhang J, Weng J. Identification of genes alternatively spliced in developing maize endosperm. PLANT BIOLOGY (STUTTGART, GERMANY) 2018; 20:59-66. [PMID: 28945323 DOI: 10.1111/plb.12631] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 09/17/2017] [Indexed: 06/07/2023]
Abstract
The process of alternative splicing is critical for the regulation of growth and development of plants. Thus far, little is known about the role of alternative splicing in the regulation of maize (Zea mays L.) endosperm development. RNA sequencing (RNA-seq) data of endosperms from two maize inbred lines, Mo17 and Ji419, at 15 and 25 days after pollination (DAP), respectively, were used to identify genes that were alternatively spliced during endosperm development. Intron retention (IR) in GRMZM2G005887 was further validated using PCR and re-sequencing technologies. In total, 49,000 alternatively spliced events and ca. 20,000 alternatively spliced genes were identified in the two maize inbred lines. Of these, 30 genes involved in amino acid biosynthesis and starch biosynthesis were identified, with IR occurring only in a specific sample, and were significantly co-expressed with ten well-known genes related to maize endosperm development. Moreover, IR in GRMZM2G005887, which encodes a cysteine synthase, was confirmed to occur only in the endosperm of Mo17 at 15 DAP, resulting in the retention of a 121-bp fragment in its 5' untranslated region. Two cis-acting regulatory elements, CAAT-box and TATA-box were observed in the retained fragment in Mo17 at 15 DAP; this could regulate the expression of this gene and influence endosperm development. The results suggest that the 30 genes with IR identified herein might be associated with maize endosperm development, and are likely to play important roles in the developing maize endosperm.
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Affiliation(s)
- S Xie
- College of Life Science, Sichuan Agricultural University, Ya'an, China
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - X Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Z Zhou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - X Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Y Huang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - J Zhang
- College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - J Weng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
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31
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Nielsen MM, Ruzanski C, Krucewicz K, Striebeck A, Cenci U, Ball SG, Palcic MM, Cuesta-Seijo JA. Crystal Structures of the Catalytic Domain of Arabidopsis thaliana Starch Synthase IV, of Granule Bound Starch Synthase From CLg1 and of Granule Bound Starch Synthase I of Cyanophora paradoxa Illustrate Substrate Recognition in Starch Synthases. FRONTIERS IN PLANT SCIENCE 2018; 9:1138. [PMID: 30123236 PMCID: PMC6086201 DOI: 10.3389/fpls.2018.01138] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 07/13/2018] [Indexed: 05/20/2023]
Abstract
Starch synthases (SSs) are responsible for depositing the majority of glucoses in starch. Structural knowledge on these enzymes that is available from the crystal structures of rice granule bound starch synthase (GBSS) and barley SSI provides incomplete information on substrate binding and active site architecture. Here we report the crystal structures of the catalytic domains of SSIV from Arabidopsis thaliana, of GBSS from the cyanobacterium CLg1 and GBSSI from the glaucophyte Cyanophora paradoxa, with all three bound to ADP and the inhibitor acarbose. The SSIV structure illustrates in detail the modes of binding for both donor and acceptor in a plant SS. CLg1GBSS contains, in the same crystal structure, examples of molecules with and without bound acceptor, which illustrates the conformational changes induced upon acceptor binding that presumably precede catalytic activity. With structures available from several isoforms of plant and non-plant SSs, as well as the closely related bacterial glycogen synthases, we analyze, at the structural level, the common elements that define a SS, the elements that are necessary for substrate binding and singularities of the GBSS family that could underlie its processivity. While the phylogeny of the SSIII/IV/V has been recently discussed, we now further report the detailed evolutionary history of the GBSS/SSI/SSII type of SSs enlightening the origin of the GBSS enzymes used in our structural analysis.
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Affiliation(s)
| | - Christian Ruzanski
- Carlsberg Research Laboratory, Copenhagen, Denmark
- † Present address: Christian Ruzanski, Novo Nordisk A/S, Måløv, Denmark Monica M. Palcic, Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | | | | | - Ugo Cenci
- UMR8576 CNRS-USTL, Unité de Glycobiologie Structurale et Fonctionnelle, Université des Sciences et Technologies de Lille, Villeneuve-d’Ascq, France
| | - Steven G. Ball
- UMR8576 CNRS-USTL, Unité de Glycobiologie Structurale et Fonctionnelle, Université des Sciences et Technologies de Lille, Villeneuve-d’Ascq, France
| | - Monica M. Palcic
- Carlsberg Research Laboratory, Copenhagen, Denmark
- † Present address: Christian Ruzanski, Novo Nordisk A/S, Måløv, Denmark Monica M. Palcic, Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Jose A. Cuesta-Seijo
- Carlsberg Research Laboratory, Copenhagen, Denmark
- *Correspondence: Jose A. Cuesta-Seijo,
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Hara-Skrzypiec A, Śliwka J, Jakuczun H, Zimnoch-Guzowska E. Quantitative trait loci for tuber blackspot bruise and enzymatic discoloration susceptibility in diploid potato. Mol Genet Genomics 2017; 293:331-342. [PMID: 29080143 PMCID: PMC5854731 DOI: 10.1007/s00438-017-1387-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 10/19/2017] [Indexed: 12/19/2022]
Abstract
Tuber tissue discolorations caused by impact (blackspot bruising) and enzymatic discoloration (ED) after tuber cutting are crucial quality traits of the cultivated potato. To understand the complex genetics of the traits, quantitative trait locus (QTL) analysis using diploid mapping population and diversity array technology (DArT) markers was performed. The phenotypic assessment included the complex evaluation of blackspot bruising susceptibility through two methods: rotating drum (BRD) and falling bolt (BFB) in combination with the evaluation of enzymatic discoloration. Because of observed in-practice relationship between bruising susceptibility and tuber starch content (TSC), analysis of starch content-corrected bruising susceptibility (SCB) was performed. QTLs for bruising were detected on chromosomes I, V with both test methods. The rotating drum method enabled the detection of additional QTLs on chromosomes VIII and XII. Analysis of SCB enabled the identification of the major QTL on chromosome V and two weaker QTLs on chromosomes VIII and XII, independently of starch content. The QTL for bruising detected on chromosome I overlapped with the most significant QTL for tuber starch content. This QTL was not significant for starch content-corrected bruising susceptibility, and the effect of the QTL on chromosome V was enhanced for this trait. The QTL analysis of ED revealed the contribution of seven QTLs for the trait, located on six chromosomes, including these detected for the first time: a major locus on chromosome V and minor QTLs on chromosomes VII and X, which were specific for the trait. The QTL for ED on chromosome VIII was co-localized with the marker for polyphenol oxidase (POT32). The phenotypic correlation between bruising and ED was confirmed in QTL analyses of both traits, and the QTLs detected for these traits overlapped on chromosomes I, V, and VIII. Our results should provide a basis for further studies on candidate genes affecting blackspot bruise susceptibility and enzymatic discoloration.
