1
|
Omondi EO, Lin CY, Huang SM, Liao CA, Lin YP, Oliva R, van Zonneveld M. Landscape genomics reveals genetic signals of environmental adaptation of African wild eggplants. Ecol Evol 2024; 14:e11662. [PMID: 38983700 PMCID: PMC11232056 DOI: 10.1002/ece3.11662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 06/03/2024] [Accepted: 06/18/2024] [Indexed: 07/11/2024] Open
Abstract
Crop wild relatives (CWR) provide a valuable resource for improving crops. They possess desirable traits that confer resilience to various environmental stresses. To fully utilize crop wild relatives in breeding and conservation programs, it is important to understand the genetic basis of their adaptation. Landscape genomics associates environments with genomic variation and allows for examining the genetic basis of adaptation. Our study examined the differences in allele frequency of 15,416 single nucleotide polymorphisms (SNPs) generated through genotyping by sequencing approach among 153 accessions of 15 wild eggplant relatives and two cultivated species from Africa, the principal hotspot of these wild relatives. We also explored the correlation between these variations and the bioclimatic and soil conditions at their collection sites, providing a comprehensive understanding of the genetic signals of environmental adaptation in African wild eggplant. Redundancy analysis (RDA) results showed that the environmental variation explained 6% while the geographical distances among the collection sites explained 15% of the genomic variation in the eggplant wild relative populations when controlling for population structure. Our findings indicate that even though environmental factors are not the main driver of selection in eggplant wild relatives, it is influential in shaping the genomic variation over time. The selected environmental variables and candidate SNPs effectively revealed grouping patterns according to the environmental characteristics of sampling sites. Using four genotype-environment association methods, we detected 396 candidate SNPs (2.5% of the initial SNPs) associated with eight environmental factors. Some of these SNPs signal genes involved in pathways that help adapt to environmental stresses such as drought, heat, cold, salinity, pests, and diseases. These candidate SNPs will be useful for marker-assisted improvement and characterizing the germplasm of this crop for developing climate-resilient eggplant varieties. The study provides a model for applying landscape genomics to other crops' wild relatives.
Collapse
Affiliation(s)
- Emmanuel O Omondi
- Genetic Resources and Seed Unit World Vegetable Center Tainan Taiwan
| | - Chen-Yu Lin
- Biotechnology, World Vegetable Center Tainan Taiwan
| | | | - Cheng-An Liao
- Department of Horticulture National Taiwan University Taipei Taiwan
| | - Ya-Ping Lin
- Biotechnology, World Vegetable Center Tainan Taiwan
| | - Ricardo Oliva
- Plant Pathology World Vegetable Center Tainan Taiwan
| | | |
Collapse
|
2
|
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.
Collapse
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
| | | |
Collapse
|
3
|
Gramazio P, Alonso D, Arrones A, Villanueva G, Plazas M, Toppino L, Barchi L, Portis E, Ferrante P, Lanteri S, Rotino GL, Giuliano G, Vilanova S, Prohens J. Conventional and new genetic resources for an eggplant breeding revolution. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6285-6305. [PMID: 37419672 DOI: 10.1093/jxb/erad260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 07/05/2023] [Indexed: 07/09/2023]
Abstract
Eggplant (Solanum melongena) is a major vegetable crop with great potential for genetic improvement owing to its large and mostly untapped genetic diversity. It is closely related to over 500 species of Solanum subgenus Leptostemonum that belong to its primary, secondary, and tertiary genepools and exhibit a wide range of characteristics useful for eggplant breeding, including traits adaptive to climate change. Germplasm banks worldwide hold more than 19 000 accessions of eggplant and related species, most of which have yet to be evaluated. Nonetheless, eggplant breeding using the cultivated S. melongena genepool has yielded significantly improved varieties. To overcome current breeding challenges and for adaptation to climate change, a qualitative leap forward in eggplant breeding is necessary. The initial findings from introgression breeding in eggplant indicate that unleashing the diversity present in its relatives can greatly contribute to eggplant breeding. The recent creation of new genetic resources such as mutant libraries, core collections, recombinant inbred lines, and sets of introgression lines will be another crucial element and will require the support of new genomics tools and biotechnological developments. The systematic utilization of eggplant genetic resources supported by international initiatives will be critical for a much-needed eggplant breeding revolution to address the challenges posed by climate change.
Collapse
Affiliation(s)
- Pietro Gramazio
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - David Alonso
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Andrea Arrones
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Gloria Villanueva
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Mariola Plazas
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Laura Toppino
- CREA Research Centre for Genomics and Bioinformatics, Via Paullese 28, 26836 Montanaso Lombardo, LO, Italy
| | - Lorenzo Barchi
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics, University of Turin, Largo P. Braccini 2, 10095 Grugliasco, TO, Italy
| | - Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics, University of Turin, Largo P. Braccini 2, 10095 Grugliasco, TO, Italy
| | - Paola Ferrante
- Agenzia Nazionale Per Le Nuove Tecnologie, L'energia e Lo Sviluppo Economico Sostenibile (ENEA), Casaccia Research Centre, Rome, Italy
| | - Sergio Lanteri
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics, University of Turin, Largo P. Braccini 2, 10095 Grugliasco, TO, Italy
| | - Giuseppe Leonardo Rotino
- CREA Research Centre for Genomics and Bioinformatics, Via Paullese 28, 26836 Montanaso Lombardo, LO, Italy
| | - Giovanni Giuliano
- Agenzia Nazionale Per Le Nuove Tecnologie, L'energia e Lo Sviluppo Economico Sostenibile (ENEA), Casaccia Research Centre, Rome, Italy
| | - Santiago Vilanova
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| |
Collapse
|
4
|
Mohanty S, Mishra BK, Dasgupta M, Acharya GC, Singh S, Naresh P, Bhue S, Dixit A, Sarkar A, Sahoo MR. Deciphering phenotyping, DNA barcoding, and RNA secondary structure predictions in eggplant wild relatives provide insights for their future breeding strategies. Sci Rep 2023; 13:13829. [PMID: 37620406 PMCID: PMC10449851 DOI: 10.1038/s41598-023-40797-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 08/16/2023] [Indexed: 08/26/2023] Open
Abstract
Eggplant or aubergine (Solanum melongena L.) and its wild cousins, comprising 13 clades with 1500 species, have an unprecedented demand across the globe. Cultivated eggplant has a narrow molecular diversity that hinders eggplant breeding advancements. Wild eggplants need resurgent attention to broaden eggplant breeding resources. In this study, we emphasized phenotypic and genotypic discriminations among 13 eggplant species deploying chloroplast-plastid (Kim matK) and nuclear (ITS2) short gene sequences (400-800 bp) at DNA barcode region followed by ITS2 secondary structure predictions. The identification efficiency at the Kim matK region was higher (99-100%) than in the ITS2 region (80-90%). The eggplant species showed 13 unique secondary structures with a central ring with various helical orientations. Principal component analysis (PCoA) provides the descriptor-wise phenotypic clustering, which is essential for trait-specific breeding. Groups I and IV are categorized under scarlet complexes S. aethiopicum, S. trilobatum, and S. melongena (wild and cultivated). Group II represented the gboma clade (S. macrocarpon, S. wrightii, S. sisymbriifolium, and S. aculeatissimum), and group III includes S. mammosum, and S. torvum with unique fruit shape and size. The present study would be helpful in genetic discrimination, biodiversity conservation, and the safe utilization of wild eggplants.
