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Tagiakas RI, Avdikos ID, Goula A, Koutis K, Nianiou-Obeidat I, Mavromatis AG. Characterization and evaluation of Greek tomato landraces for productivity and fruit quality traits related to sustainable low-input farming systems. FRONTIERS IN PLANT SCIENCE 2022; 13:994530. [PMID: 36578333 PMCID: PMC9791058 DOI: 10.3389/fpls.2022.994530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Tomato is one of the most important horticultural species all over the world, having high level of consumption and employing many people, both in the primary sector (farmers) and in the secondary sector (traders, seed companies and processors). Nowadays, the use of commercial tomato F1 hybrids tends to prevail because of high yield potential and homogeneity of fruits which are often characterized by lack of quality and sensory characteristics. In contrast, tomato landraces have outstanding quality traits, such as high concentration of antioxidants and organoleptic compounds, as well as often include desirable genes in their genome for adaptability, plasticity, response to low-input conditions, and high fruit nutritional value. Thus, they are appropriate material in the use of sustainable agricultural management systems or as gene donors for the development of new type of tomato cultivars suitable for low-input farming systems. The present experimental study refers to 22 Greek tomato landraces and two commercial cultivars (cv. Macedonia and the F1 hybrid Formula) used as controls, which were characterized by phenotypical markers and evaluated under low-input sustainable farming conditions. Specifically, during this research, measurements were taken regarding yield potential (early production, number of fruits per plant, fruit weight, total yield) and fruit quality traits, such as physicochemical characteristics (pH, acidity, and soluble solid components - Brixο) also according to nutritional value (content of ascorbic acid, lycopene, total carotenoids, and total phenolics) of tomato fruits. In the most promising landraces (cv. Milo Chalkidiki, cv. Eratiras, cv. Lotos, cv. Aspros lotos, cv. Pantaroza, cv. Karabola and cv. Kardia Vodiou), having comparable yield and fruit quality traits with commercial cultivars, intrapopulation "Pure line selection" method, under low-input farming conditions was applied for two years. Following this approach, we succeed to determine the level of yield potential and provide information for the nutritive value and utilization of typical tomato landraces, improving their yield and fruit quality traits, following a mild intrapopulation selection under low-input farming conditions. This data pipeline is expected to be of interest for organic farmers and processors of high nutritive tomato products, with low carbon footprint for the environment.
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Affiliation(s)
- R. I. Tagiakas
- Aristotle University, Lab of Genetics and Plant Breeding, School of Agriculture, Thessaloniki, Greece
| | - I. D. Avdikos
- International Hellenic University, Lab of Horticulture, Thessaloniki, Greece
| | - A. Goula
- Aristotle University, Lab of Food Engineering and Processing, School of Agriculture, Thessaloniki, Greece
| | - K. Koutis
- Aegilops, Network for Biodiversity, Volos, Greece
| | - Irini Nianiou-Obeidat
- Aristotle University, Lab of Genetics and Plant Breeding, School of Agriculture, Thessaloniki, Greece
| | - A. G. Mavromatis
- Aristotle University, Lab of Genetics and Plant Breeding, School of Agriculture, Thessaloniki, Greece
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Pons C, Casals J, Palombieri S, Fontanet L, Riccini A, Rambla JL, Ruggiero A, Figás MDR, Plazas M, Koukounaras A, Picarella ME, Sulli M, Fisher J, Ziarsolo P, Blanca J, Cañizares J, Cammareri M, Vitiello A, Batelli G, Kanellis A, Brouwer M, Finkers R, Nikoloudis K, Soler S, Giuliano G, Grillo S, Grandillo S, Zamir D, Mazzucato A, Causse M, Díez MJ, Prohens J, Monforte AJ, Granell A. Atlas of phenotypic, genotypic and geographical diversity present in the European traditional tomato. HORTICULTURE RESEARCH 2022; 9:uhac112. [PMID: 35795386 PMCID: PMC9252105 DOI: 10.1093/hr/uhac112] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
The Mediterranean basin countries are considered secondary centres of tomato diversification. However, information on phenotypic and allelic variation of local tomato materials is still limited. Here we report on the evaluation of the largest traditional tomato collection, which includes 1499 accessions from Southern Europe. Analyses of 70 traits revealed a broad range of phenotypic variability with different distributions among countries, with the culinary end use within each country being the main driver of tomato diversification. Furthermore, eight main tomato types (phenoclusters) were defined by integrating phenotypic data, country of origin, and end use. Genome-wide association study (GWAS) meta-analyses identified associations in 211 loci, 159 of which were novel. The multidimensional integration of phenoclusters and the GWAS meta-analysis identified the molecular signatures for each traditional tomato type and indicated that signatures originated from differential combinations of loci, which in some cases converged in the same tomato phenotype. Our results provide a roadmap for studying and exploiting this untapped tomato diversity.