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Affiliation(s)
- Agnieszka Hara-Skrzypiec
- Plant Breeding and Acclimatization Institute, National Research Institute, Młochów, Platanowa 19, 05-831, Młochów, Poland.
| | - J Śliwka
- Plant Breeding and Acclimatization Institute, National Research Institute, Młochów, Platanowa 19, 05-831, Młochów, Poland
| | - H Jakuczun
- Plant Breeding and Acclimatization Institute, National Research Institute, Młochów, Platanowa 19, 05-831, Młochów, Poland
| | - E Zimnoch-Guzowska
- Plant Breeding and Acclimatization Institute, National Research Institute, Młochów, Platanowa 19, 05-831, Młochów, Poland
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Carpenter MA, Shaw M, Cooper RD, Frew TJ, Butler RC, Murray SR, Moya L, Coyne CJ, Timmerman-Vaughan GM. Association mapping of starch chain length distribution and amylose content in pea (Pisum sativum L.) using carbohydrate metabolism candidate genes. BMC PLANT BIOLOGY 2017; 17:132. [PMID: 28764648 PMCID: PMC5540500 DOI: 10.1186/s12870-017-1080-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 07/21/2017] [Indexed: 05/24/2023]
Abstract
BACKGROUND Although starch consists of large macromolecules composed of glucose units linked by α-1,4-glycosidic linkages with α-1,6-glycosidic branchpoints, variation in starch structural and functional properties is found both within and between species. Interest in starch genetics is based on the importance of starch in food and industrial processes, with the potential of genetics to provide novel starches. The starch metabolic pathway is complex but has been characterized in diverse plant species, including pea. RESULTS To understand how allelic variation in the pea starch metabolic pathway affects starch structure and percent amylose, partial sequences of 25 candidate genes were characterized for polymorphisms using a panel of 92 diverse pea lines. Variation in the percent amylose composition of extracted seed starch and (amylopectin) chain length distribution, one measure of starch structure, were characterized for these lines. Association mapping was undertaken to identify polymorphisms associated with the variation in starch chain length distribution and percent amylose, using a mixed linear model that incorporated population structure and kinship. Associations were found for polymorphisms in seven candidate genes plus Mendel's r locus (which conditions the round versus wrinkled seed phenotype). The genes with associated polymorphisms are involved in the substrate supply, chain elongation and branching stages of the pea carbohydrate and starch metabolic pathways. CONCLUSIONS The association of polymorphisms in carbohydrate and starch metabolic genes with variation in amylopectin chain length distribution and percent amylose may help to guide manipulation of pea seed starch structural and functional properties through plant breeding.
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Affiliation(s)
- Margaret A Carpenter
- The New Zealand Institute for Plant & Food Research Limited, PO Box 4704, Christchurch, New Zealand
| | - Martin Shaw
- The New Zealand Institute for Plant & Food Research Limited, PO Box 4704, Christchurch, New Zealand
| | - Rebecca D Cooper
- The New Zealand Institute for Plant & Food Research Limited, PO Box 4704, Christchurch, New Zealand
| | - Tonya J Frew
- The New Zealand Institute for Plant & Food Research Limited, PO Box 4704, Christchurch, New Zealand
| | - Ruth C Butler
- The New Zealand Institute for Plant & Food Research Limited, PO Box 4704, Christchurch, New Zealand
| | - Sarah R Murray
- The New Zealand Institute for Plant & Food Research Limited, PO Box 4704, Christchurch, New Zealand
| | - Leire Moya
- The New Zealand Institute for Plant & Food Research Limited, PO Box 4704, Christchurch, New Zealand
| | - Clarice J Coyne
- USDA-ARS Western Regional Plant Introduction Station, 59 Johnson Hall, WSU Pullman, Pullman, Washington, WA 99164-6402, USA
| | - Gail M Timmerman-Vaughan
- The New Zealand Institute for Plant & Food Research Limited, PO Box 4704, Christchurch, New Zealand.
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MacNeill GJ, Mehrpouyan S, Minow MAA, Patterson JA, Tetlow IJ, Emes MJ. Starch as a source, starch as a sink: the bifunctional role of starch in carbon allocation. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:4433-4453. [PMID: 28981786 DOI: 10.1093/jxb/erx291] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Starch commands a central role in the carbon budget of the majority of plants on earth, and its biological role changes during development and in response to the environment. Throughout the life of a plant, starch plays a dual role in carbon allocation, acting as both a source, releasing carbon reserves in leaves for growth and development, and as a sink, either as a dedicated starch store in its own right (in seeds and tubers), or as a temporary reserve of carbon contributing to sink strength, in organs such as flowers, fruits, and developing non-starchy seeds. The presence of starch in tissues and organs thus has a profound impact on the physiology of the growing plant as its synthesis and degradation governs the availability of free sugars, which in turn control various growth and developmental processes. This review attempts to summarize the large body of information currently available on starch metabolism and its relationship to wider aspects of carbon metabolism and plant nutrition. It highlights gaps in our knowledge and points to research areas that show promise for bioengineering and manipulation of starch metabolism in order to achieve more desirable phenotypes such as increased yield or plant biomass.
