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Pons C, Casals J, Brower M, Sacco A, Riccini A, Hendrickx P, Figás MDR, Fisher J, Grandillo S, Mazzucato A, Soler S, Zamir D, Causse M, Díez MJ, Finkers R, Prohens J, Monforte AJ, Granell A. Diversity and genetic architecture of agro-morphological traits in a core collection of European traditional tomato. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5896-5916. [PMID: 37527560 PMCID: PMC10540738 DOI: 10.1093/jxb/erad306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 07/28/2023] [Indexed: 08/03/2023]
Abstract
European traditional tomato varieties have been selected by farmers given their consistent performance and adaptation to local growing conditions. Here we developed a multipurpose core collection, comprising 226 accessions representative of the genotypic, phenotypic, and geographical diversity present in European traditional tomatoes, to investigate the basis of their phenotypic variation, gene×environment interactions, and stability for 33 agro-morphological traits. Comparison of the traditional varieties with a modern reference panel revealed that some traditional varieties displayed excellent agronomic performance and high trait stability, as good as or better than that of their modern counterparts. We conducted genome-wide association and genome-wide environment interaction studies and detected 141 quantitative trait loci (QTLs). Out of those, 47 QTLs were associated with the phenotype mean (meanQTLs), 41 with stability (stbQTLs), and 53 QTL-by-environment interactions (QTIs). Most QTLs displayed additive gene actions, with the exception of stbQTLs, which were mostly recessive and overdominant QTLs. Both common and specific loci controlled the phenotype mean and stability variation in traditional tomato; however, a larger proportion of specific QTLs was observed, indicating that the stability gene regulatory model is the predominant one. Developmental genes tended to map close to meanQTLs, while genes involved in stress response, hormone metabolism, and signalling were found within regions affecting stability. A total of 137 marker-trait associations for phenotypic means and stability were novel, and therefore our study enhances the understanding of the genetic basis of valuable agronomic traits and opens up a new avenue for an exploitation of the allelic diversity available within European traditional tomato germplasm.
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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
| | - Matthijs Brower
- Wageningen University & Research, Plant Breeding, POB 386, NL-6700 AJ Wageningen, The Netherlands
| | - Adriana Sacco
- Institute of Biosciences and BioResources (IBBR), National Research Council of Italy (CNR), Via Università 133, 80055 Portici, Italy
| | - Alessandro Riccini
- Department of Agriculture and Forest Sciences (DAFNE), Università degli Studi della Tuscia, Viterbo, Italy
| | - Patrick Hendrickx
- Wageningen University & Research, Plant Breeding, POB 386, NL-6700 AJ Wageningen, The Netherlands
| | - Maria del Rosario Figás
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, València, Spain
| | - Josef Fisher
- Hebrew University of Jerusalem, Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Rehovot, Israel
| | - 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
| | - Salvador Soler
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, València, Spain
| | - Dani Zamir
- Hebrew University of Jerusalem, Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Rehovot, Israel
| | - Mathilde Causse
- INRAE, UR1052, Génétique et Amélioration des Fruits et Légumes 67 Allée des Chênes, 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
| | - Richard Finkers
- Wageningen University & Research, Plant Breeding, POB 386, NL-6700 AJ Wageningen, The Netherlands
| | - 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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Recent Large-Scale Genotyping and Phenotyping of Plant Genetic Resources of Vegetatively Propagated Crops. PLANTS 2021; 10:plants10020415. [PMID: 33672381 PMCID: PMC7926561 DOI: 10.3390/plants10020415] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/19/2021] [Accepted: 02/19/2021] [Indexed: 12/12/2022]
Abstract
Several recent national and international projects have focused on large-scale genotyping of plant genetic resources in vegetatively propagated crops like fruit and berries, potatoes and woody ornamentals. The primary goal is usually to identify true-to-type plant material, detect possible synonyms, and investigate genetic diversity and relatedness among accessions. A secondary goal may be to create sustainable databases that can be utilized in research and breeding for several years ahead. Commonly applied DNA markers (like microsatellite DNA and SNPs) and next-generation sequencing each have their pros and cons for these purposes. Methods for large-scale phenotyping have lagged behind, which is unfortunate since many commercially important traits (yield, growth habit, storability, and disease resistance) are difficult to score. Nevertheless, the analysis of gene action and development of robust DNA markers depends on environmentally controlled screening of very large sets of plant material. Although more time-consuming, co-operative projects with broad-scale data collection are likely to produce more reliable results. In this review, we will describe some of the approaches taken in genotyping and/or phenotyping projects concerning a wide variety of vegetatively propagated crops.
