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Blanca J, Pons C, Montero-Pau J, Sanchez-Matarredona D, Ziarsolo P, Fontanet L, Fisher J, Plazas M, Casals J, Rambla JL, Riccini A, Palombieri S, Ruggiero A, Sulli M, Grillo S, Kanellis A, Giuliano G, Finkers R, Cammareri M, Grandillo S, Mazzucato A, Causse M, Díez MJ, Prohens J, Zamir D, Cañizares J, Monforte AJ, Granell A. European traditional tomatoes galore: a result of farmers' selection of a few diversity-rich loci. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3431-3445. [PMID: 35358313 PMCID: PMC9162183 DOI: 10.1093/jxb/erac072] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
A comprehensive collection of 1254 tomato accessions, corresponding to European traditional and modern varieties, early domesticated varieties, and wild relatives, was analyzed by genotyping by sequencing. A continuous genetic gradient between the traditional and modern varieties was observed. European traditional tomatoes displayed very low genetic diversity, with only 298 polymorphic loci (95% threshold) out of 64 943 total variants. European traditional tomatoes could be classified into several genetic groups. Two main clusters consisting of Spanish and Italian accessions showed higher genetic diversity than the remaining varieties, suggesting that these regions might be independent secondary centers of diversity with a different history. Other varieties seem to be the result of a more recent complex pattern of migrations and hybridizations among the European regions. Several polymorphic loci were associated in a genome-wide association study with fruit morphological traits in the European traditional collection. The corresponding alleles were found to contribute to the distinctive phenotypic characteristic of the genetic varietal groups. The few highly polymorphic loci associated with morphological traits in an otherwise a low-diversity population suggests a history of balancing selection, in which tomato farmers likely maintained the morphological variation by inadvertently applying a high selective pressure within different varietal types.
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Affiliation(s)
- Jose Blanca
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV-UPV), Universitat Politècnica de València, València, Spain
| | - Clara Pons
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV-UPV), 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
| | | | - David Sanchez-Matarredona
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV-UPV), Universitat Politècnica de València, València, Spain
| | - Peio Ziarsolo
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV-UPV), Universitat Politècnica de València, València, Spain
| | | | - Josef Fisher
- Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Mariola Plazas
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV-UPV), Universitat Politècnica de València, València, Spain
| | - Joan Casals
- Department of Agri-Food Engineering and Biotechnology/Miquel Agustí Foundation, UPC-BarcelonaTech, Campus Baix Llobregat, Esteve Terrades 8, 08860 Castelldefels, Spain
| | - Jose Luis Rambla
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, València, Spain
| | - Alessandro Riccini
- Department of Agriculture and Forest Sciences (DAFNE), Università degli Studi della Tuscia, Viterbo, Italy
| | | | - Alessandra Ruggiero
- Institute of Biosciences and BioResources (IBBR), National Research Council of Italy (CNR), Via Università 133, 80055 Portici, Italy
| | - Maria Sulli
- 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
| | - Angelos Kanellis
- Group of Biotechnology of Pharmaceutical Plants, Laboratory of Pharmacognosy, Department of Pharmaceutical Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Giovanni Giuliano
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Casaccia Research Centre, Rome, Italy
| | - Richard Finkers
- Plant Breeding, Wageningen University and Research, POB 386, 6700 AJ Wageningen, The Netherlands
| | - Maria Cammareri
- 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
| | - 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, Centre de Recherche PACA, Domaine Saint Maurice, 67 Allée des Chênes, CS 60094, 84143 Montfavet, France
| | - Maria José Díez
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV-UPV), Universitat Politècnica de València, València, Spain
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV-UPV), Universitat Politècnica de València, València, Spain
| | - Dani Zamir
- Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Joaquin Cañizares
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV-UPV), Universitat Politècnica de València, València, Spain
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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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Breeding for Resistance to Fusarium Wilt of Tomato: A Review. Genes (Basel) 2021; 12:genes12111673. [PMID: 34828278 PMCID: PMC8624629 DOI: 10.3390/genes12111673] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/21/2021] [Accepted: 10/21/2021] [Indexed: 01/22/2023] Open
Abstract
For over a century, breeders have worked to develop tomato (Solanum lycopersicum) cultivars with resistance to Fusarium wilt (Fol) caused by the soilborne fungus Fusarium oxysporum f. sp. lycopersici. Host resistance is the most effective strategy for the management of this disease. For each of the three Fol races, resistance has been introgressed from wild tomato species, predominately in the form of R genes. The I, I-2, I-3, and I-7 R genes have each been identified, as well as the corresponding Avr effectors in the fungus with the exception of Avr7. The mechanisms by which the R gene protein products recognize these effectors, however, has not been elucidated. Extensive genetic mapping, gene cloning, and genome sequencing efforts support the development of tightly-linked molecular markers, which greatly expedite tomato breeding and the development of elite, Fol resistant cultivars. These resources also provide important tools for pyramiding resistance genes and should support the durability of host resistance.
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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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Efremov GI, Slugina MA, Shchennikova AV, Kochieva EZ. Differential Regulation of Phytoene Synthase PSY1 During Fruit Carotenogenesis in Cultivated and Wild Tomato Species ( Solanum section Lycopersicon). PLANTS 2020; 9:plants9091169. [PMID: 32916928 PMCID: PMC7569967 DOI: 10.3390/plants9091169] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/31/2020] [Accepted: 09/07/2020] [Indexed: 12/17/2022]
Abstract
In plants, carotenoids define fruit pigmentation and are involved in the processes of photo-oxidative stress defense and phytohormone production; a key enzyme responsible for carotene synthesis in fruit is phytoene synthase 1 (PSY1). Tomatoes (Solanum section Lycopersicon) comprise cultivated (Solanum lycopersicum) as well as wild species with different fruit color and are a good model to study carotenogenesis in fleshy fruit. In this study, we identified homologous PSY1 genes in five Solanum section Lycopersicon species, including domesticated red-fruited S. lycopersicum and wild yellow-fruited S. cheesmaniae and green-fruited S. chilense, S. habrochaites and S. pennellii. PSY1 homologs had a highly conserved structure, including key motifs in the active and catalytic sites, suggesting that PSY1 enzymatic function is similar in green-fruited wild tomato species and preserved in red-fruited S. lycopersicum. PSY1 mRNA expression directly correlated with carotenoid content in ripe fruit of the analyzed tomato species, indicating differential transcriptional regulation. Analysis of the PSY1 promoter and 5′-UTR sequence revealed over 30 regulatory elements involved in response to light, abiotic stresses, plant hormones, and parasites, suggesting that the regulation of PSY1 expression may affect the processes of fruit senescence, seed maturation and dormancy, and pathogen resistance. The revealed differences between green-fruited and red-fruited Solanum species in the structure of the PSY1 promoter/5′-UTR, such as the acquisition of ethylene-responsive element by S. lycopersicum, could reflect the effects of domestication on the transcriptional mechanisms regulating PSY1 expression, including induction of carotenogenesis during fruit ripening, which would contribute to red coloration in mature fruit.
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Esposito S, Cardi T, Campanelli G, Sestili S, Díez MJ, Soler S, Prohens J, Tripodi P. ddRAD sequencing-based genotyping for population structure analysis in cultivated tomato provides new insights into the genomic diversity of Mediterranean 'da serbo' type long shelf-life germplasm. HORTICULTURE RESEARCH 2020; 7:134. [PMID: 32922806 PMCID: PMC7459340 DOI: 10.1038/s41438-020-00353-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/10/2020] [Accepted: 06/19/2020] [Indexed: 05/26/2023]
Abstract
Double digest restriction-site associated sequencing (ddRAD-seq) is a flexible and cost-effective strategy for providing in-depth insights into the genetic architecture of germplasm collections. Using this methodology, we investigated the genomic diversity of a panel of 288 diverse tomato (Solanum lycopersicum L.) accessions enriched in 'da serbo' (called 'de penjar' in Spain) long shelf life (LSL) materials (152 accessions) mostly originating from Italy and Spain. The rest of the materials originate from different countries and include landraces for fresh consumption, elite cultivars, heirlooms, and breeding lines. Apart from their LSL trait, 'da serbo' landraces are of remarkable interest for their resilience. We identified 32,799 high-quality SNPs, which were used for model ancestry population structure and non-parametric hierarchical clustering. Six genetic subgroups were revealed, clearly separating most 'da serbo' landraces, but also the Spanish germplasm, suggesting a subdivision of the population based on type and geographical provenance. Linkage disequilibrium (LD) in the collection decayed very rapidly within <5 kb. We then investigated SNPs showing contrasted minor frequency allele (MAF) in 'da serbo' materials, resulting in the identification of high frequencies in this germplasm of several mutations in genes related to stress tolerance and fruit maturation such as CTR1 and JAR1. Finally, a mini-core collection of 58 accessions encompassing most of the diversity was selected for further exploitation of key traits. Our findings suggest the presence of a genetic footprint of the 'da serbo' germplasm selected in the Mediterranean basin. Moreover, we provide novel insights on LSL 'da serbo' germplasm as a promising source of alleles for tolerance to stresses.
