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Gaber DA, Berthelot C, Blaudez D, Kovács GM, Franken P. Impact of dark septate endophytes on salt stress alleviation of tomato plants. Front Microbiol 2023; 14:1124879. [PMID: 37415811 PMCID: PMC10320394 DOI: 10.3389/fmicb.2023.1124879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 05/19/2023] [Indexed: 07/08/2023] Open
Abstract
Fungal endophytes can improve plant tolerance to abiotic stress conditions. Dark septate endophytes (DSEs) belong to phylogenetically non-related groups of root colonizing fungi among the Ascomycota with high melanin-producing activities. They can be isolated from roots of more than 600 plant species in diverse ecosystems. Still the knowledge about their interaction with host plants and their contribution to stress alleviation is limited. The current work aimed to test the abilities of three DSEs (Periconia macrospinosa, Cadophora sp., Leptodontidium sp.) to alleviate moderate and high salt stress in tomato plants. By including an albino mutant, the role of melanin for the interaction with plants and salt stress alleviation could also be tested. P. macrospinosa and Cadophora sp. improved shoot and root growth 6 weeks after inoculation under moderate and high salt stress conditions. No matter how much salt stress was applied, macroelement (P, N, and C) contents were unaffected by DSE inoculation. The four tested DSE strains successfully colonized the roots of tomato, but the colonization level was clearly reduced in the albino mutant of Leptodontidium sp. Any difference in the effects on plant growth between the Leptodontidium sp. wild type strain and the albino mutant could, however, not be observed. These results show that particular DSEs are able to increase salt tolerance as they promote plant growth specifically under stress condition. Increased plant biomasses combined with stable nutrient contents resulted in higher P uptake in shoots of inoculated plants at moderate and high salt conditions and higher N uptake in the absence of salt stress in all inoculated plants, in P. macrospinosa-inoculated plants at moderate salt condition and in all inoculated plants except the albino mutants at high salt condition. In summary, melanin in DSEs seems to be important for the colonization process, but does not influence growth, nutrient uptake or salt tolerance of plants.
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Affiliation(s)
- Dalia A. Gaber
- Leibniz-Institute of Vegetable and Ornamental Crops, Grossbeeren, Germany
- Erfurt Research Centre for Horticultural Crops, University of Applied Sciences, Erfurt, Germany
- Department of Botany and Microbiology, Faculty of Science, Assiut University, Assiut, Egypt
| | - Charlotte Berthelot
- Université de Lorraine, CNRS, LIEC, Nancy, France
- CTIFL, Centre de Carquefou, Carquefou, France
| | | | - Gábor M. Kovács
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Budapest, Hungary
- Centre for Agricultural Research, Plant Protection Institute, Budapest, Hungary
| | - Philipp Franken
- Leibniz-Institute of Vegetable and Ornamental Crops, Grossbeeren, Germany
- Erfurt Research Centre for Horticultural Crops, University of Applied Sciences, Erfurt, Germany
- Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
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Nakayama H, Ichihashi Y, Kimura S. Diversity of tomato leaf form provides novel insights into breeding. BREEDING SCIENCE 2023; 73:76-85. [PMID: 37168814 PMCID: PMC10165341 DOI: 10.1270/jsbbs.22061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 08/29/2022] [Indexed: 05/13/2023]
Abstract
Tomato (Solanum lycopersicum L.) is cultivated widely globally. The crop exhibits tremendous morphological variations because of its long breeding history. Apart from the commercial tomato varieties, wild species and heirlooms are grown in certain regions of the world. Since the fruit constitutes the edible part, much of the agronomical research is focused on it. However, recent studies have indicated that leaf morphology influences fruit quality. As leaves are specialized photosynthetic organs and the vascular systems transport the photosynthetic products to sink organs, the architectural characteristics of the leaves have a strong influence on the final fruit quality. Therefore, comprehensive research focusing on both the fruit and leaf morphology is required for further tomato breeding. This review summarizes an overview of knowledge of the basic tomato leaf development, morphological diversification, and molecular mechanisms behind them and emphasizes its importance in breeding. Finally, we discuss how these findings and knowledge can be applied to future tomato breeding.
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Affiliation(s)
- Hokuto Nakayama
- Graduate School of Science, Department of Biological Sciences, The University of Tokyo, Science Build. #2, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-0033, Japan
- Department of Plant Biology, University of California Davis, One Shields Avenue, Davis, CA 95616, U.S.A.
- Corresponding author (e-mail: )
| | | | - Seisuke Kimura
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-Ku, Kyoto 603-8555, Japan
- Center for Plant Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-Ku, Kyoto 603-8555, Japan
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Genomics, Proteomics, and Metabolomics Approaches to Improve Abiotic Stress Tolerance in Tomato Plant. Int J Mol Sci 2023; 24:ijms24033025. [PMID: 36769343 PMCID: PMC9918255 DOI: 10.3390/ijms24033025] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
To explore changes in proteins and metabolites under stress circumstances, genomics, proteomics, and metabolomics methods are used. In-depth research over the previous ten years has gradually revealed the fundamental processes of plants' responses to environmental stress. Abiotic stresses, which include temperature extremes, water scarcity, and metal toxicity brought on by human activity and urbanization, are a major cause for concern, since they can result in unsustainable warming trends and drastically lower crop yields. Furthermore, there is an emerging reliance on agrochemicals. Stress is responsible for physiological transformations such as the formation of reactive oxygen, stomatal opening and closure, cytosolic calcium ion concentrations, metabolite profiles and their dynamic changes, expression of stress-responsive genes, activation of potassium channels, etc. Research regarding abiotic stresses is lacking because defense feedbacks to abiotic factors necessitate regulating the changes that activate multiple genes and pathways that are not properly explored. It is clear from the involvement of these genes that plant stress response and adaptation are complicated processes. Targeting the multigenicity of plant abiotic stress responses caused by genomic sequences, transcripts, protein organization and interactions, stress-specific and cellular transcriptome collections, and mutant screens can be the first step in an integrative approach. Therefore, in this review, we focused on the genomes, proteomics, and metabolomics of tomatoes under abiotic stress.
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Rai GK, Kumar P, Choudhary SM, Kosser R, Khanday DM, Choudhary S, Kumar B, Magotra I, Kumar RR, Ram C, Rouphael Y, Corrado G, Behera TK. Biomimetic Strategies for Developing Abiotic Stress-Tolerant Tomato Cultivars: An Overview. PLANTS (BASEL, SWITZERLAND) 2022; 12:86. [PMID: 36616215 PMCID: PMC9823378 DOI: 10.3390/plants12010086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/17/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
The tomato is one of the most important vegetables in the world. The demand for tomatoes is high in virtually any country, owing to their gastronomic versatility and nutritional and aromatic value. Drought, salinity, and inadequate temperature can be major factors in diminishing yield, affecting physiological and biochemical processes and altering various metabolic pathways, from the aggregation of low molecular-weight substances to the transcription of specific genes. Various biotechnological tools can be used to alter the tomato genes so that this species can more rapidly or better adapt to abiotic stress. These approaches range from the introgression of genes coding for specific enzymes for mitigating a prevailing stress to genetic modifications that alter specific metabolic pathways to help tomato perceive environmental cues and/or withstand adverse conditions. In recent years, environmental and social concerns and the high complexity of the plant response may increase the attention of applied plant biotechnology toward biomimetic strategies, generally defined as all the approaches that seek to develop more sustainable and acceptable strategies by imitating nature's time-tested solutions. In this review, we provide an overview of some of the genetic sequences and molecules that were the objects of biotechnological intervention in tomato as examples of approaches to achieve tolerance to abiotic factors, improving existing nature-based mechanisms and solutions (biomimetic biotechnological approaches (BBA)). Finally, we discuss implications and perspectives within the GMO debate, proposing that crops modified with BBA should receive less stringent regulation.