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Cirilli M, Micali S, Aranzana MJ, Arús P, Babini A, Barreneche T, Bink M, Cantin CM, Ciacciulli A, Cos-Terrer JE, Drogoudi P, Eduardo I, Foschi S, Giovannini D, Guerra W, Liverani A, Pacheco I, Pascal T, Quilot-Turion B, Verde I, Rossini L, Bassi D. The Multisite PeachRefPop Collection: A True Cultural Heritage and International Scientific Tool for Fruit Trees. PLANT PHYSIOLOGY 2020; 184:632-646. [PMID: 32727910 PMCID: PMC7536698 DOI: 10.1104/pp.19.01412] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 07/17/2020] [Indexed: 05/21/2023]
Abstract
Plants have evolved a range of adaptive mechanisms that adjust their development and physiology to variable external conditions, particularly in perennial species subjected to long-term interplay with the environment. Exploiting the allelic diversity within available germplasm and leveraging the knowledge of the mechanisms regulating genotype interaction with the environment are crucial to address climatic challenges and assist the breeding of novel cultivars with improved resilience. The development of multisite collections is of utmost importance for the conservation and utilization of genetic materials and will greatly facilitate the dissection of genotype-by-environment interaction. Such resources are still lacking for perennial trees, especially with the intrinsic difficulties of successful propagation, material exchange, and living collection maintenance. This work describes the concept, design, and realization of the first multisite peach (Prunus persica) reference collection (PeachRefPop) located across different European countries and sharing the same experimental design. Other than an invaluable tool for scientific studies in perennial species, PeachRefPop provides a milestone in an international collaborative project for the conservation and exploitation of European peach germplasm resources and, ultimately, as a true heritage for future generations.
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Affiliation(s)
- Marco Cirilli
- Department of Agricultural and Environmental Sciences, University of Milan, 20133 Milan, Italy
| | - Sabrina Micali
- Consiglio Per La Ricerca In Agricoltura E L'analisi Dell'Economia Agraria, Research Centre for Olive, Fruit, and Citrus Crops, 00134 Rome, Italy
| | - Maria José Aranzana
- Institut de Recerca i Tecnologia Agroalimentàries, Centre de Recerca en Agrigenòmica Consejo Superior de Investigaciones Científicas, Institut de Recerca i Tecnologia Agroalimentàries, Universitat Autònoma de Barcelona, Universitat de Barcelona, Campus UAB, 08193 Barcelona, Spain
| | - Pere Arús
- Institut de Recerca i Tecnologia Agroalimentàries, Centre de Recerca en Agrigenòmica Consejo Superior de Investigaciones Científicas, Institut de Recerca i Tecnologia Agroalimentàries, Universitat Autònoma de Barcelona, Universitat de Barcelona, Campus UAB, 08193 Barcelona, Spain
| | - Annarosa Babini
- Phytosanitary Service, Regione Emilia-Romagna, 40128 Bologna, Italy
| | - Teresa Barreneche
- Université de Bordeaux, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, France
| | - Marco Bink
- Hendrix Genetics Research, Technology, and Services, 5830 AC Boxmeer, The Netherlands
| | - Celia M Cantin
- Institut de Recerca i Tecnologia Agroalimentàries, Centre de Recerca en Agrigenòmica Consejo Superior de Investigaciones Científicas, Institut de Recerca i Tecnologia Agroalimentàries, Universitat Autònoma de Barcelona, Universitat de Barcelona, Campus UAB, 08193 Barcelona, Spain
| | - Angelo Ciacciulli
- Department of Agricultural and Environmental Sciences, University of Milan, 20133 Milan, Italy
| | | | - Pavlina Drogoudi
- Hellenic Agricultural Organization 'Demeter', Department of Deciduous Fruit Trees, Institute of Plant Breeding and Genetic Resources, 59200 Naoussa, Greece