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Affiliation(s)
- Salvatore Esposito
- CREA Research Centre for Vegetable and Ornamental Crops, Pontecagnano, (SA) Italy
| | - Teodoro Cardi
- CREA Research Centre for Vegetable and Ornamental Crops, Pontecagnano, (SA) Italy
| | - Gabriele Campanelli
- CREA Research Centre for Vegetable and Ornamental Crops, Monsampolo del Tronto (AP), Tronto, Italy
| | - Sara Sestili
- CREA Research Centre for Vegetable and Ornamental Crops, Monsampolo del Tronto (AP), Tronto, Italy
| | - María José Díez
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Salvador Soler
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Pasquale Tripodi
- CREA Research Centre for Vegetable and Ornamental Crops, Pontecagnano, (SA) Italy
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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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Induced Plant Defenses Against Herbivory in Cultivated and Wild Tomato. J Chem Ecol 2019; 45:693-707. [DOI: 10.1007/s10886-019-01090-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/17/2019] [Accepted: 07/21/2019] [Indexed: 10/26/2022]
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Bac-Molenaar JA, Mol S, Verlaan MG, van Elven J, Kim HK, Klinkhamer PGL, Leiss KA, Vrieling K. Trichome Independent Resistance against Western Flower Thrips in Tomato. PLANT & CELL PHYSIOLOGY 2019; 60:1011-1024. [PMID: 30715458 PMCID: PMC6534821 DOI: 10.1093/pcp/pcz018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 01/29/2019] [Indexed: 05/26/2023]
Abstract
Western flower thrips (WFT) are a major pest on many crops, including tomato. Thrips cause yield losses, not only through feeding damage, but also by the transmission of viruses of which the Tomato Spotted Wilt Virus is the most important one. In cultivated tomato, genetic diversity is extremely low, and all commercial lines are susceptible to WFT. Several wild relatives are WFT resistant and these resistances are based on glandular trichome-derived traits. Introgression of these traits in cultivated lines did not lead to WFT resistant commercial varieties so far. In this study, we investigated WFT resistance in cultivated tomato using a F2 population derived from a cross between a WFT susceptible and a WFT resistant cultivated tomato line. We discovered that this WFT resistance is independent of glandular trichome density or trichome-derived volatile profiles and is associated with three QTLs on chromosomes 4, 5 and 10. Foliar metabolic profiles of F3 families with low and high WFT feeding damage were clearly different. We identified α-tomatine and a phenolic compound as potential defensive compounds. Their causality and interaction need further investigation. Because this study is based on cultivated tomato lines, our findings can directly be used in nowadays breeding programs.
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Affiliation(s)
- Johanna A Bac-Molenaar
- Plant Sciences and Natural Products Lab, Institute of Biology Leiden, Sylviusweg 72, BE Leiden, The Netherlands
- Wageningen University and Research, Violierenweg 1, MV Bleiswijk, The Netherlands
| | - Selena Mol
- Plant Sciences and Natural Products Lab, Institute of Biology Leiden, Sylviusweg 72, BE Leiden, The Netherlands
- Rijk Zwaan Breeding B.V, Burgemeester Crezeelaan 40, KX De Lier, The Netherlands
| | - Maarten G Verlaan
- Rijk Zwaan Breeding B.V, Burgemeester Crezeelaan 40, KX De Lier, The Netherlands
| | - Joke van Elven
- Rijk Zwaan Breeding B.V, Burgemeester Crezeelaan 40, KX De Lier, The Netherlands
| | - Hye Kyong Kim
- Plant Sciences and Natural Products Lab, Institute of Biology Leiden, Sylviusweg 72, BE Leiden, The Netherlands
| | - Peter G L Klinkhamer
- Plant Sciences and Natural Products Lab, Institute of Biology Leiden, Sylviusweg 72, BE Leiden, The Netherlands
| | - Kirsten A Leiss
- Plant Sciences and Natural Products Lab, Institute of Biology Leiden, Sylviusweg 72, BE Leiden, The Netherlands
- Wageningen University and Research, Violierenweg 1, MV Bleiswijk, The Netherlands
| | - Klaas Vrieling
- Plant Sciences and Natural Products Lab, Institute of Biology Leiden, Sylviusweg 72, BE Leiden, The Netherlands
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10
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Wang T, Li HT, Zhu H, Qi SY, Zhang YM, Zhang ZJ, Zou QD. Comparative Analyses of Genetic Variation in a Tomato (Solanum lycopersicum L.) Germplasm Collection with Single Nucleotide Polymorphism and Insertion-Deletion Markers. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419020182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Wang X, Chen Y, Thomas CL, Ding G, Xu P, Shi D, Grandke F, Jin K, Cai H, Xu F, Yi B, Broadley MR, Shi L. Genetic variants associated with the root system architecture of oilseed rape (Brassica napus L.) under contrasting phosphate supply. DNA Res 2017; 24:407-417. [PMID: 28430897 PMCID: PMC5737433 DOI: 10.1093/dnares/dsx013] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 03/29/2017] [Indexed: 12/29/2022] Open
Abstract
Breeding crops with ideal root system architecture for efficient absorption of phosphorus is an important strategy to reduce the use of phosphate fertilizers. To investigate genetic variants leading to changes in root system architecture, 405 oilseed rape cultivars were genotyped with a 60K Brassica Infinium SNP array in low and high P environments. A total of 285 single-nucleotide polymorphisms were associated with root system architecture traits at varying phosphorus levels. Nine single-nucleotide polymorphisms corroborate a previous linkage analysis of root system architecture quantitative trait loci in the BnaTNDH population. One peak single-nucleotide polymorphism region on A3 was associated with all root system architecture traits and co-localized with a quantitative trait locus for primary root length at low phosphorus. Two more single-nucleotide polymorphism peaks on A5 for root dry weight at low phosphorus were detected in both growth systems and co-localized with a quantitative trait locus for the same trait. The candidate genes identified on A3 form a haplotype ‘BnA3Hap’, that will be important for understanding the phosphorus/root system interaction and for the incorporation into Brassica napus breeding programs.
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Affiliation(s)
- Xiaohua Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Yanling Chen
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Catherine L Thomas
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12?5RD, UK
| | - Guangda Ding
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Ping Xu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Dexu Shi
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Fabian Grandke
- Department of Plant Breeding, IFZ Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Giessen 35392, Germany
| | - Kemo Jin
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Hongmei Cai
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Martin R Broadley
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12?5RD, UK
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
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12
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Ohyama A, Shirasawa K, Matsunaga H, Negoro S, Miyatake K, Yamaguchi H, Nunome T, Iwata H, Fukuoka H, Hayashi T. Bayesian QTL mapping using genome-wide SSR markers and segregating population derived from a cross of two commercial F 1 hybrids of tomato. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1601-1616. [PMID: 28477044 DOI: 10.1007/s00122-017-2913-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 04/27/2017] [Indexed: 06/07/2023]
Abstract
Using newly developed euchromatin-derived genomic SSR markers and a flexible Bayesian mapping method, 13 significant agricultural QTLs were identified in a segregating population derived from a four-way cross of tomato. So far, many QTL mapping studies in tomato have been performed for progeny obtained from crosses between two genetically distant parents, e.g., domesticated tomatoes and wild relatives. However, QTL information of quantitative traits related to yield (e.g., flower or fruit number, and total or average weight of fruits) in such intercross populations would be of limited use for breeding commercial tomato cultivars because individuals in the populations have specific genetic backgrounds underlying extremely different phenotypes between the parents such as large fruit in domesticated tomatoes and small fruit in wild relatives, which may not be reflective of the genetic variation in tomato breeding populations. In this study, we constructed F2 population derived from a cross between two commercial F1 cultivars in tomato to extract QTL information practical for tomato breeding. This cross corresponded to a four-way cross, because the four parental lines of the two F1 cultivars were considered to be the founders. We developed 2510 new expressed sequence tag (EST)-based (euchromatin-derived) genomic SSR markers and selected 262 markers from these new SSR markers and publicly available SSR markers to construct a linkage map. QTL analysis for ten agricultural traits of tomato was performed based on the phenotypes and marker genotypes of F2 plants using a flexible Bayesian method. As results, 13 QTL regions were detected for six traits by the Bayesian method developed in this study.
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Affiliation(s)
- Akio Ohyama
- National Agriculture and Food Research Organization (NARO), Institute of Vegetable and Floriculture Science (NIVFS), 3-1-1 Kannondai, Tsukuba, Ibaraki, 305-8519, Japan.