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Affiliation(s)
- Gyanendra Kumar Rai
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu 180009, India
| | - Pradeep Kumar
- Division of Integrated Farming System, ICAR—Central Arid Zone Research Institute, Jodhpur 342003, India
| | - Sadiya Maryam Choudhary
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu 180009, India
| | - Rafia Kosser
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu 180009, India
| | - Danish Mushtaq Khanday
- Division of Plant Breeding and Genetics, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu 180009, India
| | - Shallu Choudhary
- Division of Entomology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu 180009, India
| | - Bupesh Kumar
- Division of Plant Breeding and Genetics, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu 180009, India
| | - Isha Magotra
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu 180009, India
| | - Ranjit Ranjan Kumar
- Division of Biochemistry, ICAR—Indian Agricultural Research Institute, New Delhi 110001, India
| | - Chet Ram
- Division of Crop Improvement, ICAR—Central Institute for Arid Horticulture, Bikaner 334006, India
| | - Youssef Rouphael
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055 Naples, Italy
| | - Giandomenico Corrado
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055 Naples, Italy
| | - Tusar Kanti Behera
- ICAR—Indian Institute of Vegetable Research, Jakhini (Shahanshapur), Varanasi 221305, India
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Metwally RA, Abdelhameed RE, Soliman SA, Al-Badwy AH. Potential use of beneficial fungal microorganisms and C-phycocyanin extract for enhancing seed germination, seedling growth and biochemical traits of Solanum lycopersicum L. BMC Microbiol 2022; 22:108. [PMID: 35448979 PMCID: PMC9027073 DOI: 10.1186/s12866-022-02509-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 03/21/2022] [Indexed: 12/03/2022] Open
Abstract
Background Biopriming as a new technique of seed treatment involves the application of beneficial microorganisms on the seed surface to stimulate seed germination, plant growth, and protect the seed from soil and seed-borne pathogens. The present investigation was carried out on seed germination, seedling vigor and biochemical traits of one of the most important vegetable crops (Tomato, Solanum lycopersicum L.). The treatments comprised viz. T1: Non primed seeds (Control), T2: Hydropriming, T3: Biopriming with C-phycocyanin (C-PC) (Spirulina platensis extract), T4: Biopriming with Trichoderma asperellum, T5: Biopriming with T. viride, T6: Biopriming with Beauveria bassiana. Results Extraction and purification of C-phycocyanin (C-PC) from the dry S. platensis powder using various methods was performed. The purity after dialyses was 0.49 and its ultimate purity (A620/A280) after ion-exchange chromatography was 4.64. The results on tomato seedlings revealed that the maximum germination percentage (100%), germination index (15.46 and 15.12), seedling length (10.67 cm), seedling dry weight (1.73 and 1.97 mg) and seedling length vigor index (1066.7) were recorded for tomato biopriming with T. viride, and B. bassiana (T5 and T6). Moreover, the quantitative estimation of total carbohydrates and total free amino acids contents in bioprimed tomato seedlings indicated a significantly higher amount with T. viride, followed by those bioprimed with T. asperellum, B. bassiana and C-PC extract. Conclusion Thus, our results indicated that biopriming of tomato seeds with beneficial fungal inoculants and C-PC was very effective. The most operative biostimulants were those bioprimed with T. viride and B. bassiana compared to other biostimulants (T. asperellum and C-PC). Therefore, to ensure sustainable agriculture, this study offers new possibilities for the biopriming application as an alternative and ecological management strategy to chemical treatment and provides a valuable basis for improving seed germination.
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Affiliation(s)
- Rabab A Metwally
- Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig, 44519, Egypt
| | - Reda E Abdelhameed
- Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig, 44519, Egypt.
| | - Shereen A Soliman
- Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig, 44519, Egypt
| | - Asmaa H Al-Badwy
- Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig, 44519, Egypt
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Yuste-Lisbona FJ, Jiménez-Gómez JM, Capel C, Lozano R. Effective Mapping by Sequencing to Isolate Causal Mutations in the Tomato Genome. Methods Mol Biol 2021; 2264:89-103. [PMID: 33263905 DOI: 10.1007/978-1-0716-1201-9_7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Forward genetic analysis remains as one of the most powerful tools for assessing gene functions, although the identification of the causal mutation responsible for a given phenotype has been a tedious and time-consuming task until recently. Advances in deep sequencing technologies have provided new approaches for the exploitation of natural and artificially induced genetic diversity, thus accelerating the discovery of novel allelic variants. In this chapter, a mapping-by-sequencing forward genetics approach is described to identify causal mutations in tomato (Solanum lycopersicum L.), a major crop species that is also a model species for plant biology and breeding.
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Affiliation(s)
- Fernando J Yuste-Lisbona
- Centro de Investigación en Biotecnología Agroalimentaria, Departamento de Biología y Geología, Universidad de Almería, Almería, Spain
| | - José M Jiménez-Gómez
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Carmen Capel
- Centro de Investigación en Biotecnología Agroalimentaria, Departamento de Biología y Geología, Universidad de Almería, Almería, Spain
| | - Rafael Lozano
- Centro de Investigación en Biotecnología Agroalimentaria, Departamento de Biología y Geología, Universidad de Almería, Almería, Spain.
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Goh WWB, Wong L. The Birth of Bio-data Science: Trends, Expectations, and Applications. GENOMICS, PROTEOMICS & BIOINFORMATICS 2020; 18:5-15. [PMID: 32428604 PMCID: PMC7393550 DOI: 10.1016/j.gpb.2020.01.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 12/02/2019] [Accepted: 02/26/2020] [Indexed: 12/23/2022]
Affiliation(s)
- Wilson Wen Bin Goh
- (1)School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.
| | - Limsoon Wong
- (2)Department of Computer Science, National University of Singapore, Singapore 117417, Singapore.
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Borgohain P, Saha B, Agrahari R, Chowardhara B, Sahoo S, van der Vyver C, Panda SK. SlNAC2 overexpression in Arabidopsis results in enhanced abiotic stress tolerance with alteration in glutathione metabolism. PROTOPLASMA 2019; 256:1065-1077. [PMID: 30919132 DOI: 10.1007/s00709-019-01368-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 03/18/2019] [Indexed: 05/26/2023]
Abstract
Plant NAC (NAM, ATAF, and CUC) transcription factors (TF) have important roles to play in abiotic stress responses through activation of a battery of functional genes/transcriptional regulators responsible for stress tolerance. Here we report the cloning of a novel Solanum lycopersicum L., NAC2 TF having 960 nucleotides long CDS (GenBank: KT740994.1). Phylogenetic analysis depicted the similarity of SlNAC2 to other orthologs. SlNAC2 was overexpressed in Arabidopsis thaliana to assess and characterize its role in plant abiotic stress responses. The transgenic events were first confirmed by genomic DNA PCR and qRT PCR; then the T3 generation plants were used for stress assays. Soil stress assay depicted better survivability of the transgenic plants under both salt (NaCl) and drought (PEG) stress. The transgenic plants showed enhanced endurance; with better antioxidative response, reduced accumulation of reactive oxygen species (ROS) molecules and better retention of water in tissue. This study for the very first time analyzed the different stakeholders of the glutathione metabolism in SlNAC2 overexpressing transgenic lines on exposure to both salinity and PEG stress. The expression of the two genes (ɤ-ECS, GS) responsible for glutathione biosynthesis increased with SlNAC2 overexpression. Further glutathione reductase responsible for reduction of glutathione disulfide (GSSG) to glutathione (GSH) also increased significantly which suggested the regulation of glutathione metabolism as a mechanism for the osmotic stress tolerance conferred to plants upon NAC overexpression.
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Affiliation(s)
- Pankaj Borgohain
- Plant Functional Genomics Laboratory, Department of Life Science and Bioinformatics, Assam University, Silchar, 788011, India
| | - Bedabrata Saha
- Plant Functional Genomics Laboratory, Department of Life Science and Bioinformatics, Assam University, Silchar, 788011, India
| | - Rajkishan Agrahari
- Plant Functional Genomics Laboratory, Department of Life Science and Bioinformatics, Assam University, Silchar, 788011, India
| | - Bhaben Chowardhara
- Plant Functional Genomics Laboratory, Department of Life Science and Bioinformatics, Assam University, Silchar, 788011, India
| | - Smita Sahoo
- Plant Functional Genomics Laboratory, Department of Life Science and Bioinformatics, Assam University, Silchar, 788011, India
| | - Christell van der Vyver
- Institute for Plant Biotechnology, Department of Genetics, University of Stellenbosch, Stellenbosch, 7602, South Africa
| | - Sanjib Kumar Panda
- Plant Functional Genomics Laboratory, Department of Life Science and Bioinformatics, Assam University, Silchar, 788011, India.