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Affiliation(s)
- Clara Pons
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, València, Spain
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, València, Spain
| | - Joan Casals
- Department of Agri-Food Engineering and Biotechnology/Miquel Agustí Foundation, Universitat Politècnica de Catalunya, Campus Baix Llobregat, Esteve Terrades 8, 08860 Castelldefels, Spain
| | - Samuela Palombieri
- Institute of Biosciences and BioResources (IBBR), National Research Council of Italy (CNR), Via Università 133, 80055 Portici, Italy
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, 01100 Viterbo, Italy
| | - Lilian Fontanet
- INRAE, UR1052, Génétique et Amélioration des Fruits et Légumes 67 Allé des Chênes, Centre de Recherche PACA, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
- HM Clause, Portes-lès-Valence, France
| | - Alessandro Riccini
- Department of Agriculture and Forest Sciences (DAFNE), Università degli Studi della Tuscia, Viterbo,Italy
| | - Jose Luis Rambla
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, València, Spain
| | - Alessandra Ruggiero
- Institute of Biosciences and BioResources (IBBR), National Research Council of Italy (CNR), Via Università 133, 80055 Portici, Italy
| | - Maria del Rosario Figás
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, València, Spain
| | - Mariola Plazas
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, València, Spain
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, València, Spain
| | - Athanasios Koukounaras
- Aristotle University of Thessaloniki, School of Agriculture, Laboratory of Vegetable Crops, Thessaloniki, 54124 Greece
| | - Maurizio E Picarella
- Department of Agriculture and Forest Sciences (DAFNE), Università degli Studi della Tuscia, Viterbo,Italy
| | - Maria Sulli
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Casaccia Research Centre, Rome, Italy
| | - Josef Fisher
- Hebrew University of Jerusalem, Robert H Smith Inst Plant Sci & Genet Agr, Rehovot, Israel
| | - Peio Ziarsolo
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, València, Spain
| | - Jose Blanca
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, València, Spain
| | - Joaquin Cañizares
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, València, Spain
| | - Maria Cammareri
- Institute of Biosciences and BioResources (IBBR), National Research Council of Italy (CNR), Via Università 133, 80055 Portici, Italy
| | - Antonella Vitiello
- Institute of Biosciences and BioResources (IBBR), National Research Council of Italy (CNR), Via Università 133, 80055 Portici, Italy
| | - Giorgia Batelli
- Institute of Biosciences and BioResources (IBBR), National Research Council of Italy (CNR), Via Università 133, 80055 Portici, Italy
| | - Angelos Kanellis
- Group of Biotechnology of Pharmaceutical Plants, Laboratory of Pharmacognosy, Department of Pharmaceutical Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Matthijs Brouwer
- Wageningen Univ & Res, Plant Breeding, POB 386, NL-6700 AJ Wageningen, Netherlands
| | - Richard Finkers
- Wageningen Univ & Res, Plant Breeding, POB 386, NL-6700 AJ Wageningen, Netherlands
| | | | - Salvador Soler
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, València, Spain
| | - Giovanni Giuliano
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Casaccia Research Centre, Rome, Italy
| | - Stephania Grillo
- Institute of Biosciences and BioResources (IBBR), National Research Council of Italy (CNR), Via Università 133, 80055 Portici, Italy
| | - Silvana Grandillo
- Institute of Biosciences and BioResources (IBBR), National Research Council of Italy (CNR), Via Università 133, 80055 Portici, Italy
| | - Dani Zamir
- Hebrew University of Jerusalem, Robert H Smith Inst Plant Sci & Genet Agr, Rehovot, Israel
| | - Andrea Mazzucato
- Department of Agriculture and Forest Sciences (DAFNE), Università degli Studi della Tuscia, Viterbo,Italy
| | - Mathilde Causse
- INRAE, UR1052, Génétique et Amélioration des Fruits et Légumes 67 Allé des Chênes, Centre de Recherche PACA, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
| | - Maria José Díez
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, València, Spain
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, València, Spain
| | - Antonio Jose Monforte
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, València, Spain
| | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, València, Spain
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Thole V, Vain P, Martin C. Effect of Elevated Temperature on Tomato Post-Harvest Properties. PLANTS 2021; 10:plants10112359. [PMID: 34834722 PMCID: PMC8623658 DOI: 10.3390/plants10112359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 10/22/2021] [Accepted: 10/27/2021] [Indexed: 11/16/2022]
Abstract
The fleshy fruit of tomato (Solanum lycopersicum) is a commodity used worldwide as a fresh or processed product. Like many crops, tomato plants and harvested fruits are susceptible to the onset of climate change. Temperature plays a key role in tomato fruit production and ripening, including softening, development of fruit colour, flavour and aroma. The combination of climate change and the drive to reduce carbon emission and energy consumption is likely to affect tomato post-harvest storage conditions. In this study, we investigated the effect of an elevated storage temperature on tomato shelf life and fungal susceptibility. A collection of 41 genotypes with low and high field performance at elevated temperature, including different growth, fruit and market types, was used to assess post-harvest performances. A temperature increase from 18–20 °C to 26 °C reduced average shelf life of fruit by 4 days ± 1 day and increased fungal susceptibility by 11% ± 5% across all genotypes. We identified tomato varieties that exhibit both favourable post-harvest fruit quality and high field performance at elevated temperature. This work contributes to efforts to enhance crop resilience by selecting for thermotolerance combined with traits suitable to maintain and improve fruit quality, shelf life and pathogen susceptibility under changing climate conditions.