- NARO, NIVFS, 360 Kusawa, Ano, Tsu, Mie, 514-2392, Japan.
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
| | | | - Satomi Negoro
- NARO, NIVFS, 360 Kusawa, Ano, Tsu, Mie, 514-2392, Japan
| | - Koji Miyatake
- NARO, NIVFS, 360 Kusawa, Ano, Tsu, Mie, 514-2392, Japan
| | | | | | - Hiroyoshi Iwata
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Hiroyuki Fukuoka
- NARO, Institute of Vegetable and Tea Science (NIVTS), 360 Kusawa, Ano, Tsu, Mie, 514-2392, Japan
- Takii & Company, Limited, 1360 Hari, Konan, Shiga, 520-3231, Japan
| | - Takeshi Hayashi
- NARO, Institute of Crop Science (NICS), 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan.
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13
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Ren J, Chen L, Jin X, Zhang M, You FM, Wang J, Frenkel V, Yin X, Nevo E, Sun D, Luo MC, Peng J. Solar Radiation-Associated Adaptive SNP Genetic Differentiation in Wild Emmer Wheat, Triticum dicoccoides. FRONTIERS IN PLANT SCIENCE 2017; 8:258. [PMID: 28352272 PMCID: PMC5348526 DOI: 10.3389/fpls.2017.00258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 02/10/2017] [Indexed: 05/06/2023]
Abstract
Whole-genome scans with large number of genetic markers provide the opportunity to investigate local adaptation in natural populations and identify candidate genes under positive selection. In the present study, adaptation genetic differentiation associated with solar radiation was investigated using 695 polymorphic SNP markers in wild emmer wheat originated in a micro-site at Yehudiyya, Israel. The test involved two solar radiation niches: (1) sun, in-between trees; and (2) shade, under tree canopy, separated apart by a distance of 2-4 m. Analysis of molecular variance showed a small (0.53%) but significant portion of overall variation between the sun and shade micro-niches, indicating a non-ignorable genetic differentiation between sun and shade habitats. Fifty SNP markers showed a medium (0.05 ≤ FST ≤ 0.15) or high genetic differentiation (FST > 0.15). A total of 21 outlier loci under positive selection were identified by using four different FST -outlier testing algorithms. The markers and genome locations under positive selection are consistent with the known patterns of selection. These results suggested that genetic differentiation between sun and shade habitats is substantial, radiation-associated, and therefore ecologically determined. Hence, the results of this study reflected effects of natural selection through solar radiation on EST-related SNP genetic diversity, resulting presumably in different adaptive complexes at a micro-scale divergence. The present work highlights the evolutionary theory and application significance of solar radiation-driven natural selection in wheat improvement.
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Affiliation(s)
- Jing Ren
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou UniversityDezhou, China
| | - Liang Chen
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Chinese Academy of SciencesWuhan, China
| | - Xiaoli Jin
- Department of Agronomy and the Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang UniversityHangzhou, China
| | - Miaomiao Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Chinese Academy of SciencesWuhan, China
| | - Frank M. You
- Cereal Research Centre, Agriculture and Agri-Food CanadaWinnipeg, MB, Canada
| | - Jirui Wang
- Department of Plant Sciences, University of CaliforniaDavis, CA, USA
| | - Vladimir Frenkel
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of HaifaHaifa, Israel
| | - Xuegui Yin
- Department of Biotechnology, College of Agriculture, Guangdong Ocean UniversityZhanjiang, China
| | - Eviatar Nevo
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of HaifaHaifa, Israel
| | - Dongfa Sun
- Department of Agronomy, College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of CaliforniaDavis, CA, USA
| | - Junhua Peng
- Department of Biotechnology, College of Agriculture, Guangdong Ocean UniversityZhanjiang, China
- The State Key Lab of Crop Breeding Technology Innovation and Integration, China National Seed Group Co. Ltd.Wuhan, China
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14
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Berdugo-Cely J, Valbuena RI, Sánchez-Betancourt E, Barrero LS, Yockteng R. Genetic diversity and association mapping in the Colombian Central Collection of Solanum tuberosum L. Andigenum group using SNPs markers. PLoS One 2017; 12:e0173039. [PMID: 28257509 PMCID: PMC5336250 DOI: 10.1371/journal.pone.0173039] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Accepted: 02/14/2017] [Indexed: 01/03/2023] Open
Abstract
The potato (Solanum tuberosum L.) is the fourth most important crop food in the world and Colombia has one of the most important collections of potato germplasm in the world (the Colombian Central Collection-CCC). Little is known about its potential as a source of genetic diversity for molecular breeding programs. In this study, we analyzed 809 Andigenum group accessions from the CCC using 5968 SNPs to determine: 1) the genetic diversity and population structure of the Andigenum germplasm and 2) the usefulness of this collection to map qualitative traits across the potato genome. The genetic structure analysis based on principal components, cluster analyses, and Bayesian inference revealed that the CCC can be subdivided into two main groups associated with their ploidy level: Phureja (diploid) and Andigena (tetraploid). The Andigena population was more genetically diverse but less genetically substructured than the Phureja population (three vs. five subpopulations, respectively). The association mapping analysis of qualitative morphological data using 4666 SNPs showed 23 markers significantly associated with nine morphological traits. The present study showed that the CCC is a highly diverse germplasm collection genetically and phenotypically, useful to implement association mapping in order to identify genes related to traits of interest and to assist future potato genetic breeding programs.
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Affiliation(s)
- Jhon Berdugo-Cely
- Colombian Agricultural Research Corporation (CORPOICA)-Mosquera, Cundinamarca, Colombia
| | - Raúl Iván Valbuena
- Colombian Agricultural Research Corporation (CORPOICA)-Mosquera, Cundinamarca, Colombia
| | | | - Luz Stella Barrero
- Colombian Agricultural Research Corporation (CORPOICA)-Mosquera, Cundinamarca, Colombia
| | - Roxana Yockteng
- Colombian Agricultural Research Corporation (CORPOICA)-Mosquera, Cundinamarca, Colombia
- Muséum National d’Histoire Naturelle, UMR-CNRS 7205, Paris, France
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15
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Satková P, Starý T, Plešková V, Zapletalová M, Kašparovský T, Činčalová-Kubienová L, Luhová L, Mieslerová B, Mikulík J, Lochman J, Petřivalský M. Diverse responses of wild and cultivated tomato to BABA, oligandrin and Oidium neolycopersici infection. ANNALS OF BOTANY 2017; 119:829-840. [PMID: 27660055 PMCID: PMC5378190 DOI: 10.1093/aob/mcw188] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 06/06/2016] [Accepted: 08/05/2016] [Indexed: 05/10/2023]
Abstract
Background and Aims Current strategies for increased crop protection of susceptible tomato plants against pathogen infections include treatment with synthetic chemicals, application of natural pathogen-derived compounds or transfer of resistance genes from wild tomato species within breeding programmes. In this study, a series of 45 genes potentially involved in defence mechanisms was retrieved from the genome sequence of inbred reference tomato cultivar Solanum lycopersicum 'Heinz 1706'. The aim of the study was to analyse expression of these selected genes in wild and cultivated tomato plants contrasting in resistance to the biotrophic pathogen Oidium neolycopersici , the causative agent of powdery mildew. Plants were treated either solely with potential resistance inducers or by inducers together with the pathogen. Methods The resistance against O. neolycopersici infection as well as RT-PCR-based analysis of gene expression in response to the oomycete elicitor oligandrin and chemical agent β-aminobutyric acid (BABA) were investigated in the highly susceptible domesticated inbred genotype Solanum lycopersicum 'Amateur' and resistant wild genotype Solanum habrochaites . Key Results Differences in basal expression levels of defensins, germins, β-1,3-glucanases, heveins, chitinases, osmotins and PR1 proteins in non-infected and non-elicited plants were observed between the highly resistant and susceptible genotypes. Moreover, these defence genes showed an extensive up-regulation following O. neolycopersici infection in both genotypes. Application of BABA and elicitin induced expression of multiple defence-related transcripts and, through different mechanisms, enhanced resistance against powdery mildew in the susceptible tomato genotype. Conclusions The results indicate that non-specific resistance in the resistant genotype S. habrochaites resulted from high basal levels of transcripts with proven roles in defence processes. In the susceptible genotype S. lycopersicum 'Amateur', oligandrin- and BABA-induced resistance involved different signalling pathways, with BABA-treated leaves displaying direct activation of the ethylene-dependent signalling pathway, in contrast to previously reported jasmonic acid-mediated signalling for elicitins.