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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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Pérez‐Martín F, Yuste‐Lisbona FJ, Pineda B, Angarita‐Díaz MP, García‐Sogo B, Antón T, Sánchez S, Giménez E, Atarés A, Fernández‐Lozano A, Ortíz‐Atienza A, García‐Alcázar M, Castañeda L, Fonseca R, Capel C, Goergen G, Sánchez J, Quispe JL, Capel J, Angosto T, Moreno V, Lozano R. A collection of enhancer trap insertional mutants for functional genomics in tomato. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:1439-1452. [PMID: 28317264 PMCID: PMC5633825 DOI: 10.1111/pbi.12728] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 03/03/2017] [Accepted: 03/15/2017] [Indexed: 05/06/2023]
Abstract
With the completion of genome sequencing projects, the next challenge is to close the gap between gene annotation and gene functional assignment. Genomic tools to identify gene functions are based on the analysis of phenotypic variations between a wild type and its mutant; hence, mutant collections are a valuable resource. In this sense, T-DNA collections allow for an easy and straightforward identification of the tagged gene, serving as the basis of both forward and reverse genetic strategies. This study reports on the phenotypic and molecular characterization of an enhancer trap T-DNA collection in tomato (Solanum lycopersicum L.), which has been produced by Agrobacterium-mediated transformation using a binary vector bearing a minimal promoter fused to the uidA reporter gene. Two genes have been isolated from different T-DNA mutants, one of these genes codes for a UTP-glucose-1-phosphate uridylyltransferase involved in programmed cell death and leaf development, which means a novel gene function reported in tomato. Together, our results support that enhancer trapping is a powerful tool to identify novel genes and regulatory elements in tomato and that this T-DNA mutant collection represents a highly valuable resource for functional analyses in this fleshy-fruited model species.
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Affiliation(s)
- Fernando Pérez‐Martín
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL)Universidad de AlmeríaAlmeríaSpain
| | | | - Benito Pineda
- Instituto de Biología Molecular y Celular de Plantas (UPV‐CSIC)Universidad Politécnica de ValenciaValenciaSpain
| | - María Pilar Angarita‐Díaz
- Instituto de Biología Molecular y Celular de Plantas (UPV‐CSIC)Universidad Politécnica de ValenciaValenciaSpain
| | - Begoña García‐Sogo
- Instituto de Biología Molecular y Celular de Plantas (UPV‐CSIC)Universidad Politécnica de ValenciaValenciaSpain
| | - Teresa Antón
- Instituto de Biología Molecular y Celular de Plantas (UPV‐CSIC)Universidad Politécnica de ValenciaValenciaSpain
| | - Sibilla Sánchez
- Instituto de Biología Molecular y Celular de Plantas (UPV‐CSIC)Universidad Politécnica de ValenciaValenciaSpain
| | - Estela Giménez
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL)Universidad de AlmeríaAlmeríaSpain
| | - Alejandro Atarés
- Instituto de Biología Molecular y Celular de Plantas (UPV‐CSIC)Universidad Politécnica de ValenciaValenciaSpain
| | - Antonia Fernández‐Lozano
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL)Universidad de AlmeríaAlmeríaSpain
| | - Ana Ortíz‐Atienza
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL)Universidad de AlmeríaAlmeríaSpain
| | - Manuel García‐Alcázar
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL)Universidad de AlmeríaAlmeríaSpain
| | - Laura Castañeda
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL)Universidad de AlmeríaAlmeríaSpain
| | - Rocío Fonseca
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL)Universidad de AlmeríaAlmeríaSpain
| | - Carmen Capel
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL)Universidad de AlmeríaAlmeríaSpain
| | - Geraldine Goergen
- Instituto de Biología Molecular y Celular de Plantas (UPV‐CSIC)Universidad Politécnica de ValenciaValenciaSpain
| | - Jorge Sánchez
- Instituto de Biología Molecular y Celular de Plantas (UPV‐CSIC)Universidad Politécnica de ValenciaValenciaSpain
| | - Jorge L. Quispe
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL)Universidad de AlmeríaAlmeríaSpain
| | - Juan Capel
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL)Universidad de AlmeríaAlmeríaSpain
| | - Trinidad Angosto
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL)Universidad de AlmeríaAlmeríaSpain
| | - Vicente Moreno
- Instituto de Biología Molecular y Celular de Plantas (UPV‐CSIC)Universidad Politécnica de ValenciaValenciaSpain
| | - Rafael Lozano
- Centro de Investigación en Biotecnología Agroalimentaria (BITAL)Universidad de AlmeríaAlmeríaSpain
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Fulop D, Ranjan A, Ofner I, Covington MF, Chitwood DH, West D, Ichihashi Y, Headland L, Zamir D, Maloof JN, Sinha NR. A New Advanced Backcross Tomato Population Enables High Resolution Leaf QTL Mapping and Gene Identification. G3 (BETHESDA, MD.) 2016; 6:3169-3184. [PMID: 27510891 PMCID: PMC5068939 DOI: 10.1534/g3.116.030536] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 08/01/2016] [Indexed: 12/23/2022]
Abstract
Quantitative Trait Loci (QTL) mapping is a powerful technique for dissecting the genetic basis of traits and species differences. Established tomato mapping populations between domesticated tomato (Solanum lycopersicum) and its more distant interfertile relatives typically follow a near isogenic line (NIL) design, such as the S. pennellii Introgression Line (IL) population, with a single wild introgression per line in an otherwise domesticated genetic background. Here, we report on a new advanced backcross QTL mapping resource for tomato, derived from a cross between the M82 tomato cultivar and S. pennellii This so-called Backcrossed Inbred Line (BIL) population is comprised of a mix of BC2 and BC3 lines, with domesticated tomato as the recurrent parent. The BIL population is complementary to the existing S. pennellii IL population, with which it shares parents. Using the BILs, we mapped traits for leaf complexity, leaflet shape, and flowering time. We demonstrate the utility of the BILs for fine-mapping QTL, particularly QTL initially mapped in the ILs, by fine-mapping several QTL to single or few candidate genes. Moreover, we confirm the value of a backcrossed population with multiple introgressions per line, such as the BILs, for epistatic QTL mapping. Our work was further enabled by the development of our own statistical inference and visualization tools, namely a heterogeneous hidden Markov model for genotyping the lines, and by using state-of-the-art sparse regression techniques for QTL mapping.
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Affiliation(s)
- Daniel Fulop
- Department of Plant Biology, University of California at Davis, California 95616
| | - Aashish Ranjan
- Department of Plant Biology, University of California at Davis, California 95616
| | - Itai Ofner
- Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Michael F Covington
- Department of Plant Biology, University of California at Davis, California 95616
| | - Daniel H Chitwood
- Department of Plant Biology, University of California at Davis, California 95616
| | - Donelly West
- Department of Plant Biology, University of California at Davis, California 95616
| | - Yasunori Ichihashi
- Department of Plant Biology, University of California at Davis, California 95616
| | - Lauren Headland
- Department of Plant Biology, University of California at Davis, California 95616
| | - Daniel Zamir
- Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Julin N Maloof
- Department of Plant Biology, University of California at Davis, California 95616
| | - Neelima R Sinha
- Department of Plant Biology, University of California at Davis, California 95616
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12
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Ranjan A, Budke JM, Rowland SD, Chitwood DH, Kumar R, Carriedo L, Ichihashi Y, Zumstein K, Maloof JN, Sinha NR. eQTL Regulating Transcript Levels Associated with Diverse Biological Processes in Tomato. PLANT PHYSIOLOGY 2016; 172:328-40. [PMID: 27418589 PMCID: PMC5074602 DOI: 10.1104/pp.16.00289] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 07/11/2016] [Indexed: 05/18/2023]
Abstract
Variation in gene expression, in addition to sequence polymorphisms, is known to influence developmental, physiological, and metabolic traits in plants. Genetic mapping populations have facilitated identification of expression quantitative trait loci (eQTL), the genetic determinants of variation in gene expression patterns. We used an introgression population developed from the wild desert-adapted Solanum pennellii and domesticated tomato (Solanum lycopersicum) to identify the genetic basis of transcript level variation. We established the effect of each introgression on the transcriptome and identified approximately 7,200 eQTL regulating the steady-state transcript levels of 5,300 genes. Barnes-Hut t-distributed stochastic neighbor embedding clustering identified 42 modules revealing novel associations between transcript level patterns and biological processes. The results showed a complex genetic architecture of global transcript abundance pattern in tomato. Several genetic hot spots regulating a large number of transcript level patterns relating to diverse biological processes such as plant defense and photosynthesis were identified. Important eQTL regulating transcript level patterns were related to leaf number and complexity as well as hypocotyl length. Genes associated with leaf development showed an inverse correlation with photosynthetic gene expression, but eQTL regulating genes associated with leaf development and photosynthesis were dispersed across the genome. This comprehensive eQTL analysis details the influence of these loci on plant phenotypes and will be a valuable community resource for investigations on the genetic effects of eQTL on phenotypic traits in tomato.
