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Martina M, Zayas A, Portis E, Di Nardo G, Polli MF, Comino C, Gilardi G, Martin E, Acquadro A. The Dark Side of the pollen: BSA-seq identified genomic regions linked to male sterility in globe artichoke. BMC Plant Biol 2024; 24:415. [PMID: 38760683 PMCID: PMC11100218 DOI: 10.1186/s12870-024-05119-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 05/08/2024] [Indexed: 05/19/2024]
Abstract
Globe artichoke (Cynara cardunculus var. scolymus; 2n = 2x = 34) is a food crop consumed for its immature flower heads. Traditionally, globe artichoke varietal types are vegetatively propagated. However, seed propagation makes it possible to treat the crop as annual, increasing field uniformity and reducing farmers costs, as well as pathogens diffusion. Despite globe artichoke's significant agricultural value and the critical role of heterosis in the development of superior varieties, the production of hybrids remains challenging without a reliable system for large-scale industrial seed production. Male sterility (MS) presents a promising avenue for overcoming these challenges by simplifying the hybridization process and enabling cost-effective seed production. However, within the Cynara genus, genic male sterility has been linked to three recessive loci in globe artichoke, with no definitive genetic mechanism elucidated to date. A 250 offsprings F2 population, derived from a cross between a MS globe artichoke and a male fertile (MF) cultivated cardoon (C. cardunculus var. altilis) and fitting a monogenic segregation model (3:1), was analyzed through BSA-seq, aiming at the identification of genomic regions/genes affecting male sterility. Four QTL regions were identified on chromosomes 4, 12, and 14. By analyzing the sequence around the highest pick on chromosome 14, a cytochrome P450 (CYP703A2) was identified, carrying a deleterious substitution (R/Q) fixed in the male sterile parent. A single dCAPS marker was developed around this SNP, allowing the discrimination between MS and MF genotypes within the population, suitable for applications in plant breeding programs. A 3D model of the protein was generated by homology modeling, revealing that the mutated amino acid is part of a highly conserved motif crucial for protein folding.
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Affiliation(s)
- Matteo Martina
- DISAFA, Plant Genetics and Breeding, University of Turin, Turin, Italy
| | - Aldana Zayas
- IICAR (Instituto de Investigaciones en Ciencias Agrarias de Rosario), CONICET, Campo Exp. J.F. Villarino, Zavalla, Santa Fe, Argentina
| | - Ezio Portis
- DISAFA, Plant Genetics and Breeding, University of Turin, Turin, Italy
| | - Giovanna Di Nardo
- DBIOS, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | | | - Cinzia Comino
- DISAFA, Plant Genetics and Breeding, University of Turin, Turin, Italy
| | - Gianfranco Gilardi
- DBIOS, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Eugenia Martin
- IICAR (Instituto de Investigaciones en Ciencias Agrarias de Rosario), CONICET, Campo Exp. J.F. Villarino, Zavalla, Santa Fe, Argentina.
| | - Alberto Acquadro
- DISAFA, Plant Genetics and Breeding, University of Turin, Turin, Italy.
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Martina M, De Rosa V, Magon G, Acquadro A, Barchi L, Barcaccia G, De Paoli E, Vannozzi A, Portis E. Revitalizing agriculture: next-generation genotyping and -omics technologies enabling molecular prediction of resilient traits in the Solanaceae family. Front Plant Sci 2024; 15:1278760. [PMID: 38375087 PMCID: PMC10875072 DOI: 10.3389/fpls.2024.1278760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 01/22/2024] [Indexed: 02/21/2024]
Abstract
This review highlights -omics research in Solanaceae family, with a particular focus on resilient traits. Extensive research has enriched our understanding of Solanaceae genomics and genetics, with historical varietal development mainly focusing on disease resistance and cultivar improvement but shifting the emphasis towards unveiling resilience mechanisms in genebank-preserved germplasm is nowadays crucial. Collecting such information, might help researchers and breeders developing new experimental design, providing an overview of the state of the art of the most advanced approaches for the identification of the genetic elements laying behind resilience. Building this starting point, we aim at providing a useful tool for tackling the global agricultural resilience goals in these crops.
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Affiliation(s)
- Matteo Martina
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
| | - Valeria De Rosa
- Department of Agricultural, Food, Environmental and Animal Sciences (DI4A), University of Udine, Udine, Italy
| | - Gabriele Magon
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padua, Legnaro, Italy
| | - Alberto Acquadro
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
| | - Lorenzo Barchi
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
| | - Gianni Barcaccia
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padua, Legnaro, Italy
| | - Emanuele De Paoli
- Department of Agricultural, Food, Environmental and Animal Sciences (DI4A), University of Udine, Udine, Italy
| | - Alessandro Vannozzi
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padua, Legnaro, Italy
| | - Ezio Portis
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
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Poczai P, D’Agostino N, Deanna R, Portis E. Editorial: Solanaceae VIII: biodiversity, climate change and breeding. Front Genet 2023; 14:1348372. [PMID: 38174047 PMCID: PMC10763236 DOI: 10.3389/fgene.2023.1348372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Affiliation(s)
- Péter Poczai
- Botany and Mycology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
- Museomics Research Group, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Nunzio D’Agostino
- University of Naples Federico II, Department of Agricultural Sciences, Portici, Italy
| | - Rocio Deanna
- University of Colorado, Boulder, CO, United States
- Instituto Multidisciplinario de Biología Vegetal (IMBIV, CONICET-UNC), Córdoba, Argentina
| | - Ezio Portis
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Turin, Grugliasco, Italy
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Magon G, De Rosa V, Martina M, Falchi R, Acquadro A, Barcaccia G, Portis E, Vannozzi A, De Paoli E. Boosting grapevine breeding for climate-smart viticulture: from genetic resources to predictive genomics. Front Plant Sci 2023; 14:1293186. [PMID: 38148866 PMCID: PMC10750425 DOI: 10.3389/fpls.2023.1293186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 11/27/2023] [Indexed: 12/28/2023]
Abstract
The multifaceted nature of climate change is increasing the urgency to select resilient grapevine varieties, or generate new, fitter cultivars, to withstand a multitude of new challenging conditions. The attainment of this goal is hindered by the limiting pace of traditional breeding approaches, which require decades to result in new selections. On the other hand, marker-assisted breeding has proved useful when it comes to traits governed by one or few genes with great effects on the phenotype, but its efficacy is still restricted for complex traits controlled by many loci. On these premises, innovative strategies are emerging which could help guide selection, taking advantage of the genetic diversity within the Vitis genus in its entirety. Multiple germplasm collections are also available as a source of genetic material for the introgression of alleles of interest via adapted and pioneering transformation protocols, which present themselves as promising tools for future applications on a notably recalcitrant species such as grapevine. Genome editing intersects both these strategies, not only by being an alternative to obtain focused changes in a relatively rapid way, but also by supporting a fine-tuning of new genotypes developed with other methods. A review on the state of the art concerning the available genetic resources and the possibilities of use of innovative techniques in aid of selection is presented here to support the production of climate-smart grapevine genotypes.
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Affiliation(s)
- Gabriele Magon
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padova, Agripolis, Viale dell’Università 16, Legnaro, Italy
| | - Valeria De Rosa
- Department of Agricultural, Food, Environmental and Animal Sciences (DI4A), University of Udine, Via delle Scienze, 206, Udine, Italy
| | - Matteo Martina
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Largo P. Braccini 2, Grugliasco, Italy
| | - Rachele Falchi
- Department of Agricultural, Food, Environmental and Animal Sciences (DI4A), University of Udine, Via delle Scienze, 206, Udine, Italy
| | - Alberto Acquadro
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Largo P. Braccini 2, Grugliasco, Italy
| | - Gianni Barcaccia
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padova, Agripolis, Viale dell’Università 16, Legnaro, Italy
| | - Ezio Portis
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Largo P. Braccini 2, Grugliasco, Italy
| | - Alessandro Vannozzi
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padova, Agripolis, Viale dell’Università 16, Legnaro, Italy
| | - Emanuele De Paoli
- Department of Agricultural, Food, Environmental and Animal Sciences (DI4A), University of Udine, Via delle Scienze, 206, Udine, Italy
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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. Plant J 2023; 116:1667-1680. [PMID: 37682777 DOI: 10.1111/tpj.16455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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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. J Exp Bot 2023; 74:6285-6305. [PMID: 37419672 DOI: 10.1093/jxb/erad260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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Martina M, Acquadro A, Portis E, Barchi L, Lanteri S. Diversity analyses in two ornamental and large-genome Ranunculaceae species based on a low-cost Klenow NGS-based protocol. Front Plant Sci 2023; 14:1187205. [PMID: 37360724 PMCID: PMC10289064 DOI: 10.3389/fpls.2023.1187205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 05/26/2023] [Indexed: 06/28/2023]
Abstract
Persian buttercup (Ranunculus asiaticus L.) and poppy anemone (Anemone coronaria L.) are ornamental, outcrossing, perennial species belonging to the Ranunculaceae family, characterized by large and highly repetitive genomes. We applied K-seq protocol in both species to generate high-throughput sequencing data and produce a large number of genetic polymorphisms. The technique entails the application of Klenow polymerase-based PCR using short primers designed by analyzing k-mer sets in the genome sequence. To date the genome sequence of both species has not been released, thus we designed primer sets based on the reference the genome sequence of the related species Aquilegia oxysepala var. kansuensis (Brühl). A whole of 11,542 SNPs were selected for assessing genetic diversity of eighteen commercial varieties of R. asiaticus, while 1,752 SNPs for assessing genetic diversity in six cultivars of A. coronaria. UPGMA dendrograms were constructed and in R. asiaticus integrated in with PCA analysis. This study reports the first molecular fingerprinting within Persian buttercup, while the results obtained in poppy anemone were compared with a previously published SSR-based fingerprinting, proving K-seq to be an efficient protocol for the genotyping of complex genetic backgrounds.
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Gaccione L, Martina M, Barchi L, Portis E. A Compendium for Novel Marker-Based Breeding Strategies in Eggplant. Plants (Basel) 2023; 12:1016. [PMID: 36903876 PMCID: PMC10005326 DOI: 10.3390/plants12051016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Arrones A, Mangino G, Alonso D, Plazas M, Prohens J, Portis E, Barchi L, Giuliano G, Vilanova S, Gramazio P. Mutations in the SmAPRR2 transcription factor suppressing chlorophyll pigmentation in the eggplant fruit peel are key drivers of a diversified colour palette. Front Plant Sci 2022; 13:1025951. [PMID: 36388476 PMCID: PMC9647125 DOI: 10.3389/fpls.2022.1025951] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/03/2022] [Indexed: 06/01/2023]
Abstract
Understanding the mechanisms by which chlorophylls are synthesized in the eggplant (Solanum melongena) fruit peel is of great relevance for eggplant breeding. A multi-parent advanced generation inter-cross (MAGIC) population and a germplasm collection have been screened for green pigmentation in the fruit peel and used to identify candidate genes for this trait. A genome-wide association study (GWAS) performed with 420 MAGIC individuals revealed a major association on chromosome 8 close to a gene similar to APRR2. Two variants in SmAPRR2, predicted as having a high impact effect, were associated with the absence of fruit chlorophyll pigmentation in the MAGIC population, and a large deletion of 5.27 kb was found in two reference genomes of accessions without chlorophyll in the fruit peel. The validation of the candidate gene SmAPRR2 was performed by its sequencing in a set of MAGIC individuals and through its de novo assembly in 277 accessions from the G2P-SOL eggplant core collection. Two additional mutations in SmAPRR2 associated with the lack of chlorophyll were identified in the core collection set. The phylogenetic analysis of APRR2 reveals orthology within Solanaceae and suggests that specialization of APRR2-like genes occurred independently in Cucurbitaceae and Solanaceae. A strong geographical differentiation was observed in the frequency of predominant mutations in SmAPRR2, resulting in a lack of fruit chlorophyll pigmentation and suggesting that this phenotype may have arisen and been selected independently several times. This study represents the first identification of a major gene for fruit chlorophyll pigmentation in the eggplant fruit.
