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Sun R, Chen S, Chen X, Liu X, Zhang F, Wu J, Su L. Enzymatic treatment to improve permeability and quality of cherry tomatoes for production of dried products. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:2718-2727. [PMID: 37997286 DOI: 10.1002/jsfa.13156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 11/02/2023] [Accepted: 11/23/2023] [Indexed: 11/25/2023]
Abstract
BACKGROUND Cherry tomatoes are nutritious and favored by consumers. Processing them into dried cherry tomatoes can prolong their storage life and improve their flavor. The pretreatment of tomato pericarp is crucial for the subsequent processing. However, the traditional physical and chemical treatments of tomato pericarp generally cause nutrient loss and environmental pollution. RESULTS In this study, a novel enzymatic method for cherry tomatoes was performed using mixed enzymes containing cutinase, cellulase and pectinase. Results showed that the pericarp permeability of cherry tomatoes was effectively improved due to enzymatic treatment. Changes in the microscopic structure and composition of the cuticle were revealed. After treatment with different concentrations of enzymes, cherry tomatoes exhibited higher pericarp permeability and sensory quality to varying degrees. The lycopene content and total polyphenol content significantly increased 2.4- and 1.45-fold, respectively. In addition, the satisfactory effect of the six-time reuse of enzymes on cherry tomatoes could still reach the same level as the initial effect, which effectively reduced the cost of production. CONCLUSIONS This study revealed for the first time that a mixed enzymatic treatment consisting of cutinase, pectinase and cellulase could effectively degrade the cuticle, enhance the pericarp permeability and improve the quality of cherry tomatoes, with the advantages of being mildly controllable and environmentally friendly, providing a new strategy for the processing of dried cherry tomatoes. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Ruyu Sun
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, Wuxi, China
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
| | - Shiheng Chen
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, Wuxi, China
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
| | - Xiaoqian Chen
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, Wuxi, China
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
| | - Xiaqing Liu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, Wuxi, China
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
| | - Fengshan Zhang
- Shangdong Huatai Paper Co. Ltd & Shangdong Yellow Triangle Biotechnology Industry Research Institute Co. Ltd, Dongying, China
| | - Jing Wu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, Wuxi, China
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
| | - Lingqia Su
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, Wuxi, China
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
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2
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Ji D, Liu W, Jiang L, Chen T. Cuticles and postharvest life of tomato fruit: A rigid cover for aerial epidermis or a multifaceted guard of freshness? Food Chem 2023; 411:135484. [PMID: 36682164 DOI: 10.1016/j.foodchem.2023.135484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 01/04/2023] [Accepted: 01/11/2023] [Indexed: 01/20/2023]
Abstract
Fruit cuticle is a specialized cell wall hydrophobic architecture covering the aerial surfaces of fruit, which forms the interface between the fruit and its environment. As a specialized seed-bearing organ, fruit utilize cuticles as physical barriers, water permeation regulator and resistance to pathogens, thus appealing extensive research interests for its potential values in developing postharvest freshness-keeping strategies. Here, we provide an overview for the composition and functions of fruit cuticles, mainly focusing on its functions in mechanical support, water permeability barrier and protection over pathogens, further introduce key mechanisms implicated in fruit cuticle biosynthesis. Moreover, currently available state-of-art techniques for examining compositional diversity and architecture of fruit are also compared.
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Affiliation(s)
- Dongchao Ji
- School of Life Sciences and Medicine, Shandong University of Technology, Xincun West Road 266, Zhangdian District, Zibo, Shandong 255049, China; Key Laboratory of Plant Resources, Institute of Botany, Innovative Academy of Seed Design, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Haidian District, Beijing 100093, China; University of Chinese Academy of Sciences, Yuquan Road 19(A), Shijingshan District, Beijing 100049, China
| | - Wei Liu
- Key Laboratory of Plant Resources, Institute of Botany, Innovative Academy of Seed Design, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Haidian District, Beijing 100093, China; University of Chinese Academy of Sciences, Yuquan Road 19(A), Shijingshan District, Beijing 100049, China
| | - Libo Jiang
- School of Life Sciences and Medicine, Shandong University of Technology, Xincun West Road 266, Zhangdian District, Zibo, Shandong 255049, China
| | - Tong Chen
- Key Laboratory of Plant Resources, Institute of Botany, Innovative Academy of Seed Design, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Haidian District, Beijing 100093, China; University of Chinese Academy of Sciences, Yuquan Road 19(A), Shijingshan District, Beijing 100049, China; Key Laboratory of Post-Harvest Handling of Fruits, Ministry of Agriculture, Nanxincun 20, Xiangshan, Haidian District, Beijing 100093, China.
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3
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Escórcio R, Bento A, Tomé AS, Correia VG, Rodrigues R, Moreira CJS, Marion D, Bakan B, Silva Pereira C. Finding a Needle in a Haystack: Producing Antimicrobial Cutin-Derived Oligomers from Tomato Pomace. ACS SUSTAINABLE CHEMISTRY & ENGINEERING 2022; 10:11415-11427. [PMID: 36061097 PMCID: PMC9428892 DOI: 10.1021/acssuschemeng.2c03437] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/22/2022] [Indexed: 05/14/2023]
Abstract
Agro-industrial residues comprise a rich diversity of plant polymers and bioactive compounds, constituting promising sources for the development of materials, including bioplastics, and food supplements, among other applications. In particular, the polyester cutin is abundant in fruit peel, a plentiful constituent of pomace agro-industrial residues. The potential of diverse fruit pomaces as a source for the development of cutin-derived materials/products has been extensively sought out. This study expands the established knowledge: it sets proof of concept for the production of antimicrobial oligomers from cutin-rich materials isolated in a single step from tomato pomaces generated by two remote agro-industries. Specifically, it first analyzed how the chemical signature (nuclear magnetic resonance (NMR) and gas chromatography-mass spectrometry (GC-MS)) of a pomace (and of its major constituents) mirrors that of the corresponding cutin-rich material isolated using an ionic liquid extractant. The cutin-rich materials were then deconstructed (using mild hydrolyses), and the resultant mixtures were chemically characterized and screened for bactericidal activity against Escherichia coli and Staphylococcus aureus. The presence of esterified structures, linear and/or branched, likely comprising dioic acids as a major building block (but not exclusively) is a prerequisite for activity against E. coli but not against S. aureus that was susceptible to monomers as well. Further studies are required to optimize the production of broad bactericidal oligomers from any cutin-rich pomace source, moving ahead toward their circular usage.
