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Diouf I, Derivot L, Koussevitzky S, Carretero Y, Bitton F, Moreau L, Causse M. Genetic basis of phenotypic plasticity and genotype × environment interactions in a multi-parental tomato population. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5365-5376. [PMID: 32474596 PMCID: PMC7501811 DOI: 10.1093/jxb/eraa265] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 05/25/2020] [Indexed: 05/25/2023]
Abstract
Deciphering the genetic basis of phenotypic plasticity and genotype × environment interactions (G×E) is of primary importance for plant breeding in the context of global climate change. Tomato (Solanum lycopersicum) is a widely cultivated crop that can grow in different geographical habitats and that displays a great capacity for expressing phenotypic plasticity. We used a multi-parental advanced generation intercross (MAGIC) tomato population to explore G×E and plasticity for multiple traits measured in a multi-environment trial (MET) comprising optimal cultural conditions together with water deficit, salinity, and heat stress over 12 environments. Substantial G×E was observed for all the traits measured. Different plasticity parameters were estimated by employing Finlay-Wilkinson and factorial regression models and these were used together with genotypic means for quantitative trait loci (QTL) mapping analyses. In addition, mixed linear models were also used to investigate the presence of QTL × environment interactions. The results highlighted a complex genetic architecture of tomato plasticity and G×E. Candidate genes that might be involved in the occurrence of G×E are proposed, paving the way for functional characterization of stress response genes in tomato and for breeding climate-adapted cultivars.
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Affiliation(s)
| | | | | | | | | | - Laurence Moreau
- UMR GQE-Le Moulon, INRA, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
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Esposito S, Cardi T, Campanelli G, Sestili S, Díez MJ, Soler S, Prohens J, Tripodi P. ddRAD sequencing-based genotyping for population structure analysis in cultivated tomato provides new insights into the genomic diversity of Mediterranean 'da serbo' type long shelf-life germplasm. HORTICULTURE RESEARCH 2020; 7:134. [PMID: 32922806 PMCID: PMC7459340 DOI: 10.1038/s41438-020-00353-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/10/2020] [Accepted: 06/19/2020] [Indexed: 05/26/2023]
Abstract
Double digest restriction-site associated sequencing (ddRAD-seq) is a flexible and cost-effective strategy for providing in-depth insights into the genetic architecture of germplasm collections. Using this methodology, we investigated the genomic diversity of a panel of 288 diverse tomato (Solanum lycopersicum L.) accessions enriched in 'da serbo' (called 'de penjar' in Spain) long shelf life (LSL) materials (152 accessions) mostly originating from Italy and Spain. The rest of the materials originate from different countries and include landraces for fresh consumption, elite cultivars, heirlooms, and breeding lines. Apart from their LSL trait, 'da serbo' landraces are of remarkable interest for their resilience. We identified 32,799 high-quality SNPs, which were used for model ancestry population structure and non-parametric hierarchical clustering. Six genetic subgroups were revealed, clearly separating most 'da serbo' landraces, but also the Spanish germplasm, suggesting a subdivision of the population based on type and geographical provenance. Linkage disequilibrium (LD) in the collection decayed very rapidly within <5 kb. We then investigated SNPs showing contrasted minor frequency allele (MAF) in 'da serbo' materials, resulting in the identification of high frequencies in this germplasm of several mutations in genes related to stress tolerance and fruit maturation such as CTR1 and JAR1. Finally, a mini-core collection of 58 accessions encompassing most of the diversity was selected for further exploitation of key traits. Our findings suggest the presence of a genetic footprint of the 'da serbo' germplasm selected in the Mediterranean basin. Moreover, we provide novel insights on LSL 'da serbo' germplasm as a promising source of alleles for tolerance to stresses.