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Affiliation(s)
- Andrea Arrones
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Giulio Mangino
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - David Alonso
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Mariola Plazas
- 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
| | - Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics and Breeding, University of Turin, Grugliasco, Italy
| | - Lorenzo Barchi
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics and Breeding, University of Turin, Grugliasco, 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, Valencia, Spain
| | - Pietro Gramazio
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, Valencia, Spain
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Martina M, Acquadro A, Gulino D, Brusco F, Rabaglio M, Portis E, Lanteri S. First genetic maps development and QTL mining in Ranunculus asiaticus L. through ddRADseq. Front Plant Sci 2022; 13:1009206. [PMID: 36212343 PMCID: PMC9539318 DOI: 10.3389/fpls.2022.1009206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
Persian Buttercup (Ranunculus asiaticus L.; 2x=2n=16; estimated genome size: 7.6Gb) is an ornamental and perennial crop native of Asia Minor and Mediterranean basin, marketed both as cut flower or potted plant. Currently new varieties are developed by selecting plants carrying desirable traits in segregating progenies obtained by controlled mating, which are propagated through rhizomes or micro-propagated in vitro. In order to escalate selection efficiency and respond to market requests, more knowledge of buttercup genetics would facilitate the identification of markers associated with loci and genes controlling key ornamental traits, opening the way for molecular assisted breeding programs. Reduced-representation sequencing (RRS) represents a powerful tool for plant genotyping, especially in case of large genomes such as the one of buttercup, and have been applied for the development of high-density genetic maps in several species. We report on the development of the first molecular-genetic maps in R. asiaticus based on of a two-way pseudo-testcross strategy. A double digest restriction-site associated DNA (ddRAD) approach was applied for genotyping two F1 mapping populations, whose female parents were a genotype of a so called 'ponpon' and of a 'double flower' varieties, while the common male parental ('Cipro') was a genotype producing a simple flower. The ddRAD generated a total of ~2Gb demultiplexed reads, resulting in an average of 8,3M reads per line. The sstacks pipeline was applied for the construction of a mock reference genome based on sequencing data, and SNP markers segregating in only one of the parents were retained for map construction by treating the F1 population as a backcross. The four parental maps (two of the female parents and two of the common male parent) were aligned with 106 common markers and 8 linkage groups were identified, corresponding to the haploid chromosome number of the species. An average of 586 markers were associated with each parental map, with a marker density ranging from 1 marker/cM to 4.4 markers/cM. The developed maps were used for QTL analysis for flower color, leading to the identification of major QTLs for purple pigmentation. These results contribute to dissect on the genetics of Persian buttercup, enabling the development of new approaches for future varietal development.
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Affiliation(s)
- Matteo Martina
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
| | - Alberto Acquadro
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
| | - Davide Gulino
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
| | | | | | - Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
| | - Sergio Lanteri
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
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Rau D, Attene G, Rodriguez M, Baghino L, Pisanu AB, Sanna D, Acquadro A, Portis E, Comino C. The Population Structure of a Globe Artichoke Worldwide Collection, as Revealed by Molecular and Phenotypic Analyzes. Front Plant Sci 2022; 13:898740. [PMID: 35865281 PMCID: PMC9294547 DOI: 10.3389/fpls.2022.898740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/13/2022] [Indexed: 05/27/2023]
Abstract
The knowledge of the organization of the domesticated gene pool of crop species is an essential requirement to understand crop evolution, to rationalize conservation programs, and to support practical decisions in plant breeding. Here, we integrate simple sequence repeat (SSR) analysis and phenotypic characterization to investigate a globe artichoke collection that comprises most of the varieties cultivated worldwide. We show that the cultivated gene pool of globe artichoke includes five distinct genetic groups associated with the major phenotypic typologies: Catanesi (which based on our analysis corresponds to Violetti di Provenza), Spinosi, Violetti di Toscana, Romaneschi, and Macau. We observed that 17 and 11% of the molecular and phenotypic variance, respectively, is between these groups, while within groups, strong linkage disequilibrium and heterozygote excess are evident. The divergence between groups for quantitative traits correlates with the average broad-sense heritability within the groups. The phenotypic divergence between groups for both qualitative and quantitative traits is strongly and positively correlated with SSR divergence (FST) between groups. All this implies a low population size and strong bottleneck effects, and indicates a long history of clonal propagation and selection during the evolution of the domesticated gene pool of globe artichoke. Moreover, the comparison between molecular and phenotypic population structures suggests that harvest time, plant architecture (i.e., plant height, stem length), leaf spininess, head morphology (i.e., head shape, bract shape, spininess) together with the number of heads per plant were the main targets of selection during the evolution of the cultivated germplasm. We emphasize our findings in light of the potential exploitation of this collection for association mapping studies.
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Affiliation(s)
- Domenico Rau
- Dipartimento di Agraria, Sezione di Agronomia, Coltivazioni Erbacee e Genetica (SACEG), Università degli Studi di Sassari, Sassari, Italy
| | - Giovanna Attene
- Dipartimento di Agraria, Sezione di Agronomia, Coltivazioni Erbacee e Genetica (SACEG), Università degli Studi di Sassari, Sassari, Italy
| | - Monica Rodriguez
- Dipartimento di Agraria, Sezione di Agronomia, Coltivazioni Erbacee e Genetica (SACEG), Università degli Studi di Sassari, Sassari, Italy
| | - Limbo Baghino
- Agenzia AGRIS Sardegna (Servizio Ricerca sui Sistemi Colturali Erbacei, Settore Innovazione dei Modelli Gestionali e Studio Della Biodiversità Nelle Colture Intensive), Oristano, Italy
| | - Anna Barbara Pisanu
- Agenzia AGRIS Sardegna (Servizio Ricerca sui Sistemi Colturali Erbacei, Settore Innovazione dei Modelli Gestionali e Studio Della Biodiversità Nelle Colture Intensive), Oristano, Italy
| | - Davide Sanna
- Agenzia AGRIS Sardegna (Servizio Ricerca sui Sistemi Colturali Erbacei, Settore Innovazione dei Modelli Gestionali e Studio Della Biodiversità Nelle Colture Intensive), Oristano, Italy
| | - Alberto Acquadro
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA), Genetica Vegetale (Plant Genetics), Università degli Studi di Torino, Turin, Italy
| | - Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA), Genetica Vegetale (Plant Genetics), Università degli Studi di Torino, Turin, Italy
| | - Cinzia Comino
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA), Genetica Vegetale (Plant Genetics), Università degli Studi di Torino, Turin, Italy
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Poczai P, D’Agostino N, Deanna R, Portis E. Editorial: Solanaceae VII: Biology, Genetics, and Evolution. Front Genet 2022; 13:932421. [PMID: 35812731 PMCID: PMC9261279 DOI: 10.3389/fgene.2022.932421] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 05/12/2022] [Indexed: 12/02/2022] Open
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Cerruti E, Gisbert C, Drost HG, Valentino D, Portis E, Barchi L, Prohens J, Lanteri S, Comino C, Catoni M. Grafting vigour is associated with DNA de-methylation in eggplant. Hortic Res 2021; 8:241. [PMID: 34719687 PMCID: PMC8558322 DOI: 10.1038/s41438-021-00660-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 07/20/2021] [Accepted: 07/30/2021] [Indexed: 05/08/2023]
Abstract
In horticulture, grafting is a popular technique used to combine positive traits from two different plants. This is achieved by joining the plant top part (scion) onto a rootstock which contains the stem and roots. Rootstocks can provide resistance to stress and increase plant production, but despite their wide use, the biological mechanisms driving rootstock-induced alterations of the scion phenotype remain largely unknown. Given that epigenetics plays a relevant role during distance signalling in plants, we studied the genome-wide DNA methylation changes induced in eggplant (Solanum melongena) scion using two interspecific rootstocks to increase vigour. We found that vigour was associated with a change in scion gene expression and a genome-wide hypomethylation in the CHH context. Interestingly, this hypomethylation correlated with the downregulation of younger and potentially more active long terminal repeat retrotransposable elements (LTR-TEs), suggesting that graft-induced epigenetic modifications are associated with both physiological and molecular phenotypes in grafted plants. Our results indicate that the enhanced vigour induced by heterografting in eggplant is associated with epigenetic modifications, as also observed in some heterotic hybrids.
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Affiliation(s)
- Elisa Cerruti
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Carmina Gisbert
- Institute for Conservation & Improvement of Valencian Agrodiversity (COMAV), Universitat Politècnica de València, Valencia, Spain
| | - Hajk-Georg Drost
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Computational Biology Group, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Danila Valentino
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
| | - Ezio Portis
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
| | - Lorenzo Barchi
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
| | - Jaime Prohens
- Institute for Conservation & Improvement of Valencian Agrodiversity (COMAV), Universitat Politècnica de València, Valencia, Spain
| | - Sergio Lanteri
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
| | - Cinzia Comino
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, Grugliasco, Italy.
| | - Marco Catoni
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK.
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom.
- Institute for Sustainable Plant Protection, National Research Council of Italy, Torino, Italy.
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Barchi L, Rabanus‐Wallace MT, Prohens J, Toppino L, Padmarasu S, Portis E, Rotino GL, Stein N, Lanteri S, Giuliano G. Improved genome assembly and pan-genome provide key insights into eggplant domestication and breeding. Plant J 2021; 107:579-596. [PMID: 33964091 PMCID: PMC8453987 DOI: 10.1111/tpj.15313] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 05/20/2023]
Abstract
Eggplant (Solanum melongena L.) is an important horticultural crop and one of the most widely grown vegetables from the Solanaceae family. It was domesticated from a wild, prickly progenitor carrying small, round, non-anthocyanic fruits. We obtained a novel, highly contiguous genome assembly of the eggplant '67/3' reference line, by Hi-C retrofitting of a previously released short read- and optical mapping-based assembly. The sizes of the 12 chromosomes and the fraction of anchored genes in the improved assembly were comparable to those of a chromosome-level assembly. We resequenced 23 accessions of S. melongena representative of the worldwide phenotypic, geographic, and genetic diversity of the species, and one each from the closely related species Solanum insanum and Solanum incanum. The eggplant pan-genome contained approximately 51.5 additional megabases and 816 additional genes compared with the reference genome, while the pan-plastome showed little genetic variation. We identified 53 selective sweeps related to fruit color, prickliness, and fruit shape in the nuclear genome, highlighting selection leading to the emergence of present-day S. melongena cultivars from its wild ancestors. Candidate genes underlying the selective sweeps included a MYBL1 repressor and CHALCONE ISOMERASE (for fruit color), homologs of Arabidopsis GLABRA1 and GLABROUS INFLORESCENCE STEMS2 (for prickliness), and orthologs of tomato FW2.2, OVATE, LOCULE NUMBER/WUSCHEL, SUPPRESSOR OF OVATE, and CELL SIZE REGULATOR (for fruit size/shape), further suggesting that selection for the latter trait relied on a common set of orthologous genes in tomato and eggplant.