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Affiliation(s)
- Pavla Satková
- Department of Biochemistry, Faculty of Science, Palacký University, Šlechtitelů 27, 78371 Olomouc, Czech Republic
| | - Tomáš Starý
- Department of Biochemistry, Faculty of Science, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic
| | - Veronika Plešková
- Department of Biochemistry, Faculty of Science, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic
| | - Martina Zapletalová
- Department of Biochemistry, Faculty of Science, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic
| | - Tomáš Kašparovský
- Department of Biochemistry, Faculty of Science, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic
| | - Lucie Činčalová-Kubienová
- Department of Biochemistry, Faculty of Science, Palacký University, Šlechtitelů 27, 78371 Olomouc, Czech Republic
| | - Lenka Luhová
- Department of Biochemistry, Faculty of Science, Palacký University, Šlechtitelů 27, 78371 Olomouc, Czech Republic
| | - Barbora Mieslerová
- Department of Botany, Faculty of Science, Palacký University, Šlechtitelů 27, 78371 Olomouc, Czech Republic
| | - Jaromír Mikulík
- Laboratory of Growth Regulators & Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University & Institute of Experimental Botany ASCR, Šlechtitelů 27, 78371 Olomouc, Czech Republic
| | - Jan Lochman
- Department of Biochemistry, Faculty of Science, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic
| | - Marek Petřivalský
- Department of Biochemistry, Faculty of Science, Palacký University, Šlechtitelů 27, 78371 Olomouc, Czech Republic
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16
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Barrantes W, López-Casado G, García-Martínez S, Alonso A, Rubio F, Ruiz JJ, Fernández-Muñoz R, Granell A, Monforte AJ. Exploring New Alleles Involved in Tomato Fruit Quality in an Introgression Line Library of Solanum pimpinellifolium. FRONTIERS IN PLANT SCIENCE 2016; 7:1172. [PMID: 27582742 PMCID: PMC4987366 DOI: 10.3389/fpls.2016.01172] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 07/21/2016] [Indexed: 05/22/2023]
Abstract
We have studied a genomic library of introgression lines from the Solanum pimpinellifolium accession TO-937 into the genetic background of the "Moneymaker" cultivar in order to evaluate the accession's breeding potential. Overall, no deleterious phenotypes were observed, and the plants and fruits were phenotypically very similar to those of "Moneymaker," which confirms the feasibility of translating the current results into elite breeding programs. We identified chromosomal regions associated with traits that were both vegetative (plant vigor, trichome density) and fruit-related (morphology, organoleptic quality, color). A trichome-density locus was mapped on chromosome 10 that had not previously been associated with insect resistance, which indicates that the increment of trichomes by itself does not confer resistance. A large number of quantitative trait loci (QTLs) have been identified for fruit weight. Interestingly, fruit weight QTLs on chromosomes 1 and 10 showed a magnitude effect similar to that of QTLs previously defined as important in domestication and diversification. Low variability was observed for fruit-shape-related traits. We were, however, able to identify a QTL for shoulder height, although the effects were quite low, thus demonstrating the suitability of the current population for QTL detection. Regarding organoleptic traits, consistent QTLs were detected for soluble solid content (SSC). Interestingly, QTLs on chromosomes 2 and 9 increased SSC but did not affect fruit weight, making them quite promising for introduction in modern cultivars. Three ILs with introgressions on chromosomes 1, 2, and 10 increased the internal fruit color, making them candidates for increasing the color of modern cultivars. Comparing the QTL detection between this IL population and a recombinant inbred line population from the same cross, we found that QTL stability across generations depended on the trait, as it was very high for fruit weight but low for organoleptic traits. This difference in QTL stability may be due to a predominant additive gene action for QTLs involved in fruit weight, whereas epistatic and genetic background interactions are most likely important for the other traits.
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Affiliation(s)
- Walter Barrantes
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Polytechnic University of ValenciaValencia, Spain
- Estación Experimental Agrícola Fabio Baudrit Moreno, Universidad de Costa RicaAlajuela, Costa Rica
| | - Gloria López-Casado
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Consejo Superior de Investigaciones Científicas, University of MalagaAlgarrobo-Costa, Spain
| | - Santiago García-Martínez
- Departamento de Biología Aplicada, Escuela Politécnica Superior de Orihuela, Universidad Miguel HernándezOrihuela, Spain
| | - Aranzazu Alonso
- Departamento de Biología Aplicada, Escuela Politécnica Superior de Orihuela, Universidad Miguel HernándezOrihuela, Spain
| | - Fernando Rubio
- Departamento de Biología Aplicada, Escuela Politécnica Superior de Orihuela, Universidad Miguel HernándezOrihuela, Spain
| | - Juan J. Ruiz
- Departamento de Biología Aplicada, Escuela Politécnica Superior de Orihuela, Universidad Miguel HernándezOrihuela, Spain
| | - Rafael Fernández-Muñoz
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Consejo Superior de Investigaciones Científicas, University of MalagaAlgarrobo-Costa, Spain
| | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Polytechnic University of ValenciaValencia, Spain
| | - Antonio J. Monforte
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Polytechnic University of ValenciaValencia, Spain
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17
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McDaniel T, Tosh CR, Gatehouse AMR, George D, Robson M, Brogan B. Novel resistance mechanisms of a wild tomato against the glasshouse whitefly. AGRONOMY FOR SUSTAINABLE DEVELOPMENT 2016; 36:14. [PMID: 32355506 PMCID: PMC7175684 DOI: 10.1007/s13593-016-0351-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/05/2016] [Indexed: 05/13/2023]
Abstract
The glasshouse whitefly, Trialeurodes vaporariorum, is an important pest of many crop plants including tomato, Solanum lycopersicum. Many wild tomato species exhibit a higher resistance to whiteflies. Therefore, locating the source of this enhanced resistance and breeding it into commercial tomato species is an important strategy to reduce the impact of pests on crops. Here, we assessed the pest resistance of Lycopersicon pimpinellifolium by comparing oviposition and feeding data from T. vaporariorum on this wild tomato species with data collected from a susceptible commercial tomato, S. lycopersicum var. 'Elegance'. The location of resistance factors was examined by use of electrical penetration graph (EPG) studies on these tomato species. Results show that whiteflies preferentially settled on the commercial tomato more often in 80 % of the replicates when given free choice between the two tomato species and laid significantly fewer eggs on L. pimpinellifolium. Whiteflies exhibited a shorter duration of the second feeding bout, reduced pathway phase probing, longer salivation in the phloem and more non-probing activities in the early stages of the EPG on the wild tomato species compared to the commercial tomato. These findings evidence that a dual mode of resistance is present in this wild tomato against T. vaporariorum: a post-penetration, pre-phloem resistance mechanism and a phloem-located factor, which to the best of our knowledge is the first time that evidence for this has been presented. These findings can be used to inform future breeding strategies to increase the resistance of commercial tomato varieties against this important pest.
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Affiliation(s)
- Thomas McDaniel
- School of Biology, Newcastle University, Devonshire Building, Newcastle-upon-Tyne, NE1 7RU UK
| | - Colin R. Tosh
- School of Biology, Newcastle University, Devonshire Building, Newcastle-upon-Tyne, NE1 7RU UK
| | | | - David George
- Stockbridge Technology Centre, Cawood, Selby, North Yorkshire, YO8 3TZ UK
| | - Michelle Robson
- School of Biology, Newcastle University, Devonshire Building, Newcastle-upon-Tyne, NE1 7RU UK
| | - Barry Brogan
- School of Biology, Newcastle University, Devonshire Building, Newcastle-upon-Tyne, NE1 7RU UK
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18
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Identification of Genetic Differentiation between Waxy and Common Maize by SNP Genotyping. PLoS One 2015; 10:e0142585. [PMID: 26566240 PMCID: PMC4643885 DOI: 10.1371/journal.pone.0142585] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 10/23/2015] [Indexed: 11/18/2022] Open
Abstract
Waxy maize (Zea mays L. var. ceratina) is an important vegetable and economic crop that is thought to have originated from cultivated flint maize and most recently underwent divergence from common maize. In this study, a total of 110 waxy and 110 common maize inbred lines were genotyped with 3072 SNPs to evaluate the genetic diversity, population structure, and linkage disequilibrium decay as well as identify putative loci that are under positive selection. The results revealed abundant genetic diversity in the studied panel and that genetic diversity was much higher in common than in waxy maize germplasms. Principal coordinate analysis and neighbor-joining cluster analysis consistently classified the 220 accessions into two major groups and a mixed group with mixed ancestry. Subpopulation structure in both waxy and common maize sets were associated with the germplasm origin and corresponding heterotic groups. The LD decay distance (1500–2000 kb) in waxy maize was lower than that in common maize. Fourteen candidate loci were identified as under positive selection between waxy and common maize at the 99% confidence level. The information from this study can assist waxy maize breeders by enhancing parental line selection and breeding program design.
