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Barchi L, Aprea G, Rabanus-Wallace MT, Toppino L, Alonso D, Portis E, Lanteri S, Gaccione L, Omondi E, van Zonneveld M, Schafleitner R, Ferrante P, Börner A, Stein N, Díez MJ, Lefebvre V, Salinier J, Boyaci HF, Finkers R, Brouwer M, Bovy AG, Rotino GL, Prohens J, Giuliano G. Analysis of >3400 worldwide eggplant accessions reveals two independent domestication events and multiple migration-diversification routes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1667-1680. [PMID: 37682777 DOI: 10.1111/tpj.16455] [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: 12/13/2022] [Accepted: 08/26/2023] [Indexed: 09/10/2023]
Abstract
Eggplant (Solanum melongena) is an important Solanaceous crop, widely cultivated and consumed in Asia, the Mediterranean basin, and Southeast Europe. Its domestication centers and migration and diversification routes are still a matter of debate. We report the largest georeferenced and genotyped collection to this date for eggplant and its wild relatives, consisting of 3499 accessions from seven worldwide genebanks, originating from 105 countries in five continents. The combination of genotypic and passport data points to the existence of at least two main centers of domestication, in Southeast Asia and the Indian subcontinent, with limited genetic exchange between them. The wild and weedy eggplant ancestor S. insanum shows admixture with domesticated S. melongena, similar to what was described for other fruit-bearing Solanaceous crops such as tomato and pepper and their wild ancestors. After domestication, migration and admixture of eggplant populations from different regions have been less conspicuous with respect to tomato and pepper, thus better preserving 'local' phenotypic characteristics. The data allowed the identification of misclassified and putatively duplicated accessions, facilitating genebank management. All the genetic, phenotypic, and passport data have been deposited in the Open Access G2P-SOL database, and constitute an invaluable resource for understanding the domestication, migration and diversification of this cosmopolitan vegetable.
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Affiliation(s)
- Lorenzo Barchi
- DISAFA - Plant Genetics, University of Turin, Grugliasco, Torino, 10095, Italy
| | - Giuseppe Aprea
- ENEA, Casaccia Res Ctr, Via Anguillarese 301, Rome, 00123, Italy
| | - M Timothy Rabanus-Wallace
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Seeland, OT Gatersleben, 06466, Germany
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Australia
| | - Laura Toppino
- CREA, Research Centre for Genomics and Bioinformatics, Via Paullese 28, Montanaso Lombardo, LO 26836, Italy
| | - David Alonso
- Universitat Politècnica de València, Camino de Vera 14, Valencia, 46022, Spain
| | - Ezio Portis
- DISAFA - Plant Genetics, University of Turin, Grugliasco, Torino, 10095, Italy
| | - Sergio Lanteri
- DISAFA - Plant Genetics, University of Turin, Grugliasco, Torino, 10095, Italy
| | - Luciana Gaccione
- DISAFA - Plant Genetics, University of Turin, Grugliasco, Torino, 10095, Italy
| | | | | | | | - Paola Ferrante
- ENEA, Casaccia Res Ctr, Via Anguillarese 301, Rome, 00123, Italy
| | - Andreas Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Seeland, OT Gatersleben, 06466, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Seeland, OT Gatersleben, 06466, Germany
- Department of Crop Sciences, Center for Integrated Breeding Research (CiBreed), Georg-August-University, Von Siebold Str. 8, Göttingen, 37075, Germany
| | - Maria José Díez
- Universitat Politècnica de València, Camino de Vera 14, Valencia, 46022, Spain
| | | | - Jérémy Salinier
- INRAE, GAFL, Montfavet, F-84140, France
- CIRAD La Réunion et Mayotte, UMR PVBMT Saint-Pierre, La Réunion, France
| | - Hatice Filiz Boyaci
- Department of Horticulture, Faculty of Agriculture, University of Recep Tayyip Erdogan, Rize, Turkey
| | - Richard Finkers
- Wageningen University & Research WUR, Wageningen, The Netherlands
- GenNovation B.V., Wageningen, The Netherlands
| | - Matthijs Brouwer
- Wageningen University & Research WUR, Wageningen, The Netherlands
| | - Arnaud G Bovy
- Wageningen University & Research WUR, Wageningen, The Netherlands
| | - Giuseppe Leonardo Rotino
- CREA, Research Centre for Genomics and Bioinformatics, Via Paullese 28, Montanaso Lombardo, LO 26836, Italy
| | - Jaime Prohens
- Universitat Politècnica de València, Camino de Vera 14, Valencia, 46022, Spain
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Gaccione L, Martina M, Barchi L, Portis E. A Compendium for Novel Marker-Based Breeding Strategies in Eggplant. PLANTS (BASEL, SWITZERLAND) 2023; 12:1016. [PMID: 36903876 PMCID: PMC10005326 DOI: 10.3390/plants12051016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/06/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
The worldwide production of eggplant is estimated at about 58 Mt, with China, India and Egypt being the major producing countries. Breeding efforts in the species have mainly focused on increasing productivity, abiotic and biotic tolerance/resistance, shelf-life, the content of health-promoting metabolites in the fruit rather than decreasing the content of anti-nutritional compounds in the fruit. From the literature, we collected information on mapping quantitative trait loci (QTLs) affecting eggplant's traits following a biparental or multi-parent approach as well as genome-wide association (GWA) studies. The positions of QTLs were lifted according to the eggplant reference line (v4.1) and more than 700 QTLs were identified, here organized into 180 quantitative genomic regions (QGRs). Our findings thus provide a tool to: (i) determine the best donor genotypes for specific traits; (ii) narrow down QTL regions affecting a trait by combining information from different populations; (iii) pinpoint potential candidate genes.