Collapse
Affiliation(s)
- Sansuta Mohanty
- Central Horticultural Experiment Station, ICAR-Indian Institute of Horticultural Research, Bhubaneswar, Odisha, 751019, India
- Department of Molecular Biology and Biotechnology, Institute of Agricultural Sciences (IAS), Siksha O Anusandhan, Deemed to be University, Bhubaneswar, Odisha, 751003, India
| | - Bandana Kumari Mishra
- Central Horticultural Experiment Station, ICAR-Indian Institute of Horticultural Research, Bhubaneswar, Odisha, 751019, India
- Trident Academy of Creative Technology, Bhubaneswar, Odisha, 751024, India
| | - Madhumita Dasgupta
- ICAR Research Complex for Northeastern Hill Region, Manipur Centre, Imphal, Manipur, 795004, India
- Department of Molecular Biology and Biotechnology, Institute of Agricultural Sciences (IAS), Siksha O Anusandhan, Deemed to be University, Bhubaneswar, Odisha, 751003, India
| | - Gobinda Chandra Acharya
- Central Horticultural Experiment Station, ICAR-Indian Institute of Horticultural Research, Bhubaneswar, Odisha, 751019, India
| | - Satyapriya Singh
- Central Horticultural Experiment Station, ICAR-Indian Institute of Horticultural Research, Bhubaneswar, Odisha, 751019, India
| | - Ponnam Naresh
- ICAR-Indian Institute of Horticultural Research, Bengaluru, 560089, Karnataka, India
| | - Shyamlal Bhue
- Institute of Life Sciences, Bhubaneswar, Odisha, 751024, India
| | - Anshuman Dixit
- Institute of Life Sciences, Bhubaneswar, Odisha, 751024, India
| | - Arup Sarkar
- Trident Academy of Creative Technology, Bhubaneswar, Odisha, 751024, India
| | - Manas Ranjan Sahoo
- Central Horticultural Experiment Station, ICAR-Indian Institute of Horticultural Research, Bhubaneswar, Odisha, 751019, India.
| |
Collapse
|
5
|
Sotomayor DA, Ellis D, Salas A, Gomez R, Sanchez RA, Carrillo F, Giron C, Quispe V, Manrique-Carpintero NC, Anglin NL, Zorrilla C. Collecting wild potato species ( Solanum sect. Petota) in Peru to enhance genetic representation and fill gaps in ex situ collections. FRONTIERS IN PLANT SCIENCE 2023; 14:1044718. [PMID: 36794213 PMCID: PMC9923048 DOI: 10.3389/fpls.2023.1044718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 01/12/2023] [Indexed: 06/18/2023]
Abstract
Crop wild relatives (CWRs) are important sources of novel genes, due to their high variability of response to biotic and abiotic stresses, which can be invaluable for crop genetic improvement programs. Recent studies have shown that CWRs are threatened by several factors, including changes in land-use and climate change. A large proportion of CWRs are underrepresented in genebanks, making it necessary to take action to ensure their long-term ex situ conservation. With this aim, 18 targeted collecting trips were conducted during 2017/2018 in the center of origin of potato (Solanum tuberosum L.), targeting 17 diverse ecological regions of Peru. This was the first comprehensive wild potato collection in Peru in at least 20 years and encompassed most of the unique habitats of potato CWRs in the country. A total of 322 wild potato accessions were collected as seed, tubers, and whole plants for ex situ storage and conservation. They belonged to 36 wild potato species including one accession of S. ayacuchense that was not conserved previously in any genebank. Most accessions required regeneration in the greenhouse prior to long-term conservation as seed. The collected accessions help reduce genetic gaps in ex situ conserved germplasm and will allow further research questions on potato genetic improvement and conservation strategies to be addressed. These potato CWRs are available by request for research, training, and breeding purposes under the terms of the International Treaty for Plant Genetic Resources for Food and Agriculture (ITPGRFA) from the Instituto Nacional de Innovacion Agraria (INIA) and the International Potato Center (CIP) in Lima-Peru.
Collapse
Affiliation(s)
- Diego A. Sotomayor
- Direccion de Recursos Geneticos y Biotecnologia, Instituto Nacional de Innovacion Agraria (INIA), Lima, Peru
- Facultad de Ciencias, Universidad Nacional Agraria La Molina (UNALM), Lima, Peru
| | - David Ellis
- Centro Internacional de la Papa (CIP), Lima, Peru
| | | | - Rene Gomez
- Centro Internacional de la Papa (CIP), Lima, Peru
| | - Rosa A. Sanchez
- Direccion de Recursos Geneticos y Biotecnologia, Instituto Nacional de Innovacion Agraria (INIA), Lima, Peru
- Facultad de Ciencias, Universidad Nacional Agraria La Molina (UNALM), Lima, Peru
| | - Fredesvinda Carrillo
- Direccion de Recursos Geneticos y Biotecnologia, Instituto Nacional de Innovacion Agraria (INIA), Lima, Peru
| | - Carolina Giron
- Direccion de Recursos Geneticos y Biotecnologia, Instituto Nacional de Innovacion Agraria (INIA), Lima, Peru
| | | | | | - Noelle L. Anglin
- Centro Internacional de la Papa (CIP), Lima, Peru
- USDA ARS Small Grains and Potato Germplasm Unit, Aberdeen, ID, United States
| | - Cinthya Zorrilla
- Direccion de Recursos Geneticos y Biotecnologia, Instituto Nacional de Innovacion Agraria (INIA), Lima, Peru
- International Atomic Energy Agency, Plant Breeding and Genetics Section, Joint FAO/IAEA Center of Nuclear Techniques in Food and Agriculture, Vienna, Austria
| |
Collapse
|
6
|
Kapadia C, Datta R, Mahammad SM, Tomar RS, Kheni JK, Ercisli S. Genome-Wide Identification, Quantification, and Validation of Differentially Expressed miRNAs in Eggplant ( Solanum melongena L.) Based on Their Response to Ralstonia solanacearum Infection. ACS OMEGA 2023; 8:2648-2657. [PMID: 36687045 PMCID: PMC9851032 DOI: 10.1021/acsomega.2c07097] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/27/2022] [Indexed: 06/13/2023]
Abstract
MicroRNAs (miRNAs), a type of short noncoding RNA molecule (21-23 nucleotides), mediate repressive gene regulation through RNA silencing at the posttranscriptional level and play an important role in the defense response to abiotic and biotic stresses. miRNAs of the plant system have been studied in model crops for their diverse regulatory role while less is known about their significance in other plants whose genome and transcriptome data are scarce in the database, including eggplant (Solanum melongena L.). In the present study, a next-generation sequencing platform was used for the sequencing of miRNA, and real-time quantitative PCR for miRNAs was used to validate the gene expression patterns of miRNAs in Solanum melongena plantlets infected with the bacterial wilt-causing pathogen Ralstonia solanacearum (R. solanacearum). Sequence analyses showed the presence of 375 miRNAs belonging to 29 conserved families. The miR414 is highly conserved miRNA across the plant system while miR5658 and miR5021 were found exclusively in Arabidopsis thaliana surprisingly, these miRNAs were found in eggplants too. The most abundant families were miR5658 and miR414. Ppt-miR414, hvu-miR444b, stu-miR8020, and sly miR5303 were upregulated in Pusa purple long (PPL) (susceptible) at 48 h postinfection, followed by a decline after 96 h postinfection. A similar trend was obtained in ath-miR414, stu-mir5303h, alymiR847-5p, far-miR1134, ath-miR5021, ath-miR5658, osa-miR2873c, lja-miR7530, stu-miR7997c, and gra-miR8741 but at very low levels after infection in the susceptible variety, indicating their negative role in the suppression of host immunity. On the other hand, osa-miR2873c was found to be slightly increased after 96 hpi from 48 hpi. Most of the miRNAs under study showed relatively lower expression in the resistant variety Arka Nidhi after infection than in the susceptible variety. These results shed light on a deeper regulatory role of miRNAs and their targets in regulation of the plant response to bacterial infection. The present experiment and their results suggested that the higher expression of miRNA leads to a decline in host mRNA and thus shows susceptibility.
Collapse
Affiliation(s)
- Chintan Kapadia
- Department
of Plant Molecular Biology and Biotechnology, ASPEE College of Horticulture
and Forestry, Navsari Agricultural University, Navsari 396450, India
| | - Rahul Datta
- Department
of Geology and Pedology, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemedelska1, 61300 Brno, Czech Republic
| | - Saiyed Mufti Mahammad
- Department
of Plant Molecular Biology and Biotechnology, ASPEE College of Horticulture
and Forestry, Navsari Agricultural University, Navsari 396450, India
| | - Rukam Singh Tomar
- Department
of Biotechnology and Biochemistry, Junagadh
Agricultural University, Junagadh 362 001, India
| | - Jasmin Kumar Kheni
- Department
of Biotechnology and Biochemistry, Junagadh
Agricultural University, Junagadh 362 001, India
| | - Sezai Ercisli
- Department
of Horticulture, Faculty of Agriculture, Ataturk University, 25240 Erzurum, Turkey
| |
Collapse
|
7
|
González-Orenga S, Plazas M, Ribera E, Pallotti C, Boscaiu M, Prohens J, Vicente O, Fita A. Transgressive Biochemical Response to Water Stress in Interspecific Eggplant Hybrids. PLANTS (BASEL, SWITZERLAND) 2023; 12:194. [PMID: 36616323 PMCID: PMC9824389 DOI: 10.3390/plants12010194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/24/2022] [Accepted: 12/28/2022] [Indexed: 06/17/2023]
Abstract
In a climate change scenario, crop tolerance to drought must be urgently improved, as it represents an increasingly critical stress reducing agricultural yields worldwide. Although most crops are relatively sensitive to water stress, many of their wild relatives are more tolerant and may be used to improve drought tolerance in our crops. In this study, the response to drought of eggplant (Solanum melongena), its close wild relatives S. insanum and S. incanum and their interspecific hybrids with S. melongena was assessed. The plants were subjected to two treatments for 18 days: control, with irrigation every four days, and drought, with complete interruption of irrigation. Morphological and biomass traits were measured, and physiological and biochemical responses were analysed using stress biomarkers such as proline, flavonoids, and total phenolic compounds. Oxidative stress was quantified by measuring malondialdehyde (MDA) content. As a result of the drought treatment, plant development and tissue water content were seriously affected. Generally, water deficit also caused significant increases in MDA, proline, flavonoids, and total phenolics compounds. Our results comparing parental accessions reveal a better response to drought in one of the S. insanum accessions. The hybrid between S. melongena and S. incanum displayed a better response than the other hybrids and even its parents. The results obtained here might be helpful for future eggplant breeding programmes aimed at improving drought tolerance.