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Affiliation(s)
- Lorenzo Barchi
- DISAFA – Plant geneticsUniversity of TurinGrugliasco (TO)10095Italy
| | | | - Jaime Prohens
- COMAVUniversitat Politècnica de ValènciaCamino de Vera 14Valencia46022Spain
| | - Laura Toppino
- CREA Research Centre for Genomics and BioinformaticsVia Paullese 28Montanaso LombardoLO26836Italy
| | - Sudharsan Padmarasu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstr. 3Seeland06466Germany
| | - Ezio Portis
- DISAFA – Plant geneticsUniversity of TurinGrugliasco (TO)10095Italy
| | - Giuseppe Leonardo Rotino
- CREA Research Centre for Genomics and BioinformaticsVia Paullese 28Montanaso LombardoLO26836Italy
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstr. 3Seeland06466Germany
- Department of Crop SciencesCenter for Integrated Breeding Research (CiBreed)Georg‐August‐UniversityVon Siebold Str. 8Göttingen37075Germany
| | - Sergio Lanteri
- DISAFA – Plant geneticsUniversity of TurinGrugliasco (TO)10095Italy
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Pavese V, Cavalet Giorsa E, Barchi L, Acquadro A, Torello Marinoni D, Portis E, James Lucas S, Botta R. Whole-genome assembly of Corylus avellana cv'Tonda Gentile delle Langhe' using linked-reads (10X Genomics). G3 (Bethesda) 2021; 11:6272584. [PMID: 33964151 PMCID: PMC8495946 DOI: 10.1093/g3journal/jkab152] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/20/2021] [Indexed: 01/01/2023]
Abstract
The European hazelnut (Corylus avellana L.; 2n = 2x = 22) is a worldwide economically important tree nut that is cross-pollinated due to sporophytic incompatibility. Therefore, any individual plant is highly heterozygous. Cultivars are clonally propagated using mound layering, rooted suckers, and micropropagation. In recent years, the interest in this crop has increased, due to a growing demand related to the recognized health benefits of nut consumption. C. avellana cv “Tonda Gentile delle Langhe” (“TGdL”) is well-known for its high kernel quality, and the premium price paid for this cultivar is an economic benefit for producers in northern Italy. Assembly of a high-quality genome is a difficult task in many plant species because of the high level of heterozygosity. We assembled a chromosome-level genome sequence of “TGdL” with a two-step approach. First, 10X Genomics Chromium Technology was used to create a high-quality sequence, which was then assembled into scaffolds with cv “Tombul” genome as the reference. Eleven pseudomolecules were obtained, corresponding to 11 chromosomes. A total of 11,046 scaffolds remained unplaced, representing 11% of the genome (46,504,161 bp). Gene prediction, performed with Maker-P software, identified 27,791 genes (AED ≤0.4 and 92% of BUSCO completeness), whose function was analyzed with BlastP and InterProScan software. To characterize “TGdL” specific genetic mechanisms, Orthofinder was used to detect orthologs between hazelnut and closely related species. The “TGdL” genome sequence is expected to be a powerful tool to understand hazelnut genetics and allow detection of markers/genes for important traits to be used in targeted breeding programs.
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Affiliation(s)
- Vera Pavese
- Dipartimento di Scienze Agrarie, Forestali e Alimentari-DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy
| | - Emile Cavalet Giorsa
- Dipartimento di Scienze Agrarie, Forestali e Alimentari-DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy
| | - Lorenzo Barchi
- Dipartimento di Scienze Agrarie, Forestali e Alimentari-DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy
| | - Alberto Acquadro
- Dipartimento di Scienze Agrarie, Forestali e Alimentari-DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy
| | - Daniela Torello Marinoni
- Dipartimento di Scienze Agrarie, Forestali e Alimentari-DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy
| | - Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali e Alimentari-DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy
| | - Stuart James Lucas
- Sabanci University SUNUM Nanotechnology Research and Application Centre, Istanbul, Turkey
| | - Roberto Botta
- Dipartimento di Scienze Agrarie, Forestali e Alimentari-DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy
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Abstract
Tomato (Solanum lycopersicum L.) aroma is determined by the interaction of volatile compounds (VOCs) released by the tomato fruits with receptors in the nose, leading to a sensorial impression, such as "sweet", "smoky", or "fruity" aroma. Of the more than 400 VOCs released by tomato fruits, 21 have been reported as main contributors to the perceived tomato aroma. These VOCs can be grouped in five clusters, according to their biosynthetic origins. In the last decades, a vast array of scientific studies has investigated the genetic component of tomato aroma in modern tomato cultivars and their relatives. In this paper we aim to collect, compare, integrate and summarize the available literature on flavour-related QTLs in tomato. Three hundred and 5ifty nine (359) QTLs associated with tomato fruit VOCs were physically mapped on the genome and investigated for the presence of potential candidate genes. This review makes it possible to (i) pinpoint potential donors described in literature for specific traits, (ii) highlight important QTL regions by combining information from different populations, and (iii) pinpoint potential candidate genes. This overview aims to be a valuable resource for researchers aiming to elucidate the genetics underlying tomato flavour and for breeders who aim to improve tomato aroma.
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Affiliation(s)
- Matteo Martina
- DISAFA, Plant Genetics and Breeding, University of Turin, 10095 Grugliasco, Italy;
| | - Yury Tikunov
- Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands;
| | - Ezio Portis
- DISAFA, Plant Genetics and Breeding, University of Turin, 10095 Grugliasco, Italy;
- Correspondence: (E.P.); (A.G.B.); Tel.: +39-011-6708807 (E.P.); +31-317-480762 (A.G.B.)
| | - Arnaud G. Bovy
- Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands;
- Correspondence: (E.P.); (A.G.B.); Tel.: +39-011-6708807 (E.P.); +31-317-480762 (A.G.B.)
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Valentini N, Portis E, Botta R, Acquadro A, Pavese V, Cavalet Giorsa E, Torello Marinoni D. Mapping the Genetic Regions Responsible for Key Phenology-Related Traits in the European Hazelnut. Front Plant Sci 2021; 12:749394. [PMID: 35003153 PMCID: PMC8733624 DOI: 10.3389/fpls.2021.749394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/24/2021] [Indexed: 05/03/2023]
Abstract
An increasing interest in the cultivation of (European) hazelnut (Corylus avellana) is driving a demand to breed cultivars adapted to non-conventional environments, particularly in the context of incipient climate change. Given that plant phenology is so strongly determined by genotype, a rational approach to support these breeding efforts will be to identify quantitative trait loci (QTLs) and the genes underlying the basis for adaptation. The present study was designed to map QTLs for phenology-related traits, such as the timing of both male and female flowering, dichogamy, and the period required for nuts to reach maturity. The analysis took advantage of an existing linkage map developed from a population of F1 progeny bred from the cross "Tonda Gentile delle Langhe" × "Merveille de Bollwiller," consisting in 11 LG. A total of 42 QTL-harboring regions were identified. Overall, 71 QTLs were detected, 49 on the TGdL map and 22 on the MB map; among these, 21 were classified as major; 13 were detected in at least two of the seasons (stable-major QTL). In detail, 20 QTLs were identified as contributing to the time of male flowering, 15 to time of female flowering, 25 to dichogamy, and 11 to time of nut maturity. LG02 was found to harbor 16 QTLs, while 15 QTLs mapped to LG10 and 14 to LG03. Many of the QTLs were clustered with one another. The major cluster was located on TGdL_02 and consisted of mainly major QTLs governing all the analyzed traits. A search of the key genomic regions revealed 22 candidate genes underlying the set of traits being investigated. Many of them have been described in the literature as involved in processes related to flowering, control of dormancy, budburst, the switch from vegetative to reproductive growth, or the morphogenesis of flowers and seeds.
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Torello Marinoni D, Nishio S, Valentini N, Shirasawa K, Acquadro A, Portis E, Alma A, Akkak A, Pavese V, Cavalet-Giorsa E, Botta R. Development of High-Density Genetic Linkage Maps and Identification of Loci for Chestnut Gall Wasp Resistance in Castanea spp. Plants (Basel) 2020; 9:plants9081048. [PMID: 32824716 PMCID: PMC7465717 DOI: 10.3390/plants9081048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/12/2020] [Accepted: 08/13/2020] [Indexed: 11/29/2022]
Abstract
Castanea sativa is an important multipurpose species in Europe for nut and timber production as well as for its role in the landscape and in the forest ecosystem. This species has low tolerance to chestnut gall wasp (Dryocosmus kuriphilus Yasumatsu), which is a pest that was accidentally introduced into Europe in early 2000 and devastated forest and orchard trees. Resistance to the gall wasp was found in the hybrid cultivar ‘Bouche de Bétizac’ (C. sativa × C. crenata) and studied by developing genetic linkage maps using a population derived from a cross between ‘Bouche de Bétizac’ and the susceptible cultivar ‘Madonna’ (C. sativa). The high-density genetic maps were constructed using double-digest restriction site-associated DNA-seq and simple sequence repeat markers. The map of ‘Bouche de Bétizac’ consisted of 1459 loci and spanned 809.6 cM; the map of ‘Madonna’ consisted of 1089 loci and spanned 753.3 cM. In both maps, 12 linkage groups were identified. A single major QTL was recognized on the ‘Bouche de Bétizac’ map, explaining up to 67–69% of the phenotypic variance of the resistance trait (Rdk1). The Rdk1 quantitative trait loci (QTL) region included 11 scaffolds and two candidate genes putatively involved in the resistance response were identified. This study will contribute to C. sativa breeding programs and to the study of Rdk1 genes.
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Affiliation(s)
- Daniela Torello Marinoni
- Dipartimento di Scienze Agrarie, Forestali e Alimentari—DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy; (N.V.); (A.A.); (E.P.); (A.A.); (V.P.); (E.C.-G.); (R.B.)
- Correspondence:
| | - Sogo Nishio
- Institute of Fruit Tree and Tea Science, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605, Japan;
| | - Nadia Valentini
- Dipartimento di Scienze Agrarie, Forestali e Alimentari—DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy; (N.V.); (A.A.); (E.P.); (A.A.); (V.P.); (E.C.-G.); (R.B.)
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan;
| | - Alberto Acquadro
- Dipartimento di Scienze Agrarie, Forestali e Alimentari—DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy; (N.V.); (A.A.); (E.P.); (A.A.); (V.P.); (E.C.-G.); (R.B.)
| | - Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali e Alimentari—DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy; (N.V.); (A.A.); (E.P.); (A.A.); (V.P.); (E.C.-G.); (R.B.)
| | - Alberto Alma
- Dipartimento di Scienze Agrarie, Forestali e Alimentari—DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy; (N.V.); (A.A.); (E.P.); (A.A.); (V.P.); (E.C.-G.); (R.B.)
| | - Aziz Akkak
- Dipartimento di Scienze Agrarie, degli Alimenti e dell’Ambiente, Università degli Studi di Foggia, Via Napoli 25, 71121 Foggia, Italy;
| | - Vera Pavese
- Dipartimento di Scienze Agrarie, Forestali e Alimentari—DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy; (N.V.); (A.A.); (E.P.); (A.A.); (V.P.); (E.C.-G.); (R.B.)
| | - Emile Cavalet-Giorsa
- Dipartimento di Scienze Agrarie, Forestali e Alimentari—DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy; (N.V.); (A.A.); (E.P.); (A.A.); (V.P.); (E.C.-G.); (R.B.)
| | - Roberto Botta
- Dipartimento di Scienze Agrarie, Forestali e Alimentari—DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy; (N.V.); (A.A.); (E.P.); (A.A.); (V.P.); (E.C.-G.); (R.B.)