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Affiliation(s)
- Aashish Ranjan
- Department of Plant Biology, University of California, Davis, California 95616
| | - Jessica M Budke
- Department of Plant Biology, University of California, Davis, California 95616
| | - Steven D Rowland
- Department of Plant Biology, University of California, Davis, California 95616
| | - Daniel H Chitwood
- Department of Plant Biology, University of California, Davis, California 95616
| | - Ravi Kumar
- Department of Plant Biology, University of California, Davis, California 95616
| | - Leonela Carriedo
- Department of Plant Biology, University of California, Davis, California 95616
| | - Yasunori Ichihashi
- Department of Plant Biology, University of California, Davis, California 95616
| | - Kristina Zumstein
- Department of Plant Biology, University of California, Davis, California 95616
| | - Julin N Maloof
- Department of Plant Biology, University of California, Davis, California 95616
| | - Neelima R Sinha
- Department of Plant Biology, University of California, Davis, California 95616
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13
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Li Z, Peng R, Tian Y, Han H, Xu J, Yao Q. Genome-Wide Identification and Analysis of the MYB Transcription Factor Superfamily in Solanum lycopersicum. PLANT & CELL PHYSIOLOGY 2016; 57:1657-77. [PMID: 27279646 DOI: 10.1093/pcp/pcw091] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 04/29/2016] [Indexed: 05/21/2023]
Abstract
MYB proteins constitute one of the largest transcription factor families in the plant kingdom, members of which perform a variety of functions in plant biological processes. However, there are only very limited reports on the characterization of MYB transcription factors in tomato (Solanum lycopersicum). In our study, a total of 127 MYB genes have been identified in the tomato genome. A complete overview of these MYB genes is presented, including the phylogeny, gene structures, protein motifs, chromosome locations and expression patterns. The 127 SlMYB proteins could be classified into 18 subgroups based on domain similarity and phylogenetic topology. Phylogenetic analysis of SlMYBs along with MYBs from Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) indicated 14 subfamilies. Conserved motifs outside the MYB domain may reflect their functional conservation. The identified tomato MYB genes were distributed on 12 chromosomes at various densities but mainly in chromosomes 6 and 10 (12.6% and 11.8%, respectively). Genome-wide segmental and tandem duplications were also found, which may contribute to the expansion of SlMYB genes. RNA-sequencing and microarray data revealed tissue-specific and stress-responsive expression patterns of SlMYB genes. The expression profiles of SlMYB genes in response to salicylic acid (SA) and jasmonic acid methyl ester (MeJA) were also investigated by real-time PCR. Moreover, ethylene-responsive element-binding factor-associated amphiphilic repression (EAR) motifs were found in 24 SlMYB proteins. Collectively, our comprehensive analysis of SlMYB genes will facilitate future functional studies of the tomato MYB gene family and probably other Solanaceae plants.
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Affiliation(s)
- Zhenjun Li
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 2901 Beidi Rd, Shanghai 201106, PR China
| | - Rihe Peng
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 2901 Beidi Rd, Shanghai 201106, PR China
| | - Yongsheng Tian
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 2901 Beidi Rd, Shanghai 201106, PR China
| | - Hongjuan Han
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 2901 Beidi Rd, Shanghai 201106, PR China
| | - Jing Xu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 2901 Beidi Rd, Shanghai 201106, PR China
| | - Quanhong Yao
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 2901 Beidi Rd, Shanghai 201106, PR China
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14
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Campos JF, Cara B, Pérez-Martín F, Pineda B, Egea I, Flores FB, Fernandez-Garcia N, Capel J, Moreno V, Angosto T, Lozano R, Bolarin MC. The tomato mutant ars1 (altered response to salt stress 1) identifies an R1-type MYB transcription factor involved in stomatal closure under salt acclimation. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1345-56. [PMID: 26578112 DOI: 10.1111/pbi.12498] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 09/18/2015] [Accepted: 10/04/2015] [Indexed: 05/09/2023]
Abstract
A screening under salt stress conditions of a T-DNA mutant collection of tomato (Solanum lycopersicum L.) led to the identification of the altered response to salt stress 1 (ars1) mutant, which showed a salt-sensitive phenotype. Genetic analysis of the ars1 mutation revealed that a single T-DNA insertion in the ARS1 gene was responsible of the mutant phenotype. ARS1 coded for an R1-MYB type transcription factor and its expression was induced by salinity in leaves. The mutant reduced fruit yield under salt acclimation while in the absence of stress the disruption of ARS1 did not affect this agronomic trait. The stomatal behaviour of ars1 mutant leaves induced higher Na(+) accumulation via the transpiration stream, as the decreases of stomatal conductance and transpiration rate induced by salt stress were markedly lower in the mutant plants. Moreover, the mutation affected stomatal closure in a response mediated by abscisic acid (ABA). The characterization of tomato transgenic lines silencing and overexpressing ARS1 corroborates the role of the gene in regulating the water loss via transpiration under salinity. Together, our results show that ARS1 tomato gene contributes to reduce transpirational water loss under salt stress. Finally, this gene could be interesting for tomato molecular breeding, because its manipulation could lead to improved stress tolerance without yield penalty under optimal culture conditions.
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Affiliation(s)
- Juan F Campos
- Department of Stress Biology and Plant Pathology, CEBAS-CSIC, Espinardo-Murcia, Spain
| | - Beatriz Cara
- Agro-Food Biotechnology Research Centre (BITAL), University of Almeria, Almería, Spain
| | - Fernando Pérez-Martín
- Agro-Food Biotechnology Research Centre (BITAL), University of Almeria, Almería, Spain
| | - Benito Pineda
- Department of Plant Biotechnology and In Vitro Culture, IBMCP-UPV/CSIC, Valencia, Spain
| | - Isabel Egea
- Department of Stress Biology and Plant Pathology, CEBAS-CSIC, Espinardo-Murcia, Spain
| | - Francisco B Flores
- Department of Stress Biology and Plant Pathology, CEBAS-CSIC, Espinardo-Murcia, Spain
| | | | - Juan Capel
- Agro-Food Biotechnology Research Centre (BITAL), University of Almeria, Almería, Spain
| | - Vicente Moreno
- Department of Plant Biotechnology and In Vitro Culture, IBMCP-UPV/CSIC, Valencia, Spain
| | - Trinidad Angosto
- Agro-Food Biotechnology Research Centre (BITAL), University of Almeria, Almería, Spain
| | - Rafael Lozano
- Agro-Food Biotechnology Research Centre (BITAL), University of Almeria, Almería, Spain
| | - Maria C Bolarin
- Department of Stress Biology and Plant Pathology, CEBAS-CSIC, Espinardo-Murcia, Spain
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15
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Chen S, Wang X, Zhang L, Lin S, Liu D, Wang Q, Cai S, El-Tanbouly R, Gan L, Wu H, Li Y. Identification and characterization of tomato gibberellin 2-oxidases (GA2oxs) and effects of fruit-specific SlGA2ox1 overexpression on fruit and seed growth and development. HORTICULTURE RESEARCH 2016; 3:16059. [PMID: 28018605 PMCID: PMC5142509 DOI: 10.1038/hortres.2016.59] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 10/22/2016] [Accepted: 10/24/2016] [Indexed: 05/05/2023]
Abstract
Gibberellins (GAs) play a crucial role in growth and development of the tomato fruit. Previously published studies focusing on the effect of GAs on tomato fruits used chemical treatments, constitutive overexpression or silencing of GA biosynthetic and catabolic genes globally throughout the plant. Fruit-specific overexpression of GA catabolic enzyme genes GA2-oxidases (GA2oxs), however, may provide an alternative method to study the role of endogenous GAs on the fruit development. In this study, we have identified 11 SlGA2ox proteins in tomato that are classified into three subgroups. Motif analysis and multiple sequence alignments have demonstrated that all SlGA2oxs, except SlGA2ox10, have similar motif compositions and high-sequence conservation. Quantitative reverse transcription-PCR analysis has showed that SlGA2oxs exhibit differential expression patterns in tomato fruits at different developmental stages. When the fruit-specific promoter TFM7 was used to control the expression of SlGA2ox1, we observed no changes in growth and development of vegetative organs. However, fruit weight, seed number and germination rate were significantly affected. We also treated tomato fruits with GA biosynthesis inhibitor and observed phenotypes similar to those of the transgenic fruits. Furthermore, we have demonstrated that expression of cell expansion and GA responsive genes were downregulated in transgenic tomato fruits, supporting that overexpression of the SlGA2ox1 leads to reduction in endogenous GAs. This study provides additional evidence that endogenous GAs and the SlGA2ox1 gene play an important role in controlling on fruit weight, seed development and germination in tomato plant.