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A Genomic BSAseq Approach for the Characterization of QTLs Underlying Resistance to Fusarium oxysporum in Eggplant. Cells 2022; 11:cells11162548. [PMID: 36010625 PMCID: PMC9406753 DOI: 10.3390/cells11162548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/12/2022] [Accepted: 08/12/2022] [Indexed: 11/17/2022] Open
Abstract
Eggplant (Solanum melongena L.), similar to many other crops, suffers from soil-borne diseases, including Fusarium oxysporum f. sp. melongenae (Fom), causing wilting and heavy yield loss. To date, the genetic factors underlying plant responses to Fom are not well known. We previously developed a Recombinant Inbred Lines (RILs) population using as a female parent the fully resistant line ‘305E40’ and as a male parent the partially resistant line ‘67/3’. The fully resistant trait to Fom was introgressed from the allied species S. aethiopicum. In this work, the RIL population was assessed for the responses to Fom and by using a genomic mapping approach, two major QTLs on chromosomes CH02 and CH11 were identified, associated with the full and partial resistance trait to Fom, respectively. A targeted BSAseq procedure in which Illumina reads bulks of RILs grouped according to their resistance score was aligned to the appropriate reference genomes highlighted differentially enriched regions between resistant/susceptible progeny in the genomic regions underlying both QTLs. The characterization of such regions allowed us to identify the most reliable candidate genes for the two resistance traits. With the aim of revealing exclusive species-specific contigs and scaffolds inherited from the allied species and thus associated with the full resistance trait, a draft de-novo assembly of available Illumina sequences of the ‘305E40’ parent was developed to better resolve the non-recombining genomic region on its CH02 carrying the introgressed Fom resistance locus from S. aethiopicum.
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Salinier J, Lefebvre V, Besombes D, Burck H, Causse M, Daunay MC, Dogimont C, Goussopoulos J, Gros C, Maisonneuve B, McLeod L, Tobal F, Stevens R. The INRAE Centre for Vegetable Germplasm: Geographically and Phenotypically Diverse Collections and Their Use in Genetics and Plant Breeding. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11030347. [PMID: 35161327 PMCID: PMC8838894 DOI: 10.3390/plants11030347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 05/14/2023]
Abstract
The French National Research Institute for Agriculture, Food and the Environment (INRAE) conserves and distributes five vegetable collections as seeds: the aubergine* (in this article the word aubergine refers to eggplant), pepper, tomato, melon and lettuce collections, together with their wild or cultivated relatives, are conserved in Avignon, France. Accessions from the collections have geographically diverse origins, are generally well-described and fixed for traits of agronomic or scientific interest and have available passport data. In addition to currently conserving over 10,000 accessions (between 900 and 3000 accessions per crop), the centre maintains scientific collections such as core collections and bi- or multi-parental populations, which have also been genotyped with SNP markers. Each collection has its own merits and highlights, which are discussed in this review: the aubergine collection is a rich source of crop wild relatives of Solanum; the pepper, melon and lettuce collections have been screened for resistance to plant pathogens, including viruses, fungi, oomycetes and insects; and the tomato collection has been at the heart of genome-wide association studies for fruit quality traits and environmental stress tolerance.