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Barchi L, Pietrella M, Venturini L, Minio A, Toppino L, Acquadro A, Andolfo G, Aprea G, Avanzato C, Bassolino L, Comino C, Molin AD, Ferrarini A, Maor LC, Portis E, Reyes-Chin-Wo S, Rinaldi R, Sala T, Scaglione D, Sonawane P, Tononi P, Almekias-Siegl E, Zago E, Ercolano MR, Aharoni A, Delledonne M, Giuliano G, Lanteri S, Rotino GL. A chromosome-anchored eggplant genome sequence reveals key events in Solanaceae evolution. Sci Rep 2019; 9:11769. [PMID: 31409808 PMCID: PMC6692341 DOI: 10.1038/s41598-019-47985-w] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 07/05/2019] [Indexed: 11/30/2022] Open
Abstract
With approximately 450 species, spiny Solanum species constitute the largest monophyletic group in the Solanaceae family, but a high-quality genome assembly from this group is presently missing. We obtained a chromosome-anchored genome assembly of eggplant (Solanum melongena), containing 34,916 genes, confirming that the diploid gene number in the Solanaceae is around 35,000. Comparative genomic studies with tomato (S. lycopersicum), potato (S. tuberosum) and pepper (Capsicum annuum) highlighted the rapid evolution of miRNA:mRNA regulatory pairs and R-type defense genes in the Solanaceae, and provided a genomic basis for the lack of steroidal glycoalkaloid compounds in the Capsicum genus. Using parsimony methods, we reconstructed the putative chromosomal complements of the key founders of the main Solanaceae clades and the rearrangements that led to the karyotypes of extant species and their ancestors. From 10% to 15% of the genes present in the four genomes were syntenic paralogs (ohnologs) generated by the pre-γ, γ and T paleopolyploidy events, and were enriched in transcription factors. Our data suggest that the basic gene network controlling fruit ripening is conserved in different Solanaceae clades, and that climacteric fruit ripening involves a differential regulation of relatively few components of this network, including CNR and ethylene biosynthetic genes.
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Affiliation(s)
- Lorenzo Barchi
- University of Torino - DISAFA - Plant Genetics and Breeding, Largo Braccini 2, 10095, Grugliasco, Torino, Italy
| | - Marco Pietrella
- Italian National Agency for New Technologies, Energy and Sustainable Development (ENEA), Casaccia Res Ctr, Via Anguillarese 301, 00123, Roma, Italy.,Council for Agricultural Research and Economics (CREA), Research Centre for Olive, Citrus and Tree Fruit, 47121, Forlì, Italy
| | - Luca Venturini
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.,Department of Life Sciences, Natural History Museum, Cromwell Rd, Kensington, London, United Kingdom
| | - Andrea Minio
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Laura Toppino
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics, 26836, Montanaso Lombardo, LO, Italy
| | - Alberto Acquadro
- University of Torino - DISAFA - Plant Genetics and Breeding, Largo Braccini 2, 10095, Grugliasco, Torino, Italy
| | - Giuseppe Andolfo
- Department of Agricultural Sciences, University of Naples Federico II, 80055, Portici, Italy
| | - Giuseppe Aprea
- Italian National Agency for New Technologies, Energy and Sustainable Development (ENEA), Casaccia Res Ctr, Via Anguillarese 301, 00123, Roma, Italy
| | - Carla Avanzato
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Laura Bassolino
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics, 26836, Montanaso Lombardo, LO, Italy
| | - Cinzia Comino
- University of Torino - DISAFA - Plant Genetics and Breeding, Largo Braccini 2, 10095, Grugliasco, Torino, Italy
| | - Alessandra Dal Molin
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Alberto Ferrarini
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Louise Chappell Maor
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ezio Portis
- University of Torino - DISAFA - Plant Genetics and Breeding, Largo Braccini 2, 10095, Grugliasco, Torino, Italy
| | - Sebastian Reyes-Chin-Wo
- UC Davis Genome Center-GBSF, 451 Health Sciences Drive, University of California, Davis, CA, 95616, USA
| | - Riccardo Rinaldi
- University of Torino - DISAFA - Plant Genetics and Breeding, Largo Braccini 2, 10095, Grugliasco, Torino, Italy
| | - Tea Sala
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics, 26836, Montanaso Lombardo, LO, Italy
| | - Davide Scaglione
- IGA Technology Services, Via J. Linussio, 51, 33100, Udine, Italy
| | - Prashant Sonawane
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Paola Tononi
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Efrat Almekias-Siegl
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Elisa Zago
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | | | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Massimo Delledonne
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.
| | - Giovanni Giuliano
- Italian National Agency for New Technologies, Energy and Sustainable Development (ENEA), Casaccia Res Ctr, Via Anguillarese 301, 00123, Roma, Italy.
| | - Sergio Lanteri
- University of Torino - DISAFA - Plant Genetics and Breeding, Largo Braccini 2, 10095, Grugliasco, Torino, Italy.
| | - Giuseppe Leonardo Rotino
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics, 26836, Montanaso Lombardo, LO, Italy
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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. Front Plant Sci 2019; 10:1005. [PMID: 31440267 PMCID: PMC6693525 DOI: 10.3389/fpls.2019.01005] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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Cerruti E, Comino C, Acquadro A, Marconi G, Repetto AM, Pisanu AB, Pilia R, Albertini E, Portis E. Analysis of DNA Methylation Patterns Associated with In Vitro Propagated Globe Artichoke Plants Using an EpiRADseq-Based Approach. Genes (Basel) 2019; 10:E263. [PMID: 30939865 PMCID: PMC6523903 DOI: 10.3390/genes10040263] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 03/22/2019] [Accepted: 03/26/2019] [Indexed: 01/16/2023] Open
Abstract
Globe artichoke represents one of the main horticultural species of the Mediterranean basin, and 'Spinoso sardo' is the most widespread and economically relevant varietal type in Sardinia, Italy. In the last decades, in vitro culture of meristematic apices has increased the frequency of aberrant plants in open-field production. These off-type phenotypes showed highly pinnate-parted leaves and late inflorescence budding, and emerged from some branches of the true-to-type 'Spinoso sardo' plants. This phenomenon cannot be foreseen and is reversible through generations, suggesting the occurrence of epigenetic alterations. Here, we report an exploratory study on DNA methylation patterns in off-type/true-to-type globe artichoke plants, using a modified EpiRADseq technology, which allowed the identification of 2,897 differentially methylated loci (DML): 1,998 in CG, 458 in CHH, and 441 in CHG methylation contexts of which 720, 88, and 152, respectively, were in coding regions. Most of them appeared involved in primary metabolic processes, mostly linked to photosynthesis, regulation of flower development, and regulation of reproductive processes, coherently with the observed phenotype. Differences in the methylation status of some candidate genes were integrated with transcriptional analysis to test whether these two regulation levels might interplay in the emergence and spread of the 'Spinoso sardo' non-conventional phenotype.
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Affiliation(s)
- Elisa Cerruti
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, 10095 Grugliasco, Italy.
| | - Cinzia Comino
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, 10095 Grugliasco, Italy.
| | - Alberto Acquadro
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, 10095 Grugliasco, Italy.
| | - Gianpiero Marconi
- Department of Agricultural, Food, and Environmental Sciences, University of Perugia, 06121 Perugia, Italy.
| | - Anna Maria Repetto
- Agris Sardegna-Agenzia Regionale per la Ricerca in Agricoltura-Servizio Ricerca sui Sistemi Colturali Erbacei, 09123 Cagliari, Italy.
| | - Anna Barbara Pisanu
- Agris Sardegna-Agenzia Regionale per la Ricerca in Agricoltura-Servizio Ricerca sui Sistemi Colturali Erbacei, 09123 Cagliari, Italy.
| | - Roberto Pilia
- Agris Sardegna-Agenzia Regionale per la Ricerca in Agricoltura-Servizio Ricerca sui Sistemi Colturali Erbacei, 09123 Cagliari, Italy.
| | - Emidio Albertini
- Department of Agricultural, Food, and Environmental Sciences, University of Perugia, 06121 Perugia, Italy.
| | - Ezio Portis
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, 10095 Grugliasco, Italy.
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22
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Torello Marinoni D, Valentini N, Portis E, Acquadro A, Beltramo C, Mehlenbacher SA, Mockler TC, Rowley ER, Botta R. High density SNP mapping and QTL analysis for time of leaf budburst in Corylus avellana L. PLoS One 2018; 13:e0195408. [PMID: 29608620 PMCID: PMC5880404 DOI: 10.1371/journal.pone.0195408] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Accepted: 03/21/2018] [Indexed: 01/25/2023] Open
Abstract
The growing area of European hazelnut (Corylus avellana L.) is increasing, as well as the number of producing countries, and there is a pressing need for new improved cultivars. Hazelnut conventional breeding process is slow, due to the length of juvenile phase and the high heterozygosity level. The development of genetic linkage maps and the identification of molecular markers tightly linked to QTL (quantitative trait loci) of agronomic interest are essential tools for speeding up the selection of seedlings carrying desired traits through marker-assisted selection. The objectives of this study were to enrich a previous linkage map and confirm QTL related to time of leaf budburst, using an F1 population obtained by crossing Tonda Gentile delle Langhe with Merveille de Bollwiller. Genotyping-by-Sequencing was used to identify a total of 9,999 single nucleotide polymorphism markers. Well saturated linkage maps were constructed for each parent using the double pseudo-testcross mapping strategy. A reciprocal translocation was detected in Tonda Gentile delle Langhe between two non-homologous chromosomes. Applying a bioinformatic approach, we were able to disentangle ‘pseudo-linkage’ between markers, removing markers around the translocation breakpoints and obtain a linear order of the markers for the two chromosomes arms, for each linkage group involved in the translocation. Twenty-nine QTL for time of leaf budburst were identified, including a stably expressed region on LG_02 of the Tonda Gentile delle Langhe map. The stability of these QTL and their coding sequence content indicates promise for the identification of specific chromosomal regions carrying key genes involved in leaf budburst.
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Affiliation(s)
- Daniela Torello Marinoni
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli Studi di Torino, Grugliasco, Torino, Italy
| | - Nadia Valentini
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli Studi di Torino, Grugliasco, Torino, Italy
| | - Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli Studi di Torino, Grugliasco, Torino, Italy
- * E-mail:
| | - Alberto Acquadro
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli Studi di Torino, Grugliasco, Torino, Italy
| | - Chiara Beltramo
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli Studi di Torino, Grugliasco, Torino, Italy
| | - Shawn A. Mehlenbacher
- Department of Horticulture, Oregon State University, Corvallis, Oregon, United States of America
| | - Todd C. Mockler
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Erik R. Rowley
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Roberto Botta
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli Studi di Torino, Grugliasco, Torino, Italy
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23
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Portis E, Lanteri S, Barchi L, Portis F, Valente L, Toppino L, Rotino GL, Acquadro A. Comprehensive Characterization of Simple Sequence Repeats in Eggplant ( Solanum melongena L.) Genome and Construction of a Web Resource. Front Plant Sci 2018; 9:401. [PMID: 29643862 PMCID: PMC5883146 DOI: 10.3389/fpls.2018.00401] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 03/13/2018] [Indexed: 05/21/2023]
Abstract
We have characterized the simple sequence repeat (SSR) markers of the eggplant (Solanum melongena) using a recent high quality sequence of its whole genome. We found nearly 133,000 perfect SSRs, a density of 125.5 SSRs/Mbp, and also about 178,400 imperfect SSRs. Of the perfect SSRs, 15.6% were complex, with two stretches of repeats separated by an intervening block of <100 nt. Di- and trinucleotide SSRs accounted, respectively, for 43 and 37% of the total. The SSRs were classified according to their number of repeats and overall length, and were assigned to their linkage group. We found 2,449 of the perfect SSRs in 2,086 genes, with an overall density of 18.5 SSRs/Mbp across the gene space; 3,524 imperfect SSRs were present in 2,924 genes at a density of 26.7 SSRs/Mbp. Putative functions were assigned via ontology to genes containing at least one SSR. Using this data we developed an "Eggplant Microsatellite DataBase" (EgMiDB) which permits identification of SSR markers in terms of their location on the genome, type of repeat (perfect vs. imperfect), motif type, sequence, repeat number and genomic/gene context. It also suggests forward and reverse primers. We employed an in silico PCR analysis to validate these SSR markers, using as templates two CDS sets and three assembled transcriptomes obtained from diverse eggplant accessions.