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Affiliation(s)
- Gregory J MacNeill
- Department of Molecular and Cellular Biology, College of Biological Science, Summerlee Science Complex, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Sahar Mehrpouyan
- Department of Molecular and Cellular Biology, College of Biological Science, Summerlee Science Complex, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Mark A A Minow
- Department of Molecular and Cellular Biology, College of Biological Science, Summerlee Science Complex, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Jenelle A Patterson
- Department of Molecular and Cellular Biology, College of Biological Science, Summerlee Science Complex, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Ian J Tetlow
- Department of Molecular and Cellular Biology, College of Biological Science, Summerlee Science Complex, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Michael J Emes
- Department of Molecular and Cellular Biology, College of Biological Science, Summerlee Science Complex, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
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Sweetlove LJ, Nielsen J, Fernie AR. Engineering central metabolism - a grand challenge for plant biologists. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:749-763. [PMID: 28004455 DOI: 10.1111/tpj.13464] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Revised: 12/14/2016] [Accepted: 12/15/2016] [Indexed: 06/06/2023]
Abstract
The goal of increasing crop productivity and nutrient-use efficiency is being addressed by a number of ambitious research projects seeking to re-engineer photosynthetic biochemistry. Many of these projects will require the engineering of substantial changes in fluxes of central metabolism. However, as has been amply demonstrated in simpler systems such as microbes, central metabolism is extremely difficult to rationally engineer. This is because of multiple layers of regulation that operate to maintain metabolic steady state and because of the highly connected nature of central metabolism. In this review we discuss new approaches for metabolic engineering that have the potential to address these problems and dramatically improve the success with which we can rationally engineer central metabolism in plants. In particular, we advocate the adoption of an iterative 'design-build-test-learn' cycle using fast-to-transform model plants as test beds. This approach can be realised by coupling new molecular tools to incorporate multiple transgenes in nuclear and plastid genomes with computational modelling to design the engineering strategy and to understand the metabolic phenotype of the engineered organism. We also envisage that mutagenesis could be used to fine-tune the balance between the endogenous metabolic network and the introduced enzymes. Finally, we emphasise the importance of considering the plant as a whole system and not isolated organs: the greatest increase in crop productivity will be achieved if both source and sink metabolism are engineered.
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Affiliation(s)
- Lee J Sweetlove
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE41128, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800, Lyngby, Denmark
- Science for Life Laboratory, Royal Institute of Technology, SE17121, Stockholm, Sweden
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
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Functional and structural characterization of plastidic starch phosphorylase during barley endosperm development. PLoS One 2017; 12:e0175488. [PMID: 28407006 PMCID: PMC5391026 DOI: 10.1371/journal.pone.0175488] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 03/27/2017] [Indexed: 12/03/2022] Open
Abstract
The production of starch is essential for human nutrition and represents a major metabolic flux in the biosphere. The biosynthesis of starch in storage organs like barley endosperm operates via two main pathways using different substrates: starch synthases use ADP-glucose to produce amylose and amylopectin, the two major components of starch, whereas starch phosphorylase (Pho1) uses glucose-1-phosphate (G1P), a precursor for ADP-glucose production, to produce α-1,4 glucans. The significance of the Pho1 pathway in starch biosynthesis has remained unclear. To elucidate the importance of barley Pho1 (HvPho1) for starch biosynthesis in barley endosperm, we analyzed HvPho1 protein production and enzyme activity levels throughout barley endosperm development and characterized structure-function relationships of HvPho1. The molecular mechanisms underlying the initiation of starch granule biosynthesis, that is, the enzymes and substrates involved in the initial transition from simple sugars to polysaccharides, remain unclear. We found that HvPho1 is present as an active protein at the onset of barley endosperm development. Notably, purified recombinant protein can catalyze the de novo production of α-1,4-glucans using HvPho1 from G1P as the sole substrate. The structural properties of HvPho1 provide insights into the low affinity of HvPho1 for large polysaccharides like starch or amylopectin. Our results suggest that HvPho1 may play a role during the initiation of starch biosynthesis in barley.
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Van Harsselaar JK, Lorenz J, Senning M, Sonnewald U, Sonnewald S. Genome-wide analysis of starch metabolism genes in potato (Solanum tuberosum L.). BMC Genomics 2017; 18:37. [PMID: 28056783 PMCID: PMC5217216 DOI: 10.1186/s12864-016-3381-z] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 12/06/2016] [Indexed: 12/11/2022] Open
Abstract
Background Starch is the principle constituent of potato tubers and is of considerable importance for food and non-food applications. Its metabolism has been subject of extensive research over the past decades. Despite its importance, a description of the complete inventory of genes involved in starch metabolism and their genome organization in potato plants is still missing. Moreover, mechanisms regulating the expression of starch genes in leaves and tubers remain elusive with regard to differences between transitory and storage starch metabolism, respectively. This study aimed at identifying and mapping the complete set of potato starch genes, and to study their expression pattern in leaves and tubers using different sets of transcriptome data. Moreover, we wanted to uncover transcription factors co-regulated with starch accumulation in tubers in order to get insight into the regulation of starch metabolism. Results We identified 77 genomic loci encoding enzymes involved in starch metabolism. Novel isoforms of many enzymes were found. Their analysis will help to elucidate mechanisms of starch biosynthesis and degradation. Expression analysis of starch genes led to the identification of tissue-specific isoenzymes suggesting differences in the transcriptional regulation of starch metabolism between potato leaf and tuber tissues. Selection of genes predominantly expressed in developing potato tubers and exhibiting an expression pattern indicative for a role in starch biosynthesis enabled the identification of possible transcriptional regulators of tuber starch biosynthesis by co-expression analysis. Conclusions This study provides the annotation of the complete set of starch metabolic genes in potato plants and their genomic localizations. Novel, so far undescribed, enzyme isoforms were revealed. Comparative transcriptome analysis enabled the identification of tuber- and leaf-specific isoforms of starch genes. This finding suggests distinct regulatory mechanisms in transitory and storage starch metabolism. Putative regulatory proteins of starch biosynthesis in potato tubers have been identified by co-expression and their expression was verified by quantitative RT-PCR. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3381-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jessica K Van Harsselaar
- Department of Biology, Division of Biochemistry, Friedrich-Alexander-University Erlangen-Nuremberg, Staudtstrasse 5, 91058, Erlangen, Germany
| | - Julia Lorenz
- Department of Biology, Division of Biochemistry, Friedrich-Alexander-University Erlangen-Nuremberg, Staudtstrasse 5, 91058, Erlangen, Germany
| | - Melanie Senning
- Department of Biology, Division of Biochemistry, Friedrich-Alexander-University Erlangen-Nuremberg, Staudtstrasse 5, 91058, Erlangen, Germany
| | - Uwe Sonnewald
- Department of Biology, Division of Biochemistry, Friedrich-Alexander-University Erlangen-Nuremberg, Staudtstrasse 5, 91058, Erlangen, Germany
| | - Sophia Sonnewald
- Department of Biology, Division of Biochemistry, Friedrich-Alexander-University Erlangen-Nuremberg, Staudtstrasse 5, 91058, Erlangen, Germany.