Collapse
Affiliation(s)
- Sara González-Orenga
- Institute for the Conservation and Improvement of Valencian Agrodiversity (COMAV), Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
- Department of Plant Biology and Soil Science, Faculty of Biology, Universidad de Vigo, Campus Lagoas-Marcosendre, 36310 Vigo, Spain
| | - Mariola Plazas
- Institute for the Conservation and Improvement of Valencian Agrodiversity (COMAV), Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Elvira Ribera
- Institute for the Conservation and Improvement of Valencian Agrodiversity (COMAV), Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Claudia Pallotti
- Institute for the Conservation and Improvement of Valencian Agrodiversity (COMAV), Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Monica Boscaiu
- Mediterranean Agroforestry Institute (IAM), Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Jaime Prohens
- Institute for the Conservation and Improvement of Valencian Agrodiversity (COMAV), Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Oscar Vicente
- Institute for the Conservation and Improvement of Valencian Agrodiversity (COMAV), Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Ana Fita
- Institute for the Conservation and Improvement of Valencian Agrodiversity (COMAV), Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| |
Collapse
|
8
|
Pisias MT, Bakala HS, McAlvay AC, Mabry ME, Birchler JA, Yang B, Pires JC. Prospects of Feral Crop De Novo Redomestication. PLANT & CELL PHYSIOLOGY 2022; 63:1641-1653. [PMID: 35639623 DOI: 10.1093/pcp/pcac072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/13/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
Modern agriculture depends on a narrow variety of crop species, leaving global food and nutritional security highly vulnerable to the adverse effects of climate change and population expansion. Crop improvement using conventional and molecular breeding approaches leveraging plant genetic diversity using crop wild relatives (CWRs) has been one approach to address these issues. However, the rapid pace of the global change requires additional innovative solutions to adapt agriculture to meet global needs. Neodomestication-the rapid and targeted introduction of domestication traits using introgression or genome editing of CWRs-is being explored as a supplementary approach. These methods show promise; however, they have so far been limited in efficiency and applicability. We propose expanding the scope of neodomestication beyond truly wild CWRs to include feral crops as a source of genetic diversity for novel crop development, in this case 'redomestication'. Feral crops are plants that have escaped cultivation and evolved independently, typically adapting to their local environments. Thus, feral crops potentially contain valuable adaptive features while retaining some domestication traits. Due to their genetic proximity to crop species, feral crops may be easier targets for de novo domestication (i.e. neodomestication via genome editing techniques). In this review, we explore the potential of de novo redomestication as an application for novel crop development by genome editing of feral crops. This approach to efficiently exploit plant genetic diversity would access an underutilized reservoir of genetic diversity that could prove important in support of global food insecurity in the face of the climate change.
Collapse
Affiliation(s)
- Michael T Pisias
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, 1201 Rollins Street, Columbia, MO 65211, USA
| | - Harmeet Singh Bakala
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, 1201 Rollins Street, Columbia, MO 65211, USA
| | - Alex C McAlvay
- Institute of Economic Botany, New York Botanical Garden, 2900 Southern Boulevard, Bronx, NY 10458, USA
| | - Makenzie E Mabry
- Florida Museum of Natural History, University of Florida, 1659 Museum Road, Gainesville, FL 32611, USA
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Tucker Hall, Columbia, MO 65211, USA
| | - Bing Yang
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, 1201 Rollins Street, Columbia, MO 65211, USA
- Donald Danforth Plant Science Center, 975 N Warson Road, St. Louis, MO 63132, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Tucker Hall, Columbia, MO 65211, USA
| |
Collapse
|
9
|
Tassone MR, Bagnaresi P, Desiderio F, Bassolino L, Barchi L, Florio FE, Sunseri F, Sirangelo TM, Rotino GL, Toppino L. A Genomic BSAseq Approach for the Characterization of QTLs Underlying Resistance to Fusarium oxysporum in Eggplant. Cells 2022; 11:2548. [PMID: 36010625 PMCID: PMC9406753 DOI: 10.3390/cells11162548] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [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.
Collapse
Affiliation(s)
- Maria Rosaria Tassone
- Council for Agricultural Research and Economics, Genomics and Bioinformatics Research Center, 26836 Montanaso Lombardo, Italy
- Department of Agricultural Science, University Mediterranea of Reggio Calabria, 89124 Reggio Calabria, Italy
| | - Paolo Bagnaresi
- Council for Agricultural Research and Economics, Genomics and Bioinformatics Research Center, 29017 Fiorenzuola d’Arda, Italy
| | - Francesca Desiderio
- Council for Agricultural Research and Economics, Genomics and Bioinformatics Research Center, 29017 Fiorenzuola d’Arda, Italy
| | - Laura Bassolino
- Council for Agricultural Research and Economics, Genomics and Bioinformatics Research Center, 26836 Montanaso Lombardo, Italy
- Council for Agricultural Research and Economics, Cereal and Industrial Crops Research Center, 40128 Bologna, Italy
| | - Lorenzo Barchi
- DISAFA, Plant Genetics and Breeding, University of Turin, 10095 Grugliasco, Italy
| | - Francesco Elia Florio
- Council for Agricultural Research and Economics, Genomics and Bioinformatics Research Center, 26836 Montanaso Lombardo, Italy
| | - Francesco Sunseri
- Department of Agricultural Science, University Mediterranea of Reggio Calabria, 89124 Reggio Calabria, Italy
| | - Tiziana Maria Sirangelo
- Council for Agricultural Research and Economics, Genomics and Bioinformatics Research Center, 26836 Montanaso Lombardo, Italy
| | - Giuseppe Leonardo Rotino
- Council for Agricultural Research and Economics, Genomics and Bioinformatics Research Center, 26836 Montanaso Lombardo, Italy
| | - Laura Toppino
- Council for Agricultural Research and Economics, Genomics and Bioinformatics Research Center, 26836 Montanaso Lombardo, Italy
| |
Collapse
|
10
|
Aubriot X, Knapp S. A revision of the "spiny solanums" of Tropical Asia ( Solanum, the Leptostemonum Clade, Solanaceae). PHYTOKEYS 2022; 198:1-270. [PMID: 36760991 PMCID: PMC9849010 DOI: 10.3897/phytokeys.198.79514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 04/20/2022] [Indexed: 06/18/2023]
Abstract
The Leptostemonum Clade, or the "spiny solanums", is the most species-rich monophyletic clade of the large cosmopolitan genus Solanum (Solanaceae) and represents almost half the species diversity of the genus. Species diversity in the clade is highest in the Americas, but significant clusters of endemic taxa occur in the Eastern Hemisphere. We present here a taxonomic revision of the 51 species of spiny solanums occurring in tropical Asia (excluding the island of New Guinea, and the lowlands of Nepal and Bhutan). Three species are described as new: Solanumkachinense X.Aubriot & S.Knapp, sp. nov. from northern Myanmar, S.peikuoense S.S.Ying, sp. nov. from Taiwan, and S.sulawesi X.Aubriot & S.Knapp, sp. nov. from northern Sulawesi, Indonesia. Of the spiny solanums occurring in the region, 38 are native and 13 are introduced from the Americas or Africa, either as adventive weeds or as cultivated plants. Phylogenetic resolution amongst these taxa is still a work in progress, so we have chosen to treat these taxa in a geographical context to aid with identification and further taxon discovery. For the native species we provide complete nomenclatural details for all recognised species and their synonyms, complete descriptions, distributions including maps, common names and uses, and preliminary conservation assessments. For the introduced taxa that have been treated in detail elsewhere we provide details of types, synonyms based on tropical Asian material, general distributions, and common names for the region. We provide lecto- or neotypifications for 67 names; 63 for native and 4 for introduced taxa. All taxa are discussed and compared to similar species; keys are provided for all taxa. We illustrate all native species with herbarium and field photographs and introduced species with field photographs only. All specimens examined for this treatment are included in Suppl. materials 1-3 as searchable files.