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Affiliation(s)
- Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari – Plant Genetics and Breeding, Università degli Studi di Torino, Turin, Italy
| | - Sergio Lanteri
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari – Plant Genetics and Breeding, Università degli Studi di Torino, Turin, Italy
- *Correspondence: Sergio Lanteri,
| | - Lorenzo Barchi
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari – Plant Genetics and Breeding, Università degli Studi di Torino, Turin, Italy
| | | | | | - Laura Toppino
- CREA-GB, Research Centre for Genomics and Bioinformatics, Lodi, Italy
| | | | - Alberto Acquadro
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari – Plant Genetics and Breeding, Università degli Studi di Torino, Turin, Italy
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Gianoglio S, Moglia A, Acquadro A, Comino C, Portis E. The genome-wide identification and transcriptional levels of DNA methyltransferases and demethylases in globe artichoke. PLoS One 2017; 12:e0181669. [PMID: 28746368 PMCID: PMC5529103 DOI: 10.1371/journal.pone.0181669] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 07/05/2017] [Indexed: 11/19/2022] Open
Abstract
Changes to the cytosine methylation status of DNA, driven by the activity of C5 methyltransferases (C5-MTases) and demethylases, exert an important influence over development, transposon movement, gene expression and imprinting. Three groups of C5-MTase enzymes have been identified in plants, namely MET (methyltransferase 1), CMT (chromomethyltransferases) and DRM (domains rearranged methyltransferases). Here the repertoire of genes encoding C5-MTase and demethylase by the globe artichoke (Cynara cardunculus var. scolymus) is described, based on sequence homology, a phylogenetic analysis and a characterization of their functional domains. A total of ten genes encoding C5-MTase (one MET, five CMTs and four DRMs) and five demethylases was identified. An analysis of their predicted product's protein structure suggested an extensive level of conservation has been retained by the C5-MTases. Transcriptional profiling based on quantitative real time PCR revealed a number of differences between the genes encoding maintenance and de novo methyltransferases, sometimes in a tissue- or development-dependent manner, which implied a degree of functional specialization.
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Affiliation(s)
- Silvia Gianoglio
- Department of Agricultural, Forest and Food Sciences, University of Torino, Grugliasco, Italy
| | - Andrea Moglia
- Department of Agricultural, Forest and Food Sciences, University of Torino, Grugliasco, Italy
| | - Alberto Acquadro
- Department of Agricultural, Forest and Food Sciences, University of Torino, Grugliasco, Italy
| | - Cinzia Comino
- Department of Agricultural, Forest and Food Sciences, University of Torino, Grugliasco, Italy
- * E-mail:
| | - Ezio Portis
- Department of Agricultural, Forest and Food Sciences, University of Torino, Grugliasco, Italy
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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: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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Acquadro A, Barchi L, Portis E, Carrasquilla-Garcia N, Tirone M, Lanteri S, Comino C. RAD2seq: an efficient protocol for plant genotyping by sequencing. ACTA ACUST UNITED AC 2016. [DOI: 10.17660/actahortic.2016.1147.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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27
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Scaglione D, Reyes-Chin-Wo S, Acquadro A, Froenicke L, Portis E, Beitel C, Tirone M, Mauro R, Lo Monaco A, Mauromicale G, Faccioli P, Cattivelli L, Rieseberg L, Michelmore R, Lanteri S. Corrigendum: The genome sequence of the outbreeding globe artichoke constructed de novo incorporating a phase-aware low-pass sequencing strategy of F1 progeny. Sci Rep 2016; 6:25323. [PMID: 27212460 PMCID: PMC4876515 DOI: 10.1038/srep25323] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
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Beltramo C, Valentini N, Portis E, Torello Marinoni D, Boccacci P, Sandoval Prando MA, Botta R. Genetic mapping and QTL analysis in European hazelnut (Corylus avellana L.). Mol Breeding 2016; 36:27. [PMID: 0 DOI: 10.1007/s11032-016-0450-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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Rinaldi R, Van Deynze A, Portis E, Rotino GL, Toppino L, Hill T, Ashrafi H, Barchi L, Lanteri S. New Insights on Eggplant/Tomato/Pepper Synteny and Identification of Eggplant and Pepper Orthologous QTL. Front Plant Sci 2016; 7:1031. [PMID: 27486463 PMCID: PMC4948011 DOI: 10.3389/fpls.2016.01031] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 06/30/2016] [Indexed: 05/20/2023]
Abstract
Eggplant, pepper, and tomato are the most exploited berry-producing vegetables within the Solanaceae family. Their genomes differ in size, but each has 12 chromosomes which have undergone rearrangements causing a redistribution of loci. The genome sequences of all three species are available but differ in coverage, assembly quality and percentage of anchorage. Determining their syntenic relationship and QTL orthology will contribute to exploit genomic resources and genetic data for key agronomic traits. The syntenic analysis between tomato and pepper based on the alignment of 34,727 tomato CDS to the pepper genome sequence, identified 19,734 unique hits. The resulting synteny map confirmed the 14 inversions and 10 translocations previously documented, but also highlighted 3 new translocations and 4 major new inversions. Furthermore, each of the 12 chromosomes exhibited a number of rearrangements involving small regions of 0.5-0.7 Mbp. Due to high fragmentation of the publicly available eggplant genome sequence, physical localization of most eggplant QTL was not possible, thus, we compared the organization of the eggplant genetic map with the genome sequence of both tomato and pepper. The eggplant/tomato syntenic map confirmed all the 10 translocations but only 9 of the 14 known inversions; on the other hand, a newly detected inversion was recognized while another one was not confirmed. The eggplant/pepper syntenic map confirmed 10 translocations and 8 inversions already detected and suggested a putative new translocation. In order to perform the assessment of eggplant and pepper QTL orthology, the eggplant and pepper sequence-based markers located in their respective genetic map were aligned onto the pepper genome. GBrowse in pepper was used as reference platform for QTL positioning. A set of 151 pepper QTL were located as well as 212 eggplant QTL, including 76 major QTL (PVE ≥ 10%) affecting key agronomic traits. Most were confirmed to cluster in orthologous chromosomal regions. Our results highlight that the availability of genome sequences for an increasing number of crop species and the development of "ultra-dense" physical maps provide new and key tools for detailed syntenic and orthology studies between related plant species.
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Affiliation(s)
- Riccardo Rinaldi
- DISAFA Plant Genetics and Breeding, University of TurinTurin, Italy
- Seed Biotechnology Center, University of California, DavisDavis, CA, USA
| | - Allen Van Deynze
- Seed Biotechnology Center, University of California, DavisDavis, CA, USA
| | - Ezio Portis
- DISAFA Plant Genetics and Breeding, University of TurinTurin, Italy
| | | | - Laura Toppino
- CREA-ORL Research Unit for Vegetable CropsMontanaso Lombardo, Italy
| | - Theresa Hill
- Seed Biotechnology Center, University of California, DavisDavis, CA, USA
| | - Hamid Ashrafi
- Seed Biotechnology Center, University of California, DavisDavis, CA, USA
| | - Lorenzo Barchi
- DISAFA Plant Genetics and Breeding, University of TurinTurin, Italy
- *Correspondence: Lorenzo Barchi
| | - Sergio Lanteri
- DISAFA Plant Genetics and Breeding, University of TurinTurin, Italy
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Toppino L, Barchi L, Lo Scalzo R, Palazzolo E, Francese G, Fibiani M, D'Alessandro A, Papa V, Laudicina VA, Sabatino L, Pulcini L, Sala T, Acciarri N, Portis E, Lanteri S, Mennella G, Rotino GL. Mapping Quantitative Trait Loci Affecting Biochemical and Morphological Fruit Properties in Eggplant (Solanum melongena L.). Front Plant Sci 2016; 7:256. [PMID: 26973692 PMCID: PMC4777957 DOI: 10.3389/fpls.2016.00256] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 02/15/2016] [Indexed: 05/19/2023]
Abstract
Eggplant berries are a source of health-promoting metabolites including antioxidant and nutraceutical compounds, mainly anthocyanins and chlorogenic acid; however, they also contain some anti-nutritional compounds such as steroidal glycoalkaloids (SGA) and saponins, which are responsible for the bitter taste of the flesh and with potential toxic effects on humans. Up to now, Quantitative Trait Loci (QTL) for the metabolic content are far from being characterized in eggplant, thus hampering the application of breeding programs aimed at improving its fruit quality. Here we report on the identification of some QTL for the fruit metabolic content in an F2 intraspecific mapping population of 156 individuals, obtained by crossing the eggplant breeding lines "305E40" × "67/3." The same population was previously employed for the development of a RAD-tag based linkage map and the identification of QTL associated to morphological and physiological traits. The mapping population was biochemically characterized for both fruit basic qualitative data, like dry matter, °Brix, sugars, and organic acids, as well as for health-related compounds such chlorogenic acid, (the main flesh monomeric phenol), the two peel anthocyanins [i.e., delphinidin-3-rutinoside (D3R) and delphinidin-3-(p- coumaroylrutinoside)-5-glucoside (nasunin)] and the two main steroidal glycoalkaloids, solasonine, and solamargine. For most of the traits, one major QTL (PVE ≥10%) was spotted and putative orthologies with other Solanaceae crops are discussed. The present results supply valuable information to eggplant breeders on the inheritance of key fruit quality traits, thus providing potential tools to assist future breeding programs.