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38
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Mitchell M, Pritchard J, Okada S, Larroque O, Yulia D, Pettolino F, Szydlowski N, Singh S, Liu Q, Ral JP. Oil Accumulation in Transgenic Potato Tubers Alters Starch Quality and Nutritional Profile. FRONTIERS IN PLANT SCIENCE 2017; 8:554. [PMID: 28446916 PMCID: PMC5388768 DOI: 10.3389/fpls.2017.00554] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 03/27/2017] [Indexed: 05/07/2023]
Abstract
Plant storage compounds such as starch and lipids are important for human and animal nutrition as well as industry. There is interest in diverting some of the carbon stored in starch-rich organs (leaves, tubers, and cereal grains) into lipids in order to improve the energy density or nutritional properties of crops as well as providing new sources of feedstocks for food and manufacturing. Previously, we generated transgenic potato plants that accumulate up to 3.3% triacylglycerol (TAG) by dry weight in the tubers, which also led to changes in starch content, starch granule morphology and soluble sugar content. The aim of this study was to investigate how TAG accumulation affects the nutritional and processing properties of high oil potatoes with a particular focus on starch structure, physical and chemical properties. Overall, TAG accumulation was correlated with increased energy density, total nitrogen, amino acids, organic acids and inorganic phosphate, which could be of potential nutritional benefit. However, TAG accumulation had negative effects on starch quality as well as quantity. Starch from high oil potatoes had lower amylose and phosphate content, reduced peak viscosity and higher gelatinization temperature. Interestingly, starch pasting properties were disproportionately affected in lines accumulating the highest levels of TAG (>2.5%) compared to those accumulating only moderate levels (0.2-1.6%). These results indicate that optimized engineering of specialized crops for food, feed, fuel and chemical industries requires careful selection of traits, and an appropriate level of transgene expression, as well as a better understanding of starch structure and carbon partitioning in plant storage organs.
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Affiliation(s)
- Madeline Mitchell
- Commonwealth Scientific and Industrial Research OrganisationCanberra, ACT, Australia
- *Correspondence: Madeline Mitchell
| | - Jenifer Pritchard
- Commonwealth Scientific and Industrial Research OrganisationCanberra, ACT, Australia
| | - Shoko Okada
- Commonwealth Scientific and Industrial Research OrganisationCanberra, ACT, Australia
| | - Oscar Larroque
- Commonwealth Scientific and Industrial Research OrganisationCanberra, ACT, Australia
| | - Dina Yulia
- Commonwealth Scientific and Industrial Research OrganisationCanberra, ACT, Australia
| | - Filomena Pettolino
- Commonwealth Scientific and Industrial Research OrganisationCanberra, ACT, Australia
| | - Nicolas Szydlowski
- Univ. Lille, CNRS, USR 3290 - MSAP - Miniaturisation pour la Synthèse l'Analyse et la ProtéomiqueLille, France
| | - Surinder Singh
- Commonwealth Scientific and Industrial Research OrganisationCanberra, ACT, Australia
| | - Qing Liu
- Commonwealth Scientific and Industrial Research OrganisationCanberra, ACT, Australia
| | - Jean-Philippe Ral
- Commonwealth Scientific and Industrial Research OrganisationCanberra, ACT, Australia
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Cai H, Chen Y, Zhang M, Cai R, Cheng B, Ma Q, Zhao Y. A novel GRAS transcription factor, ZmGRAS20, regulates starch biosynthesis in rice endosperm. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2017; 23:143-154. [PMID: 28250591 PMCID: PMC5313408 DOI: 10.1007/s12298-016-0404-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/29/2016] [Indexed: 05/07/2023]
Abstract
Starch occupies the maximal component of cereal grains and is pivotal for maize yield and quality. However, the regulatory mechanism of starch synthesis is still poorly understand. In this study, a GRAS transcription factor, ZmGRAS20, was isolated from maize inbred line B73 based on transcriptome sequencing. Quantitative real-time PCR indicated that ZmGRAS20 is specifically expressed in maize endosperm. Transient expression of ZmGRAS20-green fluorescent protein fusion protein in tobacco cells showed a nucleus and membrane localization of the protein. Transactivation assay of ZmGRAS20 demonstrated that it has no transactivation activity in yeast cells. Overexpression of ZmGRAS20 led to a chalky region of ventral endosperm with decreased starch content and defective agronomic characters in transgenic seeds. Moreover, ZmGRAS20-overexpression plants had fewer fractions of long-branched starch chains. Further scanning electron microscopy observation of ZmGRAS20 transgenic seeds exhibited altered starch granules morphology compared with wide type plants. Taken together, these results suggested that ZmGRAS20 may function as a starch synthesis regulatory factor in rice endosperm.
