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Pfister B, Shields JM, Kockmann T, Grossmann J, Abt MR, Stadler M, Zeeman SC. Tuning heterologous glucan biosynthesis in yeast to understand and exploit plant starch diversity. BMC Biol 2022; 20:207. [PMID: 36153520 PMCID: PMC9509603 DOI: 10.1186/s12915-022-01408-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/13/2022] [Indexed: 11/30/2022] Open
Abstract
Background Starch, a vital plant-derived polysaccharide comprised of branched glucans, is essential in nutrition and many industrial applications. Starch is often modified post-extraction to alter its structure and enhance its functionality. Targeted metabolic engineering of crops to produce valuable and versatile starches requires knowledge of the relationships between starch biosynthesis, structure, and properties, but systematic studies to obtain this knowledge are difficult to conduct in plants. Here we used Saccharomyces cerevisiae as a testbed to dissect the functions of plant starch biosynthetic enzymes and create diverse starch-like polymers. Results We explored yeast promoters and terminators to tune the expression levels of the starch-biosynthesis machinery from Arabidopsis thaliana. We systematically modulated the expression of each starch synthase (SS) together with a branching enzyme (BE) in yeast. Protein quantification by parallel reaction monitoring (targeted proteomics) revealed unexpected effects of glucan biosynthesis on protein abundances but showed that the anticipated broad range of SS/BE enzyme ratios was maintained during the biosynthetic process. The different SS/BE ratios clearly influenced glucan structure and solubility: The higher the SS/BE ratio, the longer the glucan chains and the more glucans were partitioned into the insoluble fraction. This effect was irrespective of the SS isoform, demonstrating that the elongation/branching ratio controls glucan properties separate from enzyme specificity. Conclusions Our results provide a quantitative framework for the in silico design of improved starch biosynthetic processes in plants. Our study also exemplifies a workflow for the rational tuning of a complex pathway in yeast, starting from the selection and evaluation of expression modules to multi-gene assembly and targeted protein monitoring during the biosynthetic process. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01408-x.
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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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3
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Seidi F, Yazdi MK, Jouyandeh M, Habibzadeh S, Munir MT, Vahabi H, Bagheri B, Rabiee N, Zarrintaj P, Saeb MR. Crystalline polysaccharides: A review. Carbohydr Polym 2022; 275:118624. [PMID: 34742405 DOI: 10.1016/j.carbpol.2021.118624] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 08/26/2021] [Accepted: 08/26/2021] [Indexed: 12/12/2022]
Abstract
The biodegradability and mechanical properties of polysaccharides are dependent on their architecture (linear or branched) as well as their crystallinity (size of crystals and crystallinity percent). The amount of crystalline zones in the polysaccharide significantly governs their ultimate properties and applications (from packaging to biomedicine). Although synthesis, characterization, and properties of polysaccharides have been the subject of several review papers, the effects of crystallization kinetics and crystalline domains on the properties and application have not been comprehensively addressed. This review places focus on different aspects of crystallization of polysaccharides as well as applications of crystalline polysaccharides. Crystallization of cellulose, chitin, chitosan, and starch, as the main members of this family, were discussed. Then, application of the aforementioned crystalline polysaccharides and nano-polysaccharides as well as their physical and chemical interactions were overviewed. This review attempts to provide a complete picture of crystallization-property relationship in polysaccharides.
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Affiliation(s)
- Farzad Seidi
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources and International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing 210037, China
| | - Mohsen Khodadadi Yazdi
- Center of Excellence in Electrochemistry, School of Chemistry, College of Science, University of Tehran, Tehran, Iran
| | - Maryam Jouyandeh
- Center of Excellence in Electrochemistry, School of Chemistry, College of Science, University of Tehran, Tehran, Iran
| | - Sajjad Habibzadeh
- Department of Chemical Engineering, Amirkabir University of Technology (Tehran Polytechnic), Tehran, Iran
| | | | - Henri Vahabi
- Université de Lorraine, CentraleSupélec, LMOPS, F-57000 Metz, France
| | - Babak Bagheri
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Navid Rabiee
- Department of Physics, Sharif University of Technology, P.O. Box 11155-9161, Tehran, Iran
| | - Payam Zarrintaj
- School of Chemical Engineering, Oklahoma State University, 420 Engineering North, Stillwater, OK 74078, United States
| | - Mohammad Reza Saeb
- Department of Polymer Technology, Faculty of Chemistry, Gdańsk University of Technology, G. Narutowicza 11/12, 80-233 Gdańsk, Poland.