Collapse
Affiliation(s)
- Xavier Aubriot
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique et Evolution, 91190, Gif-sur-Yvette, FranceThe Natural History MuseumLondonUnited Kingdom
- The Natural History Museum, Cromwell Road, London SW7 5BD, UKUniversité Paris-SaclayParisFrance
| | - Sandra Knapp
- The Natural History Museum, Cromwell Road, London SW7 5BD, UKUniversité Paris-SaclayParisFrance
| |
Collapse
|
11
|
Coulibaly M, Idohou R, Akohoue F, Peterson AT, Sawadogo M, Achigan-Dako EG. Coupling genetic structure analysis and ecological-niche modeling in Kersting’s groundnut in West Africa. Sci Rep 2022; 12:5590. [PMID: 35379846 PMCID: PMC8980027 DOI: 10.1038/s41598-022-09153-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 03/14/2022] [Indexed: 01/14/2023] Open
Abstract
Orphan legume crops play an important role in smallholder farmers’ food systems. Though less documented, they have the potential to contribute to adequate nutrition in vulnerable communities. Unfortunately, data are scarce about the potential of those crops to withstand current and future climate variations. Using Macrotyloma geocarpum as an example, we used ecological niche modeling to explore the role of ecology on the current and future distributions of genetic populations of Kersting’s groundnut. Our findings showed that: (1) the models had good predictive power, indicating that M. geocarpum’s distribution was correlated with both climatic and soil layers; (2) identity and similarity tests revealed that the two genetic groups have identical and similar environmental niches; (3) by integrating the genetic information in niche modeling, niches projections show divergence in the response of the species and genetic populations to ongoing climate change. This study highlights the importance of incorporating genetic data into Ecological Niche Modeling (ENM) approaches to obtain a finer information of species’ future distribution, and explores the implications for agricultural adaptation, with a particular focus on identifying priority actions in orphan crops conservation and breeding.
Collapse
|
12
|
Wambugu PW, Henry R. Supporting in situ conservation of the genetic diversity of crop wild relatives using genomic technologies. Mol Ecol 2022; 31:2207-2222. [PMID: 35170117 PMCID: PMC9303585 DOI: 10.1111/mec.16402] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/08/2022] [Accepted: 02/11/2022] [Indexed: 11/27/2022]
Abstract
The last decade has witnessed huge technological advances in genomics, particularly in DNA sequencing. Here, we review the actual and potential application of genomics in supporting in situ conservation of crop wild relatives (CWRs). In addition to helping in prioritization of protection of CWR taxa and in situ conservation sites, genome analysis is allowing the identification of novel alleles that need to be prioritized for conservation. Genomics is enabling the identification of potential sources of important adaptive traits that can guide the establishment or enrichment of in situ genetic reserves. Genomic tools also have the potential for developing a robust framework for monitoring and reporting genome‐based indicators of genetic diversity changes associated with factors such as land use or climate change. These tools have been demonstrated to have an important role in managing the conservation of populations, supporting sustainable access and utilization of CWR diversity, enhancing accelerated domestication of new crops and forensic genomics thus preventing misappropriation of genetic resources. Despite this great potential, many policy makers and conservation managers have failed to recognize and appreciate the need to accelerate the application of genomics to support the conservation and management of biodiversity in CWRs to underpin global food security. Funding and inadequate genomic expertise among conservation practitioners also remain major hindrances to the widespread application of genomics in conservation.
Collapse
Affiliation(s)
- Peterson W Wambugu
- Kenya Agricultural and Livestock Research Organization, Genetic Resources Research Institute, P.O. Box 30148, 00100, Nairobi, Kenya
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, 4072, Australia.,ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Queensland, Brisbane, QLD, 4072, Australia
| |
Collapse
|
13
|
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.
Collapse
|
14
|
Kamenya SN, Mikwa EO, Song B, Odeny DA. Genetics and breeding for climate change in Orphan crops. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1787-1815. [PMID: 33486565 PMCID: PMC8205878 DOI: 10.1007/s00122-020-03755-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 12/16/2020] [Indexed: 05/17/2023]
Abstract
Climate change is rapidly changing how we live, what we eat and produce, the crops we breed and the target traits. Previously underutilized orphan crops that are climate resilient are receiving much attention from the crops research community, as they are often the only crops left in the field after periods of extreme weather conditions. There are several orphan crops with incredible resilience to biotic and abiotic stresses. Some are nutritious, while others provide good sources of biofuel, medicine and other industrial raw materials. Despite these benefits, orphan crops are still lacking in important genetic and genomic resources that could be used to fast track their improvement and make their production profitable. Progress has been made in generating draft genomes of at least 28 orphan crops over the last decade, thanks to the reducing cost of sequencing. The implementation of a structured breeding program that takes advantage of additional modern crop improvement tools such as genomic selection, speed breeding, genome editing, high throughput phenotyping and breeding digitization would make rapid improvement of these orphan crops possible, but would require coordinated research investment. Other production challenges such as lack of adequate germplasm conservation, poor/non-existent seed systems and agricultural extension services, as well as poor marketing channels will also need to be improved if orphan crops were to be profitable. We review the importance of breeding orphan crops under the increasing effects of climate change, highlight existing gaps that need to be addressed and share some lessons to be learned from major crops.
Collapse
Affiliation(s)
- Sandra Ndagire Kamenya
- African Center of Excellence in Agroecology and Livelihood Systems, Uganda Martyrs University, Kampala, Uganda
| | - Erick Owuor Mikwa
- The International Crops Research Institute for the Semi-Arid Tropics - Eastern and Southern Africa, Nairobi, Kenya
| | - Bo Song
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute At Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518060, People's Republic of China.
| | - Damaris Achieng Odeny
- The International Crops Research Institute for the Semi-Arid Tropics - Eastern and Southern Africa, Nairobi, Kenya.
| |
Collapse
|
15
|
Hübner S, Kantar MB. Tapping Diversity From the Wild: From Sampling to Implementation. FRONTIERS IN PLANT SCIENCE 2021; 12:626565. [PMID: 33584776 PMCID: PMC7873362 DOI: 10.3389/fpls.2021.626565] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 01/07/2021] [Indexed: 05/05/2023]
Abstract
The diversity observed among crop wild relatives (CWRs) and their ability to flourish in unfavorable and harsh environments have drawn the attention of plant scientists and breeders for many decades. However, it is also recognized that the benefit gained from using CWRs in breeding is a potential rose between thorns of detrimental genetic variation that is linked to the trait of interest. Despite the increased interest in CWRs, little attention was given so far to the statistical, analytical, and technical considerations that should guide the sampling design, the germplasm characterization, and later its implementation in breeding. Here, we review the entire process of sampling and identifying beneficial genetic variation in CWRs and the challenge of using it in breeding. The ability to detect beneficial genetic variation in CWRs is strongly affected by the sampling design which should be adjusted to the spatial and temporal variation of the target species, the trait of interest, and the analytical approach used. Moreover, linkage disequilibrium is a key factor that constrains the resolution of searching for beneficial alleles along the genome, and later, the ability to deplete linked deleterious genetic variation as a consequence of genetic drag. We also discuss how technological advances in genomics, phenomics, biotechnology, and data science can improve the ability to identify beneficial genetic variation in CWRs and to exploit it in strive for higher-yielding and sustainable crops.