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Affiliation(s)
- Shen Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaojing Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Liying Zhang
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Shanshan Lin
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Decai Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Quanzhi Wang
- Jiangsu Polytechnic College of Agriculture and Forestry, Zhenjiang 212400, China
- Jiangsu Engineering and Technology Center for Modern Horticulture, Zhenjiang 212400, China
| | - Shanya Cai
- Jiangsu Polytechnic College of Agriculture and Forestry, Zhenjiang 212400, China
| | - Rania El-Tanbouly
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT 06269, USA
| | - Lijun Gan
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Han Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- ()
| | - Yi Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT 06269, USA
- ()
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16
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Garcia-Abellan JO, Fernandez-Garcia N, Lopez-Berenguer C, Egea I, Flores FB, Angosto T, Capel J, Lozano R, Pineda B, Moreno V, Olmos E, Bolarin MC. The tomato res mutant which accumulates JA in roots in non-stressed conditions restores cell structure alterations under salinity. PHYSIOLOGIA PLANTARUM 2015; 155:296-314. [PMID: 25582191 DOI: 10.1111/ppl.12320] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 12/17/2014] [Accepted: 12/18/2014] [Indexed: 05/21/2023]
Abstract
Jasmonic acid (JA) regulates a wide spectrum of plant biological processes, from plant development to stress defense responses. The role of JA in plant response to salt stress is scarcely known, and even less known is the specific response in root, the main plant organ responsible for ionic uptake and transport to the shoot. Here we report the characterization of the first tomato (Solanum lycopersicum) mutant, named res (restored cell structure by salinity), that accumulates JA in roots prior to exposure to stress. The res tomato mutant presented remarkable growth inhibition and displayed important morphological alterations and cellular disorganization in roots and leaves under control conditions, while these alterations disappeared when the res mutant plants were grown under salt stress. Reciprocal grafting between res and wild type (WT) (tomato cv. Moneymaker) indicated that the main organ responsible for the development of alterations was the root. The JA-signaling pathway is activated in res roots prior to stress, with transcripts levels being even higher in control condition than in salinity. Future studies on this mutant will provide significant advances in the knowledge of JA role in root in salt-stress tolerance response, as well as in the energy trade-off between plant growth and response to stress.
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Affiliation(s)
- José O Garcia-Abellan
- Department of Stress Biology and Plant Pathology, CEBAS-CSIC, P.O. Box 164, 30100, Espinardo-Murcia, Spain
| | - Nieves Fernandez-Garcia
- Department of Stress Biology and Plant Pathology, CEBAS-CSIC, P.O. Box 164, 30100, Espinardo-Murcia, Spain
| | - Carmen Lopez-Berenguer
- Department of Stress Biology and Plant Pathology, CEBAS-CSIC, P.O. Box 164, 30100, Espinardo-Murcia, Spain
| | - Isabel Egea
- Department of Stress Biology and Plant Pathology, CEBAS-CSIC, P.O. Box 164, 30100, Espinardo-Murcia, Spain
| | - Francisco B Flores
- Department of Stress Biology and Plant Pathology, CEBAS-CSIC, P.O. Box 164, 30100, Espinardo-Murcia, Spain
| | - Trinidad Angosto
- Agro-Food Biotechnology Research Centre (BITAL), University of Almería, La Cañada de San Urbano, 04120, Almería, Spain
| | - Juan Capel
- Agro-Food Biotechnology Research Centre (BITAL), University of Almería, La Cañada de San Urbano, 04120, Almería, Spain
| | - Rafael Lozano
- Agro-Food Biotechnology Research Centre (BITAL), University of Almería, La Cañada de San Urbano, 04120, Almería, Spain
| | - Benito Pineda
- Department of Plant Biotechnology and In Vitro Culture, IBMCP-UPV/CSIC, Camino de Vera s/n, 46022, Valencia, Spain
| | - Vicente Moreno
- Department of Plant Biotechnology and In Vitro Culture, IBMCP-UPV/CSIC, Camino de Vera s/n, 46022, Valencia, Spain
| | - Enrique Olmos
- Department of Stress Biology and Plant Pathology, CEBAS-CSIC, P.O. Box 164, 30100, Espinardo-Murcia, Spain
| | - Maria C Bolarin
- Department of Stress Biology and Plant Pathology, CEBAS-CSIC, P.O. Box 164, 30100, Espinardo-Murcia, Spain
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17
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Martínez-Bello L, Moritz T, López-Díaz I. Silencing C19-GA 2-oxidases induces parthenocarpic development and inhibits lateral branching in tomato plants. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:5897-910. [PMID: 26093022 PMCID: PMC4566981 DOI: 10.1093/jxb/erv300] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Gibberellins (GAs) are phytohormones that regulate a wide range of developmental processes in plants. Levels of active GAs are regulated by biosynthetic and catabolic enzymes like the GA 2-oxidases (GA2oxs). In tomato (Solanum lycopersicum L.) C19 GA2oxs are encoded by a small multigenic family of five members with some degree of redundancy. In order to investigate their roles in tomato, the silencing of all five genes in transgenic plants was induced. A significant increase in active GA4 content was found in the ovaries of transgenic plants. In addition, the transgenic unfertilized ovaries were much bigger than wild-type ovaries (about 30 times) and a certain proportion (5-37%) were able to develop parthenocarpically. Among the GA2ox family, genes GA2ox1 and -2 seem to be the most relevant for this phenotype since their expression was induced in unfertilized ovaries and repressed in developing fruits, inversely correlating with ovary growth. Interestingly, transgenic lines exhibited a significant inhibition of branching and a higher content of active GA4 in axillary buds. This phenotype was reverted, in transgenic plants, by the application of paclobutrazol, a GA biosynthesis inhibitor, suggesting a role for GAs as repressors of branching. In summary, this work demonstrates that GA 2-oxidases regulate gibberellin levels in ovaries and axillary buds of tomato plants and their silencing is responsible for parthenocarpic fruit growth and branching inhibition.