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Tamburino R, Sannino L, Cafasso D, Cantarella C, Orrù L, Cardi T, Cozzolino S, D’Agostino N, Scotti N. Cultivated Tomato ( Solanum lycopersicum L.) Suffered a Severe Cytoplasmic Bottleneck during Domestication: Implications from Chloroplast Genomes. PLANTS 2020; 9:plants9111443. [PMID: 33114641 PMCID: PMC7692331 DOI: 10.3390/plants9111443] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 12/13/2022]
Abstract
In various crops, genetic bottlenecks occurring through domestication can limit crop resilience to biotic and abiotic stresses. In the present study, we investigated nucleotide diversity in tomato chloroplast genome through sequencing seven plastomes of cultivated accessions from the Campania region (Southern Italy) and two wild species among the closest (Solanum pimpinellifolium) and most distantly related (S. neorickii) species to cultivated tomatoes. Comparative analyses among the chloroplast genomes sequenced in this work and those available in GenBank allowed evaluating the variability of plastomes and defining phylogenetic relationships. A dramatic reduction in genetic diversity was detected in cultivated tomatoes, nonetheless, a few de novo mutations, which still differentiated the cultivated tomatoes from the closest wild relative S. pimpinellifolium, were detected and are potentially utilizable as diagnostic markers. Phylogenetic analyses confirmed that S. pimpinellifolium is the closest ancestor of all cultivated tomatoes. Local accessions all clustered together and were strictly related with other cultivated tomatoes (S. lycopersicum group). Noteworthy, S. lycopersicum var. cerasiforme resulted in a mixture of both cultivated and wild tomato genotypes since one of the two analyzed accessions clustered with cultivated tomato, whereas the other with S. pimpinellifolium. Overall, our results revealed a very reduced cytoplasmic variability in cultivated tomatoes and suggest the occurrence of a cytoplasmic bottleneck during their domestication.
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Affiliation(s)
- Rachele Tamburino
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and BioResources, Via Università 133, 80055 Portici (NA), Italy; (R.T.); (L.S.)
| | - Lorenza Sannino
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and BioResources, Via Università 133, 80055 Portici (NA), Italy; (R.T.); (L.S.)
| | - Donata Cafasso
- Department of Biology, University of Naples Federico II, Via Cinthia, 80126 Naples, Italy; (D.C.); (S.C.)
| | - Concita Cantarella
- CREA Research Centre for Vegetable and Ornamental Crops, Via dei Cavalleggeri 25, 84098 Pontecagnano Faiano (SA), Italy; (C.C.); (T.C.); (N.D.)
| | - Luigi Orrù
- CREA Research Centre for Genomics and Bioinformatics, via S. Protaso 302, 29017 Fiorenzuola d’Arda (PC), Italy;
| | - Teodoro Cardi
- CREA Research Centre for Vegetable and Ornamental Crops, Via dei Cavalleggeri 25, 84098 Pontecagnano Faiano (SA), Italy; (C.C.); (T.C.); (N.D.)
| | - Salvatore Cozzolino
- Department of Biology, University of Naples Federico II, Via Cinthia, 80126 Naples, Italy; (D.C.); (S.C.)
| | - Nunzio D’Agostino
- CREA Research Centre for Vegetable and Ornamental Crops, Via dei Cavalleggeri 25, 84098 Pontecagnano Faiano (SA), Italy; (C.C.); (T.C.); (N.D.)
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 133, 80055 Portici (NA), Italy
| | - Nunzia Scotti
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and BioResources, Via Università 133, 80055 Portici (NA), Italy; (R.T.); (L.S.)
- Correspondence: ; Tel.: +39-0812-53-9482
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5
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Tomato Phenotypic Diversity Determined by Combined Approaches of Conventional and High-Throughput Tomato Analyzer Phenotyping. PLANTS 2020; 9:plants9020197. [PMID: 32033402 PMCID: PMC7076427 DOI: 10.3390/plants9020197] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/31/2020] [Accepted: 02/03/2020] [Indexed: 11/18/2022]
Abstract
Morphological variation in vegetative and fruit traits is a key determinant in unraveling phenotypic diversity. This study was designed to assess phenotypic diversity in tomatoes and examine intra- and intervarietal groups’ variability using 28 conventional descriptors (CDs) and 47 Tomato Analyzer (TA) descriptors related to plant and fruit morphometry. Comprehensive phenotyping of 150 accessions representing 21 countries discerned noticeable variability for CD vegetative traits and TA quantified fruit features, such as shape, size, and color. Hierarchical cluster analysis divided the accessions into 10 distinct classes based on fruit shape and size. Multivariate analysis was used to assess divergence in variable traits among populations. Eight principal components with an eigenvalue >1 were identified by factor analysis, which contributed 87.5% variation to the total cumulative variance with the first two components contributing 32.0% and 18.1% variance, respectively. The relationship between vegetative and fruit descriptors was explained by respective CD and TA correlation networks. There was a strong positive correlation between fruit shape and size whereas negative correlations were between fruit shape index, internal eccentricity, and proximal end shape. The combined approach of CD and TA phenotyping allowed us to unravel the phenotypic diversity of vegetative and reproductive trait variation evaluated at pre- and post-harvest stages.