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Affiliation(s)
- Huilin Cai
- National Engineering Laboratory of Crop Stress Resistance/Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, 230036 China
| | - Yulong Chen
- National Engineering Laboratory of Crop Stress Resistance/Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, 230036 China
| | - Min Zhang
- National Engineering Laboratory of Crop Stress Resistance/Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, 230036 China
| | - Ronghao Cai
- National Engineering Laboratory of Crop Stress Resistance/Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, 230036 China
| | - Beijiu Cheng
- National Engineering Laboratory of Crop Stress Resistance/Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, 230036 China
| | - Qing Ma
- National Engineering Laboratory of Crop Stress Resistance/Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, 230036 China
| | - Yang Zhao
- National Engineering Laboratory of Crop Stress Resistance/Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, 230036 China
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40
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Modeling the competition between antenna size mutant and wild type microalgae in outdoor mass culture. J Biotechnol 2016; 240:1-13. [DOI: 10.1016/j.jbiotec.2016.10.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 10/10/2016] [Accepted: 10/12/2016] [Indexed: 01/09/2023]
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Gao H, Yu X, Deng T, Sun M, Xiao X, Huang X, Chen Y, Li R. Event-specific detection of transgenic potato AV43-6-G7 using real-time and digital PCR methods. BMC Biotechnol 2016; 16:74. [PMID: 27784303 PMCID: PMC5081928 DOI: 10.1186/s12896-016-0303-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 10/13/2016] [Indexed: 01/09/2023] Open
Abstract
Background The isolation of unknown DNA sequences flanked by known sequences is an important task in the event-specific detection of GMOs. None of event-specific detection method was developed based on the junction sequence of an exogenous integrant in the transgenic potato AV43-6-G7. Results The flanking sequence between the exogenous fragment and recombinant chromosome of this potato was successfully acquired through exogenous gene 5′-RACE. The event-specific primers and Taqman probe were designed to amplify fragments spanning the exogenous DNA and potato genomic DNA. The specific real-time PCR and digital PCR detection methods for AV43-6-G7 potato were established based on primers designed according to the flanking sequences. The detection limit of the qualitative PCR assay was 0.01 % for AV43-6-G7 potato in 100 ng of potato genomic DNA, corresponding to approximately 11.6 copies of the potato haploid genome. The ddPCR assays for Potato AV43-6-G7 achieved a limit of quantification of approximately 58 target copies, with RSD ≤ 25 %. The aLOQ of this system was approximately 1.2 copies. Conclusions These results indicated that these event-specific methods would be useful for the identification of potato AV43-6-G7. Electronic supplementary material The online version of this article (doi:10.1186/s12896-016-0303-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hongwei Gao
- Shandong Entry-Exit Inspection and Quarantine Bureau of People's Republic of China, Qingdao, China.
| | - Xiaofan Yu
- Qingdao University Medical College, Qingdao, China
| | - Tingting Deng
- Chinese Academy of Inspection and Quarantine Institute, Beijing, China
| | - Min Sun
- Shandong Entry-Exit Inspection and Quarantine Bureau of People's Republic of China, Qingdao, China
| | - Xizhi Xiao
- Shandong Entry-Exit Inspection and Quarantine Bureau of People's Republic of China, Qingdao, China
| | - Xin Huang
- Chinese Academy of Inspection and Quarantine Institute, Beijing, China
| | - Ying Chen
- Chinese Academy of Inspection and Quarantine Institute, Beijing, China
| | - Ronggui Li
- Qingdao University Medical College, Qingdao, China
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Yasui Y, Hirakawa H, Ueno M, Matsui K, Katsube-Tanaka T, Yang SJ, Aii J, Sato S, Mori M. Assembly of the draft genome of buckwheat and its applications in identifying agronomically useful genes. DNA Res 2016; 23:215-24. [PMID: 27037832 PMCID: PMC4909311 DOI: 10.1093/dnares/dsw012] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 02/20/2016] [Indexed: 01/14/2023] Open
Abstract
Buckwheat (Fagopyrum esculentum Moench; 2n = 2x = 16) is a nutritionally dense annual crop widely grown in temperate zones. To accelerate molecular breeding programmes of this important crop, we generated a draft assembly of the buckwheat genome using short reads obtained by next-generation sequencing (NGS), and constructed the Buckwheat Genome DataBase. After assembling short reads, we determined 387,594 scaffolds as the draft genome sequence (FES_r1.0). The total length of FES_r1.0 was 1,177,687,305 bp, and the N50 of the scaffolds was 25,109 bp. Gene prediction analysis revealed 286,768 coding sequences (CDSs; FES_r1.0_cds) including those related to transposable elements. The total length of FES_r1.0_cds was 212,917,911 bp, and the N50 was 1,101 bp. Of these, the functions of 35,816 CDSs excluding those for transposable elements were annotated by BLAST analysis. To demonstrate the utility of the database, we conducted several test analyses using BLAST and keyword searches. Furthermore, we used the draft genome as a reference sequence for NGS-based markers, and successfully identified novel candidate genes controlling heteromorphic self-incompatibility of buckwheat. The database and draft genome sequence provide a valuable resource that can be used in efforts to develop buckwheat cultivars with superior agronomic traits.