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Affiliation(s)
- Salvatore Esposito
- CREA Research Centre for Vegetable and Ornamental Crops, Pontecagnano, (SA) Italy
| | - Teodoro Cardi
- CREA Research Centre for Vegetable and Ornamental Crops, Pontecagnano, (SA) Italy
| | - Gabriele Campanelli
- CREA Research Centre for Vegetable and Ornamental Crops, Monsampolo del Tronto (AP), Tronto, Italy
| | - Sara Sestili
- CREA Research Centre for Vegetable and Ornamental Crops, Monsampolo del Tronto (AP), Tronto, Italy
| | - María José Díez
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Salvador Soler
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Pasquale Tripodi
- CREA Research Centre for Vegetable and Ornamental Crops, Pontecagnano, (SA) Italy
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Komatsu H, Abdellatif IMY, Yuan S, Ono M, Nonaka S, Ezura H, Ariizumi T, Miura K. Genome editing in PDS genes of tomatoes by non-selection method and of Nicotiana benthamiana by one single guide RNA to edit two orthologs. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2020; 37:213-221. [PMID: 32821229 PMCID: PMC7434671 DOI: 10.5511/plantbiotechnology.20.0527b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The CRISPR/Cas9 system is widely used for targeted mutagenesis in many organisms including plants. For application of this system, tissue culture methods need to be established. In this study, detailed methods for introduction of mutations in tomato and Nicotiana benthamiana plants using the CRISPR/Cas9 system are described. The methods include tissue culture protocols for tomato and N. benthamiana. We also demonstrate the methodology to generate Cas9-free genome edited tomato plants and use of one single guide RNA (sgRNA) to edit two orthologs in N. benthamiana. The examples of editing the PHYTOENE DESATURASE (PDS) genes in these plants are also provided. The Cas9-free tomato line was obtained when tomato plants were cultured on a non-selective medium after transformation with the CRISPR/Cas9 system. Two orthologs of PDS in N. benthamiana were mutated using a sgRNA, because these orthologs contain the same nucleotide sequences with PAM motif. These mutations were inherited to the next generation. The mutations in the PDS genes resulted in an albino phenotype in tomato and N. benthamiana plants. These results demonstrate that the non-selective method is one of the ways to obtain Cas9-free genome editing in tomato plants and that the two orthologs can be edited by one sgRNA in N. benthamiana.
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Affiliation(s)
- Hiroki Komatsu
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki 305-8572, Japan
| | - Islam M. Y. Abdellatif
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki 305-8572, Japan
| | - Shaoze Yuan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki 305-8572, Japan
| | - Misaki Ono
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki 305-8572, Japan
| | - Satoko Nonaka
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki 305-8572, Japan
- Tsukuba-Plant Innovation Research Center, University of Tsukuba, Ibaraki 305-8572, Japan
| | - Hiroshi Ezura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki 305-8572, Japan
- Tsukuba-Plant Innovation Research Center, University of Tsukuba, Ibaraki 305-8572, Japan
| | - Tohru Ariizumi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki 305-8572, Japan
- Tsukuba-Plant Innovation Research Center, University of Tsukuba, Ibaraki 305-8572, Japan
- E-mail: Tel & Fax: +81-29-853-4710
| | - Kenji Miura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki 305-8572, Japan
- Tsukuba-Plant Innovation Research Center, University of Tsukuba, Ibaraki 305-8572, Japan
- E-mail: Tel & Fax: +81-29-853-6401
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54
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Mata-Nicolás E, Montero-Pau J, Gimeno-Paez E, Garcia-Carpintero V, Ziarsolo P, Menda N, Mueller LA, Blanca J, Cañizares J, van der Knaap E, Díez MJ. Exploiting the diversity of tomato: the development of a phenotypically and genetically detailed germplasm collection. HORTICULTURE RESEARCH 2020; 7:66. [PMID: 32377357 PMCID: PMC7192925 DOI: 10.1038/s41438-020-0291-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 03/06/2020] [Accepted: 03/16/2020] [Indexed: 05/19/2023]
Abstract
A collection of 163 accessions, including Solanum pimpinellifolium, Solanum lycopersicum var. cerasiforme and Solanum lycopersicum var. lycopersicum, was selected to represent the genetic and morphological variability of tomato at its centers of origin and domestication: Andean regions of Peru and Ecuador and Mesoamerica. The collection is enriched with S. lycopersicum var. cerasiforme from the Amazonian region that has not been analyzed previously nor used extensively. The collection has been morphologically characterized showing diversity for fruit, flower and vegetative traits. Their genomes were sequenced in the Varitome project and are publicly available (solgenomics.net/projects/varitome). The identified SNPs have been annotated with respect to their impact and a total number of 37,974 out of 19,364,146 SNPs have been described as high impact by the SnpEeff analysis. GWAS has shown associations for different traits, demonstrating the potential of this collection for this kind of analysis. We have not only identified known QTLs and genes, but also new regions associated with traits such as fruit color, number of flowers per inflorescence or inflorescence architecture. To speed up and facilitate the use of this information, F2 populations were constructed by crossing the whole collection with three different parents. This F2 collection is useful for testing SNPs identified by GWAs, selection sweeps or any other candidate gene. All data is available on Solanaceae Genomics Network and the accession and F2 seeds are freely available at COMAV and at TGRC genebanks. All these resources together make this collection a good candidate for genetic studies.