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Conesa MÀ, Fullana-Pericàs M, Granell A, Galmés J. Mediterranean Long Shelf-Life Landraces: An Untapped Genetic Resource for Tomato Improvement. FRONTIERS IN PLANT SCIENCE 2020; 10:1651. [PMID: 31998340 PMCID: PMC6965163 DOI: 10.3389/fpls.2019.01651] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 11/22/2019] [Indexed: 05/31/2023]
Abstract
The Mediterranean long shelf-life (LSL) tomatoes are a group of landraces with a fruit remaining sound up to 6-12 months after harvest. Most have been selected under semi-arid Mediterranean summer conditions with poor irrigation or rain-fed and thus, are drought tolerant. Besides the convergence in the latter traits, local selection criteria have been very variable, leading to a wide variation in fruit morphology and quality traits. The different soil characteristics and agricultural management techniques across the Mediterranean denote also a wide range of plant adaptive traits to different conditions. Despite the notorious traits for fruit quality and environment adaptation, the LSL landraces have been poorly exploited in tomato breeding programs, which rely basically on wild tomato species. In this review, we describe most of the information currently available for Mediterranean LSL landraces in order to highlight the importance of this genetic resource. We focus on the origin and diversity, the main selective traits, and the determinants of the extended fruit shelf-life and the drought tolerance. Altogether, the Mediterranean LSL landraces are a very valuable heritage to be revalued, since constitutes an alternative source to improve fruit quality and shelf-life in tomato, and to breed for more resilient cultivars under the predicted climate change conditions.
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Affiliation(s)
- Miquel À. Conesa
- Department Biologia-INAGEA, Universitat de les Illes Balears, Balearic Islands, Spain
| | - Mateu Fullana-Pericàs
- Department Biologia-INAGEA, Universitat de les Illes Balears, Balearic Islands, Spain
| | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, Valencia, Spain
| | - Jeroni Galmés
- Department Biologia-INAGEA, Universitat de les Illes Balears, Balearic Islands, Spain
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Tranchida-Lombardo V, Aiese Cigliano R, Anzar I, Landi S, Palombieri S, Colantuono C, Bostan H, Termolino P, Aversano R, Batelli G, Cammareri M, Carputo D, Chiusano ML, Conicella C, Consiglio F, D'Agostino N, De Palma M, Di Matteo A, Grandillo S, Sanseverino W, Tucci M, Grillo S. Whole-genome re-sequencing of two Italian tomato landraces reveals sequence variations in genes associated with stress tolerance, fruit quality and long shelf-life traits. DNA Res 2018; 25:149-160. [PMID: 29149280 PMCID: PMC5909465 DOI: 10.1093/dnares/dsx045] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 10/27/2017] [Indexed: 02/07/2023] Open
Abstract
Tomato is a high value crop and the primary model for fleshy fruit development and ripening. Breeding priorities include increased fruit quality, shelf life and tolerance to stresses. To contribute towards this goal, we re-sequenced the genomes of Corbarino (COR) and Lucariello (LUC) landraces, which both possess the traits of plant adaptation to water deficit, prolonged fruit shelf-life and good fruit quality. Through the newly developed pipeline Reconstructor, we generated the genome sequences of COR and LUC using datasets of 65.8 M and 56.4 M of 30-150 bp paired-end reads, respectively. New contigs including reads that could not be mapped to the tomato reference genome were assembled, and a total of 43, 054 and 44, 579 gene loci were annotated in COR and LUC. Both genomes showed novel regions with similarity to Solanum pimpinellifolium and Solanum pennellii. In addition to small deletions and insertions, 2, 000 and 1, 700 single nucleotide polymorphisms (SNPs) could exert potentially disruptive effects on 1, 371 and 1, 201 genes in COR and LUC, respectively. A detailed survey of the SNPs occurring in fruit quality, shelf life and stress tolerance related-genes identified several candidates of potential relevance. Variations in ethylene response components may concur in determining peculiar phenotypes of COR and LUC.