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Affiliation(s)
- Yasuo Yasui
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyou-ku, Kyoto 606-8502, Japan
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Mariko Ueno
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyou-ku, Kyoto 606-8502, Japan
| | - Katsuhiro Matsui
- NARO Kyushu Okinawa Agricultural Research Center, 2421 Suya, Koshi, Kumamoto 861-1192, Japan
| | - Tomoyuki Katsube-Tanaka
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyou-ku, Kyoto 606-8502, Japan
| | - Soo Jung Yang
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyou-ku, Kyoto 606-8502, Japan
| | - Jotaro Aii
- Faculty of Applied Life Science, Niigata University of Pharmacy and Applied Life Science, Akiha-ku, Niigata 956-8603, Japan
| | - Shingo Sato
- Faculty of Applied Life Science, Niigata University of Pharmacy and Applied Life Science, Akiha-ku, Niigata 956-8603, Japan
| | - Masashi Mori
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 308 Suematsu, Nonoichi, Ishikawa 912-8836, Japan
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Chen J, Yi Q, Cao Y, Wei B, Zheng L, Xiao Q, Xie Y, Gu Y, Li Y, Huang H, Wang Y, Hou X, Long T, Zhang J, Liu H, Liu Y, Yu G, Huang Y. ZmbZIP91 regulates expression of starch synthesis-related genes by binding to ACTCAT elements in their promoters. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:1327-38. [PMID: 26689855 DOI: 10.1093/jxb/erv527] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Starch synthesis is a key process that influences crop yield and quality, though little is known about the regulation of this complex metabolic pathway. Here, we present the identification of ZmbZIP91 as a candidate regulator of starch synthesis via co-expression analysis in maize (Zea mays L.). ZmbZIP91 was strongly associated with the expression of starch synthesis genes. Reverse tanscription-PCR (RT-PCR) and RNA in situ hybridization indicated that ZmbZIP91 is highly expressed in maize endosperm, with less expression in leaves. Particle bombardment-mediated transient expression in maize endosperm and leaf protoplasts demonstrated that ZmbZIP91 could positively regulate the expression of starch synthesis genes in both leaves and endosperm. Additionally, the Arabidopsis mutant vip1 carried a mutation in a gene (VIP1) that is homologous to ZmbZIP91, displayed altered growth with less starch in leaves, and ZmbZIP91 was able to complement this phenotype, resulting in normal starch synthesis. A yeast one-hybrid experiment and EMSAs showed that ZmbZIP91 could directly bind to ACTCAT elements in the promoters of starch synthesis genes (pAGPS1, pSSI, pSSIIIa, and pISA1). These results demonstrate that ZmbZIP91 acts as a core regulatory factor in starch synthesis by binding to ACTCAT elements in the promoters of starch synthesis genes.
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Affiliation(s)
- Jiang Chen
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Qiang Yi
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Yao Cao
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Bin Wei
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Lanjie Zheng
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Qianling Xiao
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Ying Xie
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Yong Gu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Yangping Li
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Huanhuan Huang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Yongbin Wang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Xianbin Hou
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Tiandan Long
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Junjie Zhang
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Hanmei Liu
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Yinghong Liu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Guowu Yu
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Yubi Huang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
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Cuesta-Seijo JA, Nielsen MM, Ruzanski C, Krucewicz K, Beeren SR, Rydhal MG, Yoshimura Y, Striebeck A, Motawia MS, Willats WGT, Palcic MM. In vitro Biochemical Characterization of All Barley Endosperm Starch Synthases. FRONTIERS IN PLANT SCIENCE 2016; 6:1265. [PMID: 26858729 PMCID: PMC4730117 DOI: 10.3389/fpls.2015.01265] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 12/27/2015] [Indexed: 05/18/2023]
Abstract
Starch is the main storage polysaccharide in cereals and the major source of calories in the human diet. It is synthesized by a panel of enzymes including five classes of starch synthases (SSs). While the overall starch synthase (SS) reaction is known, the functional differences between the five SS classes are poorly understood. Much of our knowledge comes from analyzing mutant plants with altered SS activities, but the resulting data are often difficult to interpret as a result of pleitropic effects, competition between enzymes, overlaps in enzyme activity and disruption of multi-enzyme complexes. Here we provide a detailed biochemical study of the activity of all five classes of SSs in barley endosperm. Each enzyme was produced recombinantly in E. coli and the properties and modes of action in vitro were studied in isolation from other SSs and other substrate modifying activities. Our results define the mode of action of each SS class in unprecedented detail; we analyze their substrate selection, temperature dependence and stability, substrate affinity and temporal abundance during barley development. Our results are at variance with some generally accepted ideas about starch biosynthesis and might lead to the reinterpretation of results obtained in planta. In particular, they indicate that granule bound SS is capable of processive action even in the absence of a starch matrix, that SSI has no elongation limit, and that SSIV, believed to be critical for the initiation of starch granules, has maltoligosaccharides and not polysaccharides as its preferred substrates.
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Affiliation(s)
| | | | | | | | | | - Maja G. Rydhal
- Department of Plant and Environmental Sciences, University of CopenhagenFrederiksberg, Copenhagen, Denmark
| | | | | | - Mohammed S. Motawia
- Department of Plant and Environmental Sciences, University of CopenhagenFrederiksberg, Copenhagen, Denmark
| | - William G. T. Willats
- Department of Plant and Environmental Sciences, University of CopenhagenFrederiksberg, Copenhagen, Denmark
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Śliwka J, Sołtys-Kalina D, Szajko K, Wasilewicz-Flis I, Strzelczyk-Żyta D, Zimnoch-Guzowska E, Jakuczun H, Marczewski W. Mapping of quantitative trait loci for tuber starch and leaf sucrose contents in diploid potato. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:131-40. [PMID: 26467474 PMCID: PMC4703618 DOI: 10.1007/s00122-015-2615-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 09/29/2015] [Indexed: 05/11/2023]
Abstract
Most QTL for leaf sucrose content map to positions that are similar to positions of QTL for tuber starch content in diploid potato. In the present study, using a diploid potato mapping population and Diversity Array Technology (DArT) markers, we identified twelve quantitative trait loci (QTL) for tuber starch content on seven potato chromosomes: I, II, III, VIII, X, XI, and XII. The most important QTL spanned a wide region of chromosome I (42.0–104.6 cM) with peaks at 63 and 84 cM which explained 17.6 and 19.2% of the phenotypic variation, respectively. ADP-glucose pyrophosphorylase (AGPase) is the key enzyme for starch biosynthesis. The gene encoding the large subunit of this enzyme, AGPaseS-a, was localized to chromosome I at 102.3 cM and accounted for 15.2% of the variance in tuber starch content. A more than 100-fold higher expression of this gene was observed in RT-qPCR assay in plants with the marker allele AGPaseS-a1334. This study is the first to report QTL for sucrose content in potato leaves. QTL for sucrose content in leaves were located on eight potato chromosomes: I, II, III, V, VIII, IX, X and XII. In 5-week-old plants, only one QTL for leaf sucrose content was detected after 8 h of darkness; four QTL were detected after 8 h of illumination. In 11-week-old plants, 6 and 3 QTL were identified after dark and light phases, respectively. Of fourteen QTL for leaf sucrose content, eleven mapped to positions that were similar to QTL for tuber starch content. These results provide genetic information for further research examining the relationships between metabolic carbon molecule sources and sinks in potato plants.