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Kovi MR, Fjellheim S, Sandve SR, Larsen A, Rudi H, Asp T, Kent MP, Rognli OA. Population Structure, Genetic Variation, and Linkage Disequilibrium in Perennial Ryegrass Populations Divergently Selected for Freezing Tolerance. FRONTIERS IN PLANT SCIENCE 2015; 6:929. [PMID: 26617611 PMCID: PMC4641910 DOI: 10.3389/fpls.2015.00929] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 10/15/2015] [Indexed: 05/15/2023]
Abstract
Low temperature is one of the abiotic stresses seriously affecting the growth of perennial ryegrass (Lolium perenne L.), and freezing tolerance is a complex trait of major agronomical importance in northern and central Europe. Understanding the genetic control of freezing tolerance would aid in the development of cultivars of perennial ryegrass with improved adaptation to frost. The plant material investigated in this study was an experimental synthetic population derived from pair-crosses among five European perennial ryegrass genotypes, representing adaptations to a range of climatic conditions across Europe. A total number of 80 individuals (24 of High frost [HF]; 29 of Low frost [LF], and 27 of Unselected [US]) from the second generation of the two divergently selected populations and an unselected (US) control population were genotyped using 278 genome-wide SNPs derived from perennial ryegrass transcriptome sequences. Our studies investigated the genetic diversity among the three experimental populations by analysis of molecular variance and population structure, and determined that the HF and LF populations are very divergent after selection for freezing tolerance, whereas the HF and US populations are more similar. Linkage disequilibrium (LD) decay varied across the seven chromosomes and the conspicuous pattern of LD between the HF and LF population confirmed their divergence in freezing tolerance. Furthermore, two F st outlier methods; finite island model (fdist) by LOSITAN and hierarchical structure model using ARLEQUIN, both detected six loci under directional selection. These outlier loci are most probably linked to genes involved in freezing tolerance, cold adaptation, and abiotic stress. These six candidate loci under directional selection for freezing tolerance might be potential marker resources for breeding perennial ryegrass cultivars with improved freezing tolerance.
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Affiliation(s)
- Mallikarjuna Rao Kovi
- Department of Plant Sciences, Centre for Integrative Genetics, Norwegian University of Life SciencesÅs, Norway
| | - Siri Fjellheim
- Department of Plant Sciences, Centre for Integrative Genetics, Norwegian University of Life SciencesÅs, Norway
| | - Simen R. Sandve
- Department of Plant Sciences, Centre for Integrative Genetics, Norwegian University of Life SciencesÅs, Norway
- Department of Animal and Aquacultural Sciences, Centre for Integrative Genetics, Norwegian University of Life SciencesÅs, Norway
| | | | - Heidi Rudi
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life SciencesÅs, Norway
| | - Torben Asp
- Department of Molecular Biology and Genetics, Aarhus UniversitySlagelse, Denmark
| | - Matthew Peter Kent
- Department of Animal and Aquacultural Sciences, Centre for Integrative Genetics, Norwegian University of Life SciencesÅs, Norway
| | - Odd Arne Rognli
- Department of Plant Sciences, Centre for Integrative Genetics, Norwegian University of Life SciencesÅs, Norway
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Sim SC, Robbins MD, Wijeratne S, Wang H, Yang W, Francis DM. Association Analysis for Bacterial Spot Resistance in a Directionally Selected Complex Breeding Population of Tomato. PHYTOPATHOLOGY 2015; 105:1437-45. [PMID: 26509802 DOI: 10.1094/phyto-02-15-0051-r] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Bacterial spot of tomato is caused by at least four species of Xanthomonas with multiple physiological races. We developed a complex breeding population for simultaneous discovery of marker-trait linkage, validation of existing quantitative trait loci (QTL), and pyramiding of resistance. Six advanced accessions with resistance from distinct sources were crossed in all combinations and their F1 hybrids were intercrossed. Over 1,100 segregating progeny were evaluated in the field following inoculation with X. euvesicatoria race T1 strains. We selected 5% of the most resistant and 5% of the most susceptible progeny for evaluation as plots in two subsequent replicated field trials inoculated with T1 and T3 (X. perforans) strains. The estimated heritability of T1 resistance was 0.32. In order to detect previously reported resistance genes, as well as novel QTL, we explored methods to correct for population structure and analysis based on single markers or haplotypes. Both single-point and haplotype analyses identified strong associations in the genomic regions known to carry Rx-3 (chromosome 5) and Rx-4/Xv3 (chromosome 11). Accounting for kinship and structure generally improved the fit of statistical models. Detection of known loci was improved by adding kinship or a combination of kinship and structure using a Q matrix from model-based clustering. Additional QTL were detected on chromosomes 1, 4, 6, and 7 for T1 resistance and chromosomes 2, 4, and 6 for T3 resistance (P < 0.01). Haplotype analysis improved our ability to trace the origin of positive alleles. These results demonstrate that both known and novel associations can be identified using complex breeding populations that have experienced directional selection.
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Affiliation(s)
- Sung-Chur Sim
- First, second, and sixth authors: Department of Horticulture and Crop Science, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster 44691; first author: Department of Bioresources Engineering, Sejong University, 98 Gunja-dong Gwangjin-gu Seoul, 143-747 Korea; second author: USDA Forage & Range Research Laboratory, Logan, UT 84322; third author: Molecular and Cellular Imaging Center, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster 44691; fourth and fifth authors: Department of Vegetable Science, China Agricultural University, Beijing 100193, China; and fourth author: Dupont Pioneer, Woodstock, ON, N4S 7V6, Canada
| | - Matthew D Robbins
- First, second, and sixth authors: Department of Horticulture and Crop Science, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster 44691; first author: Department of Bioresources Engineering, Sejong University, 98 Gunja-dong Gwangjin-gu Seoul, 143-747 Korea; second author: USDA Forage & Range Research Laboratory, Logan, UT 84322; third author: Molecular and Cellular Imaging Center, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster 44691; fourth and fifth authors: Department of Vegetable Science, China Agricultural University, Beijing 100193, China; and fourth author: Dupont Pioneer, Woodstock, ON, N4S 7V6, Canada
| | - Saranga Wijeratne
- First, second, and sixth authors: Department of Horticulture and Crop Science, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster 44691; first author: Department of Bioresources Engineering, Sejong University, 98 Gunja-dong Gwangjin-gu Seoul, 143-747 Korea; second author: USDA Forage & Range Research Laboratory, Logan, UT 84322; third author: Molecular and Cellular Imaging Center, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster 44691; fourth and fifth authors: Department of Vegetable Science, China Agricultural University, Beijing 100193, China; and fourth author: Dupont Pioneer, Woodstock, ON, N4S 7V6, Canada
| | - Hui Wang
- First, second, and sixth authors: Department of Horticulture and Crop Science, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster 44691; first author: Department of Bioresources Engineering, Sejong University, 98 Gunja-dong Gwangjin-gu Seoul, 143-747 Korea; second author: USDA Forage & Range Research Laboratory, Logan, UT 84322; third author: Molecular and Cellular Imaging Center, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster 44691; fourth and fifth authors: Department of Vegetable Science, China Agricultural University, Beijing 100193, China; and fourth author: Dupont Pioneer, Woodstock, ON, N4S 7V6, Canada
| | - Wencai Yang
- First, second, and sixth authors: Department of Horticulture and Crop Science, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster 44691; first author: Department of Bioresources Engineering, Sejong University, 98 Gunja-dong Gwangjin-gu Seoul, 143-747 Korea; second author: USDA Forage & Range Research Laboratory, Logan, UT 84322; third author: Molecular and Cellular Imaging Center, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster 44691; fourth and fifth authors: Department of Vegetable Science, China Agricultural University, Beijing 100193, China; and fourth author: Dupont Pioneer, Woodstock, ON, N4S 7V6, Canada
| | - David M Francis
- First, second, and sixth authors: Department of Horticulture and Crop Science, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster 44691; first author: Department of Bioresources Engineering, Sejong University, 98 Gunja-dong Gwangjin-gu Seoul, 143-747 Korea; second author: USDA Forage & Range Research Laboratory, Logan, UT 84322; third author: Molecular and Cellular Imaging Center, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster 44691; fourth and fifth authors: Department of Vegetable Science, China Agricultural University, Beijing 100193, China; and fourth author: Dupont Pioneer, Woodstock, ON, N4S 7V6, Canada
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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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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 DOI: 10.1371/journalpone.0137139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 08/12/2015] [Indexed: 05/26/2023] 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
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Scarano D, Rao R, Masi P, Corrado G. SSR fingerprint reveals mislabeling in commercial processed tomato products. Food Control 2015. [DOI: 10.1016/j.foodcont.2014.12.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Blanca J, Montero-Pau J, Sauvage C, Bauchet G, Illa E, Díez MJ, Francis D, Causse M, van der Knaap E, Cañizares J. Genomic variation in tomato, from wild ancestors to contemporary breeding accessions. BMC Genomics 2015; 16:257. [PMID: 25880392 PMCID: PMC4404671 DOI: 10.1186/s12864-015-1444-1] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 03/06/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Domestication modifies the genomic variation of species. Quantifying this variation provides insights into the domestication process, facilitates the management of resources used by breeders and germplasm centers, and enables the design of experiments to associate traits with genes. We described and analyzed the genetic diversity of 1,008 tomato accessions including Solanum lycopersicum var. lycopersicum (SLL), S. lycopersicum var. cerasiforme (SLC), and S. pimpinellifolium (SP) that were genotyped using 7,720 SNPs. Additionally, we explored the allelic frequency of six loci affecting fruit weight and shape to infer patterns of selection. RESULTS Our results revealed a pattern of variation that strongly supported a two-step domestication process, occasional hybridization in the wild, and differentiation through human selection. These interpretations were consistent with the observed allele frequencies for the six loci affecting fruit weight and shape. Fruit weight was strongly selected in SLC in the Andean region of Ecuador and Northern Peru prior to the domestication of tomato in Mesoamerica. Alleles affecting fruit shape were differentially selected among SLL genetic subgroups. Our results also clarified the biological status of SLC. True SLC was phylogenetically positioned between SP and SLL and its fruit morphology was diverse. SLC and "cherry tomato" are not synonymous terms. The morphologically-based term "cherry tomato" included some SLC, contemporary varieties, as well as many admixtures between SP and SLL. Contemporary SLL showed a moderate increase in nucleotide diversity, when compared with vintage groups. CONCLUSIONS This study presents a broad and detailed representation of the genomic variation in tomato. Tomato domestication seems to have followed a two step-process; a first domestication in South America and a second step in Mesoamerica. The distribution of fruit weight and shape alleles supports that domestication of SLC occurred in the Andean region. Our results also clarify the biological status of SLC as true phylogenetic group within tomato. We detect Ecuadorian and Peruvian accessions that may represent a pool of unexplored variation that could be of interest for crop improvement.