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Affiliation(s)
- Valentina Tranchida-Lombardo
- National Research Council of Italy Institute of Biosciences and Bioresources (CNR-IBBR), Via Università 133, 80055 Portici, Italy
| | | | - Irantzu Anzar
- Sequentia Biotech Calle Comte D'Urgel 240, 08036 Barcelona, Spain
| | - Simone Landi
- National Research Council of Italy Institute of Biosciences and Bioresources (CNR-IBBR), Via Università 133, 80055 Portici, Italy
| | - Samuela Palombieri
- National Research Council of Italy Institute of Biosciences and Bioresources (CNR-IBBR), Via Università 133, 80055 Portici, Italy
| | - Chiara Colantuono
- Department of Agricultural Sciences, University of Naples Federico II, Via Universita' 100, 80055 Portici, Italy
| | - Hamed Bostan
- Department of Agricultural Sciences, University of Naples Federico II, Via Universita' 100, 80055 Portici, Italy
| | - Pasquale Termolino
- National Research Council of Italy Institute of Biosciences and Bioresources (CNR-IBBR), Via Università 133, 80055 Portici, Italy
| | - Riccardo Aversano
- Department of Agricultural Sciences, University of Naples Federico II, Via Universita' 100, 80055 Portici, Italy
| | - Giorgia Batelli
- National Research Council of Italy Institute of Biosciences and Bioresources (CNR-IBBR), Via Università 133, 80055 Portici, Italy
| | - Maria Cammareri
- National Research Council of Italy Institute of Biosciences and Bioresources (CNR-IBBR), Via Università 133, 80055 Portici, Italy
| | - Domenico Carputo
- Department of Agricultural Sciences, University of Naples Federico II, Via Universita' 100, 80055 Portici, Italy
| | - Maria Luisa Chiusano
- Department of Agricultural Sciences, University of Naples Federico II, Via Universita' 100, 80055 Portici, Italy
| | - Clara Conicella
- National Research Council of Italy Institute of Biosciences and Bioresources (CNR-IBBR), Via Università 133, 80055 Portici, Italy
| | - Federica Consiglio
- National Research Council of Italy Institute of Biosciences and Bioresources (CNR-IBBR), Via Università 133, 80055 Portici, Italy
| | - Nunzio D'Agostino
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro Di Ricerca Orticultura e Florovivaismo (CREA-OF), Via Cavalleggeri, 25, 84098 Pontecagnano Faiano SA, Italy
| | - Monica De Palma
- National Research Council of Italy Institute of Biosciences and Bioresources (CNR-IBBR), Via Università 133, 80055 Portici, Italy
| | - Antonio Di Matteo
- Department of Agricultural Sciences, University of Naples Federico II, Via Universita' 100, 80055 Portici, Italy
| | - Silvana Grandillo
- National Research Council of Italy Institute of Biosciences and Bioresources (CNR-IBBR), Via Università 133, 80055 Portici, Italy
| | | | - Marina Tucci
- National Research Council of Italy Institute of Biosciences and Bioresources (CNR-IBBR), Via Università 133, 80055 Portici, Italy
| | - Stefania Grillo
- National Research Council of Italy Institute of Biosciences and Bioresources (CNR-IBBR), Via Università 133, 80055 Portici, Italy
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8
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A Critical View of Different Botanical, Molecular, and Chemical Techniques Used in Authentication of Plant Materials for Cosmetic Applications. COSMETICS 2018. [DOI: 10.3390/cosmetics5020030] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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9
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Twenty Years of Tomato Breeding at EPSO-UMH: Transfer Resistance from Wild Types to Local Landraces—From the First Molecular Markers to Genotyping by Sequencing (GBS). DIVERSITY 2018. [DOI: 10.3390/d10010012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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10
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Abstract
Landraces are key elements of agricultural biodiversity that have long been considered a source of useful traits. Their importance goes beyond subsistence agriculture and the essential need to preserve genetic diversity, because landraces are farmer-developed populations that are often adapted to environmental conditions of significance to tackle environmental concerns. It is therefore increasingly important to identify adaptive traits in crop landraces and understand their molecular basis. This knowledge is potentially useful for promoting more sustainable agricultural techniques, reducing the environmental impact of high-input cropping systems, and diminishing the vulnerability of agriculture to global climate change. In this review, we present an overview of the opportunities and limitations offered by landraces’ genomics. We discuss how rapid advances in DNA sequencing techniques, plant phenotyping, and recombinant DNA-based biotechnology encourage both the identification and the validation of the genomic signature of local adaptation in crop landraces. The integration of ‘omics’ sciences, molecular population genetics, and field studies can provide information inaccessible with earlier technological tools. Although empirical knowledge on the genetic and genomic basis of local adaptation is still fragmented, it is predicted that genomic scans for adaptation will unlock an intraspecific molecular diversity that may be different from that of modern varieties.