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Affiliation(s)
- Rita Escórcio
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Avenida da República, 2780-157 Oeiras, Portugal
| | - Artur Bento
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Avenida da República, 2780-157 Oeiras, Portugal
| | - Ana S. Tomé
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Avenida da República, 2780-157 Oeiras, Portugal
| | - Vanessa G. Correia
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Avenida da República, 2780-157 Oeiras, Portugal
| | - Rúben Rodrigues
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Avenida da República, 2780-157 Oeiras, Portugal
| | - Carlos J. S. Moreira
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Avenida da República, 2780-157 Oeiras, Portugal
| | - Didier Marion
- Research
Unit Biopolymers Interaction Assemblies, INRAE, 44316 Nantes, France
| | - Bénédicte Bakan
- Research
Unit Biopolymers Interaction Assemblies, INRAE, 44316 Nantes, France
| | - Cristina Silva Pereira
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Avenida da República, 2780-157 Oeiras, Portugal
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4
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Petit J, Bres C, Reynoud N, Lahaye M, Marion D, Bakan B, Rothan C. Unraveling Cuticle Formation, Structure, and Properties by Using Tomato Genetic Diversity. FRONTIERS IN PLANT SCIENCE 2021; 12:778131. [PMID: 34912361 PMCID: PMC8667768 DOI: 10.3389/fpls.2021.778131] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/02/2021] [Indexed: 05/29/2023]
Abstract
The tomato (Solanum lycopersicum) fruit has a thick, astomatous cuticle that has become a model for the study of cuticle formation, structure, and properties in plants. Tomato is also a major horticultural crop and a long-standing model for research in genetics, fruit development, and disease resistance. As a result, a wealth of genetic resources and genomic tools have been established, including collections of natural and artificially induced genetic diversity, introgression lines of genome fragments from wild relatives, high-quality genome sequences, phenotype and gene expression databases, and efficient methods for genetic transformation and editing of target genes. This mini-review reports the considerable progresses made in recent years in our understanding of cuticle by using and generating genetic diversity for cuticle-associated traits in tomato. These include the synthesis of the main cuticle components (cutin and waxes), their role in the structure and properties of the cuticle, their interaction with other cell wall polymers as well as the regulation of cuticle formation. It also addresses the opportunities offered by the untapped germplasm diversity available in tomato and the current strategies available to exploit them.
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Affiliation(s)
- Johann Petit
- INRAE, Univ. Bordeaux, UMR BFP, Villenave d’Ornon, France
| | - Cécile Bres
- INRAE, Univ. Bordeaux, UMR BFP, Villenave d’Ornon, France
| | - Nicolas Reynoud
- Unité Biopolymères, Interactions, Assemblages, INRAE, Nantes, France
| | - Marc Lahaye
- Unité Biopolymères, Interactions, Assemblages, INRAE, Nantes, France
| | - Didier Marion
- Unité Biopolymères, Interactions, Assemblages, INRAE, Nantes, France
| | - Bénédicte Bakan
- Unité Biopolymères, Interactions, Assemblages, INRAE, Nantes, France
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5
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Reimer JJ, Thiele B, Biermann RT, Junker-Frohn LV, Wiese-Klinkenberg A, Usadel B, Wormit A. Tomato leaves under stress: a comparison of stress response to mild abiotic stress between a cultivated and a wild tomato species. PLANT MOLECULAR BIOLOGY 2021; 107:177-206. [PMID: 34677706 PMCID: PMC8553704 DOI: 10.1007/s11103-021-01194-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 09/16/2021] [Indexed: 05/03/2023]
Abstract
Tomato is one of the most produced crop plants on earth and growing in the fields and greenhouses all over the world. Breeding with known traits of wild species can enhance stress tolerance of cultivated crops. In this study, we investigated responses of the transcriptome as well as primary and secondary metabolites in leaves of a cultivated and a wild tomato to several abiotic stresses such as nitrogen deficiency, chilling or warmer temperatures, elevated light intensities and combinations thereof. The wild species responded different to varied temperature conditions compared to the cultivated tomato. Nitrogen deficiency caused the strongest responses and induced in particular the secondary metabolism in both species but to much higher extent in the cultivated tomato. Our study supports the potential of a targeted induction of valuable secondary metabolites in green residues of horticultural production, that will otherwise only be composted after fruit harvest. In particular, the cultivated tomato showed a strong induction in the group of mono caffeoylquinic acids in response to nitrogen deficiency. In addition, the observed differences in stress responses between cultivated and wild tomato can lead to new breeding targets for better stress tolerance.
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Affiliation(s)
- Julia J Reimer
- Institute for Biology I, RWTH Aachen University, Worringer Weg 3, 52074, Aachen, Germany
- Bioeconomy Science Center, c/o Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- Forschungszentrum Jülich GmbH, PtJ, 52425, Jülich, Germany
| | - Björn Thiele
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, Plant Sciences (IBG-2), 52425, Jülich, Germany
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, Agrosphere (IBG-3), 52425, Jülich, Germany
- Bioeconomy Science Center, c/o Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Robin T Biermann
- Institute for Biology I, RWTH Aachen University, Worringer Weg 3, 52074, Aachen, Germany
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ) e.V., 14979, Großbeeren, Germany
| | - Laura V Junker-Frohn
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, Plant Sciences (IBG-2), 52425, Jülich, Germany
- Bioeconomy Science Center, c/o Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Anika Wiese-Klinkenberg
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, Plant Sciences (IBG-2), 52425, Jülich, Germany
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, Bioinformatics (IBG-4), 52425, Jülich, Germany
- Bioeconomy Science Center, c/o Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Björn Usadel
- Institute for Biology I, RWTH Aachen University, Worringer Weg 3, 52074, Aachen, Germany
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, Plant Sciences (IBG-2), 52425, Jülich, Germany
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, Bioinformatics (IBG-4), 52425, Jülich, Germany
- Bioeconomy Science Center, c/o Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- Heinrich-Heine-University, Chair of Biological Data Science, 40225, Düsseldorf, Germany
| | - Alexandra Wormit
- Institute for Biology I, RWTH Aachen University, Worringer Weg 3, 52074, Aachen, Germany.