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Affiliation(s)
- Liliam Martínez-Bello
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia (UPV)-Consejo Superior de Investigaciones Científicas (CSIC), Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
| | - Thomas Moritz
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Science, S-90183 Umeå, Sweden
| | - Isabel López-Díaz
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia (UPV)-Consejo Superior de Investigaciones Científicas (CSIC), Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
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18
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Dardelle F, Le Mauff F, Lehner A, Loutelier-Bourhis C, Bardor M, Rihouey C, Causse M, Lerouge P, Driouich A, Mollet JC. Pollen tube cell walls of wild and domesticated tomatoes contain arabinosylated and fucosylated xyloglucan. ANNALS OF BOTANY 2015; 115:55-66. [PMID: 25434027 PMCID: PMC4284112 DOI: 10.1093/aob/mcu218] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 09/22/2014] [Accepted: 09/23/2014] [Indexed: 05/24/2023]
Abstract
BACKGROUND AND AIMS In flowering plants, fertilization relies on the delivery of the sperm cells carried by the pollen tube to the ovule. During the tip growth of the pollen tube, proper assembly of the cell wall polymers is required to maintain the mechanical properties of the cell wall. Xyloglucan (XyG) is a cell wall polymer known for maintaining the wall integrity and thus allowing cell expansion. In most angiosperms, the XyG of somatic cells is fucosylated, except in the Asterid clade (including the Solanaceae), where the fucosyl residues are replaced by arabinose, presumably due to an adaptive and/or selective diversification. However, it has been shown recently that XyG of Nicotiana alata pollen tubes is mostly fucosylated. The objective of the present work was to determine whether such structural differences between somatic and gametophytic cells are a common feature of Nicotiana and Solanum (more precisely tomato) genera. METHODS XyGs of pollen tubes of domesticated (Solanum lycopersicum var. cerasiforme and var. Saint-Pierre) and wild (S. pimpinellifolium and S. peruvianum) tomatoes and tobacco (Nicotiana tabacum) were analysed by immunolabelling, oligosaccharide mass profiling and GC-MS analyses. KEY RESULTS Pollen tubes from all the species were labelled with the mAb CCRC-M1, a monoclonal antibody that recognizes epitopes associated with fucosylated XyG motifs. Analyses of the cell wall did not highlight major structural differences between previously studied N. alata and N. tabacum XyG. In contrast, XyG of tomato pollen tubes contained fucosylated and arabinosylated motifs. The highest levels of fucosylated XyG were found in pollen tubes from the wild species. CONCLUSIONS The results clearly indicate that the male gametophyte (pollen tube) and the sporophyte have structurally different XyG. This suggests that fucosylated XyG may have an important role in the tip growth of pollen tubes, and that they must have a specific set of functional XyG fucosyltransferases, which are yet to be characterized.
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Affiliation(s)
- Flavien Dardelle
- Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale (Glyco-MEV), EA 4358, Normandy University, IRIB, VASI, 76821 Mont-Saint-Aignan Cedex, France, COBRA, UMR6014 and FR3038, Normandy University, INSA Rouen, CNRS, IRCOF, 76821 Mont-Saint-Aignan Cedex, France, Laboratoire Polymères, Biopolymères, Surfaces, UMR CNRS 6270, Normandy University, 76821 Mont-Saint-Aignan Cedex, France and Génétique et Amélioration des Fruits et Légumes, INRA UR1052, 84143 Montfavet Cedex, France
| | - François Le Mauff
- Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale (Glyco-MEV), EA 4358, Normandy University, IRIB, VASI, 76821 Mont-Saint-Aignan Cedex, France, COBRA, UMR6014 and FR3038, Normandy University, INSA Rouen, CNRS, IRCOF, 76821 Mont-Saint-Aignan Cedex, France, Laboratoire Polymères, Biopolymères, Surfaces, UMR CNRS 6270, Normandy University, 76821 Mont-Saint-Aignan Cedex, France and Génétique et Amélioration des Fruits et Légumes, INRA UR1052, 84143 Montfavet Cedex, France
| | - Arnaud Lehner
- Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale (Glyco-MEV), EA 4358, Normandy University, IRIB, VASI, 76821 Mont-Saint-Aignan Cedex, France, COBRA, UMR6014 and FR3038, Normandy University, INSA Rouen, CNRS, IRCOF, 76821 Mont-Saint-Aignan Cedex, France, Laboratoire Polymères, Biopolymères, Surfaces, UMR CNRS 6270, Normandy University, 76821 Mont-Saint-Aignan Cedex, France and Génétique et Amélioration des Fruits et Légumes, INRA UR1052, 84143 Montfavet Cedex, France
| | - Corinne Loutelier-Bourhis
- Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale (Glyco-MEV), EA 4358, Normandy University, IRIB, VASI, 76821 Mont-Saint-Aignan Cedex, France, COBRA, UMR6014 and FR3038, Normandy University, INSA Rouen, CNRS, IRCOF, 76821 Mont-Saint-Aignan Cedex, France, Laboratoire Polymères, Biopolymères, Surfaces, UMR CNRS 6270, Normandy University, 76821 Mont-Saint-Aignan Cedex, France and Génétique et Amélioration des Fruits et Légumes, INRA UR1052, 84143 Montfavet Cedex, France
| | - Muriel Bardor
- Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale (Glyco-MEV), EA 4358, Normandy University, IRIB, VASI, 76821 Mont-Saint-Aignan Cedex, France, COBRA, UMR6014 and FR3038, Normandy University, INSA Rouen, CNRS, IRCOF, 76821 Mont-Saint-Aignan Cedex, France, Laboratoire Polymères, Biopolymères, Surfaces, UMR CNRS 6270, Normandy University, 76821 Mont-Saint-Aignan Cedex, France and Génétique et Amélioration des Fruits et Légumes, INRA UR1052, 84143 Montfavet Cedex, France
| | - Christophe Rihouey
- Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale (Glyco-MEV), EA 4358, Normandy University, IRIB, VASI, 76821 Mont-Saint-Aignan Cedex, France, COBRA, UMR6014 and FR3038, Normandy University, INSA Rouen, CNRS, IRCOF, 76821 Mont-Saint-Aignan Cedex, France, Laboratoire Polymères, Biopolymères, Surfaces, UMR CNRS 6270, Normandy University, 76821 Mont-Saint-Aignan Cedex, France and Génétique et Amélioration des Fruits et Légumes, INRA UR1052, 84143 Montfavet Cedex, France
| | - Mathilde Causse
- Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale (Glyco-MEV), EA 4358, Normandy University, IRIB, VASI, 76821 Mont-Saint-Aignan Cedex, France, COBRA, UMR6014 and FR3038, Normandy University, INSA Rouen, CNRS, IRCOF, 76821 Mont-Saint-Aignan Cedex, France, Laboratoire Polymères, Biopolymères, Surfaces, UMR CNRS 6270, Normandy University, 76821 Mont-Saint-Aignan Cedex, France and Génétique et Amélioration des Fruits et Légumes, INRA UR1052, 84143 Montfavet Cedex, France
| | - Patrice Lerouge
- Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale (Glyco-MEV), EA 4358, Normandy University, IRIB, VASI, 76821 Mont-Saint-Aignan Cedex, France, COBRA, UMR6014 and FR3038, Normandy University, INSA Rouen, CNRS, IRCOF, 76821 Mont-Saint-Aignan Cedex, France, Laboratoire Polymères, Biopolymères, Surfaces, UMR CNRS 6270, Normandy University, 76821 Mont-Saint-Aignan Cedex, France and Génétique et Amélioration des Fruits et Légumes, INRA UR1052, 84143 Montfavet Cedex, France
| | - Azeddine Driouich
- Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale (Glyco-MEV), EA 4358, Normandy University, IRIB, VASI, 76821 Mont-Saint-Aignan Cedex, France, COBRA, UMR6014 and FR3038, Normandy University, INSA Rouen, CNRS, IRCOF, 76821 Mont-Saint-Aignan Cedex, France, Laboratoire Polymères, Biopolymères, Surfaces, UMR CNRS 6270, Normandy University, 76821 Mont-Saint-Aignan Cedex, France and Génétique et Amélioration des Fruits et Légumes, INRA UR1052, 84143 Montfavet Cedex, France
| | - Jean-Claude Mollet
- Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale (Glyco-MEV), EA 4358, Normandy University, IRIB, VASI, 76821 Mont-Saint-Aignan Cedex, France, COBRA, UMR6014 and FR3038, Normandy University, INSA Rouen, CNRS, IRCOF, 76821 Mont-Saint-Aignan Cedex, France, Laboratoire Polymères, Biopolymères, Surfaces, UMR CNRS 6270, Normandy University, 76821 Mont-Saint-Aignan Cedex, France and Génétique et Amélioration des Fruits et Légumes, INRA UR1052, 84143 Montfavet Cedex, France
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Bauchet G, Munos S, Sauvage C, Bonnet J, Grivet L, Causse M. Genes involved in floral meristem in tomato exhibit drastically reduced genetic diversity and signature of selection. BMC PLANT BIOLOGY 2014; 14:279. [PMID: 25325924 PMCID: PMC4210547 DOI: 10.1186/s12870-014-0279-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 10/06/2014] [Indexed: 05/12/2023]
Abstract
BACKGROUND Domestication and selection of crops have notably reshaped fruit morphology. With its large phenotypic diversity, tomato (Solanum lycopersicum) illustrates this evolutive trend. Genes involved in flower meristem development are known to regulate also fruit morphology. To decipher the genetic variation underlying tomato fruit morphology, we assessed the nucleotide diversity and selection footprints of candidate genes involved in flower and fruit development and performed genome-wide association studies. RESULTS Thirty candidate genes were selected according to their similarity with genes involved in meristem development or their known causal function in Arabidopsis thaliana. In tomato, these genes and flanking regions were sequenced in a core collection of 96 accessions (including cultivated, cherry-type and wild relative accessions) maximizing the molecular diversity, using the Roche 454 technology. A total amount of 17 Mb was sequenced allowing the discovery of 6,106 single nucleotide polymorphisms (SNPs). The annotation of the 30 gene regions identified 231 exons carrying 517 SNPs. Subsequently, the nucleotide diversity (π) and the neutral evolution of each region were compared against genome-wide values within the collection, using a SNP array carrying 7,667 SNPs mainly distributed in coding sequences.About half of the genes revealed footprints of selection and polymorphisms putatively involved in fruit size variation by showing negative Tajima's D and nucleotide diversity reduction in cultivated tomato compared to its wild relative. Among the candidates, FW2.2 and BAM1 sequences revealed selection footprints within their promoter regions suggesting their potential involvement in their regulation. Two associations co-localized with previously identified loci: LC (locule number) and Ovate (fruit shape). CONCLUSION Compared to whole genome genotypic data, a drastic reduction of nucleotide diversity was shown for several candidate genes. Strong selection patterns were identified in 15 candidates highlighting the critical role of meristem maintenance genes as well as the impact of domestication on candidates. The study highlighted a set of polymorphisms putatively important in the evolution of these genes.