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Affiliation(s)
- Laura Toppino
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria-ORL, Unità di Ricerca per l'OrticolturaMontanaso Lombardo, Italy
| | - Lorenzo Barchi
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Plant Genetics and Breeding, University of TurinTurin, Italy
| | - Roberto Lo Scalzo
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria-IAA, Unità di Ricerca per i Processi dell'Industria AgroalimentareMilano, Italy
| | - Eristanna Palazzolo
- Dipartimento di Scienze Agrarie e Forestali, Università degli Studi di PalermoPalermo, Italy
| | - Gianluca Francese
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria-ORT, Centro di Ricerca per l'OrticolturaPontecagnano-Faiano, Italy
| | - Marta Fibiani
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria-IAA, Unità di Ricerca per i Processi dell'Industria AgroalimentareMilano, Italy
| | - Antonietta D'Alessandro
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria-ORT, Centro di Ricerca per l'OrticolturaPontecagnano-Faiano, Italy
| | - Vincenza Papa
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria-IAA, Unità di Ricerca per i Processi dell'Industria AgroalimentareMilano, Italy
| | - Vito A. Laudicina
- Dipartimento di Scienze Agrarie e Forestali, Università degli Studi di PalermoPalermo, Italy
| | - Leo Sabatino
- Dipartimento di Scienze Agrarie e Forestali, Università degli Studi di PalermoPalermo, Italy
| | - Laura Pulcini
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria-ORA, Unità di Ricerca per l'OrticolturaMonsampolo del Tronto, Italy
| | - Tea Sala
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria-ORL, Unità di Ricerca per l'OrticolturaMontanaso Lombardo, Italy
| | - Nazzareno Acciarri
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria-ORA, Unità di Ricerca per l'OrticolturaMonsampolo del Tronto, Italy
| | - Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Plant Genetics and Breeding, University of TurinTurin, Italy
| | - Sergio Lanteri
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Plant Genetics and Breeding, University of TurinTurin, Italy
| | - Giuseppe Mennella
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria-ORT, Centro di Ricerca per l'OrticolturaPontecagnano-Faiano, Italy
| | - Giuseppe L. Rotino
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria-ORL, Unità di Ricerca per l'OrticolturaMontanaso Lombardo, Italy
- *Correspondence: Giuseppe L. Rotino
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Portis E, Cericola F, Barchi L, Toppino L, Acciarri N, Pulcini L, Sala T, Lanteri S, Rotino GL. Association Mapping for Fruit, Plant and Leaf Morphology Traits in Eggplant. PLoS One 2015; 10:e0135200. [PMID: 26284782 PMCID: PMC4540451 DOI: 10.1371/journal.pone.0135200] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 07/18/2015] [Indexed: 11/18/2022] Open
Abstract
An eggplant (Solanum melongena) association panel of 191 accessions, comprising a mixture of breeding lines, old varieties and landrace selections was SNP genotyped and phenotyped for key breeding fruit and plant traits at two locations over two seasons. A genome-wide association (GWA) analysis was performed using the mixed linear model, which takes into account both a kinship matrix and the sub-population membership of the accessions. Overall, 194 phenotype/genotype associations were uncovered, relating to 30 of the 33 measured traits. These associations involved 79 SNP loci mapping to 39 distinct chromosomal regions distributed over all 12 eggplant chromosomes. A comparison of the map positions of these SNPs with those of loci derived from conventional linkage mapping showed that GWA analysis both validated many of the known controlling loci and detected a large number of new marker/trait associations. Exploiting established syntenic relationships between eggplant chromosomes and those of tomato and pepper recognized orthologous regions in ten eggplant chromosomes harbouring genes influencing breeders’ traits.
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Affiliation(s)
- Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA)—Plant Genetics and Breeding, University of Torino, I-10095 Grugliasco, Torino, Italy
| | - Fabio Cericola
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA)—Plant Genetics and Breeding, University of Torino, I-10095 Grugliasco, Torino, Italy
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria—CREA, Research Unit for Vegetable Crops, I-26836 Montanaso Lombardo, Lodi, Italy
| | - Lorenzo Barchi
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA)—Plant Genetics and Breeding, University of Torino, I-10095 Grugliasco, Torino, Italy
| | - Laura Toppino
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria—CREA, Research Unit for Vegetable Crops, I-26836 Montanaso Lombardo, Lodi, Italy
| | - Nazzareno Acciarri
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria—CREA, Research Unit for Vegetable Crops, I-63030 Monsampolo del Tronto, Ascoli Piceno, Italy
| | - Laura Pulcini
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria—CREA, Research Unit for Vegetable Crops, I-63030 Monsampolo del Tronto, Ascoli Piceno, Italy
| | - Tea Sala
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria—CREA, Research Unit for Vegetable Crops, I-26836 Montanaso Lombardo, Lodi, Italy
| | - Sergio Lanteri
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA)—Plant Genetics and Breeding, University of Torino, I-10095 Grugliasco, Torino, Italy
| | - Giuseppe Leonardo Rotino
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria—CREA, Research Unit for Vegetable Crops, I-26836 Montanaso Lombardo, Lodi, Italy
- * E-mail:
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Portis E, Cericola F, Barchi L, Toppino L, Acciarri N, Pulcini L, Sala T, Lanteri S, Rotino GL. Association Mapping for Fruit, Plant and Leaf Morphology Traits in Eggplant. PLoS One 2015. [PMID: 26284782 DOI: 10.1371/jounal.pone.0135200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023] Open
Abstract
An eggplant (Solanum melongena) association panel of 191 accessions, comprising a mixture of breeding lines, old varieties and landrace selections was SNP genotyped and phenotyped for key breeding fruit and plant traits at two locations over two seasons. A genome-wide association (GWA) analysis was performed using the mixed linear model, which takes into account both a kinship matrix and the sub-population membership of the accessions. Overall, 194 phenotype/genotype associations were uncovered, relating to 30 of the 33 measured traits. These associations involved 79 SNP loci mapping to 39 distinct chromosomal regions distributed over all 12 eggplant chromosomes. A comparison of the map positions of these SNPs with those of loci derived from conventional linkage mapping showed that GWA analysis both validated many of the known controlling loci and detected a large number of new marker/trait associations. Exploiting established syntenic relationships between eggplant chromosomes and those of tomato and pepper recognized orthologous regions in ten eggplant chromosomes harbouring genes influencing breeders' traits.
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Affiliation(s)
- Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA)-Plant Genetics and Breeding, University of Torino, I-10095 Grugliasco, Torino, Italy
| | - Fabio Cericola
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA)-Plant Genetics and Breeding, University of Torino, I-10095 Grugliasco, Torino, Italy; Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria-CREA, Research Unit for Vegetable Crops, I-26836 Montanaso Lombardo, Lodi, Italy
| | - Lorenzo Barchi
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA)-Plant Genetics and Breeding, University of Torino, I-10095 Grugliasco, Torino, Italy
| | - Laura Toppino
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria-CREA, Research Unit for Vegetable Crops, I-26836 Montanaso Lombardo, Lodi, Italy
| | - Nazzareno Acciarri
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria-CREA, Research Unit for Vegetable Crops, I-63030 Monsampolo del Tronto, Ascoli Piceno, Italy
| | - Laura Pulcini
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria-CREA, Research Unit for Vegetable Crops, I-63030 Monsampolo del Tronto, Ascoli Piceno, Italy
| | - Tea Sala
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria-CREA, Research Unit for Vegetable Crops, I-26836 Montanaso Lombardo, Lodi, Italy
| | - Sergio Lanteri
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA)-Plant Genetics and Breeding, University of Torino, I-10095 Grugliasco, Torino, Italy
| | - Giuseppe Leonardo Rotino
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria-CREA, Research Unit for Vegetable Crops, I-26836 Montanaso Lombardo, Lodi, Italy
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Cericola F, Portis E, Lanteri S, Toppino L, Barchi L, Acciarri N, Pulcini L, Sala T, Rotino GL. Linkage disequilibrium and genome-wide association analysis for anthocyanin pigmentation and fruit color in eggplant. BMC Genomics 2014; 15:896. [PMID: 25311640 PMCID: PMC4210512 DOI: 10.1186/1471-2164-15-896] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 10/06/2014] [Indexed: 11/26/2022] Open
Abstract
Background The genome-wide association (GWA) approach represents an alternative to biparental linkage mapping for determining the genetic basis of trait variation. Both approaches rely on recombination to re-arrange the genome, and seek to establish correlations between phenotype and genotype. The major advantages of GWA lie in being able to sample a much wider range of the phenotypic and genotypic variation present, in being able to exploit multiple rounds of historical recombination in many different lineages and to include multiple accessions of direct relevance to crop improvement. Results A 191 accessions eggplant (Solanum melongena L.) association panel, comprising a mixture of breeding lines, old varieties and landrace selections originating from Asia and the Mediterranean Basin, was SNP genotyped and scored for anthocyanin pigmentation and fruit color at two locations over two years. The panel formed two major clusters, reflecting geographical provenance and fruit type. The global level of linkage disequilibrium was 3.4 cM. A mixed linear model appeared to be the most appropriate for GWA. A set of 56 SNP locus/phenotype associations was identified and the genomic regions harboring these loci were distributed over nine of the 12 eggplant chromosomes. The associations were compared with the location of known QTL for the same traits. Conclusion The GWA mapping approach was effective in validating a number of established QTL and, thanks to the wide diversity captured by the panel, was able to detect a series of novel marker/trait associations. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-896) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA) - Plant Genetics and Breeding, University of Torino, Largo P, Braccini 2, I-10095 Grugliasco, Torino, Italy.
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Portis E, Barchi L, Toppino L, Lanteri S, Acciarri N, Felicioni N, Fusari F, Barbierato V, Cericola F, Valè G, Rotino GL. QTL mapping in eggplant reveals clusters of yield-related loci and orthology with the tomato genome. PLoS One 2014; 9:e89499. [PMID: 24586828 PMCID: PMC3931786 DOI: 10.1371/journal.pone.0089499] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 01/21/2014] [Indexed: 11/18/2022] Open
Abstract
In spite of its widespread cultivation and nutritional and economic importance, the eggplant (Solanum melongena L.) genome has not been extensively explored. A lack of knowledge of the patterns of inheritance of key agronomic traits has hindered the exploitation of marker technologies to accelerate its genetic improvement. An already established F2 intraspecific population of eggplant bred from the cross ‘305E40’ x ‘67/3’ was phenotyped for 20 agronomically relevant traits at two sites. Up to seven quantitative trait loci (QTL) per trait were identified and the percentage of the phenotypic variance (PV) explained per QTL ranged from 4 to 93%. Not all the QTL were detectable at both sites, but for each trait at least one major QTL (PV explained ≥10%) was identified. Although no detectable QTL x environment interaction was found, some QTL identified were location-specific. Many of the fruit-related QTL clustered within specific chromosomal regions, reflecting either linkage and/or pleiotropy. Evidence for putative tomato orthologous QTL/genes was obtained for several of the eggplant QTL. Information regarding the inheritance of key agronomic traits was obtained. Some of the QTL, along with their respective linked markers, may be useful in the context of marker-assisted breeding.