- Bioeconomy Science Center, c/o Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.
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6
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Uluisik S. Chemical and structural quality traits during postharvest ripening regulated by chromosome segments from a wild relative of tomato Solanum pennellii IL4-2 and IL5-1. J Food Biochem 2021; 45:e13858. [PMID: 34251032 DOI: 10.1111/jfbc.13858] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 06/11/2021] [Accepted: 06/27/2021] [Indexed: 11/29/2022]
Abstract
Tomato is usually harvested at an early ripening stage with high firmness suitable for storage and transportation but lacks many quality parameters such as sugars, organic acids, and phenolics. In a recent study, we have selected introgression lines (ILs) IL4-2 and IL5-1, developed from a cross between the Solanum pennellii and the Solanum lycopersicum M82, that exhibit differentiated postharvest shelf-life characteristics in the fruit compared to M82 and the rest of the ILs. Here, we first structurally and biochemically characterized IL4-2, IL5-1, and their parent M82 to decipher the cell wall mechanistic difference between soft (IL4-2) and firm (IL5-1) lines at two postharvest ripening periods. Generally, IL4-2 had more active cell wall modifications in terms of ripening-related gene expression, water-soluble pectin, and cell wall structure under the microscope, which probably makes this line softer than IL5-1. We also evaluated these lines based on commercial quality parameters, sugars, phenolics, organic, and amino acids to gain insight into their commercial and functional quality and reveal noticeable differences. In summary, the contribution of the S. pennellii IL5-1 and IL4-2 to the shelf life of the tomato was structurally characterized, and the component differences meeting the quality criteria were revealed.
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Affiliation(s)
- Selman Uluisik
- Burdur Food Agriculture and Livestock Vocational School, Burdur Mehmet Akif Ersoy University, Burdur, Turkey
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7
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Zhu D, Le Y, Zhang R, Li X, Lin Z. A global survey of the gene network and key genes for oil accumulation in cultivated tetraploid cottons. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1170-1182. [PMID: 33382517 PMCID: PMC8196633 DOI: 10.1111/pbi.13538] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/03/2020] [Accepted: 12/20/2020] [Indexed: 05/14/2023]
Abstract
To enrich our knowledge about gene network of fatty acid biosynthesis in cottonseed, we conducted comparative transcriptome to reveal the differences in gene expression between Gossypium hirsutum and Gossypium barbadense during cottonseed development. The prolonged expression period and increased expression abundance of oil-related genes are the main reasons for producing high seed oil content (SOC) in G. barbadense, which manifested as the bias of homeologous gene expression in Dt-subgenome after 25 day postanthesis (DPA). The dynamic expression profile showed that SAD6 and FATA are more important for oil biosynthesis in G. barbadense than that in G. hirsutum. Three key transcription factors, WRI1, NF-YB6 and DPBF2, showed their elite roles in regulating seed oil in cotton. We observed that sequence variations in the promoter region of BCCP2 genes might contribute to its divergence in expression level between the two species. Based on the quantitative trait loci (QTL) information of the seed oil content and utilizing additional G. barbadense introgression lines (ILs), we propose 21 candidate genes on the basis of their differential expression level, of which the GbSWEET and the GbACBP6 showed the potential functional to improve the oil content. Taken together, studying the different expression of oil-related genes and their genetic regulation mechanisms between G. hirsutum and G. barbadense provide new insights to understanding the mechanism of fatty acid biosynthesis network and fatty acid genetic improving breeding in cotton.
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Affiliation(s)
- De Zhu
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Sciences & TechnologyHuazhong Agricultural UniversityWuhanHubeiChina
| | - Yu Le
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Sciences & TechnologyHuazhong Agricultural UniversityWuhanHubeiChina
| | - Ruiting Zhang
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Sciences & TechnologyHuazhong Agricultural UniversityWuhanHubeiChina
| | - Xiaojing Li
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Sciences & TechnologyHuazhong Agricultural UniversityWuhanHubeiChina
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Sciences & TechnologyHuazhong Agricultural UniversityWuhanHubeiChina
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8
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Barraj Barraj R, Segado P, Moreno-González R, Heredia A, Fernández-Muñoz R, Domínguez E. Genome-wide QTL analysis of tomato fruit cuticle deposition and composition. HORTICULTURE RESEARCH 2021; 8:113. [PMID: 33931622 PMCID: PMC8087829 DOI: 10.1038/s41438-021-00548-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 03/22/2021] [Accepted: 04/01/2021] [Indexed: 05/24/2023]
Abstract
Genetics of traits related to fruit cuticle deposition and composition was studied in two red-fruited tomato species. Two mapping populations derived from the cross between the cultivated tomato (Solanum lycopersicum L.) and its closest relative wild species Solanum pimpinellifolium L. were employed to conduct a QTL analysis. A combination of fruit cuticle deposition, components and anatomical traits were investigated and the individual effect of each QTL evaluated. A total of 70 QTLs were identified, indicating that all the cuticle traits analyzed have a complex polygenic nature. A combination of additive and epistatic interactions was observed for all the traits, with positive contribution of both parental lines to most of them. Colocalization of QTLs for various traits uncovered novel genomic regions producing extensive changes in the cuticle. Cuticle density emerges as an important trait since it can modulate cuticle thickness and invagination thus providing a strategy for sustaining mechanical strength without compromising palatability. Two genomic regions, located in chromosomes 1 and 12, are responsible for the negative interaction between cuticle waxes and phenolics identified in tomato fruit. Several candidate genes, including transcription factors and structural genes, are postulated and their expression analyzed throughout development.