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Affiliation(s)
- Guillaume Bauchet
- />INRA, UR1052, Génétique et Amélioration des Fruits et Légumes (GAFL), 67 Allée des Chênes Domaine Saint Maurice – CS60094, 84143 Montfavet Cedex, France
- />Syngenta Seeds, 12 chemin de l’Hobit, 31790 Saint Sauveur, France
| | - Stéphane Munos
- />INRA, UR1052, Génétique et Amélioration des Fruits et Légumes (GAFL), 67 Allée des Chênes Domaine Saint Maurice – CS60094, 84143 Montfavet Cedex, France
- />Present address: INRA, UMR CNRS-INRA 441-2594, 24 Chemin de Borde Rouge – Auzeville - CS 52627, 31326 Castanet Tolosan Cedex, France
| | - Christopher Sauvage
- />INRA, UR1052, Génétique et Amélioration des Fruits et Légumes (GAFL), 67 Allée des Chênes Domaine Saint Maurice – CS60094, 84143 Montfavet Cedex, France
| | - Julien Bonnet
- />Syngenta Seeds, 12 chemin de l’Hobit, 31790 Saint Sauveur, France
| | - Laurent Grivet
- />Syngenta Seeds, 12 chemin de l’Hobit, 31790 Saint Sauveur, France
| | - Mathilde Causse
- />INRA, UR1052, Génétique et Amélioration des Fruits et Légumes (GAFL), 67 Allée des Chênes Domaine Saint Maurice – CS60094, 84143 Montfavet Cedex, France
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Ichihashi Y, Sinha NR. From genome to phenome and back in tomato. CURRENT OPINION IN PLANT BIOLOGY 2014; 18:9-15. [PMID: 24440917 DOI: 10.1016/j.pbi.2013.12.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 12/03/2013] [Accepted: 12/20/2013] [Indexed: 05/05/2023]
Abstract
The tomato is an ideal plant species for genomic and evolutionary studies. Thanks to recent technical advances, a plethora of information relating to tomato genomics has been generated. In addition, various phenotypes related to morphology, physiology and yield have been investigated in tomato and its wild relatives. In this review, we summarize recent key findings in tomato genomics that used both developmental and evolutionary approaches to link the genome to phenome. Combined, these perspectives allow us to look at the trends in tomato evolution in addition to providing insight into the future direction of research that can utilize this unique model species.
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Affiliation(s)
- Yasunori Ichihashi
- Department of Plant Biology, University of California Davis, Davis, CA 95616, USA; Center for Sustainable Resource Science, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | - Neelima R Sinha
- Department of Plant Biology, University of California Davis, Davis, CA 95616, USA.
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Iquebal MA, S, Arora V, Verma N, Rai A, Kumar D. First whole genome based microsatellite DNA marker database of tomato for mapping and variety identification. BMC PLANT BIOLOGY 2013; 13:197. [PMCID: PMC3881501 DOI: 10.1186/1471-2229-13-197] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 11/26/2013] [Indexed: 05/29/2023]
Abstract
Background The cultivated tomato is second most consumed vegetable of the world and is an important part of a diverse and balanced diet as a rich source of vitamins, minerals, phenolic antioxidants and antioxidant lycopene having anti-cancer properties. To reap benefit of genomics of the domestic tomato (Solanum lycopersicum L.) unravelled by Tomato Genome Consortium (The Tomato Genome Consortium, 2012), the bulk mining of its markers in totality is imperative and critically required. The solgenomics has limited number of microsatellite DNA markers (2867) pertaining to solanaceae family. As these markers are of linkage map having relative distance, the choice of selected markers based on absolute distance as of physical map is missing. Only limited microsatellite markers with limitations are reported for variety identification thus there is a need for more markers supplementing DUS test and also for traceability of product in global market. Description We present here the first whole genome based microsatellite DNA marker database of tomato, TomSatDB (Tomato MicroSatellite Database) with more than 1.4 million markers mined in-silico, using MIcroSAtellite (MISA) tool. To cater the customized needs of wet lab, features with a novelty of an automated primer designing tool is added. TomSatDB (http://cabindb.iasri.res.in/tomsatdb), a user-friendly and freely accessible tool offers chromosome wise as well as location wise search of primers. It is an online relational database based on “three-tier architecture” that catalogues information of microsatellites in MySQL and user-friendly interface developed using PHP (Hypertext Pre Processor). Conclusion Besides abiotic stress, tomato is known to have biotic stress due to its susceptibility over 200 diseases caused by pathogenic fungi, bacteria, viruses and nematodes. These markers are expected to pave the way of germplasm management over abiotic and biotic stress as well as improvement through molecular breeding, leading to increased tomato productivity in India as well as other parts of the world. In era of IPR the new variety can be identified based on allelic variation among varieties supplementing DUS test and product traceability.
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Affiliation(s)
- Mir A Iquebal
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, Library Avenue, New Delhi 110012, India
| | - Sarika
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, Library Avenue, New Delhi 110012, India
| | - Vasu Arora
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, Library Avenue, New Delhi 110012, India
| | - Nidhi Verma
- Germplasm Exchange Unit, National Bureau of Plant Genetic Resources (NBPGR), New Delhi 110012, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, Library Avenue, New Delhi 110012, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, Library Avenue, New Delhi 110012, India
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Chitwood DH, Kumar R, Headland LR, Ranjan A, Covington MF, Ichihashi Y, Fulop D, Jiménez-Gómez JM, Peng J, Maloof JN, Sinha NR. A quantitative genetic basis for leaf morphology in a set of precisely defined tomato introgression lines. THE PLANT CELL 2013; 25:2465-81. [PMID: 23872539 PMCID: PMC3753377 DOI: 10.1105/tpc.113.112391] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 05/27/2013] [Accepted: 07/05/2013] [Indexed: 05/18/2023]
Abstract
Introgression lines (ILs), in which genetic material from wild tomato species is introgressed into a domesticated background, have been used extensively in tomato (Solanum lycopersicum) improvement. Here, we genotype an IL population derived from the wild desert tomato Solanum pennellii at ultrahigh density, providing the exact gene content harbored by each line. To take advantage of this information, we determine IL phenotypes for a suite of vegetative traits, ranging from leaf complexity, shape, and size to cellular traits, such as stomatal density and epidermal cell phenotypes. Elliptical Fourier descriptors on leaflet outlines provide a global analysis of highly heritable, intricate aspects of leaf morphology. We also demonstrate constraints between leaflet size and leaf complexity, pavement cell size, and stomatal density and show independent segregation of traits previously assumed to be genetically coregulated. Meta-analysis of previously measured traits in the ILs shows an unexpected relationship between leaf morphology and fruit sugar levels, which RNA-Seq data suggest may be attributable to genetically coregulated changes in fruit morphology or the impact of leaf shape on photosynthesis. Together, our results both improve upon the utility of an important genetic resource and attest to a complex, genetic basis for differences in leaf morphology between natural populations.