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Pfister B, Zeeman SC, Rugen MD, Field RA, Ebenhöh O, Raguin A. Theoretical and experimental approaches to understand the biosynthesis of starch granules in a physiological context. PHOTOSYNTHESIS RESEARCH 2020; 145:55-70. [PMID: 31955343 PMCID: PMC7308250 DOI: 10.1007/s11120-019-00704-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 12/19/2019] [Indexed: 06/10/2023]
Abstract
Starch, a plant-derived insoluble carbohydrate composed of glucose polymers, is the principal carbohydrate in our diet and a valuable raw material for industry. The properties of starch depend on the arrangement of glucose units within the constituent polymers. However, key aspects of starch structure and the underlying biosynthetic processes are not well understood, limiting progress towards targeted improvement of our starch crops. In particular, the major component of starch, amylopectin, has a complex three-dimensional, branched architecture. This architecture stems from the combined actions of a multitude of enzymes, each having broad specificities that are difficult to capture experimentally. In this review, we reflect on experimental approaches and limitations to decipher the enzymes' specificities and explore possibilities for in silico simulations of these activities. We believe that the synergy between experimentation and simulation is needed for the correct interpretation of experimental data and holds the potential to greatly advance our understanding of the overall starch biosynthetic process. We furthermore propose that the formation of glucan secondary structures, concomitant with its synthesis, is a previously overlooked factor that directly affects amylopectin architecture through its impact on enzyme function.
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Affiliation(s)
- Barbara Pfister
- Department of Biology, Institute of Molecular Plant Biology, ETH Zurich, 8092, Zurich, Switzerland
| | - Samuel C Zeeman
- Department of Biology, Institute of Molecular Plant Biology, ETH Zurich, 8092, Zurich, Switzerland
| | - Michael D Rugen
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Robert A Field
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Oliver Ebenhöh
- Department of Biology, Institute of Quantitative and Theoretical Biology, Heinrich-Heine University, 40225, Düsseldorf, Germany
- Department of Biology, Cluster of Excellence on Plant Sciences, Institute of Quantitative and Theoretical Biology, Heinrich-Heine University, 40225, Düsseldorf, Germany
| | - Adélaïde Raguin
- Department of Biology, Institute of Quantitative and Theoretical Biology, Heinrich-Heine University, 40225, Düsseldorf, Germany.
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Balakrishna AK, Wazed MA, Farid M. A Review on the Effect of High Pressure Processing (HPP) on Gelatinization and Infusion of Nutrients. Molecules 2020; 25:E2369. [PMID: 32443759 PMCID: PMC7287844 DOI: 10.3390/molecules25102369] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/13/2020] [Accepted: 05/18/2020] [Indexed: 12/29/2022] Open
Abstract
High pressure processing (HPP) is a novel technology that involves subjecting foods to high hydrostatic pressures of the order of 100-600 MPa. This technology has been proven successful for inactivation of numerous microorganisms, spores and enzymes in foods, leading to increased shelf life. HPP is not limited to cold pasteurization, but has many other applications. The focus of this paper is to explore other applications of HPP, such as gelatinization, forced water absorption and infusion of nutrients. The use of high pressure in producing cold gelatinizing effects, imparting unique properties to food and improving food quality will be also discussed, highlighting the latest published studies and the innovative methods adopted.
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Affiliation(s)
| | | | - Mohammed Farid
- Department of Chemical and Materials Engineering, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand; (A.K.B.); (M.A.W.)