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Burban E, Tenaillon MI, Le Rouzic A. Gene network simulations provide testable predictions for the molecular domestication syndrome. Genetics 2021; 220:6440055. [PMID: 34849852 DOI: 10.1093/genetics/iyab214] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/15/2021] [Indexed: 11/14/2022] Open
Abstract
The domestication of plant species lead to repeatable morphological evolution, often referred to as the phenotypic domestication syndrome. Domestication is also associated with important genomic changes, such as the loss of genetic diversity compared to adequately large wild populations, and modifications of gene expression patterns. Here, we explored theoretically the effect of a domestication-like scenario on the evolution of gene regulatory networks. We ran population genetics simulations in which individuals were featured by their genotype (an interaction matrix encoding a gene regulatory network) and their gene expressions, representing the phenotypic level. Our domestication scenario included a population bottleneck and a selection switch mimicking human-mediated directional and canalizing selection, i.e., change in the optimal gene expression level and selection towards more stable expression across environments. We showed that domestication profoundly alters genetic architectures. Based on four examples of plant domestication scenarios, our simulations predict (i) a drop in neutral allelic diversity, (ii) a change in gene expression variance that depends upon the domestication scenario, (iii) transient maladaptive plasticity, (iv) a deep rewiring of the gene regulatory networks, with a trend towards gain of regulatory interactions, and (v) a global increase in the genetic correlations among gene expressions, with a loss of modularity in the resulting coexpression patterns and in the underlying networks. We provide empirically testable predictions on the differences of genetic architectures between wild and domesticated forms. The characterization of such systematic evolutionary changes in the genetic architecture of traits contributes to define a molecular domestication syndrome.
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Affiliation(s)
- Ewen Burban
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198, Gif-sur-Yvette, France.,CNRS, Univ. Rennes, ECOBIO-UMR 6553, F-35000 Rennes, France
| | - Maud I Tenaillon
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, 91190, Gif-sur-Yvette, France
| | - Arnaud Le Rouzic
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198, Gif-sur-Yvette, France
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Rosa-Martínez E, García-Martínez MD, Adalid-Martínez AM, Pereira-Dias L, Casanova C, Soler E, Figàs MR, Raigón MD, Plazas M, Soler S, Prohens J. Fruit composition profile of pepper, tomato and eggplant varieties grown under uniform conditions. Food Res Int 2021; 147:110531. [PMID: 34399509 DOI: 10.1016/j.foodres.2021.110531] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/10/2021] [Accepted: 06/14/2021] [Indexed: 11/29/2022]
Abstract
The study of the diversity within and between major Solanaceae crops (pepper, tomato, eggplant) is of interest for the selection and development of balanced diets. We have measured thirty-six major fruit composition traits, encompassing sugars, organic acids, antioxidants and minerals, in a set of 10 accessions per crop for pepper, tomato and eggplant, grown under the same cultivation conditions. The aim was to evaluate the diversity within species and to provide an accurate comparison of fruit composition among species by reducing to a minimum the environmental effect. Pepper, tomato and eggplant had a clearly distinct composition profile. Pepper showed the highest average content in total sugars and organic acids. Fructose and glucose were the major sugar compounds in the three species, although in pepper and tomato sucrose was present only in trace amounts. Citric acid was the major organic acid in pepper and tomato, while in eggplant it was malic acid. Pepper and eggplant had the highest total antioxidant activity. Vitamin C content was much higher in pepper than in tomato and eggplant, while eggplant accumulated high concentrations of chlorogenic acid. Furthermore, eggplant was the species with higher content in most minerals, particularly for K, Mg and Cu, while pepper was the richest in Fe. Due to their complementary nutritional profiles, a combined regular consumption of the three vegetables would supply more than 20% of the Dietary Reference Intake of several of the analysed phytochemicals. The large diversity within each species is of interest for selecting varieties with better nutritional and organoleptic profiles, as well as for breeding new cultivars.
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Affiliation(s)
- Elena Rosa-Martínez
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain.
| | - María Dolores García-Martínez
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Ana María Adalid-Martínez
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Leandro Pereira-Dias
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Cristina Casanova
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Elena Soler
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - María Rosario Figàs
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - María Dolores Raigón
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Mariola Plazas
- Meridiem Seeds S.L., Paraje Lo Soler 2, 30700, Torre-Pacheco, Spain
| | - Salvador Soler
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
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