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Affiliation(s)
- Estefanía Mata-Nicolás
- Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana. COMAV. Universitat Politècnica de València, Valencia, Spain
| | - Javier Montero-Pau
- Department of Biochemistry and Molecular Biology, Universitat de València, Valencia, Spain
| | - Esther Gimeno-Paez
- Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana. COMAV. Universitat Politècnica de València, Valencia, Spain
| | - Víctor Garcia-Carpintero
- Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana. COMAV. Universitat Politècnica de València, Valencia, Spain
| | - Peio Ziarsolo
- Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana. COMAV. Universitat Politècnica de València, Valencia, Spain
| | | | | | - José Blanca
- Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana. COMAV. Universitat Politècnica de València, Valencia, Spain
| | - Joaquín Cañizares
- Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana. COMAV. Universitat Politècnica de València, Valencia, Spain
| | - Esther van der Knaap
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Georgia, GA USA
- Department of Horticulture, University of Georgia, Georgia, GA USA
| | - María José Díez
- Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana. COMAV. Universitat Politècnica de València, Valencia, Spain
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55
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Gaston A, Osorio S, Denoyes B, Rothan C. Applying the Solanaceae Strategies to Strawberry Crop Improvement. TRENDS IN PLANT SCIENCE 2020; 25:130-140. [PMID: 31699520 DOI: 10.1016/j.tplants.2019.10.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/20/2019] [Accepted: 10/03/2019] [Indexed: 05/24/2023]
Abstract
Strawberry is a fruit crop species of major horticultural importance, for which fruit quality and the control of flowering (for fruit yield), runnering (for vegetative propagation), and the trade-off between the two are main breeding targets. The octoploid cultivated strawberry has a limited genetic basis. This raises the question of how to identify important gene targets and successfully exploit them for strawberry improvement. In this Opinion article we propose to apply to woodland strawberry, a wild diploid species displaying wide diversity, the strategies successfully employed in recent years for the identification of genetic variations underlying fruit quality and fruit yield traits in solanaceous crops (tomato, potato). Next we propose to use gene editing technologies to translate the findings to cultivated strawberry.
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Affiliation(s)
- Amelia Gaston
- INRA and University of Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, France
| | - Sonia Osorio
- Department of Molecular Biology and Biochemistry, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', University of Málaga - Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus de Teatinos, 29071 Málaga, Spain
| | - Béatrice Denoyes
- INRA and University of Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, France.
| | - Christophe Rothan
- INRA and University of Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, France.
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56
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Quinet M, Angosto T, Yuste-Lisbona FJ, Blanchard-Gros R, Bigot S, Martinez JP, Lutts S. Tomato Fruit Development and Metabolism. FRONTIERS IN PLANT SCIENCE 2019; 10:1554. [PMID: 31850035 PMCID: PMC6895250 DOI: 10.3389/fpls.2019.01554] [Citation(s) in RCA: 146] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 11/07/2019] [Indexed: 05/20/2023]
Abstract
Tomato (Solanum lycopersicum L.) belongs to the Solanaceae family and is the second most important fruit or vegetable crop next to potato (Solanum tuberosum L.). It is cultivated for fresh fruit and processed products. Tomatoes contain many health-promoting compounds including vitamins, carotenoids, and phenolic compounds. In addition to its economic and nutritional importance, tomatoes have become the model for the study of fleshy fruit development. Tomato is a climacteric fruit and dramatic metabolic changes occur during its fruit development. In this review, we provide an overview of our current understanding of tomato fruit metabolism. We begin by detailing the genetic and hormonal control of fruit development and ripening, after which we document the primary metabolism of tomato fruits, with a special focus on sugar, organic acid, and amino acid metabolism. Links between primary and secondary metabolic pathways are further highlighted by the importance of pigments, flavonoids, and volatiles for tomato fruit quality. Finally, as tomato plants are sensitive to several abiotic stresses, we briefly summarize the effects of adverse environmental conditions on tomato fruit metabolism and quality.