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11
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Landi S, De Lillo A, Nurcato R, Grillo S, Esposito S. In-field study on traditional Italian tomato landraces: The constitutive activation of the ROS scavenging machinery reduces effects of drought stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2017; 118:150-160. [PMID: 28633087 DOI: 10.1016/j.plaphy.2017.06.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 05/31/2017] [Accepted: 06/12/2017] [Indexed: 05/18/2023]
Abstract
The involvement and the efficiency of the antioxidants scavenging system upon drought were examined by comparing traditional tomato landraces with respect to an industrial commercial genotype (Red Setter); for the first time, comprehensive analyses of physiological, biochemical and molecular parameters were investigated directly under real field conditions, in a typical agricultural environment of Southern Italy. The characterization of the responses upon drought evidenced peculiar changes in stomatal conductance, ascorbate peroxidase and catalase activities and expression in drought tolerant tomato landraces, with respect to the industrial genotype. An in silico analysis (promoter and co-expression study) coupled to a phylogenetic investigation of selected enzymes was performed, reinforcing the hypothesis of a basal activation of ROS scavenging machinery in the Mediterranean landraces. Thus our data suggest a constitutive increase in the expression and activities of specific enzymes involved in ROS detoxification that can play a pivotal role in the drought response shown by tomato landraces. Therefore, traditional landraces could represent an important source of useful genetic variability for the improvement of commercial varieties; their ROS detoxifying capabilities denote peculiar aspects worth being explored to better describe their specific stress tolerance.
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Affiliation(s)
- Simone Landi
- Institute of Biosciences and Bioresources, Research Division, National Research Council of Italy (IBBR-CNR), Portici, 80055, Naples, Italy; Dipartimento di Biologia, Università di Napoli ''Federico II'', Via Cinthia, I-80126 Napoli, Italy
| | - Alessia De Lillo
- Dipartimento di Biologia, Università di Napoli ''Federico II'', Via Cinthia, I-80126 Napoli, Italy
| | - Roberta Nurcato
- Institute of Biosciences and Bioresources, Research Division, National Research Council of Italy (IBBR-CNR), Portici, 80055, Naples, Italy
| | - Stefania Grillo
- Institute of Biosciences and Bioresources, Research Division, National Research Council of Italy (IBBR-CNR), Portici, 80055, Naples, Italy
| | - Sergio Esposito
- Dipartimento di Biologia, Università di Napoli ''Federico II'', Via Cinthia, I-80126 Napoli, Italy.
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Baldina S, Picarella ME, Troise AD, Pucci A, Ruggieri V, Ferracane R, Barone A, Fogliano V, Mazzucato A. Metabolite Profiling of Italian Tomato Landraces with Different Fruit Types. FRONTIERS IN PLANT SCIENCE 2016; 7:664. [PMID: 27242865 PMCID: PMC4872001 DOI: 10.3389/fpls.2016.00664] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 04/29/2016] [Indexed: 05/18/2023]
Abstract
Increased interest toward traditional tomato varieties is fueled by the need to rescue desirable organoleptic traits and to improve the quality of fresh and processed tomatoes in the market. In addition, the phenotypic and genetic variation preserved in tomato landraces represents a means to understand the genetic basis of traits related to health and organoleptic aspects and improve them in modern varieties. To establish a framework for this approach, we studied the content of several metabolites in a panel of Italian tomato landraces categorized into three broad fruit type classes (flattened/ribbed, pear/oxheart, round/elongate). Three modern hybrids, corresponding to the three fruit shape typologies, were included as reference. Red ripe fruits were morphologically characterized and biochemically analyzed for their content in glycoalkaloids, phenols, amino acids, and Amadori products. The round/elongate types showed a higher content in glycoalkaloids, whereas flattened types had higher levels of phenolic compounds. Flattened tomatoes were also rich in total amino acids and in particular in glutamic acid. Multivariate analysis of amino acid content clearly separated the three classes of fruit types. Making allowance of the very low number of genotypes, phenotype-marker relationships were analyzed after retrieving single nucleotide polymorphisms (SNPs) among the landraces available in the literature. Sixty-six markers were significantly associated with the studied traits. The positions of several of these SNPs showed correspondence with already described genomic regions and QTLs supporting the reliability of the association. Overall the data indicated that significant changes in quality-related metabolites occur depending on the genetic background in traditional tomato germplasm, frequently according to specific fruit shape categories. Such a variability is suitable to harness association mapping for metabolic quality traits using this germplasm as an experimental population, paving the way for investigating their genetic/molecular basis, and facilitating breeding for quality-related compounds in tomato fruits.