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Affiliation(s)
- José Blanca
- Institute for the Conservation and Improvement of Agricultural Biodiversity (COMAV), Polytechnic University of Valencia, Camino de Vera 8E, 46022, Valencia, Spain.
| | - Javier Montero-Pau
- Institute for the Conservation and Improvement of Agricultural Biodiversity (COMAV), Polytechnic University of Valencia, Camino de Vera 8E, 46022, Valencia, Spain.
| | - Christopher Sauvage
- INRA, UR 1052 Unité de Génétique et Amélioration des Fruits et Légumes, Domaine Saint-Maurice, 67 Allée des Chênes CS60094, 84143, Montfavet Cedex, France.
| | - Guillaume Bauchet
- INRA, UR 1052 Unité de Génétique et Amélioration des Fruits et Légumes, Domaine Saint-Maurice, 67 Allée des Chênes CS60094, 84143, Montfavet Cedex, France. .,Syngenta seeds, 12 chemin de l'hobit, 31790, Saint-Sauveur, France.
| | - Eudald Illa
- Department of Horticulture and Crop Science, The Ohio State University/Ohio Agricultural Research and Development Center, Wooster, OH, 44691, USA.
| | - María José Díez
- Institute for the Conservation and Improvement of Agricultural Biodiversity (COMAV), Polytechnic University of Valencia, Camino de Vera 8E, 46022, Valencia, Spain.
| | - David Francis
- Department of Horticulture and Crop Science, The Ohio State University/Ohio Agricultural Research and Development Center, Wooster, OH, 44691, USA.
| | - Mathilde Causse
- INRA, UR 1052 Unité de Génétique et Amélioration des Fruits et Légumes, Domaine Saint-Maurice, 67 Allée des Chênes CS60094, 84143, Montfavet Cedex, France.
| | - Esther van der Knaap
- Department of Horticulture and Crop Science, The Ohio State University/Ohio Agricultural Research and Development Center, Wooster, OH, 44691, USA.
| | - Joaquín Cañizares
- Institute for the Conservation and Improvement of Agricultural Biodiversity (COMAV), Polytechnic University of Valencia, Camino de Vera 8E, 46022, Valencia, Spain.
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Menda N, Strickler SR, Edwards JD, Bombarely A, Dunham DM, Martin GB, Mejia L, Hutton SF, Havey MJ, Maxwell DP, Mueller LA. Analysis of wild-species introgressions in tomato inbreds uncovers ancestral origins. BMC PLANT BIOLOGY 2014; 14:287. [PMID: 25348801 PMCID: PMC4219026 DOI: 10.1186/s12870-014-0287-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 10/15/2014] [Indexed: 05/03/2023]
Abstract
BACKGROUND Decades of intensive tomato breeding using wild-species germplasm have resulted in the genomes of domesticated germplasm (Solanum lycopersicum) being intertwined with introgressions from their wild relatives. Comparative analysis of genomes among cultivated tomatoes and wild species that have contributed genetic variation can help identify desirable genes, such as those conferring disease resistance. The ability to identify introgression position, borders, and contents can reveal ancestral origins and facilitate harnessing of wild variation in crop breeding. RESULTS Here we present the whole-genome sequences of two tomato inbreds, Gh13 and BTI-87, both carrying the begomovirus resistance locus Ty-3 introgressed from wild tomato species. Introgressions of different sizes on chromosome 6 of Gh13 and BTI-87, both corresponding to the Ty-3 region, were identified as from a source close to the wild species S. chilense. Other introgressions were identified throughout the genomes of the inbreds and showed major differences in the breeding pedigrees of the two lines. Interestingly, additional large introgressions from the close tomato relative S. pimpinellifolium were identified in both lines. Some of the polymorphic regions were attributed to introgressions in the reference Heinz 1706 genome, indicating wild genome sequences in the reference tomato genome. CONCLUSIONS The methods developed in this work can be used to delineate genome introgressions, and subsequently contribute to development of molecular markers to aid phenotypic selection, fine mapping and discovery of candidate genes for important phenotypes, and for identification of novel variation for tomato improvement. These universal methods can easily be applied to other crop plants.
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Affiliation(s)
- Naama Menda
- />Boyce Thompson Institute for Plant Research, 533 Tower Rd, Ithaca, NY 14853 USA
| | - Susan R Strickler
- />Boyce Thompson Institute for Plant Research, 533 Tower Rd, Ithaca, NY 14853 USA
| | - Jeremy D Edwards
- />Boyce Thompson Institute for Plant Research, 533 Tower Rd, Ithaca, NY 14853 USA
| | - Aureliano Bombarely
- />Boyce Thompson Institute for Plant Research, 533 Tower Rd, Ithaca, NY 14853 USA
| | - Diane M Dunham
- />Boyce Thompson Institute for Plant Research, 533 Tower Rd, Ithaca, NY 14853 USA
| | - Gregory B Martin
- />Boyce Thompson Institute for Plant Research, 533 Tower Rd, Ithaca, NY 14853 USA
- />Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853 USA
| | - Luis Mejia
- />Facultad de Agronomía, Universidad de San Carlos de Guatemala, Guatemala City, 01012 Guatemala
| | - Samuel F Hutton
- />University of Florida, Gulf Coast Research and Education Center, 14625 CR 672, Wimauma, FL 33598 USA
| | - Michael J Havey
- />USDA-ARS Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, WI 53706 USA
| | - Douglas P Maxwell
- />Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Lukas A Mueller
- />Boyce Thompson Institute for Plant Research, 533 Tower Rd, Ithaca, NY 14853 USA
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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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Aflitos S, Schijlen E, de Jong H, de Ridder D, Smit S, Finkers R, Wang J, Zhang G, Li N, Mao L, Bakker F, Dirks R, Breit T, Gravendeel B, Huits H, Struss D, Swanson-Wagner R, van Leeuwen H, van Ham RCHJ, Fito L, Guignier L, Sevilla M, Ellul P, Ganko E, Kapur A, Reclus E, de Geus B, van de Geest H, Te Lintel Hekkert B, van Haarst J, Smits L, Koops A, Sanchez-Perez G, van Heusden AW, Visser R, Quan Z, Min J, Liao L, Wang X, Wang G, Yue Z, Yang X, Xu N, Schranz E, Smets E, Vos R, Rauwerda J, Ursem R, Schuit C, Kerns M, van den Berg J, Vriezen W, Janssen A, Datema E, Jahrman T, Moquet F, Bonnet J, Peters S. Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 80:136-48. [PMID: 25039268 DOI: 10.1111/tpj.12616] [Citation(s) in RCA: 228] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 06/23/2014] [Accepted: 07/01/2014] [Indexed: 05/20/2023]
Abstract
We explored genetic variation by sequencing a selection of 84 tomato accessions and related wild species representative of the Lycopersicon, Arcanum, Eriopersicon and Neolycopersicon groups, which has yielded a huge amount of precious data on sequence diversity in the tomato clade. Three new reference genomes were reconstructed to support our comparative genome analyses. Comparative sequence alignment revealed group-, species- and accession-specific polymorphisms, explaining characteristic fruit traits and growth habits in the various cultivars. Using gene models from the annotated Heinz 1706 reference genome, we observed differences in the ratio between non-synonymous and synonymous SNPs (dN/dS) in fruit diversification and plant growth genes compared to a random set of genes, indicating positive selection and differences in selection pressure between crop accessions and wild species. In wild species, the number of single-nucleotide polymorphisms (SNPs) exceeds 10 million, i.e. 20-fold higher than found in most of the crop accessions, indicating dramatic genetic erosion of crop and heirloom tomatoes. In addition, the highest levels of heterozygosity were found for allogamous self-incompatible wild species, while facultative and autogamous self-compatible species display a lower heterozygosity level. Using whole-genome SNP information for maximum-likelihood analysis, we achieved complete tree resolution, whereas maximum-likelihood trees based on SNPs from ten fruit and growth genes show incomplete resolution for the crop accessions, partly due to the effect of heterozygous SNPs. Finally, results suggest that phylogenetic relationships are correlated with habitat, indicating the occurrence of geographical races within these groups, which is of practical importance for Solanum genome evolution studies.