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Affiliation(s)
- Muriel Quinet
- Groupe de Recherche en Physiologie Végétale, Earth and Life Institute, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Trinidad Angosto
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL), Universidad de Almería, Almería, Spain
| | - Fernando J. Yuste-Lisbona
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL), Universidad de Almería, Almería, Spain
| | - Rémi Blanchard-Gros
- Groupe de Recherche en Physiologie Végétale, Earth and Life Institute, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Servane Bigot
- Groupe de Recherche en Physiologie Végétale, Earth and Life Institute, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | | | - Stanley Lutts
- Groupe de Recherche en Physiologie Végétale, Earth and Life Institute, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
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57
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Chaudhary J, Alisha A, Bhatt V, Chandanshive S, Kumar N, Mir Z, Kumar A, Yadav SK, Shivaraj SM, Sonah H, Deshmukh R. Mutation Breeding in Tomato: Advances, Applicability and Challenges. PLANTS (BASEL, SWITZERLAND) 2019; 8:E128. [PMID: 31091747 PMCID: PMC6572636 DOI: 10.3390/plants8050128] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/09/2019] [Accepted: 05/11/2019] [Indexed: 02/04/2023]
Abstract
Induced mutagenesis is one of the most effective strategies for trait improvement without altering the well-optimized genetic background of the cultivars. In this review, several currently accessible methods such as physical, chemical and insertional mutagenesis have been discussed concerning their efficient exploration for the tomato crop improvement. Similarly, challenges for the adaptation of genome-editing, a newly developed technique providing an opportunity to induce precise mutation, have been addressed. Several efforts of genome-editing have been demonstrated in tomato and other crops, exploring its effectiveness and convenience for crop improvement. Descriptive data compiled here from such efforts will be helpful for the efficient exploration of technological advances. However, uncertainty about the regulation of genome-edited crops is still a significant concern, particularly when timely trait improvement in tomato cultivars is needed. In this regard, random approaches of induced mutagenesis are still promising if efficiently explored in breeding applications. Precise identification of casual mutation is a prerequisite for the molecular understanding of the trait development as well as its utilization for the breeding program. Recent advances in sequencing techniques provide an opportunity for the precise detection of mutagenesis-induced sequence variations at a large scale in the genome. Here, we reviewed several novel next-generation sequencing based mutation mapping approaches including Mutmap, MutChromeSeq, and whole-genome sequencing-based mapping which has enormous potential to accelerate the mutation breeding in tomato. The proper utilization of the existing well-characterized tomato mutant resources combined with novel mapping approaches would inevitably lead to rapid enhancement of tomato quality and yield. This article provides an overview of the principles and applications of mutagenesis approaches in tomato and discusses the current progress and challenges involved in tomato mutagenesis research.
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Affiliation(s)
- Juhi Chaudhary
- Department of Biology, Oberlin College, Oberlin, OH 44074, USA.
| | - Alisha Alisha
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab 140308, India.
| | - Vacha Bhatt
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab 140308, India.
| | - Sonali Chandanshive
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab 140308, India.
| | - Nirbhay Kumar
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab 140308, India.
| | - Zahoor Mir
- National Research Center on Plant Biotechnology, New Delhi, Delhi 110012, India.
| | - Ashwini Kumar
- Division of Plant Pathology, ICAR-IARI, New Delhi, Delhi 110001, Inida.
| | - Satish K Yadav
- National Bureau of Plant Genetic Resources, New Delhi, Delhi 110012, India.
| | - S M Shivaraj
- Faculté des sciences de l'agriculture et de l'alimentation (FSAA), Université Laval, Quebec, QC G1V 0A6, Canada.
| | - Humira Sonah
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab 140308, India.
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab 140308, India.
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58
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Herrera-Téllez VI, Cruz-Olmedo AK, Plasencia J, Gavilanes-Ruíz M, Arce-Cervantes O, Hernández-León S, Saucedo-García M. The Protective Effect of Trichoderma asperellum on Tomato Plants against Fusarium oxysporum and Botrytis cinerea Diseases Involves Inhibition of Reactive Oxygen Species Production. Int J Mol Sci 2019; 20:ijms20082007. [PMID: 31022849 PMCID: PMC6514666 DOI: 10.3390/ijms20082007] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 04/17/2019] [Accepted: 04/17/2019] [Indexed: 11/17/2022] Open
Abstract
Trichoderma species are fungi widely employed as plant-growth-promoting agents and for biological control. Several commercial and laboratory-made solid formulations for mass production of Trichoderma have been reported. In this study, we evaluated a solid kaolin-based formulation to promote the absortion/retention of Trichoderma asperellum in the substrate for growing tomato plants. The unique implementation of this solid formulation resulted in an increased growth of the tomato plants, both in roots and shoots after 40 days of its application. Plants were challenged with two fungal pathogens, Fusarium oxysporum and Botrytis cinerea, and pretreatment with T. asperellum resulted in less severe wilting and stunting symptoms than non-treated plants. Treatment with T. asperellum formulation inhibited Reactive Oxygen Species (ROS) production in response to the pathogens in comparison to plants that were only challenged with both pathogens. These results suggest that decrease in ROS levels contribute to the protective effects exerted by T. asperellum in tomato.