Collapse
Affiliation(s)
- Sariel Hübner
- Galilee Research Institute (MIGAL), Tel-Hai College, Qiryat Shemona, Israel
- *Correspondence: Sariel Hübner,
| | - Michael B. Kantar
- Department of Tropical Plant and Soil Sciences, University of Hawai’i at Mânoa, Honolulu, HI, United States
| |
Collapse
|
16
|
Performance of a Set of Eggplant (Solanum melongena) Lines With Introgressions From Its Wild Relative S. incanum Under Open Field and Screenhouse Conditions and Detection of QTLs. AGRONOMY-BASEL 2020. [DOI: 10.3390/agronomy10040467] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Introgression lines (ILs) of eggplant (Solanum melongena) represent a resource of high value for breeding and the genetic analysis of important traits. We have conducted a phenotypic evaluation in two environments (open field and screenhouse) of 16 ILs from the first set of eggplant ILs developed so far. Each of the ILs carries a single marker-defined chromosomal segment from the wild eggplant relative S. incanum (accession MM577) in the genetic background of S. melongena (accession AN-S-26). Seventeen agronomic traits were scored to test the performance of ILs compared to the recurrent parent and of identifying QTLs for the investigated traits. Significant morphological differences were found between parents, and the hybrid was heterotic for vigour-related traits. Despite the presence of large introgressed fragments from a wild exotic parent, individual ILs did not display differences with respect to the recipient parent for most traits, although significant genotype × environment interaction (G × E ) was detected for most traits. Heritability values for the agronomic traits were generally low to moderate. A total of ten stable QTLs scattered across seven chromosomes was detected. For five QTLs, the S. incanum introgression was associated with higher mean values for plant- and flower-related traits, including vigour prickliness and stigma length. For one flower- and four fruit-related-trait QTLs, including flower peduncle and fruit pedicel lengths and fruit weight, the S. incanum introgression was associated with lower mean values for fruit-related traits. Evidence of synteny to other previously reported in eggplant populations was found for three of the fruit-related QTLs. The other seven stable QTLs are new, demonstrating that eggplant ILs are of great interest for eggplant breeding under different environments.
Collapse
|
17
|
Ramirez‐Villegas J, Khoury CK, Achicanoy HA, Mendez AC, Diaz MV, Sosa CC, Debouck DG, Kehel Z, Guarino L. A gap analysis modelling framework to prioritize collecting for ex situ conservation of crop landraces. DIVERS DISTRIB 2020. [DOI: 10.1111/ddi.13046] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Julian Ramirez‐Villegas
- International Center for Tropical Agriculture (CIAT) Cali Colombia
- CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS), c/o CIAT Cali Colombia
| | - Colin K. Khoury
- International Center for Tropical Agriculture (CIAT) Cali Colombia
- United States Department of Agriculture Agricultural Research Service National Laboratory for Genetic Resources Preservation Fort Collins CO USA
- Department of Biology Saint Louis University St. Louis MO USA
| | | | - Andres C. Mendez
- International Center for Tropical Agriculture (CIAT) Cali Colombia
| | | | | | | | - Zakaria Kehel
- International Center for Agricultural Research in the Dry Areas (ICARDA) Rabat Morocco
| | | |
Collapse
|
18
|
García-Fortea E, Lluch-Ruiz A, Pineda-Chaza BJ, García-Pérez A, Bracho-Gil JP, Plazas M, Gramazio P, Vilanova S, Moreno V, Prohens J. A highly efficient organogenesis protocol based on zeatin riboside for in vitro regeneration of eggplant. BMC PLANT BIOLOGY 2020; 20:6. [PMID: 31906864 PMCID: PMC6945591 DOI: 10.1186/s12870-019-2215-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 12/22/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND Efficient organogenesis induction in eggplant (Solanum melongena L.) is required for multiple in vitro culture applications. In this work, we aimed at developing a universal protocol for efficient in vitro regeneration of eggplant mainly based on the use of zeatin riboside (ZR). We evaluated the effect of seven combinations of ZR with indoleacetic acid (IAA) for organogenic regeneration in five genetically diverse S. melongena and one S. insanum L. accessions using two photoperiod conditions. In addition, the effect of six different concentrations of indolebutyric acid (IBA) in order to promote rooting was assessed to facilitate subsequent acclimatization of plants. The ploidy level of regenerated plants was studied. RESULTS In a first experiment with accessions MEL1 and MEL3, significant (p < 0.05) differences were observed for the four factors evaluated for organogenesis from cotyledon, hypocotyl and leaf explants, with the best results obtained (9 and 11 shoots for MEL1 and MEL3, respectively) using cotyledon tissue, 16 h light / 8 h dark photoperiod conditions, and medium E6 (2 mg/L of ZR and 0 mg/L of IAA). The best combination of conditions was tested in the other four accessions and confirmed its high regeneration efficiency per explant when using both cotyledon and hypocotyl tissues. The best rooting media was R2 (1 mg/L IBA). The analysis of ploidy level revealed that between 25 and 50% of the regenerated plantlets were tetraploid. CONCLUSIONS An efficient protocol for organogenesis of both cultivated and wild accessions of eggplant, based on the use of ZR, is proposed. The universal protocol developed may be useful for fostering in vitro culture applications in eggplant requiring regeneration of plants and, in addition, allows developing tetraploid plants without the need of antimitotic chemicals.
Collapse
Affiliation(s)
- Edgar García-Fortea
- Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camí de Vera s/n, 46022, Valencia, Spain
| | - Agustín Lluch-Ruiz
- Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camí de Vera s/n, 46022, Valencia, Spain
| | - Benito José Pineda-Chaza
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, 46022, Valencia, Spain
| | - Ana García-Pérez
- Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camí de Vera s/n, 46022, Valencia, Spain
| | - Juan Pablo Bracho-Gil
- Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camí de Vera s/n, 46022, Valencia, Spain
| | - Mariola Plazas
- Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camí de Vera s/n, 46022, Valencia, Spain
| | - Pietro Gramazio
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8572, Japan
| | - Santiago Vilanova
- Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camí de Vera s/n, 46022, Valencia, Spain
| | - Vicente Moreno
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, 46022, Valencia, Spain
| | - Jaime Prohens
- Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camí de Vera s/n, 46022, Valencia, Spain.
| |
Collapse
|
19
|
Barchi L, Acquadro A, Alonso D, Aprea G, Bassolino L, Demurtas O, Ferrante P, Gramazio P, Mini P, Portis E, Scaglione D, Toppino L, Vilanova S, Díez MJ, Rotino GL, Lanteri S, Prohens J, Giuliano G. Single Primer Enrichment Technology (SPET) for High-Throughput Genotyping in Tomato and Eggplant Germplasm. FRONTIERS IN PLANT SCIENCE 2019; 10:1005. [PMID: 31440267 PMCID: PMC6693525 DOI: 10.3389/fpls.2019.01005] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 07/18/2019] [Indexed: 05/20/2023]
Abstract
Single primer enrichment technology (SPET) is a new, robust, and customizable solution for targeted genotyping. Unlike genotyping by sequencing (GBS), and like DNA chips, SPET is a targeted genotyping technology, relying on the sequencing of a region flanking a primer. Its reliance on single primers, rather than on primer pairs, greatly simplifies panel design, and allows higher levels of multiplexing than PCR-based genotyping. Thanks to the sequencing of the regions surrounding the target SNP, SPET allows the discovery of thousands of closely linked, novel SNPs. In order to assess the potential of SPET for high-throughput genotyping in plants, a panel comprising 5k target SNPs, designed both on coding regions and introns/UTRs, was developed for tomato and eggplant. Genotyping of two panels composed of 400 tomato and 422 eggplant accessions, comprising both domesticated material and wild relatives, generated a total of 12,002 and 30,731 high confidence SNPs, respectively, which comprised both target and novel SNPs in an approximate ratio of 1:1.6, and 1:5.5 in tomato and eggplant, respectively. The vast majority of the markers was transferrable to related species that diverged up to 3.4 million years ago (Solanum pennellii for tomato and S. macrocarpon for eggplant). Maximum Likelihood phylogenetic trees and PCA outputs obtained from the whole dataset highlighted genetic relationships among accessions and species which were congruent with what was previously reported in literature. Better discrimination among domesticated accessions was achieved by using the target SNPs, while better discrimination among wild species was achieved using the whole SNP dataset. Our results reveal that SPET genotyping is a robust, high-throughput technology for genetic fingerprinting, with a high degree of cross-transferability between crops and their cultivated and wild relatives, and allows identification of duplicates and mislabeled accessions in genebanks.