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Affiliation(s)
- Daniel H. Chitwood
- Department of Plant Biology, University of California, Davis, California 95616
| | - Ravi Kumar
- Department of Plant Biology, University of California, Davis, California 95616
| | - Lauren R. Headland
- Department of Plant Biology, University of California, Davis, California 95616
| | - Aashish Ranjan
- Department of Plant Biology, University of California, Davis, California 95616
| | | | - Yasunori Ichihashi
- Department of Plant Biology, University of California, Davis, California 95616
| | - Daniel Fulop
- Department of Plant Biology, University of California, Davis, California 95616
| | | | - Jie Peng
- Department of Statistics, University of California, Davis, California 95616
| | - Julin N. Maloof
- Department of Plant Biology, University of California, Davis, California 95616
| | - Neelima R. Sinha
- Department of Plant Biology, University of California, Davis, California 95616
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Motamayor JC, Mockaitis K, Schmutz J, Haiminen N, III DL, Cornejo O, Findley SD, Zheng P, Utro F, Royaert S, Saski C, Jenkins J, Podicheti R, Zhao M, Scheffler BE, Stack JC, Feltus FA, Mustiga GM, Amores F, Phillips W, Marelli JP, May GD, Shapiro H, Ma J, Bustamante CD, Schnell RJ, Main D, Gilbert D, Parida L, Kuhn DN. The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color. Genome Biol 2013; 14:r53. [PMID: 23731509 PMCID: PMC4053823 DOI: 10.1186/gb-2013-14-6-r53] [Citation(s) in RCA: 154] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 04/09/2013] [Accepted: 06/03/2013] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Theobroma cacao L. cultivar Matina 1-6 belongs to the most cultivated cacao type. The availability of its genome sequence and methods for identifying genes responsible for important cacao traits will aid cacao researchers and breeders. RESULTS We describe the sequencing and assembly of the genome of Theobroma cacao L. cultivar Matina 1-6. The genome of the Matina 1-6 cultivar is 445 Mbp, which is significantly larger than a sequenced Criollo cultivar, and more typical of other cultivars. The chromosome-scale assembly, version 1.1, contains 711 scaffolds covering 346.0 Mbp, with a contig N50 of 84.4 kbp, a scaffold N50 of 34.4 Mbp, and an evidence-based gene set of 29,408 loci. Version 1.1 has 10x the scaffold N50 and 4x the contig N50 as Criollo, and includes 111 Mb more anchored sequence. The version 1.1 assembly has 4.4% gap sequence, while Criollo has 10.9%. Through a combination of haplotype, association mapping and gene expression analyses, we leverage this robust reference genome to identify a promising candidate gene responsible for pod color variation. We demonstrate that green/red pod color in cacao is likely regulated by the R2R3 MYB transcription factor TcMYB113, homologs of which determine pigmentation in Rosaceae, Solanaceae, and Brassicaceae. One SNP within the target site for a highly conserved trans-acting siRNA in dicots, found within TcMYB113, seems to affect transcript levels of this gene and therefore pod color variation. CONCLUSIONS We report a high-quality sequence and annotation of Theobroma cacao L. and demonstrate its utility in identifying candidate genes regulating traits.
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Affiliation(s)
| | - Keithanne Mockaitis
- Department of Biology, and Center for Genomics and Bioinformatics, Indiana University, 915 E. Third St, Bloomington, IN, 47405, USA
| | - Jeremy Schmutz
- Mars, Incorporated, 6885 Elm Street, McLean, VA, 22101, USA
- HudsonAlpha Institute for Biotechnology, 601 Genome Way NW, Huntsville, AL, 35806, USA
| | - Niina Haiminen
- IBM T J Watson Research, Yorktown Heights, NY, 10598, USA
| | - Donald Livingstone III
- Mars, Incorporated, 6885 Elm Street, McLean, VA, 22101, USA
- United States Department of Agriculture-Agriculture Research Service, Subtropical Horticulture Research Station, 13601 Old Cutler Rd, Miami, FL, 33158, USA
| | - Omar Cornejo
- Department of Genetics, Stanford University, 300 Pasteur Dr, Stanford, CA, 94305, USA
| | - Seth D Findley
- Mars, Incorporated, 6885 Elm Street, McLean, VA, 22101, USA
| | - Ping Zheng
- Department of Horticulture, Washington State University, Johnson Hall, Pullman, WA, 99164, USA
| | - Filippo Utro
- IBM T J Watson Research, Yorktown Heights, NY, 10598, USA
| | - Stefan Royaert
- United States Department of Agriculture-Agriculture Research Service, Subtropical Horticulture Research Station, 13601 Old Cutler Rd, Miami, FL, 33158, USA
| | - Christopher Saski
- Clemson University Genomics Institute, 105 Collings Street, Clemson, SC, 29634, USA
| | - Jerry Jenkins
- Mars, Incorporated, 6885 Elm Street, McLean, VA, 22101, USA
- HudsonAlpha Institute for Biotechnology, 601 Genome Way NW, Huntsville, AL, 35806, USA
| | - Ram Podicheti
- Center for Genomics and Bioinformatics and School of Informatics and Computing, Indiana University, 919 E 10th St, Bloomington, IN, 47408, USA
| | - Meixia Zhao
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Brian E Scheffler
- United States Department of Agriculture-Agriculture Research Service, Genomics and Bioinformatics Research Unit, 141 Experiment Station Road, Stoneville, MS, 38776, USA
| | - Joseph C Stack
- Mars, Incorporated, 6885 Elm Street, McLean, VA, 22101, USA
| | - Frank A Feltus
- Clemson University Genomics Institute, 105 Collings Street, Clemson, SC, 29634, USA
| | | | - Freddy Amores
- Estación Experimental Tropical Pichilingue, Instituto Nacional Autónomo de Investigaciones Agropecuarias (INIAP), Código Postal 24, Km 5 vía Quevedo - El Empalme, Quevedo, Ecuador
| | - Wilbert Phillips
- Programa de Mejoramiento de Cacao, CATIE 7170, Turrialba, Costa Rica
| | | | - Gregory D May
- National Center for Genome Resources, 2935 Rodeo Park Drive E, Santa Fe, NM, 87505, USA
| | - Howard Shapiro
- Mars, Incorporated, 6885 Elm Street, McLean, VA, 22101, USA
| | - Jianxin Ma
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Carlos D Bustamante
- Department of Genetics, Stanford University, 300 Pasteur Dr, Stanford, CA, 94305, USA
| | - Raymond J Schnell
- Mars, Incorporated, 6885 Elm Street, McLean, VA, 22101, USA
- United States Department of Agriculture-Agriculture Research Service, Subtropical Horticulture Research Station, 13601 Old Cutler Rd, Miami, FL, 33158, USA
| | - Dorrie Main
- Department of Horticulture, Washington State University, Johnson Hall, Pullman, WA, 99164, USA
| | - Don Gilbert
- Department of Biology, and Center for Genomics and Bioinformatics, Indiana University, 915 E. Third St, Bloomington, IN, 47405, USA
| | - Laxmi Parida
- IBM T J Watson Research, Yorktown Heights, NY, 10598, USA
| | - David N Kuhn
- United States Department of Agriculture-Agriculture Research Service, Subtropical Horticulture Research Station, 13601 Old Cutler Rd, Miami, FL, 33158, USA
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