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Affiliation(s)
- Svetlana Baldina
- Department of Agricultural and Forestry Sciences, University of TusciaViterbo, Italy
| | - Maurizio E. Picarella
- Department of Agricultural and Forestry Sciences, University of TusciaViterbo, Italy
| | - Antonio D. Troise
- Food Quality Design Group, Wageningen UniversityWageningen, Netherlands
- Department of Agricultural Sciences, University of Naples “Federico II”Napoli, Italy
| | - Anna Pucci
- Department of Agricultural and Forestry Sciences, University of TusciaViterbo, Italy
| | - Valentino Ruggieri
- Department of Agricultural Sciences, University of Naples “Federico II”Napoli, Italy
| | - Rosalia Ferracane
- Department of Agricultural Sciences, University of Naples “Federico II”Napoli, Italy
| | - Amalia Barone
- Department of Agricultural Sciences, University of Naples “Federico II”Napoli, Italy
| | - Vincenzo Fogliano
- Food Quality Design Group, Wageningen UniversityWageningen, Netherlands
| | - Andrea Mazzucato
- Department of Agricultural and Forestry Sciences, University of TusciaViterbo, Italy
- *Correspondence: Andrea Mazzucato
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Sacco A, Ruggieri V, Parisi M, Festa G, Rigano MM, Picarella ME, Mazzucato A, Barone A. Exploring a Tomato Landraces Collection for Fruit-Related Traits by the Aid of a High-Throughput Genomic Platform. PLoS One 2015; 10:e0137139. [PMID: 26393929 PMCID: PMC4579088 DOI: 10.1371/journal.pone.0137139] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 08/12/2015] [Indexed: 11/19/2022] Open
Abstract
During its evolution and domestication Solanum lycopersicum has undergone various genetic ‘bottlenecks’ and extreme inbreeding of limited genotypes. In Europe the tomato found a secondary centre for diversification, which resulted in a wide array of fruit shape variation given rise to a range of landraces that have been cultivated for centuries. Landraces represent a reservoir of genetic diversity especially for traits such as abiotic stress resistance and high fruit quality. Information about the variation present among tomato landrace populations is still limited. A collection of 123 genotypes from different geographical areas was established with the aim of capturing a wide diversity. Eighteen morphological traits were evaluated, mainly related to the fruit. About 45% of morphological variation was attributed to fruit shape, as estimated by the principal component analysis, and the dendrogram of relatedness divided the population in subgroups mainly on the basis of fruit weight and locule number. Genotyping was carried out using the tomato array platform SolCAP able to interrogate 7,720 SNPs. In the whole collection 87.1% markers were polymorphic but they decreased to 44–54% when considering groups of genotypes with different origin. The neighbour-joining tree analysis clustered the 123 genotypes into two main branches. The STRUCTURE analysis with K = 3 also divided the population on the basis of fruit size. A genomic-wide association strategy revealed 36 novel markers associated to the variation of 15 traits. The markers were mapped on the tomato chromosomes together with 98 candidate genes for the traits analyzed. Six regions were evidenced in which candidate genes co-localized with 19 associated SNPs. In addition, 17 associated SNPs were localized in genomic regions lacking candidate genes. The identification of these markers demonstrated that novel variability was captured in our germoplasm collection. They might also provide a viable indirect selection tool in future practical breeding programs.
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Affiliation(s)
- Adriana Sacco
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Valentino Ruggieri
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Mario Parisi
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria, Centro di ricerca per l’Orticoltura, Pontecagnano, Italy
| | - Giovanna Festa
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria, Centro di ricerca per l’Orticoltura, Pontecagnano, Italy
| | - Maria Manuela Rigano
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Maurizio Enea Picarella
- Department of Science and Technologies for Agriculture, Forestry, Nature and Energy (DAFNE University of Tuscia, Viterbo, Italy)
| | - Andrea Mazzucato
- Department of Science and Technologies for Agriculture, Forestry, Nature and Energy (DAFNE University of Tuscia, Viterbo, Italy)
| | - Amalia Barone
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
- * E-mail:
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14
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Maietta OW. Determinants of university–firm R&D collaboration and its impact on innovation: A perspective from a low-tech industry. RESEARCH POLICY 2015. [DOI: 10.1016/j.respol.2015.03.006] [Citation(s) in RCA: 169] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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15
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Corrado G, Piffanelli P, Caramante M, Coppola M, Rao R. SNP genotyping reveals genetic diversity between cultivated landraces and contemporary varieties of tomato. BMC Genomics 2013; 14:835. [PMID: 24279304 PMCID: PMC4046682 DOI: 10.1186/1471-2164-14-835] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 11/20/2013] [Indexed: 11/10/2022] Open
Abstract
Background The tomato (Solanum lycopersium L.) is the most widely grown vegetable in the world. It was domesticated in Latin America and Italy and Spain are considered secondary centers of diversification. This food crop has experienced severe genetic bottlenecks and modern breeding activities have been characterized by trait introgression from wild species and divergence in different market classes. Results With the aim to examine patterns of polymorphism, characterize population structure and identify putative loci under positive selection, we genotyped 214 tomato accessions (which include cultivated landraces, commercial varieties and wild relatives) using a custom-made Illumina SNP-panel. Most of the 175 successfully scored SNP loci were found to be polymorphic. Population structure analysis and estimates of genetic differentiation indicated that landraces constitute distinct sub-populations. Furthermore, contemporary varieties could be separated in groups (processing, fresh and cherry) that are consistent with the recent breeding aimed at market-class specialization. In addition, at the 95% confidence level, we identified 30, 34 and 37 loci under positive selection between landraces and each of the groups of commercial variety (cherry, processing and fresh market, respectively). Their number and genomic locations imply the presence of some extended regions with high genetic variation between landraces and contemporary varieties. Conclusions Our work provides knowledge concerning the level and distribution of genetic variation within cultivated tomato landraces and increases our understanding of the genetic subdivision of contemporary varieties. The data indicate that adaptation and selection have led to a genomic signature in cultivated landraces and that the subpopulation structure of contemporary varieties is shaped by directed breeding and largely of recent origin. The genomic characterization presented here is an essential step towards a future exploitation of the available tomato genetic resources in research and breeding programs. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-14-835) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Giandomenico Corrado
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II, via Università 100, 80055 Portici, NA, Italy.