Collapse
Affiliation(s)
| | | | - David Alonso
- COMAV, Universitat Politècnica de Valencia, Valencia, Spain
| | - Giuseppe Aprea
- ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Laura Bassolino
- CREA-GB, Research Centre for Genomics and Bioinformatics, Montanaso Lombardo, Italy
| | - Olivia Demurtas
- ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Paola Ferrante
- ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | | | - Paola Mini
- ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | | | | | - Laura Toppino
- CREA-GB, Research Centre for Genomics and Bioinformatics, Montanaso Lombardo, Italy
| | | | | | | | | | - Jaime Prohens
- COMAV, Universitat Politècnica de Valencia, Valencia, Spain
| | - Giovanni Giuliano
- ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| |
Collapse
|
20
|
|
21
|
Gramazio P, Yan H, Hasing T, Vilanova S, Prohens J, Bombarely A. Whole-Genome Resequencing of Seven Eggplant ( Solanum melongena) and One Wild Relative ( S. incanum) Accessions Provides New Insights and Breeding Tools for Eggplant Enhancement. FRONTIERS IN PLANT SCIENCE 2019; 10:1220. [PMID: 31649694 PMCID: PMC6791922 DOI: 10.3389/fpls.2019.01220] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 09/04/2019] [Indexed: 05/20/2023]
Abstract
Whole-genome resequencing provides information of great relevance for crop genetics, evolution, and breeding. Here, we present the first whole-genome resequencing study using seven eggplant (Solanum melongena) and one wild relative (Solanum incanum) accessions. These eight accessions were selected for displaying a high phenotypic and genetic diversity and for being the founder parents of an eggplant multiparent advanced generation intercrosses population. By resequencing at an average depth of 19.8× and comparing to the high-quality reference genome "67/3" over 10 million high-reliable polymorphisms were discovered, of which over 9 million (84.5%) were single nucleotide polymorphisms and more than 700,000 (6.5%) InDels. However, while for the S. melongena accessions, the variants identified ranged from 0.8 to 1.3 million, over 9 million were detected for the wild S. incanum. This confirms the narrow genetic diversity of the domesticated eggplant and suggests that introgression breeding using wild relatives can efficiently contribute to broadening the genetic basis of this crop. Differences were observed among accessions for the enrichment in genes regulating important biological processes. By analyzing the distribution of the variants, we identified the potential footprints of old introgressions from wild relatives that can help to unravel the unclear domestication and breeding history. The comprehensive annotation of these eight genomes and the information provided in this study represents a landmark in eggplant genomics and allows the development of tools for eggplant genetics and breeding.
Collapse
Affiliation(s)
- Pietro Gramazio
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
- *Correspondence: Pietro Gramazio,
| | - Haidong Yan
- School of Plant and Environmental Sciences (SPES), Virginia Tech, Blacksburg, VA, United States
| | - Tomas Hasing
- School of Plant and Environmental Sciences (SPES), Virginia Tech, Blacksburg, VA, United States
| | - Santiago Vilanova
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Aureliano Bombarely
- School of Plant and Environmental Sciences (SPES), Virginia Tech, Blacksburg, VA, United States
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| |
Collapse
|
22
|
Aubriot X, Knapp S, Syfert MM, Poczai P, Buerki S. Shedding new light on the origin and spread of the brinjal eggplant (Solanum melongena L.) and its wild relatives. AMERICAN JOURNAL OF BOTANY 2018; 105:1175-1187. [PMID: 30091787 DOI: 10.1002/ajb2.1133] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/04/2018] [Indexed: 05/11/2023]
Abstract
PREMISE OF THE STUDY While brinjal eggplant (Solanum melongena L.) is the second most important solanaceous fruit crop, we lack firm knowledge of its evolutionary relationships. This in turn limits efficient use of crop wild relatives in eggplant improvement. Here, we examine the hypothesis of linear step-wise expansion of the eggplant group from Africa to Asia. METHODS We use museum collections to generate nuclear and full-plastome data for all species of the Eggplant clade. We combine a phylogenomic approach with distribution data to infer a biogeographic scenario for the clade. KEY RESULTS The Eggplant clade has Pleistocene origins in northern Africa. Dispersals to tropical Asia gave rise to Solanum insanum, the wild progenitor of the eggplant, and to African distinct lineages of widespread and southern African species. Results suggest that spread of the species to southern Africa has been recent and likely facilitated by large mammalian herbivores, such as the African elephant and impala feeding on Solanum fruit. CONCLUSIONS Rather than a linear 'Out Of Africa' sequence, our results are more consistent with an initial dispersal event into Asia, and subsequent wide dispersal and differentiation across Africa driven by large mammalian herbivores. Our evolutionary results will affect future work on eggplant domestication and affect the use of wild relatives in breeding of this increasingly important solanaceous crop.
Collapse
Affiliation(s)
- Xavier Aubriot
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, England, UK
- Unité Mixte de Recherche 6553 Écosystèmes, Biodiversité, Évolution (ECOBIO), Observatoire des Sciences de l'Univers de Rennes, Centre National de la Recherche Scientifique, Université de Rennes 1, Rennes CEDEX, France
| | - Sandra Knapp
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, England, UK
| | - Mindy M Syfert
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, England, UK
| | - Péter Poczai
- Botany Unit, Finnish Museum of Natural History, University of Helsinki, PO Box 7, Helsinki, FI-00014, Finland
| | - Sven Buerki
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, England, UK
- Department of Biological Sciences, Boise State University, 1910 University Drive, Boise, Idaho, 83725, U.S.A
| |
Collapse
|
23
|
Gürbüz N, Uluişik S, Frary A, Frary A, Doğanlar S. Health benefits and bioactive compounds of eggplant. Food Chem 2018; 268:602-610. [PMID: 30064803 DOI: 10.1016/j.foodchem.2018.06.093] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 05/31/2018] [Accepted: 06/19/2018] [Indexed: 02/07/2023]
Abstract
Eggplant is a vegetable crop that is grown around the world and can provide significant nutritive benefits thanks to its abundance of vitamins, phenolics and antioxidants. In addition, eggplant has potential pharmaceutical uses that are just now becoming recognized. As compared to other crops in the Solanaceae, few studies have investigated eggplant's metabolic profile. Metabolomics and metabolic profiling are important platforms for assessing the chemical composition of plants and breeders are increasingly concerned about the nutritional and health benefits of crops. In this review, the historical background and classification of eggplant are shortly explained; then the beneficial phytochemicals, antioxidant activity and health effects of eggplant are discussed in detail.
Collapse
Affiliation(s)
- Nergiz Gürbüz
- Izmir Institute of Technology, Department of Molecular Biology and Genetics, 35430 Urla Izmir, Turkey
| | - Selman Uluişik
- Mehmet Akif Ersoy University, Burdur Food Agriculture and Livestock Vocational School, 15030 Burdur, Turkey
| | - Anne Frary
- Izmir Institute of Technology, Department of Molecular Biology and Genetics, 35430 Urla Izmir, Turkey.
| | - Amy Frary
- Mount Holyoke College, Department of Biological Sciences, The Biochemistry Program, 50 College St, South Hadley, MA 01075, USA.
| | - Sami Doğanlar
- Izmir Institute of Technology, Department of Molecular Biology and Genetics, 35430 Urla Izmir, Turkey.
| |
Collapse
|
24
|
Salgon S, Raynal M, Lebon S, Baptiste JM, Daunay MC, Dintinger J, Jourda C. Genotyping by Sequencing Highlights a Polygenic Resistance to Ralstonia pseudosolanacearum in Eggplant (Solanum melongena L.). Int J Mol Sci 2018; 19:E357. [PMID: 29370090 PMCID: PMC5855579 DOI: 10.3390/ijms19020357] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Revised: 01/19/2018] [Accepted: 01/22/2018] [Indexed: 12/02/2022] Open
Abstract
Eggplant cultivation is limited by numerous diseases, including the devastating bacterial wilt (BW) caused by the Ralstonia solanacearum species complex (RSSC). Within the RSSC, Ralstonia pseudosolanacearum (including phylotypes I and III) causes severe damage to all solanaceous crops, including eggplant. Therefore, the creation of cultivars resistant to R. pseudosolanacearum strains is a major goal for breeders. An intraspecific eggplant population, segregating for resistance, was created from the cross between the susceptible MM738 and the resistant EG203 lines. The population of 123 doubled haploid lines was challenged with two strains belonging to phylotypes I (PSS4) and III (R3598), which both bypass the published EBWR9 BW-resistance quantitative trait locus (QTL). Ten and three QTLs of resistance to PSS4 and to R3598, respectively, were detected and mapped. All were strongly influenced by environmental conditions. The most stable QTLs were found on chromosomes 3 and 6. Given their estimated physical position, these newly detected QTLs are putatively syntenic with BW-resistance QTLs in tomato. In particular, the QTLs' position on chromosome 6 overlaps with that of the major broad-spectrum tomato resistance QTL Bwr-6. The present study is a first step towards understanding the complex polygenic system, which underlies the high level of BW resistance of the EG203 line.
Collapse
Affiliation(s)
- Sylvia Salgon
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Unité Mixte de Recherche Peuplements Végétaux et Bio-agresseurs en Milieu Tropical (UMR PVBMT), F-97410 Saint-Pierre, France.
- Unité Mixte de Recherche Peuplements Végétaux et Bio-agresseurs en Milieu Tropical (UMR PVBMT), Université de la Réunion, F-97410 Saint-Pierre, France.