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Affiliation(s)
- Verónica I Herrera-Téllez
- Instituto de Ciencias Básicas e Ingeniería, Universidad Autónoma del Estado de Hidalgo, Pachuca-Tulancingo de Bravo Kilómetro 4.5, Mineral de la Reforma 42184, Hidalgo, Mexico.
| | - Ana K Cruz-Olmedo
- Instituto Tecnológico de Acapulco, Carr. Cayaco Puerto Marqués s/n, Del PRI, Acapulco 39905, Guerrero, Mexico.
| | - Javier Plasencia
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico.
| | - Marina Gavilanes-Ruíz
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico.
| | - Oscar Arce-Cervantes
- Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Avenida Universidad Km. 1, Rancho Universitario, Tulancingo-Santiago Tulantepec, Tulancingo 43600, Hidalgo, Mexico.
| | - Sergio Hernández-León
- Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Avenida Universidad Km. 1, Rancho Universitario, Tulancingo-Santiago Tulantepec, Tulancingo 43600, Hidalgo, Mexico.
| | - Mariana Saucedo-García
- Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Avenida Universidad Km. 1, Rancho Universitario, Tulancingo-Santiago Tulantepec, Tulancingo 43600, Hidalgo, Mexico.
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59
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Zhao J, Sauvage C, Zhao J, Bitton F, Bauchet G, Liu D, Huang S, Tieman DM, Klee HJ, Causse M. Meta-analysis of genome-wide association studies provides insights into genetic control of tomato flavor. Nat Commun 2019; 10:1534. [PMID: 30948717 PMCID: PMC6449550 DOI: 10.1038/s41467-019-09462-w] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 03/04/2019] [Indexed: 12/30/2022] Open
Abstract
Tomato flavor has changed over the course of long-term domestication and intensive breeding. To understand the genetic control of flavor, we report the meta-analysis of genome-wide association studies (GWAS) using 775 tomato accessions and 2,316,117 SNPs from three GWAS panels. We discover 305 significant associations for the contents of sugars, acids, amino acids, and flavor-related volatiles. We demonstrate that fruit citrate and malate contents have been impacted by selection during domestication and improvement, while sugar content has undergone less stringent selection. We suggest that it may be possible to significantly increase volatiles that positively contribute to consumer preferences while reducing unpleasant volatiles, by selection of the relevant allele combinations. Our results provide genetic insights into the influence of human selection on tomato flavor and demonstrate the benefits obtained from meta-analysis. Flavor is one of the most important traits for improving tomato sensory quality and consumer acceptability. Here, the authors report meta-analysis of genome-wide association studies of flavor related traits and show genetic insights into the influence of human selection during domestication and improvement.
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Affiliation(s)
- Jiantao Zhao
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, Domaine Saint Maurice, 67 Allée des Chênes CS 60094, 84143, Montfavet Cedex, France
| | - Christopher Sauvage
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, Domaine Saint Maurice, 67 Allée des Chênes CS 60094, 84143, Montfavet Cedex, France.,Syngenta, 12 Chemin de l'Hobit, Saint Sauveur, 31790, France
| | - Jinghua Zhao
- MRC Epidemiology Unit & Institute of Metabolic Science, University of Cambridge, Addrenbrooke's Hospital, Box 285, Hills Road, Cambridge, CB2 0QQ, UK.,Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge, CB1 8RN, UK
| | - Frédérique Bitton
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, Domaine Saint Maurice, 67 Allée des Chênes CS 60094, 84143, Montfavet Cedex, France
| | - Guillaume Bauchet
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, Domaine Saint Maurice, 67 Allée des Chênes CS 60094, 84143, Montfavet Cedex, France.,Boyce Thompson Institute, Cornell University, 533 Tower Rd, Ithaca, NY, 14853, USA
| | - Dan Liu
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518124, Shenzhen, Guangdong, China
| | - Sanwen Huang
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518124, Shenzhen, Guangdong, China.,Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Denise M Tieman
- Horticultural Sciences, Plant Innovation Center, University of Florida, Post Office Box 110690, Gainesville, FL, 32611, USA
| | - Harry J Klee
- Horticultural Sciences, Plant Innovation Center, University of Florida, Post Office Box 110690, Gainesville, FL, 32611, USA
| | - Mathilde Causse
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, Domaine Saint Maurice, 67 Allée des Chênes CS 60094, 84143, Montfavet Cedex, France.
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60
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Fernie AR, Gutierrez-Marcos J. From genome to phenome: genome-wide association studies and other approaches that bridge the genotype to phenotype gap. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:5-7. [PMID: 30636100 DOI: 10.1111/tpj.14219] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Affiliation(s)
- Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
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