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Soto-Cerda BJ, Diederichsen A, Duguid S, Booker H, Rowland G, Cloutier S. The potential of pale flax as a source of useful genetic variation for cultivated flax revealed through molecular diversity and association analyses. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2014; 34:2091-2107. [PMID: 26316841 PMCID: PMC4544635 DOI: 10.1007/s11032-014-0165-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 07/29/2014] [Indexed: 05/25/2023]
Abstract
Pale flax (Linum bienne Mill.) is the wild progenitor of cultivated flax (Linum usitatissimum L.) and represents the primary gene pool to broaden its genetic base. Here, a collection of 125 pale flax accessions and the Canadian flax core collection of 407 accessions were genotyped using 112 genome-wide simple sequence repeat markers and phenotyped for nine traits with the aim of conducting population structure, molecular diversity and association mapping analyses. The combined population structure analysis identified two well-supported major groups corresponding to pale and cultivated flax. The L. usitatissimum convar. crepitans accessions most closely resembled its wild progenitor, both having dehiscent capsules. The unbiased Nei's genetic distance (0.65) confirmed the strong genetic differentiation between cultivated and pale flax. Similar levels of genetic diversity were observed in both species, albeit 430 (48 %) of pale flax alleles were unique, in agreement with their high genetic differentiation. Significant associations were identified for seven and four traits in pale and cultivated flax, respectively. Favorable alleles with potentially positive effect to improve yield through yield components were identified in pale flax. The allelic frequencies of markers associated with domestication-related traits such as capsular dehiscence indicated directional selection with the most common alleles in pale flax being absent or rare in cultivated flax and vice versa. Our results demonstrated that pale flax is a potential source of novel variation to improve multiple traits in cultivated flax and that association mapping is a suitable approach to screening pale flax germplasm to identify favorable quantitative trait locus alleles.
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Affiliation(s)
- Braulio J. Soto-Cerda
- Department of Plant Science, University of Manitoba, 66 Dafoe Road, Winnipeg, MB R3T 2N2, Canada
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Rd, Winnipeg, MB R3T 2M9 Canada
- Present Address: Agriaquaculture Nutritional Genomic Center, CGNA, Genomics and Bioinformatics Unit, 4791057 Temuco, Chile
| | - Axel Diederichsen
- Plant Gene Resources of Canada, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2 Canada
| | - Scott Duguid
- Morden Research Station, Agriculture and Agri-Food Canada, 101 Route 100, Unit 100, Morden, MB R6M 1Y5 Canada
| | - Helen Booker
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
| | - Gordon Rowland
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
| | - Sylvie Cloutier
- Department of Plant Science, University of Manitoba, 66 Dafoe Road, Winnipeg, MB R3T 2N2, Canada
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Rd, Winnipeg, MB R3T 2M9 Canada
- Present Address: Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
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Yang J, Wang Y, Shen H, Yang W. In silico identification and experimental validation of insertion-deletion polymorphisms in tomato genome. DNA Res 2014; 21:429-38. [PMID: 24618211 PMCID: PMC4131836 DOI: 10.1093/dnares/dsu008] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 02/04/2014] [Indexed: 11/14/2022] Open
Abstract
Comparative analysis of the genome sequences of Solanum lycopersicum variety Heinz 1706 and S. pimpinellifolium accession LA 1589 using MUGSY software identified 145 695 insertion-deletion (InDel) polymorphisms. A selected set of 3029 candidate InDels (≥2 bp) across the entire tomato genome were subjected to PCR validation, and 82.4% could be verified. Of 2272 polymorphic InDels between LA 1589 and Heinz 1706, 61.6, 45.2, and 31.6% were polymorphic in 8 accessions of S. pimpinellifolium, 4 accessions of S. lycopersicum var. cerasiforme, and 10 varieties of S. lycopersicum, respectively. Genetic distance was 0.216 in S. pimpinellifolium, 0.202 in S. lycopersicum var. cerasiforme, and 0.108 in S. lycopersicum. The data suggested a reduction of genetic variation from S. pimpinellifolium to S. lycopersicum var. cerasiforme and S. lycopersicum. Cluster analysis showed that the 8 accessions of S. pimpinellifolium were in one group, whereas 4 accessions of S. lycopersicum var. cerasiforme and 10 varieties of S. lycopersicum were in the same group.
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Affiliation(s)
- Jingjing Yang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing 100193, China
| | - Yuanyuan Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing 100193, China
| | - Huolin Shen
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing 100193, China
| | - Wencai Yang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing 100193, China
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Ercolano MR, Sacco A, Ferriello F, D'Alessandro R, Tononi P, Traini A, Barone A, Zago E, Chiusano ML, Buson G, Delledonne M, Frusciante L. Patchwork sequencing of tomato San Marzano and Vesuviano varieties highlights genome-wide variations. BMC Genomics 2014; 15:138. [PMID: 24548308 PMCID: PMC3936818 DOI: 10.1186/1471-2164-15-138] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 01/24/2014] [Indexed: 01/08/2023] Open
Abstract
Background Investigation of tomato genetic resources is a crucial issue for better straight evolution and genetic studies as well as tomato breeding strategies. Traditional Vesuviano and San Marzano varieties grown in Campania region (Southern Italy) are famous for their remarkable fruit quality. Owing to their economic and social importance is crucial to understand the genetic basis of their unique traits. Results Here, we present the draft genome sequences of tomato Vesuviano and San Marzano genome. A 40x genome coverage was obtained from a hybrid Illumina paired-end reads assembling that combines de novo assembly with iterative mapping to the reference S. lycopersicum genome (SL2.40). Insertions, deletions and SNP variants were carefully measured. When assessed on the basis of the reference annotation, 30% of protein-coding genes are predicted to have variants in both varieties. Copy genes number and gene location were assessed by mRNA transcripts mapping, showing a closer relationship of San Marzano with reference genome. Distinctive variations in key genes and transcription/regulation factors related to fruit quality have been revealed for both cultivars. Conclusions The effort performed highlighted varieties relationships and important variants in fruit key processes useful to dissect the path from sequence variant to phenotype.
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Affiliation(s)
- Maria Raffaella Ercolano
- Department of Agriculture Sciences, University of Naples Federico II, Via Universita' 100, 80055 Portici, Italy.
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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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Fang Z, Eule-Nashoba A, Powers C, Kono TY, Takuno S, Morrell PL, Smith KP. Comparative analyses identify the contributions of exotic donors to disease resistance in a barley experimental population. G3 (BETHESDA, MD.) 2013; 3:1945-53. [PMID: 24048643 PMCID: PMC3815057 DOI: 10.1534/g3.113.007294] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 09/03/2013] [Indexed: 11/18/2022]
Abstract
Introgression of novel genetic variation into breeding populations is frequently required to facilitate response to new abiotic or biotic pressure. This is particularly true for the introduction of host pathogen resistance in plant breeding. However, the number and genomic location of loci contributed by donor parents are often unknown, complicating efforts to recover desired agronomic phenotypes. We examined allele frequency differentiation in an experimental barley breeding population subject to introgression and subsequent selection for Fusarium head blight resistance. Allele frequency differentiation between the experimental population and the base population identified three primary genomic regions putatively subject to selection for resistance. All three genomic regions have been previously identified by quantitative trait locus (QTL) and association mapping. Based on the degree of identity-by-state relative to donor parents, putative donors of resistance alleles were also identified. The successful application of comparative population genetic approaches in this barley breeding experiment suggests that the approach could be applied to other breeding populations that have undergone defined breeding and selection histories, with the potential to provide valuable information for genetic improvement.