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Singh RP, Pergolizzi G, Nepogodiev SA, de Andrade P, Kuhaudomlarp S, Field RA. Preparative and Kinetic Analysis of β-1,4- and β-1,3-Glucan Phosphorylases Informs Access to Human Milk Oligosaccharide Fragments and Analogues Thereof. Chembiochem 2020; 21:1043-1049. [PMID: 31657512 PMCID: PMC7187349 DOI: 10.1002/cbic.201900440] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/27/2019] [Indexed: 12/21/2022]
Abstract
The enzymatic synthesis of oligosaccharides depends on the availability of suitable enzymes, which remains a limitation. Without recourse to enzyme engineering or evolution approaches, herein we demonstrate the ability of wild-type cellodextrin phosphorylase (CDP: β-1,4-glucan linkage-dependent) and laminaridextrin phosphorylase (Pro_7066: β-1,3-glucan linkage-dependent) to tolerate a number of sugar-1- phosphate substrates, albeit with reduced kinetic efficiency. In spite of catalytic efficiencies of <1 % of the natural reactions, we demonstrate the utility of given phosphorylase-sugar phosphate pairs to access new-to-nature fragments of human milk oligosaccharides, or analogues thereof, in multi-milligram quantities.
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Affiliation(s)
- Ravindra Pal Singh
- Department of Biological ChemistryJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
- Present address: Food and Nutritional Biotechnology DivisionNational Agri-Food Biotechnology Institute (NABI)Main Campus, Sector 81Sahibzada Ajit Singh NagarPunjab140306India
| | - Giulia Pergolizzi
- Department of Biological ChemistryJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
| | - Sergey A. Nepogodiev
- Department of Biological ChemistryJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
| | - Peterson de Andrade
- Department of Biological ChemistryJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
| | - Sakonwan Kuhaudomlarp
- Department of Biological ChemistryJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
| | - Robert A. Field
- Department of Biological ChemistryJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
- Present address: Department of Chemistry and Manchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUK
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Kuhaudomlarp S, Stevenson CEM, Lawson DM, Field RA. The structure of a GH149 β-(1 → 3) glucan phosphorylase reveals a new surface oligosaccharide binding site and additional domains that are absent in the disaccharide-specific GH94 glucose-β-(1 → 3)-glucose (laminaribiose) phosphorylase. Proteins 2019; 87:885-892. [PMID: 31134667 PMCID: PMC6771811 DOI: 10.1002/prot.25745] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 05/07/2019] [Accepted: 05/22/2019] [Indexed: 11/08/2022]
Abstract
Glycoside phosphorylases (GPs) with specificity for β-(1 → 3)-gluco-oligosaccharides are potential candidate biocatalysts for oligosaccharide synthesis. GPs with this linkage specificity are found in two families thus far-glycoside hydrolase family 94 (GH94) and the recently discovered glycoside hydrolase family 149 (GH149). Previously, we reported a crystallographic study of a GH94 laminaribiose phosphorylase with specificity for disaccharides, providing insight into the enzyme's ability to recognize its' sugar substrate/product. In contrast to GH94, characterized GH149 enzymes were shown to have more flexible chain length specificity, with preference for substrate/product with higher degree of polymerization. In order to advance understanding of the specificity of GH149 enzymes, we herein solved X-ray crystallographic structures of GH149 enzyme Pro_7066 in the absence of substrate and in complex with laminarihexaose (G6). The overall domain organization of Pro_7066 is very similar to that of GH94 family enzymes. However, two additional domains flanking its catalytic domain were found only in the GH149 enzyme. Unexpectedly, the G6 complex structure revealed an oligosaccharide surface binding site remote from the catalytic site, which, we suggest, may be associated with substrate targeting. As such, this study reports the first structure of a GH149 phosphorylase enzyme acting on β-(1 → 3)-gluco-oligosaccharides and identifies structural elements that may be involved in defining the specificity of the GH149 enzymes.