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Affiliation(s)
- Ezio Portis
- DISAFA - Plant Genetics and Breeding, University of Torino, Grugliasco, Torino, Italy
| | - Lorenzo Barchi
- DISAFA - Plant Genetics and Breeding, University of Torino, Grugliasco, Torino, Italy
| | - Laura Toppino
- Consiglio per la Ricerca e Sperimentazione in Agricoltura - CRA-ORL, Research Unit for Vegetable Crops, Montanaso Lombardo, Lodi, Italy
| | - Sergio Lanteri
- DISAFA - Plant Genetics and Breeding, University of Torino, Grugliasco, Torino, Italy
| | - Nazzareno Acciarri
- Consiglio per la Ricerca e Sperimentazione in Agricoltura - CRA-ORA, Research Unit for Vegetable Crops, Monsampolo del Tronto, Ascoli Piceno, Italy
| | - Nazzareno Felicioni
- Consiglio per la Ricerca e Sperimentazione in Agricoltura - CRA-ORA, Research Unit for Vegetable Crops, Monsampolo del Tronto, Ascoli Piceno, Italy
| | - Fabio Fusari
- Consiglio per la Ricerca e Sperimentazione in Agricoltura - CRA-ORA, Research Unit for Vegetable Crops, Monsampolo del Tronto, Ascoli Piceno, Italy
| | - Valeria Barbierato
- Consiglio per la Ricerca e Sperimentazione in Agricoltura - CRA-ORL, Research Unit for Vegetable Crops, Montanaso Lombardo, Lodi, Italy
| | - Fabio Cericola
- DISAFA - Plant Genetics and Breeding, University of Torino, Grugliasco, Torino, Italy
| | - Giampiero Valè
- Consiglio per la Ricerca e Sperimentazione in Agricoltura - CRA-GPG, Genomic Research Centre, Fiorenzuola d'Arda, Piacenza, Italy ; Consiglio per la Ricerca e Sperimentazione in Agricoltura - CRA-RIS, Rice Research Unit, Vercelli, Italy
| | - Giuseppe Leonardo Rotino
- Consiglio per la Ricerca e Sperimentazione in Agricoltura - CRA-ORL, Research Unit for Vegetable Crops, Montanaso Lombardo, Lodi, Italy
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Pandino G, Lombardo S, Moglia A, Portis E, Lanteri S, Mauromicale G. Leaf polyphenol profile and SSR-based fingerprinting of new segregant Cynara cardunculus genotypes. Front Plant Sci 2014; 5:800. [PMID: 25653660 PMCID: PMC4300902 DOI: 10.3389/fpls.2014.00800] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 12/22/2014] [Indexed: 05/03/2023]
Abstract
The dietary value of many plant polyphenols lies in the protection given against degenerative pathologies. Their in planta role is associated with the host's defense response against biotic and abiotic stress. The polyphenol content of a given plant tissue is strongly influenced by the growing environment, but is also genetically determined. Plants belonging to the Cynara cardunculus species (globe artichoke and the cultivated and wild cardoon) accumulate substantial quantities of polyphenols mainly mono and di-caffeoylquinic acid (CQA) in their foliage. Transgressive segregation for CQA content in an F1 population bred from a cross between a globe artichoke and a cultivated cardoon led to the selection of eight segregants which accumulated more CQA in their leaves than did those of either of their parental genotypes. The selections were grown over two seasons to assess their polyphenol profile (CQAs, apigenin and luteolin derivatives and narirutin), and were also fingerprinted using a set of 217 microsatellite markers. The growing environment exerted a strong effect on polyphenol content, but two of the selections were able to accumulate up to an order of magnitude more CQA than either parent in both growing seasons. Since the species is readily vegetatively propagable, such genotypes can be straightforwardly exploited as a source of pharmaceutically valuable compounds, while their SSR-based fingerprinting will allow the genetic identity of clonally propagated material to be easily verified.
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Affiliation(s)
- Gaetano Pandino
- Dipartimento di Agricoltura, Alimentazione e Ambiente Università degli Studi di CataniaCatania, Italy
| | - Sara Lombardo
- Dipartimento di Agricoltura, Alimentazione e Ambiente Università degli Studi di CataniaCatania, Italy
| | - Andrea Moglia
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli Studi di TorinoGrugliasco, Italy
- *Correspondence: Andrea Moglia, Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli Studi di Torino, Largo Paolo Braccini 2, 10095 Grugliasco, Italy e-mail:
| | - Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli Studi di TorinoGrugliasco, Italy
| | - Sergio Lanteri
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli Studi di TorinoGrugliasco, Italy
| | - Giovanni Mauromicale
- Dipartimento di Agricoltura, Alimentazione e Ambiente Università degli Studi di CataniaCatania, Italy
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Cericola F, Portis E, Toppino L, Barchi L, Acciarri N, Ciriaci T, Sala T, Rotino GL, Lanteri S. The population structure and diversity of eggplant from Asia and the Mediterranean Basin. PLoS One 2013; 8:e73702. [PMID: 24040032 PMCID: PMC3765357 DOI: 10.1371/journal.pone.0073702] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 07/22/2013] [Indexed: 11/18/2022] Open
Abstract
A collection of 238 eggplant breeding lines, heritage varieties and selections within local landraces provenanced from Asia and the Mediterranean Basin was phenotyped with respect to key plant and fruit traits, and genotyped using 24 microsatellite loci distributed uniformly throughout the genome. STRUCTURE analysis based on the genotypic data identified two major sub-groups, which to a large extent mirrored the provenance of the entries. With the goal to identify true-breeding types, 38 of the entries were discarded on the basis of microsatellite-based residual heterozygosity, along with a further nine which were not phenotypically uniform. The remaining 191 entries were scored for a set of 19 fruit and plant traits in a replicated experimental field trial. The phenotypic data were subjected to principal component and hierarchical principal component analyses, allowing three major morphological groups to be identified. All three morphological groups were represented in both the “Occidental” and the “Oriental” germplasm, so the correlation between the phenotypic and the genotypic data sets was quite weak. The relevance of these results for evolutionary studies and the further improvement of eggplant are discussed. The population structure of the core set of germplasm shows that it can be used as a basis for an association mapping approach.
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Affiliation(s)
- Fabio Cericola
- DISAFA - Plant Genetics and Breeding, University of Torino, Grugliasco, Torino, Italy
- CRA-ORL - Research Unit for Vegetable Crops, Montanaso Lombardo, Lodi, Italy
| | - Ezio Portis
- DISAFA - Plant Genetics and Breeding, University of Torino, Grugliasco, Torino, Italy
| | - Laura Toppino
- CRA-ORL - Research Unit for Vegetable Crops, Montanaso Lombardo, Lodi, Italy
| | - Lorenzo Barchi
- DISAFA - Plant Genetics and Breeding, University of Torino, Grugliasco, Torino, Italy
| | - Nazareno Acciarri
- CRA-ORA - Research Unit for Vegetable Crops, Monsampolo del Tronto, Ascoli Piceno, Italy
| | - Tommaso Ciriaci
- CRA-ORA - Research Unit for Vegetable Crops, Monsampolo del Tronto, Ascoli Piceno, Italy
| | - Tea Sala
- CRA-ORL - Research Unit for Vegetable Crops, Montanaso Lombardo, Lodi, Italy
| | | | - Sergio Lanteri
- DISAFA - Plant Genetics and Breeding, University of Torino, Grugliasco, Torino, Italy
- * E-mail:
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Cericola F, Portis E, Toppino L, Barchi L, Acciarri N, Ciriaci T, Sala T, Rotino GL, Lanteri S. The population structure and diversity of eggplant from Asia and the Mediterranean Basin. PLoS One 2013. [PMID: 24040032 DOI: 10.1371/jounal.pone.0073702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023] Open
Abstract
A collection of 238 eggplant breeding lines, heritage varieties and selections within local landraces provenanced from Asia and the Mediterranean Basin was phenotyped with respect to key plant and fruit traits, and genotyped using 24 microsatellite loci distributed uniformly throughout the genome. STRUCTURE analysis based on the genotypic data identified two major sub-groups, which to a large extent mirrored the provenance of the entries. With the goal to identify true-breeding types, 38 of the entries were discarded on the basis of microsatellite-based residual heterozygosity, along with a further nine which were not phenotypically uniform. The remaining 191 entries were scored for a set of 19 fruit and plant traits in a replicated experimental field trial. The phenotypic data were subjected to principal component and hierarchical principal component analyses, allowing three major morphological groups to be identified. All three morphological groups were represented in both the "Occidental" and the "Oriental" germplasm, so the correlation between the phenotypic and the genotypic data sets was quite weak. The relevance of these results for evolutionary studies and the further improvement of eggplant are discussed. The population structure of the core set of germplasm shows that it can be used as a basis for an association mapping approach.
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Affiliation(s)
- Fabio Cericola
- DISAFA - Plant Genetics and Breeding, University of Torino, Grugliasco, Torino, Italy ; CRA-ORL - Research Unit for Vegetable Crops, Montanaso Lombardo, Lodi, Italy
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Scaglione D, Lanteri S, Acquadro A, Lai Z, Knapp SJ, Rieseberg L, Portis E. Large-scale transcriptome characterization and mass discovery of SNPs in globe artichoke and its related taxa. Plant Biotechnol J 2012; 10:956-69. [PMID: 22849342 DOI: 10.1111/j.1467-7652.2012.00725.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Cynara cardunculus (2n = 2× = 34) is a member of the Asteraceae family that contributes significantly to the agricultural economy of the Mediterranean basin. The species includes two cultivated varieties, globe artichoke and cardoon, which are grown mainly for food. Cynara cardunculus is an orphan crop species whose genome/transcriptome has been relatively unexplored, especially in comparison to other Asteraceae crops. Hence, there is a significant need to improve its genomic resources through the identification of novel genes and sequence-based markers, to design new breeding schemes aimed at increasing quality and crop productivity. We report the outcome of cDNA sequencing and assembly for eleven accessions of C. cardunculus. Sequencing of three mapping parental genotypes using Roche 454-Titanium technology generated 1.7 × 10⁶ reads, which were assembled into 38,726 reference transcripts covering 32 Mbp. Putative enzyme-encoding genes were annotated using the KEGG-database. Transcription factors and candidate resistance genes were surveyed as well. Paired-end sequencing was done for cDNA libraries of eight other representative C. cardunculus accessions on an Illumina Genome Analyzer IIx, generating 46 × 10⁶ reads. Alignment of the IGA and 454 reads to reference transcripts led to the identification of 195,400 SNPs with a Bayesian probability exceeding 95%; a validation rate of 90% was obtained by Sanger-sequencing of a subset of contigs. These results demonstrate that the integration of data from different NGS platforms enables large-scale transcriptome characterization, along with massive SNP discovery. This information will contribute to the dissection of key agricultural traits in C. cardunculus and facilitate the implementation of marker-assisted selection programs.
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Menin B, Comino C, Portis E, Moglia A, Cankar K, Bouwmeester HJ, Lanteri S, Beekwilder J. Genetic mapping and characterization of the globe artichoke (+)-germacrene A synthase gene, encoding the first dedicated enzyme for biosynthesis of the bitter sesquiterpene lactone cynaropicrin. Plant Sci 2012; 190:1-8. [PMID: 22608514 DOI: 10.1016/j.plantsci.2012.03.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Revised: 03/14/2012] [Accepted: 03/16/2012] [Indexed: 05/16/2023]
Abstract
Globe artichoke (Cynara cardunculus var. scolymus L., Asteraceae) is a perennial crop traditionally consumed as a vegetable in the Mediterranean countries and rich in nutraceutically and pharmaceutically active compounds, including phenolic and terpenoid compounds. Its bitter taste is caused by its high content of sesquiterpene lactones (STLs), such as cynaropicrin. The biosynthetic pathway responsible for STL biosynthesis in globe artichoke is unknown, but likely proceeds through germacrene A, as has been shown for other Asteraceae species. Here, we investigated the accumulation of cynaropicrin in different tissues of globe artichoke, and compared it to accumulation of phenolic compounds. Cynaropicrin concentration was highest in old leaves. A putative germacrene A synthase (GAS) gene was identified in a set of ~19,000 globe artichoke unigenes. When heterologously expressed in Escherichia coli, the putative globe artichoke GAS converted farnesyl diphosphate (FPP) into (+)-germacrene A. Among various tissues assayed, the level of globe artichoke GAS expression was highest in mature (six week old) leaves. A sequence polymorphism within a mapping population parent allowed the corresponding GAS gene to be positioned on a genetic map. This study reports the isolation, expression and mapping of a key gene involved in STL biosynthesis in C. cardunculus. This is a good basis for further investigation of this pathway.