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Affiliation(s)
- Rida Barraj Barraj
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Mejora Genética y Biotecnología, Estación Experimental La Mayora, Algarrobo-Costa, E-29750, Málaga, Spain
| | - Patricia Segado
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, E-29071, Málaga, Spain
| | - Rocío Moreno-González
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, E-29071, Málaga, Spain
- Departament de Bioquímica i Fisiologia and Institut de Recerca en Nutrició i Seguretat Alimentària (INSA-UB), Universitat de Barcelona (UB), E-08028, Barcelona, Spain
| | - Antonio Heredia
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, E-29071, Málaga, Spain
| | - Rafael Fernández-Muñoz
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Mejora Genética y Biotecnología, Estación Experimental La Mayora, Algarrobo-Costa, E-29750, Málaga, Spain
| | - Eva Domínguez
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Mejora Genética y Biotecnología, Estación Experimental La Mayora, Algarrobo-Costa, E-29750, Málaga, Spain.
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9
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The Role of Cutinsomes in Plant Cuticle Formation. Cells 2020; 9:cells9081778. [PMID: 32722473 PMCID: PMC7465133 DOI: 10.3390/cells9081778] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 07/10/2020] [Accepted: 07/23/2020] [Indexed: 12/21/2022] Open
Abstract
The cuticle commonly appears as a continuous lipophilic layer located at the outer epidermal cell walls of land plants. Cutin and waxes are its main components. Two methods for cutin synthesis are considered in plants. One that is based on enzymatic biosynthesis, in which cutin synthase (CUS) is involved, is well-known and commonly accepted. The other assumes the participation of specific nanostructures, cutinsomes, which are formed in physicochemical self-assembly processes from cutin precursors without enzyme involvement. Cutinsomes are formed in ground cytoplasm or, in some species, in specific cytoplasmic domains, lipotubuloid metabolons (LMs), and are most probably translocated via microtubules toward the cuticle-covered cell wall. Cutinsomes may additionally serve as platforms transporting cuticular enzymes. Presumably, cutinsomes enrich the cuticle in branched and cross-linked esterified polyhydroxy fatty acid oligomers, while CUS1 can provide both linear chains and branching cutin oligomers. These two systems of cuticle formation seem to co-operate on the surface of aboveground organs, as well as in the embryo and seed coat epidermis. This review focuses on the role that cutinsomes play in cuticle biosynthesis in S. lycopersicum, O. umbellatum and A. thaliana, which have been studied so far; however, these nanoparticles may be commonly involved in this process in different plants.
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10
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Genomic Dissection of a Wild Region in a Superior Solanum pennellii Introgression Sub-Line with High Ascorbic Acid Accumulation in Tomato Fruit. Genes (Basel) 2020; 11:genes11080847. [PMID: 32722275 PMCID: PMC7466095 DOI: 10.3390/genes11080847] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/20/2020] [Accepted: 07/22/2020] [Indexed: 11/16/2022] Open
Abstract
The Solanum pennellii introgression lines (ILs) have been exploited to map quantitative trait loci (QTLs) and identify favorable alleles that could improve fruit quality traits in tomato varieties. Over the past few years, ILs exhibiting increased content of ascorbic acid in the fruit have been selected, among which the sub-line R182. The aims of this work were to identify the genes of the wild donor S. pennellii harbored by the sub-line and to detect genes controlling ascorbic acid accumulation by using genomics tools. A Genotyping-By-Sequencing (GBS) approach confirmed that no wild introgressions were present in the sub-line besides one region on chromosome 7. By using a dense single nucleotide polymorphism (SNP) map obtained by RNA sequencing (RNA-Seq), the wild region of the sub-line was finely identified; thus, defining 39 wild genes that replaced 33 genes of the ILs genetic background (cv. M82). The differentially expressed genes mapping in the region and the variants detected among the cultivated and the wild alleles evidenced the potential role of the novel genes present in the wild region. Interestingly, one upregulated gene, annotated as a major facilitator superfamily protein, showed a novel structure in R182, with respect to the parental lines. These genes will be further investigated using gene editing strategies.
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11
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Zhu D, Li X, Wang Z, You C, Nie X, Sun J, Zhang X, Zhang D, Lin Z. Genetic dissection of an allotetraploid interspecific CSSLs guides interspecific genetics and breeding in cotton. BMC Genomics 2020; 21:431. [PMID: 32586283 PMCID: PMC7318736 DOI: 10.1186/s12864-020-06800-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/02/2020] [Indexed: 01/07/2023] Open
Abstract
Background The low genetic diversity of Upland cotton limits the potential for genetic improvement. Making full use of the genetic resources of Sea-island cotton will facilitate genetic improvement of widely cultivated Upland cotton varieties. The chromosome segments substitution lines (CSSLs) provide an ideal strategy for mapping quantitative trait loci (QTL) in interspecific hybridization. Results In this study, a CSSL population was developed by PCR-based markers assisted selection (MAS), derived from the crossing and backcrossing of Gossypium hirsutum (Gh) and G. barbadense (Gb), firstly. Then, by whole genome re-sequencing, 11,653,661 high-quality single nucleotide polymorphisms (SNPs) were identified which ultimately constructed 1211 recombination chromosome introgression segments from Gb. The sequencing-based physical map provided more accurate introgressions than the PCR-based markers. By exploiting CSSLs with mutant morphological traits, the genes responding for leaf shape and fuzz-less mutation in the Gb were identified. Based on a high-resolution recombination bin map to uncover genetic loci determining the phenotypic variance between Gh and Gb, 64 QTLs were identified for 14 agronomic traits with an interval length of 158 kb to 27 Mb. Surprisingly, multiple alleles of Gb showed extremely high value in enhancing cottonseed oil content (SOC). Conclusions This study provides guidance for studying interspecific inheritance, especially breeding researchers, for future studies using the traditional PCR-based molecular markers and high-throughput re-sequencing technology in the study of CSSLs. Available resources include candidate position for controlling cotton quality and quantitative traits, and excellent breeding materials. Collectively, our results provide insights into the genetic effects of Gb alleles on the Gh, and provide guidance for the utilization of Gb alleles in interspecific breeding.