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Affiliation(s)
- Jadwiga Śliwka
- Plant Breeding and Acclimatization Institute, National Research Institute, Młochów, Platanowa 19, 05-831 Młochów, Poland
| | - Dorota Sołtys-Kalina
- Plant Breeding and Acclimatization Institute, National Research Institute, Młochów, Platanowa 19, 05-831 Młochów, Poland
| | - Katarzyna Szajko
- Plant Breeding and Acclimatization Institute, National Research Institute, Młochów, Platanowa 19, 05-831 Młochów, Poland
| | - Iwona Wasilewicz-Flis
- Plant Breeding and Acclimatization Institute, National Research Institute, Młochów, Platanowa 19, 05-831 Młochów, Poland
| | - Danuta Strzelczyk-Żyta
- Plant Breeding and Acclimatization Institute, National Research Institute, Młochów, Platanowa 19, 05-831 Młochów, Poland
| | - Ewa Zimnoch-Guzowska
- Plant Breeding and Acclimatization Institute, National Research Institute, Młochów, Platanowa 19, 05-831 Młochów, Poland
| | - Henryka Jakuczun
- Plant Breeding and Acclimatization Institute, National Research Institute, Młochów, Platanowa 19, 05-831 Młochów, Poland
| | - Waldemar Marczewski
- Plant Breeding and Acclimatization Institute, National Research Institute, Młochów, Platanowa 19, 05-831 Młochów, Poland
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Transitory and storage starch metabolism: two sides of the same coin? Curr Opin Biotechnol 2015; 32:143-148. [DOI: 10.1016/j.copbio.2014.11.026] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 11/25/2014] [Accepted: 11/28/2014] [Indexed: 11/19/2022]
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Schwarte S, Wegner F, Havenstein K, Groth D, Steup M, Tiedemann R. Sequence variation, differential expression, and divergent evolution in starch-related genes among accessions of Arabidopsis thaliana. PLANT MOLECULAR BIOLOGY 2015; 87:489-519. [PMID: 25663508 DOI: 10.1007/s11103-015-0293-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 01/26/2015] [Indexed: 06/04/2023]
Abstract
Transitory starch metabolism is a nonlinear and highly regulated process. It originated very early in the evolution of chloroplast-containing cells and is largely based on a mosaic of genes derived from either the eukaryotic host cell or the prokaryotic endosymbiont. Initially located in the cytoplasm, starch metabolism was rewired into plastids in Chloroplastida. Relocation was accompanied by gene duplications that occurred in most starch-related gene families and resulted in subfunctionalization of the respective gene products. Starch-related isozymes were then evolutionary conserved by constraints such as internal starch structure, posttranslational protein import into plastids and interactions with other starch-related proteins. 25 starch-related genes in 26 accessions of Arabidopsis thaliana were sequenced to assess intraspecific diversity, phylogenetic relationships, and modes of selection. Furthermore, sequences derived from additional 80 accessions that are publicly available were analyzed. Diversity varies significantly among the starch-related genes. Starch synthases and phosphorylases exhibit highest nucleotide diversities, while pyrophosphatases and debranching enzymes are most conserved. The gene trees are most compatible with a scenario of extensive recombination, perhaps in a Pleistocene refugium. Most genes are under purifying selection, but disruptive selection was inferred for a few genes/substitutiones. To study transcript levels, leaves were harvested throughout the light period. By quantifying the transcript levels and by analyzing the sequence of the respective accessions, we were able to estimate whether transcript levels are mainly determined by genetic (i.e., accession dependent) or physiological (i.e., time dependent) parameters. We also identified polymorphic sites that putatively affect pattern or the level of transcripts.
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Affiliation(s)
- Sandra Schwarte
- Evolutionary Biology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, Building 26, 14476, Potsdam, Germany,
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Sołtys-Kalina D, Szajko K, Sierocka I, Śliwka J, Strzelczyk-Żyta D, Wasilewicz-Flis I, Jakuczun H, Szweykowska-Kulinska Z, Marczewski W. Novel candidate genes AuxRP and Hsp90 influence the chip color of potato tubers. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2015; 35:224. [PMID: 26612975 PMCID: PMC4648990 DOI: 10.1007/s11032-015-0415-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 11/11/2015] [Indexed: 05/11/2023]
Abstract
Potato (Solanum tuberosum L.) tubers exhibit significant variation in reducing sugar content directly after harvest, cold storage and reconditioning. Here, we performed QTL analysis for chip color, which is strongly influenced by reducing sugar content, in a diploid potato mapping population. Two QTL on chromosomes I and VI were detected for chip color after harvest and reconditioning. Only one region on chromosome VI was linked with cold-induced sweetening. Using the RT-PCR technique, we showed differential expression of the auxin-regulated protein (AuxRP) gene. The AuxRP transcript was presented in light chip color parental clone DG 97-952 and the RNA progeny of the bulk sample consisting of light chip color phenotypes after cold storage. This amplicon was absent in dark chip parental clone DG 08-26/39 and the RNA bulk sample of dark chip progeny. Genetic variation of AuxRP explained up to 16.6 and 15.2 % of the phenotypic variance after harvest and 3 months of storage at 4 °C, respectively. Using an alternative approach, the RDA-cDNA method was used to recognize 25 gene sequences, of which 11 could be assigned to potato chromosome VI. One of these genes, Heat-shock protein 90 (Hsp90), demonstrated higher mRNA and protein expression in RT-qPCR and western blotting assays in the dark chip color progeny bulk sample compared with the light chip color progeny bulk sample. Our study, for the first time, suggests that the AuxRP and Hsp90 genes are novel candidate genes capable of influencing the chip color of potato tubers.