- Association Réunionnaise pour la Modernisation de l'Economie Fruitière Légumière et Horticole (ARMEFLHOR), F-97410 Saint-Pierre, France.
| | | | - Sylvain Lebon
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Unité Mixte de Recherche Peuplements Végétaux et Bio-agresseurs en Milieu Tropical (UMR PVBMT), F-97410 Saint-Pierre, France.
| | - Jean-Michel Baptiste
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Unité Mixte de Recherche Peuplements Végétaux et Bio-agresseurs en Milieu Tropical (UMR PVBMT), F-97410 Saint-Pierre, France.
| | - Marie-Christine Daunay
- Institut National de la Recherche Agronomique (INRA), Unité de Recherche Génétique et Amélioration des Fruits et Légumes (UR GAFL), F-84143 Montfavet, France.
| | - Jacques Dintinger
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Unité Mixte de Recherche Peuplements Végétaux et Bio-agresseurs en Milieu Tropical (UMR PVBMT), F-97410 Saint-Pierre, France.
| | - Cyril Jourda
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Unité Mixte de Recherche Peuplements Végétaux et Bio-agresseurs en Milieu Tropical (UMR PVBMT), F-97410 Saint-Pierre, France.
| |
Collapse
|
25
|
Kaushik P, Gramazio P, Vilanova S, Raigón MD, Prohens J, Plazas M. Phenolics content, fruit flesh colour and browning in cultivated eggplant, wild relatives and interspecific hybrids and implications for fruit quality breeding. Food Res Int 2017; 102:392-401. [DOI: 10.1016/j.foodres.2017.09.028] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Revised: 09/01/2017] [Accepted: 09/08/2017] [Indexed: 10/18/2022]
|
26
|
Gramazio P, Prohens J, Plazas M, Mangino G, Herraiz FJ, Vilanova S. Development and Genetic Characterization of Advanced Backcross Materials and An Introgression Line Population of Solanum incanum in a S. melongena Background. FRONTIERS IN PLANT SCIENCE 2017; 8:1477. [PMID: 28912788 PMCID: PMC5582342 DOI: 10.3389/fpls.2017.01477] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 08/09/2017] [Indexed: 05/29/2023]
Abstract
Advanced backcrosses (ABs) and introgression lines (ILs) of eggplant (Solanum melongena) can speed up genetics and genomics studies and breeding in this crop. We have developed the first full set of ABs and ILs in eggplant using Solanum incanum, a wild eggplant that has a relatively high tolerance to drought, as a donor parent. The development of these ABs and IL eggplant populations had a low efficiency in the early stages, because of the lack of molecular markers and genomic tools. However, this dramatically improved after performing genotyping-by-sequencing in the first round of selfing, followed by high-resolution-melting single nucleotide polymorphism genotyping in subsequent selection steps. A set of 73 selected ABs covered 99% of the S. incanum genome, while 25 fixed immortal ILs, each carrying a single introgressed fragment in homozygosis, altogether spanned 61.7% of the S. incanum genome. The introgressed size fragment in the ILs contained between 0.1 and 10.9% of the S. incanum genome, with a mean value of 4.3%. Sixty-eight candidate genes involved in drought tolerance were identified in the set of ILs. This first set of ABs and ILs of eggplant will be extremely useful for the genetic dissection of traits of interest for eggplant, and represents an elite material for introduction into the breeding pipelines for developing new eggplant cultivars adapted to the challenges posed by the climate-change scenario.
Collapse
Affiliation(s)
- Pietro Gramazio
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de ValènciaValencia, Spain
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de ValènciaValencia, Spain
| | - Mariola Plazas
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas - Universitat Politècnica de ValènciaValencia, Spain
| | - Giulio Mangino
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de ValènciaValencia, Spain
| | - Francisco J. Herraiz
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de ValènciaValencia, Spain
| | - Santiago Vilanova
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de ValènciaValencia, Spain
| |
Collapse
|
27
|
Taher D, Solberg SØ, Prohens J, Chou YY, Rakha M, Wu TH. World Vegetable Center Eggplant Collection: Origin, Composition, Seed Dissemination and Utilization in Breeding. FRONTIERS IN PLANT SCIENCE 2017; 8:1484. [PMID: 28970840 PMCID: PMC5609569 DOI: 10.3389/fpls.2017.01484] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 08/10/2017] [Indexed: 05/19/2023]
Abstract
Eggplant is the fifth most economically important solanaceous crop after potato, tomato, pepper, and tobacco. Apart from the well-known brinjal eggplant (Solanum melongena L.), two other under-utilized eggplant species, the scarlet eggplant (S. aethiopicum L.) and the gboma eggplant (S. macrocarpon L.) are also cultivated. The taxonomy and identification of eggplant wild relatives is challenging for breeders due to the large number of related species, but recent phenotypic and genetic data and classification in primary, secondary, and tertiary genepools, as well as information on the domestication process and wild progenitors, facilitates their utilization in breeding. The World Vegetable Center (WorldVeg) holds a large public germplasm collection of eggplant, which includes the three cultivated species and more than 30 eggplant wild relatives, with more than 3,200 accessions collected from 90 countries. Over the last 15 years, more than 10,000 seed samples from the Center's eggplant collection have been shared with public and private sector entities, including other genebanks. An analysis of the global occurrences and genebank holdings of cultivated eggplants and their wild relatives reveals that the WorldVeg genebank holds the world's largest public collection of the three cultivated eggplant species. The composition, seed dissemination and utilization of germplasm from the Center's collection are highlighted. In recent years more than 1,300 accessions of eggplant have been characterized for yield and fruit quality parameters. Further screening for biotic and abiotic stresses in eggplant wild relatives is a priority, as is the need to amass more comprehensive knowledge regarding wild relatives' potential for use in breeding. However, as is the case for many other crops, wild relatives are highly under-represented in the global conservation system of eggplant genetic resources.
Collapse
Affiliation(s)
- Dalia Taher
- World Vegetable CenterTainan, Taiwan
- Vegetable Crops Research Department, Agriculture Research Center, Horticulture Research InstituteGiza, Egypt
| | - Svein Ø. Solberg
- World Vegetable CenterTainan, Taiwan
- Faculty of Applied Ecology and Agricultural Sciences, Inland Norway University of Applied SciencesElverum, Norway
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de ValènciaValencia, Spain
| | | | - Mohamed Rakha
- World Vegetable CenterTainan, Taiwan
- Horticulture Department, Faculty of Agriculture, University of KafrelsheikhKafr El-Sheikh, Egypt
| | | |
Collapse
|
28
|
Acquadro A, Barchi L, Gramazio P, Portis E, Vilanova S, Comino C, Plazas M, Prohens J, Lanteri S. Coding SNPs analysis highlights genetic relationships and evolution pattern in eggplant complexes. PLoS One 2017; 12:e0180774. [PMID: 28686642 PMCID: PMC5501601 DOI: 10.1371/journal.pone.0180774] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 06/21/2017] [Indexed: 11/18/2022] Open
Abstract
Brinjal (Solanum melongena), scarlet (S. aethiopicum) and gboma (S. macrocarpon) eggplants are three Old World domesticates. The genomic DNA of a collection of accessions belonging to the three cultivated species, along with a representation of various wild relatives, was characterized for the presence of single nucleotide polymorphisms (SNPs) using a genotype-by-sequencing approach. A total of 210 million useful reads were produced and were successfully aligned to the reference eggplant genome sequence. Out of the 75,399 polymorphic sites identified among the 76 entries in study, 12,859 were associated with coding sequence. A genetic relationships analysis, supported by the output of the FastSTRUCTURE software, identified four major sub-groups as present in the germplasm panel. The first of these clustered S. aethiopicum with its wild ancestor S. anguivi; the second, S. melongena, its wild progenitor S. insanum, and its relatives S. incanum, S. lichtensteinii and S. linneanum; the third, S. macrocarpon and its wild ancestor S. dasyphyllum; and the fourth, the New World species S. sisymbriifolium, S. torvum and S. elaeagnifolium. By applying a hierarchical FastSTRUCTURE analysis on partitioned data, it was also possible to resolve the ambiguous membership of the accessions of S. campylacanthum, S. violaceum, S. lidii, S. vespertilio and S. tomentsum, as well as to genetically differentiate the three species of New World Origin. A principal coordinates analysis performed both on the entire germplasm panel and also separately on the entries belonging to sub-groups revealed a clear separation among species, although not between each of the domesticates and their respective wild ancestors. There was no clear differentiation between either distinct cultivar groups or different geographical provenance. Adopting various approaches to analyze SNP variation provided support for interpretation of results. The genotyping-by-sequencing approach showed to be highly efficient for both quantifying genetic diversity and establishing genetic relationships among and within cultivated eggplants and their wild relatives. The relevance of these results to the evolution of eggplants, as well as to their genetic improvement, is discussed.