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Affiliation(s)
- De Zhu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Ximei Li
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.,Shandong Key Laboratory of Dryland Farming Technology/Shandong Engineering Research Center of Germplasm Innovation and Utilization of Salt-tolerant Crops, College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Zhiwei Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.,Shandong Peanut Research Institute, Qingdao, 266109, Shangdong, China
| | - Chunyuan You
- Cotton Research Institute, Shihezi Academy of Agriculture Science, Shihezi, Xinjiang, 832003, China
| | - Xinhui Nie
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Bingtuan, Agricultural College, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Jie Sun
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Bingtuan, Agricultural College, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Dawei Zhang
- Institute of Industrial Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, 830091, China.
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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12
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Sun S, Wang X, Wang K, Cui X. Dissection of complex traits of tomato in the post-genome era. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1763-1776. [PMID: 31745578 DOI: 10.1007/s00122-019-03478-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 11/09/2019] [Indexed: 06/10/2023]
Abstract
We present the main advances of dissection of complex traits in tomato by omics, the genes identified to control complex traits and the application of CRISPR/Cas9 in tomato breeding. Complex traits are believed to be under the control of multiple genes, each with different effects and interaction with environmental factors. Advance development of sequencing and molecular technologies has enabled the recognition of the genomic structure of most organisms and the identification of a nearly limitless number of markers that have made it to accelerate the speed of QTL identification and gene cloning. Meanwhile, multiomics have been used to identify the genetic variations among different tomato species, determine the expression profiles of genes in different tissues and at distinct developmental stages, and detect metabolites in different pathways and processes. The combination of these data facilitates to reveal mechanism underlying complex traits. Moreover, mutants generated by mutagens and genome editing provide relatively rich genetic variation for deciphering the complex traits and exploiting them in tomato breeding. In this article, we present the main advances of complex trait dissection in tomato by omics since the release of the tomato genome sequence in 2012. We provide further insight into some tomato complex traits because of the causal genetic variations discovered so far and explore the utilization of CRISPR/Cas9 for the modification of tomato complex traits.
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Affiliation(s)
- Shuai Sun
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaotian Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ketao Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xia Cui
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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13
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Kuhalskaya A, Wijesingha Ahchige M, Perez de Souza L, Vallarino J, Brotman Y, Alseekh S. Network Analysis Provides Insight into Tomato Lipid Metabolism. Metabolites 2020; 10:metabo10040152. [PMID: 32295308 PMCID: PMC7240963 DOI: 10.3390/metabo10040152] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/26/2020] [Accepted: 04/11/2020] [Indexed: 11/16/2022] Open
Abstract
Metabolic correlation networks have been used in several instances to obtain a deeper insight into the complexity of plant metabolism as a whole. In tomato (Solanum lycopersicum), metabolites have a major influence on taste and overall fruit quality traits. Previously a broad spectrum of metabolic and phenotypic traits has been described using a Solanum pennellii introgression-lines (ILs) population. To obtain insights into tomato fruit metabolism, we performed metabolic network analysis from existing data, covering a wide range of metabolic traits, including lipophilic and volatile compounds, for the first time. We provide a comprehensive fruit correlation network and show how primary, secondary, lipophilic, and volatile compounds connect to each other and how the individual metabolic classes are linked to yield-related phenotypic traits. Results revealed a high connectivity within and between different classes of lipophilic compounds, as well as between lipophilic and secondary metabolites. We focused on lipid metabolism and generated a gene-expression network with lipophilic metabolites to identify new putative lipid-related genes. Metabolite–transcript correlation analysis revealed key putative genes involved in lipid biosynthesis pathways. The overall results will help to deepen our understanding of tomato metabolism and provide candidate genes for transgenic approaches toward improving nutritional qualities in tomato.
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Affiliation(s)
- Anastasiya Kuhalskaya
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (A.K.); (M.W.A.); (L.P.d.S.); (J.V.); (Y.B.)
- Department of Life Sciences, Ben Gurion University of the Negev, 84105 Beersheva, Israel
| | - Micha Wijesingha Ahchige
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (A.K.); (M.W.A.); (L.P.d.S.); (J.V.); (Y.B.)
| | - Leonardo Perez de Souza
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (A.K.); (M.W.A.); (L.P.d.S.); (J.V.); (Y.B.)
| | - José Vallarino
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (A.K.); (M.W.A.); (L.P.d.S.); (J.V.); (Y.B.)
| | - Yariv Brotman
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (A.K.); (M.W.A.); (L.P.d.S.); (J.V.); (Y.B.)
- Department of Life Sciences, Ben Gurion University of the Negev, 84105 Beersheva, Israel
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (A.K.); (M.W.A.); (L.P.d.S.); (J.V.); (Y.B.)
- Centre of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
- Correspondence: ; Tel.: +49-(0)331-567-8211
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14
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Lara I, Heredia A, Domínguez E. Shelf Life Potential and the Fruit Cuticle: The Unexpected Player. FRONTIERS IN PLANT SCIENCE 2019; 10:770. [PMID: 31244879 PMCID: PMC6581714 DOI: 10.3389/fpls.2019.00770] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 05/28/2019] [Indexed: 05/18/2023]
Abstract
The plant cuticle is an extracellular barrier that protects the aerial, non-lignified parts of plants from the surrounding environment, and furthermore plays important functions in organ growth and development. The role of the cuticle in post-harvest quality of fruits is a topic currently driving a lot of interest since an increasing bulk of research data show its modulating influence on a number of important traits determining shelf life and storage potential, including water transpiration and fruit dehydration, susceptibility to rots, pests and disorders, and even firmness. Moreover, the properties of fruit cuticles keep evolving after harvest, and have also been shown to be highly responsive to the external conditions surrounding the fruit. Indeed, common post-harvest treatments will have an impact on cuticle integrity and performance that needs to be evaluated for a deeper understanding of changes in post-harvest quality. In this review, chemical and biophysical properties of fruit cuticles are summarized. An overview is also provided of post-harvest changes in cuticles and the effects thereupon of some post-harvest procedures, with the purpose of offering a comprehensive summary of currently available information. Identification of natural sources of variability in relevant quality traits would allow breeding for the improvement of post-harvest life of fruit commodities.