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Affiliation(s)
- Sakonwan Kuhaudomlarp
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Clare E M Stevenson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, UK
| | - David M Lawson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Robert A Field
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, UK
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Cornejo-Ramírez YI, Martínez-Cruz O, Del Toro-Sánchez CL, Wong-Corral FJ, Borboa-Flores J, Cinco-Moroyoqui FJ. The structural characteristics of starches and their functional properties. CYTA - JOURNAL OF FOOD 2018. [DOI: 10.1080/19476337.2018.1518343] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
| | - Oliviert Martínez-Cruz
- Departamento de Investigación y Posgrado en Alimentos, Universidad de Sonora, Hermosillo, Sonora, México. C.P
| | | | | | - Jesús Borboa-Flores
- Departamento de Investigación y Posgrado en Alimentos, Universidad de Sonora, Hermosillo, Sonora, México. C.P
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9
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Goren A, Ashlock D, Tetlow IJ. Starch formation inside plastids of higher plants. PROTOPLASMA 2018; 255:1855-1876. [PMID: 29774409 DOI: 10.1007/s00709-018-1259-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/03/2018] [Indexed: 05/09/2023]
Abstract
Starch is a water-insoluble polyglucan synthesized inside the plastid stroma within plant cells, serving a crucial role in the carbon budget of the whole plant by acting as a short-term and long-term store of energy. The highly complex, hierarchical structure of the starch granule arises from the actions of a large suite of enzyme activities, in addition to physicochemical self-assembly mechanisms. This review outlines current knowledge of the starch biosynthetic pathway operating in plant cells in relation to the micro- and macro-structures of the starch granule. We highlight the gaps in our knowledge, in particular, the relationship between enzyme function and operation at the molecular level and the formation of the final, macroscopic architecture of the granule.
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Affiliation(s)
- Asena Goren
- Department of Mathematics and Statistics, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Daniel Ashlock
- Department of Mathematics and Statistics, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Ian J Tetlow
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of Guelph, Guelph, ON, N1G 2W1, Canada.
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10
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Raguin A, Ebenhöh O. Design starch: stochastic modeling of starch granule biogenesis. Biochem Soc Trans 2017; 45:885-893. [PMID: 28673938 PMCID: PMC5652221 DOI: 10.1042/bst20160407] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 05/15/2017] [Accepted: 05/19/2017] [Indexed: 12/03/2022]
Abstract
Starch is the most widespread and abundant storage carbohydrate in plants and the main source of carbohydrate in the human diet. Owing to its remarkable properties and commercial applications, starch is still of growing interest. Its unique granular structure made of intercalated layers of amylopectin and amylose has been unraveled thanks to recent progress in microscopic imaging, but the origin of such periodicity is still under debate. Both amylose and amylopectin are made of linear chains of α-1,4-bound glucose residues, with branch points formed by α-1,6 linkages. The net difference in the distribution of chain lengths and the branching pattern of amylose (mainly linear), compared with amylopectin (racemose structure), leads to different physico-chemical properties. Amylose is an amorphous and soluble polysaccharide, whereas amylopectin is insoluble and exhibits a highly organized structure of densely packed double helices formed between neighboring linear chains. Contrarily to starch degradation that has been investigated since the early 20th century, starch production is still poorly understood. Most enzymes involved in starch growth (elongation, branching, debranching, and partial hydrolysis) are now identified. However, their specific action, their interplay (cooperative or competitive), and their kinetic properties are still largely unknown. After reviewing recent results on starch structure and starch growth and degradation enzymatic activity, we discuss recent results and current challenges for growing polysaccharides on granular surface. Finally, we highlight the importance of novel stochastic models to support the analysis of recent and complex experimental results, and to address how macroscopic properties emerge from enzymatic activity and structural rearrangements.