Collapse
Affiliation(s)
- Alberto Acquadro
- University of Turin—DISAFA—Plant Genetics and Breeding, University of Turin, Largo Braccini 2, Grugliasco, Torino, Italy
| | - Lorenzo Barchi
- University of Turin—DISAFA—Plant Genetics and Breeding, University of Turin, Largo Braccini 2, Grugliasco, Torino, Italy
| | - Pietro Gramazio
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, Valencia, Spain
| | - Ezio Portis
- University of Turin—DISAFA—Plant Genetics and Breeding, University of Turin, Largo Braccini 2, Grugliasco, Torino, Italy
| | - Santiago Vilanova
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, Valencia, Spain
| | - Cinzia Comino
- University of Turin—DISAFA—Plant Genetics and Breeding, University of Turin, Largo Braccini 2, Grugliasco, Torino, Italy
| | - Mariola Plazas
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, Camino de Vera 14, Valencia, Spain
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, Valencia, Spain
| | - Sergio Lanteri
- University of Turin—DISAFA—Plant Genetics and Breeding, University of Turin, Largo Braccini 2, Grugliasco, Torino, Italy
| |
Collapse
|
29
|
Prohens J, Gramazio P, Plazas M, Dempewolf H, Kilian B, Díez MJ, Fita A, Herraiz FJ, Rodríguez-Burruezo A, Soler S, Knapp S, Vilanova S. Introgressiomics: a new approach for using crop wild relatives in breeding for adaptation to climate change. EUPHYTICA 2017; 213:158. [PMID: 0 DOI: 10.1007/s10681-017-1938-9] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 06/23/2017] [Indexed: 05/29/2023]
|
30
|
Salgon S, Jourda C, Sauvage C, Daunay MC, Reynaud B, Wicker E, Dintinger J. Eggplant Resistance to the Ralstonia solanacearum Species Complex Involves Both Broad-Spectrum and Strain-Specific Quantitative Trait Loci. FRONTIERS IN PLANT SCIENCE 2017; 8:828. [PMID: 28580001 PMCID: PMC5437220 DOI: 10.3389/fpls.2017.00828] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 05/02/2017] [Indexed: 05/20/2023]
Abstract
Bacterial wilt (BW) is a major disease of solanaceous crops caused by the Ralstonia solanacearum species complex (RSSC). Strains are grouped into five phylotypes (I, IIA, IIB, III, and IV). Varietal resistance is the most sustainable strategy for managing BW. Nevertheless, breeding to improve cultivar resistance has been limited by the pathogen's extensive genetic diversity. Identifying the genetic bases of specific and non-specific resistance is a prerequisite to breed improvement. A major gene (ERs1) was previously mapped in eggplant (Solanum melongena L.) using an intraspecific population of recombinant inbred lines derived from the cross of susceptible MM738 (S) × resistant AG91-25 (R). ERs1 was originally found to control three strains from phylotype I, while being totally ineffective against a virulent strain from the same phylotype. We tested this population against four additional RSSC strains, representing phylotypes I, IIA, IIB, and III in order to clarify the action spectrum of ERs1. We recorded wilting symptoms and bacterial stem colonization under controlled artificial inoculation. We constructed a high-density genetic map of the population using single nucleotide polymorphisms (SNPs) developed from genotyping-by-sequencing and added 168 molecular markers [amplified fragment length polymorphisms (AFLPs), simple sequence repeats (SSRs), and sequence-related amplified polymorphisms (SRAPs)] developed previously. The new linkage map based on a total of 1,035 markers was anchored on eggplant, tomato, and potato genomes. Quantitative trait locus (QTL) mapping for resistance against a total of eight RSSC strains resulted in the detection of one major phylotype-specific QTL and two broad-spectrum QTLs. The major QTL, which specifically controls three phylotype I strains, was located at the bottom of chromosome 9 and corresponded to the previously identified major gene ERs1. Five candidate R-genes were underlying this QTL, with different alleles between the parents. The two other QTLs detected on chromosomes 2 and 5 were found to be associated with partial resistance to strains of phylotypes I, IIA, III and strains of phylotypes IIA and III, respectively. Markers closely linked to these three QTLs will be crucial for breeding eggplant with broad-spectrum resistance to BW. Furthermore, our study provides an important contribution to the molecular characterization of ERs1, which was initially considered to be a major resistance gene.
Collapse
Affiliation(s)
- Sylvia Salgon
- UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Centre de Coopération Internationale en Recherche Agronomique pour le DéveloppementSaint-Pierre, Réunion
- Association Réunionnaise pour la Modernisation de l’Economie Fruitière, Légumière et HORticoleSaint-Pierre, Réunion
- UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Université de la RéunionSaint-Pierre, Réunion
- *Correspondence: Sylvia Salgon, Jacques Dintinger,
| | - Cyril Jourda
- UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Centre de Coopération Internationale en Recherche Agronomique pour le DéveloppementSaint-Pierre, Réunion
| | - Christopher Sauvage
- UR 1052 Génétique et Amélioration des Fruits et Légumes, Institut National de la Recherche AgronomiqueMontfavet, France
| | - Marie-Christine Daunay
- UR 1052 Génétique et Amélioration des Fruits et Légumes, Institut National de la Recherche AgronomiqueMontfavet, France
| | - Bernard Reynaud
- UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Centre de Coopération Internationale en Recherche Agronomique pour le DéveloppementSaint-Pierre, Réunion
- UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Université de la RéunionSaint-Pierre, Réunion
| | - Emmanuel Wicker
- UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Centre de Coopération Internationale en Recherche Agronomique pour le DéveloppementSaint-Pierre, Réunion
- UMR Interactions Plantes-Microorganismes-Environnement, Centre de Coopération Internationale en Recherche Agronomique pour le DéveloppementMontpellier, France
| | - Jacques Dintinger
- UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Centre de Coopération Internationale en Recherche Agronomique pour le DéveloppementSaint-Pierre, Réunion
- *Correspondence: Sylvia Salgon, Jacques Dintinger,
| |
Collapse
|
31
|
Kaushik P, Prohens J, Vilanova S, Gramazio P, Plazas M. Phenotyping of Eggplant Wild Relatives and Interspecific Hybrids with Conventional and Phenomics Descriptors Provides Insight for Their Potential Utilization in Breeding. FRONTIERS IN PLANT SCIENCE 2016; 7:677. [PMID: 27242876 PMCID: PMC4871888 DOI: 10.3389/fpls.2016.00677] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 05/02/2016] [Indexed: 05/22/2023]
Abstract
Eggplant (Solanum melongena) is related to a large number of wild species that are a source of variation for breeding programmes, in particular for traits related to adaptation to climate change. However, wild species remain largely unexploited for eggplant breeding. Detailed phenotypic characterization of wild species and their hybrids with eggplant may allow identifying promising wild species and information on the genetic control and heterosis of relevant traits. We characterizated six eggplant accessions, 21 accessions of 12 wild species (the only primary genepool species S. insanum and 11 secondary genepool species) and 45 interspecific hybrids of eggplant with wild species (18 with S. insanum and 27 with secondary genepool species) using 27 conventional morphological descriptors and 20 fruit morphometric descriptors obtained with the phenomics tool Tomato Analyzer. Significant differences were observed among cultivated, wild and interspecific hybrid groups for 18 conventional and 18 Tomato Analyzer descriptors, with hybrids generally having intermediate values. Wild species were generally more variable than cultivated accessions and interspecific hybrids displayed intermediate ranges of variation and coefficient of variation (CV) values, except for fruit shape traits in which the latter were the most variable. The multivariate principal components analysis (PCA) reveals a clear separation of wild species and cultivated accessions. Interspecific hybrids with S. insanum plotted closer to cultivated eggplant, while hybrids with secondary genepool species generally clustered together with wild species. Many differences were observed among wild species for traits of agronomic interest, which allowed identifying species of greatest potential interest for eggplant breeding. Heterosis values were positive for most vigor-related traits, while for fruit size values were close to zero for hybrids with S. incanum and highly negative for hybrids with secondary genepool species. Our results allowed the identification of potentially interesting wild species and interspecific hybrids for introgression breeding in eggplant. This is an important step for broadening the genetic base of eggplant and for breeding for adaptation to climate change in this crop.
Collapse
|