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Affiliation(s)
- Isabel Lara
- Unitat de Postcollita-XaRTA, AGROTÈCNIO, Departament de Química, Universitat de Lleida, Lleida, Spain
| | - Antonio Heredia
- IHSM La Mayora, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Málaga, Spain
| | - Eva Domínguez
- IHSM La Mayora, Departamento de Mejora Genética y Biotecnología, Consejo Superior de Investigaciones Científicas, Málaga, Spain
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15
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Bac-Molenaar JA, Mol S, Verlaan MG, van Elven J, Kim HK, Klinkhamer PGL, Leiss KA, Vrieling K. Trichome Independent Resistance against Western Flower Thrips in Tomato. PLANT & CELL PHYSIOLOGY 2019; 60:1011-1024. [PMID: 30715458 PMCID: PMC6534821 DOI: 10.1093/pcp/pcz018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 01/29/2019] [Indexed: 05/26/2023]
Abstract
Western flower thrips (WFT) are a major pest on many crops, including tomato. Thrips cause yield losses, not only through feeding damage, but also by the transmission of viruses of which the Tomato Spotted Wilt Virus is the most important one. In cultivated tomato, genetic diversity is extremely low, and all commercial lines are susceptible to WFT. Several wild relatives are WFT resistant and these resistances are based on glandular trichome-derived traits. Introgression of these traits in cultivated lines did not lead to WFT resistant commercial varieties so far. In this study, we investigated WFT resistance in cultivated tomato using a F2 population derived from a cross between a WFT susceptible and a WFT resistant cultivated tomato line. We discovered that this WFT resistance is independent of glandular trichome density or trichome-derived volatile profiles and is associated with three QTLs on chromosomes 4, 5 and 10. Foliar metabolic profiles of F3 families with low and high WFT feeding damage were clearly different. We identified α-tomatine and a phenolic compound as potential defensive compounds. Their causality and interaction need further investigation. Because this study is based on cultivated tomato lines, our findings can directly be used in nowadays breeding programs.
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Affiliation(s)
- Johanna A Bac-Molenaar
- Plant Sciences and Natural Products Lab, Institute of Biology Leiden, Sylviusweg 72, BE Leiden, The Netherlands
- Wageningen University and Research, Violierenweg 1, MV Bleiswijk, The Netherlands
| | - Selena Mol
- Plant Sciences and Natural Products Lab, Institute of Biology Leiden, Sylviusweg 72, BE Leiden, The Netherlands
- Rijk Zwaan Breeding B.V, Burgemeester Crezeelaan 40, KX De Lier, The Netherlands
| | - Maarten G Verlaan
- Rijk Zwaan Breeding B.V, Burgemeester Crezeelaan 40, KX De Lier, The Netherlands
| | - Joke van Elven
- Rijk Zwaan Breeding B.V, Burgemeester Crezeelaan 40, KX De Lier, The Netherlands
| | - Hye Kyong Kim
- Plant Sciences and Natural Products Lab, Institute of Biology Leiden, Sylviusweg 72, BE Leiden, The Netherlands
| | - Peter G L Klinkhamer
- Plant Sciences and Natural Products Lab, Institute of Biology Leiden, Sylviusweg 72, BE Leiden, The Netherlands
| | - Kirsten A Leiss
- Plant Sciences and Natural Products Lab, Institute of Biology Leiden, Sylviusweg 72, BE Leiden, The Netherlands
- Wageningen University and Research, Violierenweg 1, MV Bleiswijk, The Netherlands
| | - Klaas Vrieling
- Plant Sciences and Natural Products Lab, Institute of Biology Leiden, Sylviusweg 72, BE Leiden, The Netherlands
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16
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Calafiore R, Aliberti A, Ruggieri V, Olivieri F, Rigano MM, Barone A. Phenotypic and Molecular Selection of a Superior Solanum pennellii Introgression Sub-Line Suitable for Improving Quality Traits of Cultivated Tomatoes. FRONTIERS IN PLANT SCIENCE 2019; 10:190. [PMID: 30853967 PMCID: PMC6395448 DOI: 10.3389/fpls.2019.00190] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 02/05/2019] [Indexed: 05/21/2023]
Abstract
The Solanum pennellii Introgression Line (IL) population can be exploited to identify favorable alleles that can improve yield and fruit quality traits in commercial tomato varieties. Over the past few years, we have selected ILs that exhibit increased content of antioxidant compounds in the fruit compared to the cultivar M82, which represents the genetic background in which the different wild regions of the S. pennellii ILs were included. Recently, we have identified seven sub-lines of the IL7-3 accumulating different amounts of antioxidants in the ripe fruit. Since the wild region carried on chromosome 7 induces a low fruit production in IL7-3, the first aim of the present work was to evaluate yield performances of the selected sub-lines in three experimental fields located in the South of Italy. Another aim was to confirm in the same lines the high levels of antioxidants and evaluate other fruit quality traits. On red ripe fruit, the levels of soluble solids content, firmness, and ascorbic acid (AsA) were highly variable among the sub-lines grown in three environmental conditions, evidencing a significant genotype by environment interaction for soluble solids and AsA content. Only one sub-line (coded R182) exhibited a significantly higher firmness, even though no differences were observed for this trait between the parental lines M82 and IL7-3. The same sub-line showed significantly higher AsA content compared to M82, thus resembling IL7-3. Even though IL7-3 always exhibited a significantly lower yield, all the sub-lines showed yield variability over the three trials. Interestingly, the sub-line R182, selected for its better performances in terms of fruit quality, in all the trials showed a production comparable to that of the control line M82. A group of species-specific molecular markers was tested on R182 and on the parental genotypes in order to better define the wild genomic regions carried by the elite line R182. In these regions three candidate genes that could increase the level of AsA in the fruit were identified. In the future, the line R182 could be used as pre-breeding material in order to obtain new varieties improved for nutritional traits.