| | - Iban Eduardo
- Institut de Recerca i Tecnologia Agroalimentàries, Centre de Recerca en Agrigenòmica Consejo Superior de Investigaciones Científicas, Institut de Recerca i Tecnologia Agroalimentàries, Universitat Autònoma de Barcelona, Universitat de Barcelona, Campus UAB, 08193 Barcelona, Spain
| | - Stefano Foschi
- Centro Ricerche Produzioni Vegetali, 47522 Cesena, Italy
| | - Daniela Giovannini
- Consiglio per la Ricerca in Agricoltura e L'Analisi Del'Economia Agraria, Research Centre for Olive, Fruit, and Citrus Crops, 47121 Forlì, Italy
| | | | - Alessandro Liverani
- Consiglio per la Ricerca in Agricoltura e L'Analisi Del'Economia Agraria, Research Centre for Olive, Fruit, and Citrus Crops, 47121 Forlì, Italy
| | - Igor Pacheco
- Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, 7830490 Macul, Chile
| | - Thierry Pascal
- Institut National de Recherche pour L'Agriculture, L'Alimentation et L'Environnement, Génétique et Amélioration des Fruits et Légumes, F-84143 Montfavet, France
| | - Benedicte Quilot-Turion
- Institut National de Recherche pour L'Agriculture, L'Alimentation et L'Environnement, Génétique et Amélioration des Fruits et Légumes, F-84143 Montfavet, France
| | - Ignazio Verde
- Consiglio Per La Ricerca In Agricoltura E L'analisi Dell'Economia Agraria, Research Centre for Olive, Fruit, and Citrus Crops, 00134 Rome, Italy
| | - Laura Rossini
- Department of Agricultural and Environmental Sciences, University of Milan, 20133 Milan, Italy
| | - Daniele Bassi
- Department of Agricultural and Environmental Sciences, University of Milan, 20133 Milan, Italy
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Chinese Fir Breeding in the High-Throughput Sequencing Era: Insights from SNPs. FORESTS 2019. [DOI: 10.3390/f10080681] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Knowledge on population diversity and structure is of fundamental importance for conifer breeding programs. In this study, we concentrated on the development and application of high-density single nucleotide polymorphism (SNP) markers through a high-throughput sequencing technique termed as specific-locus amplified fragment sequencing (SLAF-seq) for the economically important conifer tree species, Chinese fir (Cunninghamia lanceolata). Based on the SLAF-seq, we successfully established a high-density SNP panel consisting of 108,753 genomic SNPs from Chinese fir. This SNP panel facilitated us in gaining insight into the genetic base of the Chinese fir advance breeding population with 221 genotypes for its genetic variation, relationship and diversity, and population structure status. Overall, the present population appears to have considerable genetic variability. Most (94.15%) of the variability was attributed to the genetic differentiation of genotypes, very limited (5.85%) variation occurred on the population (sub-origin set) level. Correspondingly, low FST (0.0285–0.0990) values were seen for the sub-origin sets. When viewing the genetic structure of the population regardless of its sub-origin set feature, the present SNP data opened a new population picture where the advanced Chinese fir breeding population could be divided into four genetic sets, as evidenced by phylogenetic tree and population structure analysis results, albeit some difference in membership of the corresponding set (cluster vs. group). It also suggested that all the genetic sets were admixed clades revealing a complex relationship of the genotypes of this population. With a step wise pruning procedure, we captured a core collection (core 0.650) harboring 143 genotypes that maintains all the allele, diversity, and specific genetic structure of the whole population. This generalist core is valuable for the Chinese fir advanced breeding program and further genetic/genomic studies.
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