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Affiliation(s)
- Zhou Fang
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Amber Eule-Nashoba
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Carol Powers
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Thomas Y. Kono
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Shohei Takuno
- Graduate University for Advanced Studies, Hayama, Kanagawa 240-0193, Japan
| | - Peter L. Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Kevin P. Smith
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
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Ren J, Chen L, Sun D, You FM, Wang J, Peng Y, Nevo E, Beiles A, Sun D, Luo MC, Peng J. SNP-revealed genetic diversity in wild emmer wheat correlates with ecological factors. BMC Evol Biol 2013; 13:169. [PMID: 23937410 PMCID: PMC3751623 DOI: 10.1186/1471-2148-13-169] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 08/02/2013] [Indexed: 11/10/2022] Open
Abstract
Background Patterns of genetic diversity between and within natural plant populations and their driving forces are of great interest in evolutionary biology. However, few studies have been performed on the genetic structure and population divergence in wild emmer wheat using a large number of EST-related single nucleotide polymorphism (SNP) markers. Results In the present study, twenty-five natural wild emmer wheat populations representing a wide range of ecological conditions in Israel and Turkey were used. Genetic diversity and genetic structure were investigated using over 1,000 SNP markers. A moderate level of genetic diversity was detected due to the biallelic property of SNP markers. Clustering based on Bayesian model showed that grouping pattern is related to the geographical distribution of the wild emmer wheat. However, genetic differentiation between populations was not necessarily dependent on the geographical distances. A total of 33 outlier loci under positive selection were identified using a FST-outlier method. Significant correlations between loci and ecogeographical factors were observed. Conclusions Natural selection appears to play a major role in generating adaptive structures in wild emmer wheat. SNP markers are appropriate for detecting selectively-channeled adaptive genetic diversity in natural populations of wild emmer wheat. This adaptive genetic diversity is significantly associated with ecological factors.
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Affiliation(s)
- Jing Ren
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
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Ren J, Sun D, Chen L, You FM, Wang J, Peng Y, Nevo E, Sun D, Luo MC, Peng J. Genetic diversity revealed by single nucleotide polymorphism markers in a worldwide germplasm collection of durum wheat. Int J Mol Sci 2013; 14:7061-88. [PMID: 23538839 PMCID: PMC3645677 DOI: 10.3390/ijms14047061] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 02/23/2013] [Accepted: 03/01/2013] [Indexed: 11/25/2022] Open
Abstract
Evaluation of genetic diversity and genetic structure in crops has important implications for plant breeding programs and the conservation of genetic resources. Newly developed single nucleotide polymorphism (SNP) markers are effective in detecting genetic diversity. In the present study, a worldwide durum wheat collection consisting of 150 accessions was used. Genetic diversity and genetic structure were investigated using 946 polymorphic SNP markers covering the whole genome of tetraploid wheat. Genetic structure was greatly impacted by multiple factors, such as environmental conditions, breeding methods reflected by release periods of varieties, and gene flows via human activities. A loss of genetic diversity was observed from landraces and old cultivars to the modern cultivars released during periods of the Early Green Revolution, but an increase in cultivars released during the Post Green Revolution. Furthermore, a comparative analysis of genetic diversity among the 10 mega ecogeographical regions indicated that South America, North America, and Europe possessed the richest genetic variability, while the Middle East showed moderate levels of genetic diversity.
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Affiliation(s)
- Jing Ren
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Chinese Academy of Sciences, Wuhan 430074, Hubei, China; E-Mails: (J.R.); (D.S.); (L.C.)
- Graduate University of Chinese Academy of Sciences, Beijing 100049, China
| | - Daokun Sun
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Chinese Academy of Sciences, Wuhan 430074, Hubei, China; E-Mails: (J.R.); (D.S.); (L.C.)
| | - Liang Chen
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Chinese Academy of Sciences, Wuhan 430074, Hubei, China; E-Mails: (J.R.); (D.S.); (L.C.)
| | - Frank M. You
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; E-Mails: (F.M.Y.); (J.W.)
- Cereal Research Centre, Agriculture and Agri-Food Canada, Winnipeg, MB R3T 2M9, Canada
| | - Jirui Wang
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; E-Mails: (F.M.Y.); (J.W.)
| | - Yunliang Peng
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu 610066, Sichuan, China; E-Mail:
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel; E-Mail:
| | - Dongfa Sun
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430071, Hubei, China; E-Mail:
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; E-Mails: (F.M.Y.); (J.W.)
| | - Junhua Peng
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Chinese Academy of Sciences, Wuhan 430074, Hubei, China; E-Mails: (J.R.); (D.S.); (L.C.)
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA
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Sim SC, Van Deynze A, Stoffel K, Douches DS, Zarka D, Ganal MW, Chetelat RT, Hutton SF, Scott JW, Gardner RG, Panthee DR, Mutschler M, Myers JR, Francis DM. High-density SNP genotyping of tomato (Solanum lycopersicum L.) reveals patterns of genetic variation due to breeding. PLoS One 2012; 7:e45520. [PMID: 23029069 PMCID: PMC3447764 DOI: 10.1371/journal.pone.0045520] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 08/21/2012] [Indexed: 01/17/2023] Open
Abstract
The effects of selection on genome variation were investigated and visualized in tomato using a high-density single nucleotide polymorphism (SNP) array. 7,720 SNPs were genotyped on a collection of 426 tomato accessions (410 inbreds and 16 hybrids) and over 97% of the markers were polymorphic in the entire collection. Principal component analysis (PCA) and pairwise estimates of F(st) supported that the inbred accessions represented seven sub-populations including processing, large-fruited fresh market, large-fruited vintage, cultivated cherry, landrace, wild cherry, and S. pimpinellifolium. Further divisions were found within both the contemporary processing and fresh market sub-populations. These sub-populations showed higher levels of genetic diversity relative to the vintage sub-population. The array provided a large number of polymorphic SNP markers across each sub-population, ranging from 3,159 in the vintage accessions to 6,234 in the cultivated cherry accessions. Visualization of minor allele frequency revealed regions of the genome that distinguished three representative sub-populations of cultivated tomato (processing, fresh market, and vintage), particularly on chromosomes 2, 4, 5, 6, and 11. The PCA loadings and F(st) outlier analysis between these three sub-populations identified a large number of candidate loci under positive selection on chromosomes 4, 5, and 11. The extent of linkage disequilibrium (LD) was examined within each chromosome for these sub-populations. LD decay varied between chromosomes and sub-populations, with large differences reflective of breeding history. For example, on chromosome 11, decay occurred over 0.8 cM for processing accessions and over 19.7 cM for fresh market accessions. The observed SNP variation and LD decay suggest that different patterns of genetic variation in cultivated tomato are due to introgression from wild species and selection for market specialization.
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Affiliation(s)
- Sung-Chur Sim
- Department of Horticulture and Crop Science, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster, Ohio, United States of America
| | - Allen Van Deynze
- Seed Biotechnology Center, University of California Davis, Davis, California, United States of America
| | - Kevin Stoffel
- Seed Biotechnology Center, University of California Davis, Davis, California, United States of America
| | - David S. Douches
- Department of Crop and Soil Sciences, Michigan State University, East Lansing, Michigan, United States of America
| | - Daniel Zarka
- Department of Crop and Soil Sciences, Michigan State University, East Lansing, Michigan, United States of America
| | | | - Roger T. Chetelat
- C. M. Rick Tomato Genetic Resource Center, University of California Davis, Davis, California, United States of America
| | - Samuel F. Hutton
- University of Florida, Gulf Coast Research and Education Center, Wimauma, Florida, United States of America
| | - John W. Scott
- University of Florida, Gulf Coast Research and Education Center, Wimauma, Florida, United States of America
| | - Randolph G. Gardner
- Department of Horticultural Science, North Carolina State University, Mountain Horticultural Crops Research and Extension Center, Mills River, North Carolina, United States of America
| | - Dilip R. Panthee
- Department of Horticultural Science, North Carolina State University, Mountain Horticultural Crops Research and Extension Center, Mills River, North Carolina, United States of America
| | - Martha Mutschler
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York, United States of America
| | - James R. Myers
- Department of Horticulture, Oregon State University, Corvallis, Oregon, United States of America
| | - David M. Francis
- Department of Horticulture and Crop Science, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster, Ohio, United States of America
- * E-mail:
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