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Affiliation(s)
| | | | | | | | | | - Amalia Barone
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
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17
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Rett-Cadman S, Colle M, Mansfeld B, Barry CS, Wang Y, Weng Y, Gao L, Fei Z, Grumet R. QTL and Transcriptomic Analyses Implicate Cuticle Transcription Factor SHINE as a Source of Natural Variation for Epidermal Traits in Cucumber Fruit. FRONTIERS IN PLANT SCIENCE 2019; 10:1536. [PMID: 31827480 PMCID: PMC6890859 DOI: 10.3389/fpls.2019.01536] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 11/04/2019] [Indexed: 05/11/2023]
Abstract
The fruit surface is a unique tissue with multiple roles influencing fruit development, post-harvest storage and quality, and consumer acceptability. Serving as the first line of protection against herbivores, pathogens, and abiotic stress, the surface can vary markedly among species, cultivars within species, and developmental stage. In this study we explore developmental changes and natural variation of cucumber (Cucumis sativus L.) fruit surface properties using two cucumber lines which vary greatly for these traits and for which draft genomes and a single nucleotide polymorphism (SNP) array are available: Chinese fresh market type, Chinese Long '9930' (CL9930), and pickling type, 'Gy14'. Thin-section samples were prepared from the mid-region of fruit harvested at 0, 4, 8, 12, 16, 20, 24 and 30 days post pollination (dpp), stained with Sudan IV and evaluated for cuticle thickness, depth of wax intercalation between epidermal cells, epidermal cell size and shape, and number and size of lipid droplets. 'Gy14' is characterized by columnar shaped epidermal cells, a 2-3 fold thicker cuticular layer than CL9930, increased cuticular intercalations between cells and a larger number and larger sized lipid droplets. In both lines maximal deposition of cuticle and increase in epidermal size coincided with exponential fruit growth and was largely completed by approximately 16 dpp. Phenotyping and quantitative trait locus mapping (QTL) of fruit sampled from an F7:F8 Gy14 × CL9930 recombinant inbred line (RIL) population identified QTL regions on chromosomes 1, 4 and 5. Strong QTL for epidermal cell height, cuticle thickness, intercalation depth, and diameter of lipid droplets co-localized on chromosome 1. SSR markers on chromosome 1 were used to screen for recombinants in an extended RIL population to refine the QTL region. Further fine mapping by KASP assay combined with gene expression profiling suggested a small number of candidate genes. Tissue specificity, developmental analysis of expression, allelic diversity and gene function implicate the regulatory factor CsSHINE1/WIN1 as a source of natural variation for cucumber fruit epidermal traits.
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Affiliation(s)
- Stephanie Rett-Cadman
- Department of Horticulture and Graduate Program in Plant Breeding, Genetics and Biotechnology, Michigan State University, East Lansing, MI, United States
| | - Marivi Colle
- Department of Horticulture and Graduate Program in Plant Breeding, Genetics and Biotechnology, Michigan State University, East Lansing, MI, United States
| | - Ben Mansfeld
- Department of Horticulture and Graduate Program in Plant Breeding, Genetics and Biotechnology, Michigan State University, East Lansing, MI, United States
| | - Cornelius S. Barry
- Department of Horticulture and Graduate Program in Plant Breeding, Genetics and Biotechnology, Michigan State University, East Lansing, MI, United States
| | - Yuhui Wang
- Department of Horticulture, University of Wisconsin, Madison, WI, United States
- USDA-ARS, Vegetable Crops Research Unit, Madison, WI, United States
| | - Yiqun Weng
- Department of Horticulture, University of Wisconsin, Madison, WI, United States
- USDA-ARS, Vegetable Crops Research Unit, Madison, WI, United States
| | - Lei Gao
- Boyce Thompson Institute, Cornell University, Ithaca, NY, United States
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY, United States
| | - Rebecca Grumet
- Department of Horticulture and Graduate Program in Plant Breeding, Genetics and Biotechnology, Michigan State University, East Lansing, MI, United States
- *Correspondence: Rebecca Grumet,
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18
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Garbowicz K, Liu Z, Alseekh S, Tieman D, Taylor M, Kuhalskaya A, Ofner I, Zamir D, Klee HJ, Fernie AR, Brotman Y. Quantitative Trait Loci Analysis Identifies a Prominent Gene Involved in the Production of Fatty Acid-Derived Flavor Volatiles in Tomato. MOLECULAR PLANT 2018; 11:1147-1165. [PMID: 29960108 DOI: 10.1016/j.molp.2018.06.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 06/12/2018] [Accepted: 06/13/2018] [Indexed: 06/08/2023]
Abstract
To gain insight into the genetic regulation of lipid metabolism in tomato, we conducted metabolic trait loci (mQTL) analysis following the lipidomic profiling of fruit pericarp and leaf tissue of the Solanum pennellii introgression lines (IL). To enhance mapping resolution for selected fruit-specific mQTL, we profiled the lipids in a subset of independently derived S. pennellii backcross inbred lines, as well as in a near-isogenic sub-IL population. We identified a putative lecithin:cholesterol acyltransferase that controls the levels of several lipids, and two members of the class III lipase family, LIP1 and LIP2, that were associated with decreased levels of diacylglycerols (DAGs) and triacylglycerols (TAGs). Lipases of this class cleave fatty acids from the glycerol backbone of acylglycerols. The released fatty acids serve as precursors of flavor volatiles. We show that LIP1 expression correlates with fatty acid-derived volatile levels. We further confirm the function of LIP1 in TAG and DAG breakdown and volatile synthesis using transgenic plants. Taken together, our study extensively characterized the genetic architecture of lipophilic compounds in tomato and demonstrated at molecular level that release of free fatty acids from the glycerol backbone can have a major impact on downstream volatile synthesis.
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Affiliation(s)
- Karolina Garbowicz
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Zhongyuan Liu
- Horticultural Sciences, Plant Innovation Center, University of Florida, Gainesville, FL, USA
| | - Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany; Center of Plant System Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Denise Tieman
- Horticultural Sciences, Plant Innovation Center, University of Florida, Gainesville, FL, USA
| | - Mark Taylor
- Horticultural Sciences, Plant Innovation Center, University of Florida, Gainesville, FL, USA
| | | | - Itai Ofner
- Robert H. Smith Institute of Plant Sciences and Genetics, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Dani Zamir
- Robert H. Smith Institute of Plant Sciences and Genetics, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Harry J Klee
- Horticultural Sciences, Plant Innovation Center, University of Florida, Gainesville, FL, USA
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany; Center of Plant System Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Yariv Brotman
- Department of Life Sciences, Ben-Gurion University of the Negev, Beersheba, Israel.