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Affiliation(s)
- Adélaïde Raguin
- Institute of Quantitative and Theoretical Biology, Heinrich-Heine University, Düsseldorf 40225, Germany
| | - Oliver Ebenhöh
- Institute of Quantitative and Theoretical Biology, Heinrich-Heine University, Düsseldorf 40225, Germany
- Cluster of Excellence on Plant Sciences, Institute of Quantitative and Theoretical Biology, Heinrich-Heine University, Düsseldorf 40225, Germany
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11
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Pfister B, Sánchez-Ferrer A, Diaz A, Lu K, Otto C, Holler M, Shaik FR, Meier F, Mezzenga R, Zeeman SC. Recreating the synthesis of starch granules in yeast. eLife 2016; 5:e15552. [PMID: 27871361 PMCID: PMC5119888 DOI: 10.7554/elife.15552] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 10/08/2016] [Indexed: 11/13/2022] Open
Abstract
Starch, as the major nutritional component of our staple crops and a feedstock for industry, is a vital plant product. It is composed of glucose polymers that form massive semi-crystalline granules. Its precise structure and composition determine its functionality and thus applications; however, there is no versatile model system allowing the relationships between the biosynthetic apparatus, glucan structure and properties to be explored. Here, we expressed the core Arabidopsis starch-biosynthesis pathway in Saccharomyces cerevisiae purged of its endogenous glycogen-metabolic enzymes. Systematic variation of the set of biosynthetic enzymes illustrated how each affects glucan structure and solubility. Expression of the complete set resulted in dense, insoluble granules with a starch-like semi-crystalline organization, demonstrating that this system indeed simulates starch biosynthesis. Thus, the yeast system has the potential to accelerate starch research and help create a holistic understanding of starch granule biosynthesis, providing a basis for the targeted biotechnological improvement of crops.
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Affiliation(s)
| | | | - Ana Diaz
- Paul Scherrer Institut, Villigen, Switzerland
| | - Kuanjen Lu
- Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Caroline Otto
- Department of Biology, ETH Zürich, Zürich, Switzerland
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Karlström A, Calle F, Salazar S, Morante N, Dufour D, Ceballos H. Biological Implications in Cassava for the Production of Amylose-Free Starch: Impact on Root Yield and Related Traits. FRONTIERS IN PLANT SCIENCE 2016; 7:604. [PMID: 27242813 PMCID: PMC4873506 DOI: 10.3389/fpls.2016.00604] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 04/19/2016] [Indexed: 05/20/2023]
Abstract
Cassava (Manihot esculenta, Crantz) is an important food security crop, but it is becoming an important raw material for different industrial applications. Cassava is the second most important source of starch worldwide. Novel starch properties are of interest to the starch industry, and one them is the recently identified amylose-free (waxy) cassava starch. Waxy mutants have been found in different crops and have been often associated with a yield penalty. There are ongoing efforts to develop commercial cassava varieties with amylose-free starch. However, little information is available regarding the biological and agronomic implications of starch mutations in cassava, nor in other root and tuber crops. In this study, siblings from eight full-sib families, segregating for the waxy trait, were used to determine if the mutation has implications for yield, dry matter content (DMC) and harvest index in cassava. A total of 87 waxy and 87 wild-type starch genotypes from the eight families were used in the study. The only significant effect of starch type was on DMC (p < 0.01), with waxy clones having a 0.8% lower content than their wild type counterparts. There was no effect of starch type on fresh root yield (FRY), adjusted FRY and harvest index. It is not clear if lower DMC is a pleiotropic effect of the waxy starch mutation or else the result of linked genes introgressed along with the mutation. It is expected that commercial waxy cassava varieties will have competitive FRYs but special efforts will be required to attain adequate DMCs. This study contributes to the limited knowledge available of the impact of starch mutations on the agronomic performance of root and tuber crops.
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Affiliation(s)
- Amanda Karlström
- Department of Plant Breeding, Swedish University of Agricultural Sciences, AlnarpSweden
- Centro Internacional de Agricultura Tropical, PalmiraColombia
| | - Fernando Calle
- Centro Internacional de Agricultura Tropical, PalmiraColombia
| | - Sandra Salazar
- Centro Internacional de Agricultura Tropical, PalmiraColombia
| | - Nelson Morante
- Centro Internacional de Agricultura Tropical, PalmiraColombia
| | - Dominique Dufour
- Centro Internacional de Agricultura Tropical, PalmiraColombia
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR Qualisud, MontpellierFrance
| | - Hernán Ceballos
- Centro Internacional de Agricultura Tropical, PalmiraColombia
- *Correspondence: Hernán Ceballos,
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