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Chemotype and genotype combined analysis applied to tomato (Lycopersicon esculentum Mill.) analytical traceability. J Food Compost Anal 2011. [DOI: 10.1016/j.jfca.2010.06.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Digilio MC, Corrado G, Sasso R, Coppola V, Iodice L, Pasquariello M, Bossi S, Maffei ME, Coppola M, Pennacchio F, Rao R, Guerrieri E. Molecular and chemical mechanisms involved in aphid resistance in cultivated tomato. THE NEW PHYTOLOGIST 2010; 187:1089-1101. [PMID: 20546139 DOI: 10.1111/j.1469-8137.2010.03314.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
*An integrated approach has been used to obtain an understanding of the molecular and chemical mechanisms underlying resistance to aphids in cherry-like tomato (Solanum lycopersicum) landraces from the Campania region (southern Italy). The aphid-parasitoid system Macrosiphum euphorbiae-Aphidius ervi was used to describe the levels of resistance against aphids in two tomato accessions (AN5, AN7) exhibiting high yield and quality traits and lacking the tomato Mi gene. *Aphid development and reproduction, flight response by the aphid parasitoid A. ervi, gas chromatography-mass spectrometry headspace analysis of plant volatile organic compounds and transcriptional analysis of aphid responsive genes were performed on selected tomato accessions and on a susceptible commercial variety (M82). *When compared with the cultivated variety, M82, AN5 and AN7 showed a significant reduction of M. euphorbiae fitness, the release of larger amounts of specific volatile organic compounds that are attractive to the aphid parasitoid A. ervi, a constitutively higher level of expression of plant defence genes and differential enhancement of plant indirect resistance induced by aphid feeding. *These results provide new insights on how local selection can offer the possibility of the development of innovative genetic strategies to increase tomato resistance against aphids.
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Affiliation(s)
- Maria Cristina Digilio
- Dipartimento di Entomologia e Zoologia agraria 'Filippo Silvestri', Università di Napoli 'Federico II', Via Università 100, 80055 Portici (NA), Italy
| | - Giandomenico Corrado
- Dipartimento di Scienze del Suolo della Pianta e dell'Ambiente, Università di Napoli 'Federico II', Via Università 100, 80055 Portici (NA), Italy
| | - Raffaele Sasso
- Istituto per la Protezione delle Piante, Consiglio Nazionale delle Ricerche, Via Università 133, 80055 Portici (NA), Italy
| | - Valentina Coppola
- Dipartimento di Scienze del Suolo della Pianta e dell'Ambiente, Università di Napoli 'Federico II', Via Università 100, 80055 Portici (NA), Italy
| | - Luigi Iodice
- Istituto per la Protezione delle Piante, Consiglio Nazionale delle Ricerche, Via Università 133, 80055 Portici (NA), Italy
| | - Marianna Pasquariello
- Dipartimento di Scienze del Suolo della Pianta e dell'Ambiente, Università di Napoli 'Federico II', Via Università 100, 80055 Portici (NA), Italy
| | - Simone Bossi
- Dipartimento di Biologia Vegetale, Unità di Fisiologia Vegetale, Università di Torino - Centro della Innovazione, Via Quarello 11/A, 10135 Torino, Italy
| | - Massimo E Maffei
- Dipartimento di Biologia Vegetale, Unità di Fisiologia Vegetale, Università di Torino - Centro della Innovazione, Via Quarello 11/A, 10135 Torino, Italy
| | - Mariangela Coppola
- Dipartimento di Scienze del Suolo della Pianta e dell'Ambiente, Università di Napoli 'Federico II', Via Università 100, 80055 Portici (NA), Italy
| | - Francesco Pennacchio
- Dipartimento di Entomologia e Zoologia agraria 'Filippo Silvestri', Università di Napoli 'Federico II', Via Università 100, 80055 Portici (NA), Italy
| | - Rosa Rao
- Dipartimento di Scienze del Suolo della Pianta e dell'Ambiente, Università di Napoli 'Federico II', Via Università 100, 80055 Portici (NA), Italy
| | - Emilio Guerrieri
- Istituto per la Protezione delle Piante, Consiglio Nazionale delle Ricerche, Via Università 133, 80055 Portici (NA), Italy
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