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Petit J, Bres C, Mauxion JP, Bakan B, Rothan C. Breeding for cuticle-associated traits in crop species: traits, targets, and strategies. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5369-5387. [PMID: 29036305 DOI: 10.1093/jxb/erx341] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 09/14/2017] [Indexed: 05/18/2023]
Abstract
Improving crop productivity and quality while promoting sustainable agriculture have become major goals in plant breeding. The cuticle is a natural film covering the aerial organs of plants and consists of lipid polyesters covered and embedded with wax. The cuticle protects plants against water loss and pathogens and affects traits with strong impacts on crop quality such as, for horticultural crops, fruit brightness, cracking, russeting, netting, and shelf life. Here we provide an overview of the most important cuticle-associated traits that can be targeted for crop improvement. To date, most studies on cuticle-associated traits aimed at crop breeding have been done on fleshy fruits. Less information is available for staple crops such as rice, wheat or maize. Here we present new insights into cuticle formation and properties resulting from the study of genetic resources available for the various crop species. Our review also covers the current strategies and tools aimed at exploiting available natural and artificially induced genetic diversity and the technologies used to transfer the beneficial alleles affecting cuticle-associated traits to commercial varieties.
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Affiliation(s)
- Johann Petit
- UMR 1332 BFP, INRA, Univ. Bordeaux, F-33140 Villenave d'Ornon, France
| | - Cécile Bres
- UMR 1332 BFP, INRA, Univ. Bordeaux, F-33140 Villenave d'Ornon, France
| | | | | | - Christophe Rothan
- UMR 1332 BFP, INRA, Univ. Bordeaux, F-33140 Villenave d'Ornon, France
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20
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Cohen H, Szymanski J, Aharoni A, Dominguez E. Assimilation of 'omics' strategies to study the cuticle layer and suberin lamellae in plants. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5389-5400. [PMID: 29040673 DOI: 10.1093/jxb/erx348] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The assembly of the lipophilic cuticle layer and suberin lamellae, approximately 450 million years ago, was a major evolutionary development that enabled plants to colonize terrestrial habitats. The cuticle layer is composed of cutin polyester and embedded cuticular waxes, whereas the suberin lamellae consist of very long chain fatty acid derivatives, glycerol, and phenolics cross-linked with alkyl ferulate-embedded waxes. Due to their substantial biological roles in plant life, the mechanisms underlying the assembly of these structures have been extensively investigated. In the last decade, the introduction of 'omics' approaches, including genomics, transcriptomics, proteomics, and metabolomics, have been key in the identification of novel genetic and chemical elements involved in the formation and function of the cuticle layer and suberin lamellae. This review summarizes contemporary studies that utilized various large-scale, 'omics' strategies in combination with novel technologies to unravel how building blocks and polymers of these lipophilic barriers are made, and moreover linking structure to function along developmental programs and stress responses. We anticipate that the studies discussed here will inspire scientists studying lipophilic barriers to integrate complementary 'omics' approaches in their efforts to tackle as yet unresolved questions and engage the main challenges of the field to date.
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Affiliation(s)
- Hagai Cohen
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Jedrzej Szymanski
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
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Schmidt MHW, Vogel A, Denton AK, Istace B, Wormit A, van de Geest H, Bolger ME, Alseekh S, Maß J, Pfaff C, Schurr U, Chetelat R, Maumus F, Aury JM, Koren S, Fernie AR, Zamir D, Bolger AM, Usadel B. De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing. THE PLANT CELL 2017; 29:2336-2348. [PMID: 29025960 PMCID: PMC5774570 DOI: 10.1105/tpc.17.00521] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 09/15/2017] [Accepted: 10/11/2017] [Indexed: 05/19/2023]
Abstract
Updates in nanopore technology have made it possible to obtain gigabases of sequence data. Prior to this, nanopore sequencing technology was mainly used to analyze microbial samples. Here, we describe the generation of a comprehensive nanopore sequencing data set with a median read length of 11,979 bp for a self-compatible accession of the wild tomato species Solanum pennellii We describe the assembly of its genome to a contig N50 of 2.5 MB. The assembly pipeline comprised initial read correction with Canu and assembly with SMARTdenovo. The resulting raw nanopore-based de novo genome is structurally highly similar to that of the reference S. pennellii LA716 accession but has a high error rate and was rich in homopolymer deletions. After polishing the assembly with Illumina reads, we obtained an error rate of <0.02% when assessed versus the same Illumina data. We obtained a gene completeness of 96.53%, slightly surpassing that of the reference S. pennellii Taken together, our data indicate that such long read sequencing data can be used to affordably sequence and assemble gigabase-sized plant genomes.
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Affiliation(s)
- Maximilian H-W Schmidt
- Institute for Botany and Molecular Genetics, BioEconomy Science Center, RWTH Aachen University, 52062 Aachen, Germany
| | - Alexander Vogel
- Institute for Botany and Molecular Genetics, BioEconomy Science Center, RWTH Aachen University, 52062 Aachen, Germany
| | - Alisandra K Denton
- Institute for Botany and Molecular Genetics, BioEconomy Science Center, RWTH Aachen University, 52062 Aachen, Germany
| | - Benjamin Istace
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Genoscope, 91057 Evry, France
| | - Alexandra Wormit
- Institute for Botany and Molecular Genetics, BioEconomy Science Center, RWTH Aachen University, 52062 Aachen, Germany
| | | | - Marie E Bolger
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Saleh Alseekh
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Janina Maß
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Christian Pfaff
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Ulrich Schurr
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Roger Chetelat
- C.M. Rick Tomato Genetics Resource Center, Department of Plant Sciences, University of California, Davis, California 95616
| | - Florian Maumus
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | - Jean-Marc Aury
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Genoscope, 91057 Evry, France
| | - Sergey Koren
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Alisdair R Fernie
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Dani Zamir
- The Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Anthony M Bolger
- Institute for Botany and Molecular Genetics, BioEconomy Science Center, RWTH Aachen University, 52062 Aachen, Germany
| | - Björn Usadel
- Institute for Botany and Molecular Genetics, BioEconomy Science Center, RWTH Aachen University, 52062 Aachen, Germany
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, 52428 Jülich, Germany
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