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Affiliation(s)
- Dorota Sołtys-Kalina
- />Plant Breeding and Acclimatization Institute, National Research Institute, Młochów, Platanowa 19, 05-831 Młochów, Poland
| | - Katarzyna Szajko
- />Plant Breeding and Acclimatization Institute, National Research Institute, Młochów, Platanowa 19, 05-831 Młochów, Poland
| | - Izabela Sierocka
- />Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Jadwiga Śliwka
- />Plant Breeding and Acclimatization Institute, National Research Institute, Młochów, Platanowa 19, 05-831 Młochów, Poland
| | - Danuta Strzelczyk-Żyta
- />Plant Breeding and Acclimatization Institute, National Research Institute, Młochów, Platanowa 19, 05-831 Młochów, Poland
| | - Iwona Wasilewicz-Flis
- />Plant Breeding and Acclimatization Institute, National Research Institute, Młochów, Platanowa 19, 05-831 Młochów, Poland
| | - Henryka Jakuczun
- />Plant Breeding and Acclimatization Institute, National Research Institute, Młochów, Platanowa 19, 05-831 Młochów, Poland
| | - Zofia Szweykowska-Kulinska
- />Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Waldemar Marczewski
- />Plant Breeding and Acclimatization Institute, National Research Institute, Młochów, Platanowa 19, 05-831 Młochów, Poland
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Cortés Sierra SP, Chavarriaga P, Ceballos H, López Carrascal CE. EVALUACIÓN DE LA EXPRESIÓN DE GENES IMPLICADOS EN LA BIOSÍNTESIS DE ALMIDÓN EN DIFERENTES VARIEDADES DE YUCA. ACTA BIOLÓGICA COLOMBIANA 2014. [DOI: 10.15446/abc.v20n2.42875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
<p>Las raíces almacenadoras de yuca representan una fuente importante de almidón. La ruta metabólica del almidón ha sido reconstruida recientemente en yuca gracias a la liberación de la secuencia completa de su genoma. En este estudio se evaluó la expresión de los genes que codifican para las enzimas Pululanasa, Isoamilasa, α-amilasa, Enzima Desproporcionante, ADP-glucosa pirofoforilasa, Almidón sintasa unida al gránulo, Enzima ramificante del almidón y Sintasa soluble del almidón, en las raíces almacenadoras de plantas de 5 y 11 meses de edad, en un grupo de cinco variedades de yuca. Se evidenciaron diferencias importantes en la expresión de estos genes entre las variedades evaluadas y entre los dos tiempos. Las variedades CM523-7 y SM1219-2 presentaron uno de los niveles más altos de expresión para los genes ADP-glucosa pirofoforilasa y Almidón sintasa unida al gránulo mientras que el gen para α-amilasa fue el más bajo en estas dos variedades. Aunque la variedad TMS60444 presentó niveles de expresión similares en genes implicados en la síntesis de almidón, fue la que presentó el mayor nivel de expresión de la α-amilasa. Estos datos se pueden correlacionar con el relativo bajo contenido de materia seca en esta variedad. Los datos de expresión génica presentados en este trabajo permitirán complementar información sobre actividad enzimática con miras a identificar los elementos más importantes en la acumulación diferencial de almidón entre variedades de yuca.</p><p><strong>ABSTRACT</strong></p><p>Cassava storage roots represent an important starch source. Recently, the starch metabolic pathway in cassava has been reconstructed thanks to the full release of its genome. In this study gene expression was evaluated for genes coding Pullulanase, Isoamylase, α-amylase, Deproportionating enzyme, ADP-glucose pyrophosphorylase, Granule bound starch synthase, Starch branching enzyme and Soluble starch synthase, in cassava storage roots 5 and 11 months old, in 5 cassava varieties. Important gene expression differences were detected both at the variety and time level. CM523-7 and SM1219-2 showed one of the highest expression levels for AGPase and GBSS genes, while α-amylase showed the lowest level in these two varieties. TMS60444 variety showed similar expression levels in starch biosynthesis-related genes, but conversely also showed the highest α-amylase expression. This correlates with the relative low dry-matter content in TMS60444. Gene expression data reported here will allow complementing actual information on enzymatic activity, in order to identify the most relevant factors in differential starch accumulation between cassava varieties.</p><br /><p> </p>
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Nayar S, Sharma R, Tyagi AK, Kapoor S. Functional delineation of rice MADS29 reveals its role in embryo and endosperm development by affecting hormone homeostasis. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:4239-53. [PMID: 23929654 PMCID: PMC3808311 DOI: 10.1093/jxb/ert231] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Rice MADS29 has recently been reported to cause programmed cell death of maternal tissues, the nucellus, and the nucellar projection during early stages of seed development. However, analyses involving OsMADS29 protein expression domains and characterization of OsMADS29 gain-of-function and knockdown phenotypes revealed novel aspects of its function in maintaining hormone homeostasis, which may have a role in the development of embryo and plastid differentiation and starch filling in endosperm cells. The MADS29 transcripts accumulated to high levels soon after fertilization; however, protein accumulation was found to be delayed by at least 4 days. Immunolocalization studies revealed that the protein accumulated initially in the dorsal-vascular trace and the outer layers of endosperm, and subsequently in the embryo and aleurone and subaleurone layers of the endosperm. Ectopic expression of MADS29 resulted in a severely dwarfed phenotype, exhibiting elevated levels of cytokinin, thereby suggesting that cytokinin biosynthesis pathway could be one of the major targets of OsMADS29. Overexpression of OsMADS29 in heterologous BY2 cells was found to mimic the effects of exogenous application of cytokinins that causes differentiation of proplastids to starch-containing amyloplasts and activation of genes involved in the starch biosynthesis pathway. Suppression of MADS29 expression by RNAi severely affected seed set. The surviving seeds were smaller in size, with developmental abnormalities in the embryo and reduced size of endosperm cells, which also contained loosely packed starch granules. Microarray analysis of overexpression and knockdown lines exhibited altered expression of genes involved in plastid biogenesis, starch biosynthesis, cytokinin signalling and biosynthesis.
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Affiliation(s)
- Saraswati Nayar
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Rita Sharma
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
- *Present address: Department of Plant Pathology, University of California, Davis, CA 95616, USA
| | - Akhilesh Kumar Tyagi
- National Institute for Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Sanjay Kapoor
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
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