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Affiliation(s)
- Barbara Menin
- DIVAPRA, Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095 Grugliasco (TO), Italy
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Scaglione D, Acquadro A, Portis E, Tirone M, Knapp SJ, Lanteri S. RAD tag sequencing as a source of SNP markers in Cynara cardunculus L. BMC Genomics 2012; 13:3. [PMID: 22214349 PMCID: PMC3269995 DOI: 10.1186/1471-2164-13-3] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2011] [Accepted: 01/03/2012] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND The globe artichoke (Cynara cardunculus L. var. scolymus) genome is relatively poorly explored, especially compared to those of the other major Asteraceae crops sunflower and lettuce. No SNP markers are in the public domain. We have combined the recently developed restriction-site associated DNA (RAD) approach with the Illumina DNA sequencing platform to effect the rapid and mass discovery of SNP markers for C. cardunculus. RESULTS RAD tags were sequenced from the genomic DNA of three C. cardunculus mapping population parents, generating 9.7 million reads, corresponding to ~1 Gbp of sequence. An assembly based on paired ends produced ~6.0 Mbp of genomic sequence, separated into ~19,000 contigs (mean length 312 bp), of which ~21% were fragments of putative coding sequence. The shared sequences allowed for the discovery of ~34,000 SNPs and nearly 800 indels, equivalent to a SNP frequency of 5.6 per 1,000 nt, and an indel frequency of 0.2 per 1,000 nt. A sample of heterozygous SNP loci was mapped by CAPS assays and this exercise provided validation of our mining criteria. The repetitive fraction of the genome had a high representation of retrotransposon sequence, followed by simple repeats, AT-low complexity regions and mobile DNA elements. The genomic k-mers distribution and CpG rate of C. cardunculus, compared with data derived from three whole genome-sequenced dicots species, provided a further evidence of the random representation of the C. cardunculus genome generated by RAD sampling. CONCLUSION The RAD tag sequencing approach is a cost-effective and rapid method to develop SNP markers in a highly heterozygous species. Our approach permitted to generate a large and robust SNP datasets by the adoption of optimized filtering criteria.
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Affiliation(s)
- Davide Scaglione
- Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095 Grugliasco (Torino), Italy
| | - Alberto Acquadro
- Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095 Grugliasco (Torino), Italy
| | - Ezio Portis
- Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095 Grugliasco (Torino), Italy
| | - Matteo Tirone
- Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095 Grugliasco (Torino), Italy
| | - Steven J Knapp
- Institute for Plant Breeding, Genetics, and Genomics, University of Georgia, 111 Riverbend Rd., 30602 Athens, Georgia USA
| | - Sergio Lanteri
- Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095 Grugliasco (Torino), Italy
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Barchi L, Lanteri S, Portis E, Acquadro A, Valè G, Toppino L, Rotino GL. Identification of SNP and SSR markers in eggplant using RAD tag sequencing. BMC Genomics 2011; 12:304. [PMID: 21663628 PMCID: PMC3128069 DOI: 10.1186/1471-2164-12-304] [Citation(s) in RCA: 170] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Accepted: 06/10/2011] [Indexed: 11/10/2022] Open
Abstract
Background The eggplant (Solanum melongena L.) genome is relatively unexplored, especially compared to those of the other major Solanaceae crops tomato and potato. In particular, no SNP markers are publicly available; on the other hand, over 1,000 SSR markers were developed and publicly available. We have combined the recently developed Restriction-site Associated DNA (RAD) approach with Illumina DNA sequencing for rapid and mass discovery of both SNP and SSR markers for eggplant. Results RAD tags were generated from the genomic DNA of a pair of eggplant mapping parents, and sequenced to produce ~17.5 Mb of sequences arrangeable into ~78,000 contigs. The resulting non-redundant genomic sequence dataset consisted of ~45,000 sequences, of which ~29% were putative coding sequences and ~70% were in common between the mapping parents. The shared sequences allowed the discovery of ~10,000 SNPs and nearly 1,000 indels, equivalent to a SNP frequency of 0.8 per Kb and an indel frequency of 0.07 per Kb. Over 2,000 of the SNPs are likely to be mappable via the Illumina GoldenGate assay. A subset of 384 SNPs was used to successfully fingerprint a panel of eggplant germplasm, producing a set of informative diversity data. The RAD sequences also included nearly 2,000 putative SSRs, and primer pairs were designed to amplify 1,155 loci. Conclusion The high throughput sequencing of the RAD tags allowed the discovery of a large number of DNA markers, which will prove useful for extending our current knowledge of the genome organization of eggplant, for assisting in marker-aided selection and for carrying out comparative genomic analyses within the Solanaceae family.
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Affiliation(s)
- Lorenzo Barchi
- DIVAPRA Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
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Barchi L, Lanteri S, Portis E, Stàgel A, Valè G, Toppino L, Rotino GL. Segregation distortion and linkage analysis in eggplant (Solanum melongena L.). Genome 2011; 53:805-15. [PMID: 20962887 DOI: 10.1139/g10-073] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
An anther-derived doubled haploid (DH) population and an F2 mapping population were developed from an intraspecific hybrid between the eggplant breeding lines 305E40 and 67/3. The former incorporates an introgressed segment from Solanum aethiopicum Gilo Group carrying the gene Rfo-sa1, which confers resistance to Fusarium oxysporum; the latter is a selection from an intraspecific cross involving two conventional eggplant varieties and lacks Rfo-sa1. Initially, 28 AFLP primer combinations (PCs) were applied to a sample of 93 F2 individuals and 93 DH individuals, from which 170 polymorphic AFLP fragments were identified. In the DH population, the segregation of 117 of these AFLPs as well as markers closely linked to Rfo-sa1 was substantially distorted, while in the F2 population, segregation distortion was restricted to just 10 markers, and thus the latter was chosen for map development. A set of 141 F2 individuals was genotyped with 73 AFLP PCs (generating 406 informative markers), 32 SSRs, 4 tomato RFLPs, and 3 CAPS markers linked to Rfo-sa1. This resulted in the assignment of 348 markers to 12 major linkage groups. The framework map covered 718.7 cM, comprising 238 markers (212 AFLPs, 22 SSRs, 1 RFLP, and the Rfo-sa1 CAPS). Marker order and inter-marker distances in this eggplant map were largely consistent with those reported in a recently published SSR-based map. From an eggplant breeding perspective, DH populations produced by anther culture appear to be subject to massive segregation distortion and thus may not be very efficient in capturing the full range of genetic variation present in the parental lines.
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Affiliation(s)
- Lorenzo Barchi
- University of Turin, Department of Exploitation and Protection of the Agricultural and Forestry Resources (DiVaPRA), Plant Genetics and Breeding, Via Grugliasco (TO), Italy
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Vallino M, Zampieri E, Murat C, Girlanda M, Picarella S, Pitet M, Portis E, Martino E, Perotto S. Specific regions in the Sod1 locus of the ericoid mycorrhizal fungus Oidiodendron maius from metal-enriched soils show a different sequence polymorphism. FEMS Microbiol Ecol 2010; 75:321-31. [DOI: 10.1111/j.1574-6941.2010.01003.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Portis E, Mauromicale G, Mauro R, Acquadro A, Scaglione D, Lanteri S. Construction of a reference molecular linkage map of globe artichoke (Cynara cardunculus var. scolymus). Theor Appl Genet 2009; 120:59-70. [PMID: 19787331 DOI: 10.1007/s00122-009-1159-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2009] [Accepted: 09/11/2009] [Indexed: 05/07/2023]
Abstract
The genome organization of globe artichoke (Cynara cardunculus var. scolymus), unlike other species belonging to Asteraceae (=Compositae) family (i.e. sunflower, lettuce and chicory), remains largely unexplored. The species is highly heterozygous and suffers marked inbreeding depression when forced to self-fertilize. Thus a two-way pseudo-testcross represents the optimal strategy for linkage analysis. Here, we report linkage maps based on the progeny of a cross between globe artichoke (C. cardunculus var. scolymus) and cultivated cardoon (C. cardunculus var. altilis). The population was genotyped using a variety of PCR-based marker platforms, resulting in the identification of 708 testcross markers suitable for map construction. The male map consisted of 177 loci arranged in 17 major linkage groups, spanning 1,015.5 cM, while female map was built with 326 loci arranged into 20 major linkage groups, spanning 1,486.8 cM. The presence of 84 loci shared between these maps and those previously developed from a cross within globe artichoke allowed for map alignment and the definition of 17 homologous linkage groups, corresponding to the haploid number of the species. This will provide a favourable property for QTL scanning; furthermore, as 25 mapped markers (8%) correspond to coding regions, it has an additional value as functional map and might represent an important genetic tool for candidate gene studies in globe artichoke.
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Affiliation(s)
- E Portis
- DIVAPRA Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095, Grugliasco (Turin), Italy
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Scaglione D, Acquadro A, Portis E, Taylor CA, Lanteri S, Knapp SJ. Ontology and diversity of transcript-associated microsatellites mined from a globe artichoke EST database. BMC Genomics 2009; 10:454. [PMID: 19785740 PMCID: PMC2760586 DOI: 10.1186/1471-2164-10-454] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Accepted: 09/28/2009] [Indexed: 12/02/2022] Open
Abstract
Background The globe artichoke (Cynara cardunculus var. scolymus L.) is a significant crop in the Mediterranean basin. Despite its commercial importance and its both dietary and pharmaceutical value, knowledge of its genetics and genomics remains scant. Microsatellite markers have become a key tool in genetic and genomic analysis, and we have exploited recently acquired EST (expressed sequence tag) sequence data (Composite Genome Project - CGP) to develop an extensive set of microsatellite markers. Results A unigene assembly was created from over 36,000 globe artichoke EST sequences, containing 6,621 contigs and 12,434 singletons. Over 12,000 of these unigenes were functionally assigned on the basis of homology with Arabidopsis thaliana reference proteins. A total of 4,219 perfect repeats, located within 3,308 unigenes was identified and the gene ontology (GO) analysis highlighted some GO term's enrichments among different classes of microsatellites with respect to their position. Sufficient flanking sequence was available to enable the design of primers to amplify 2,311 of these microsatellites, and a set of 300 was tested against a DNA panel derived from 28 C. cardunculus genotypes. Consistent amplification and polymorphism was obtained from 236 of these assays. Their polymorphic information content (PIC) ranged from 0.04 to 0.90 (mean 0.66). Between 176 and 198 of the assays were informative in at least one of the three available mapping populations. Conclusion EST-based microsatellites have provided a large set of de novo genetic markers, which show significant amounts of polymorphism both between and within the three taxa of C. cardunculus. They are thus well suited as assays for phylogenetic analysis, the construction of genetic maps, marker-assisted breeding, transcript mapping and other genomic applications in the species.
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Affiliation(s)
- Davide Scaglione
- DiVaPRA Plant Genetics and Breeding, University of Torino, via L, da Vinci 44, 10095 Grugliasco, Torino, Italy.
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Moglia A, Comino C, Portis E, Acquadro A, De Vos RCH, Beekwilder J, Lanteri S. Isolation and mapping of a C3'H gene (CYP98A49) from globe artichoke, and its expression upon UV-C stress. Plant Cell Rep 2009; 28:963-74. [PMID: 19301010 DOI: 10.1007/s00299-009-0695-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Revised: 02/10/2009] [Accepted: 03/01/2009] [Indexed: 05/04/2023]
Abstract
Globe artichoke represents a natural source of phenolic compounds with dicaffeoylquinic acids along with their biosynthetic precursor chlorogenic acid (5-caffeoylquinic acid) as the predominant molecules. We report the isolation and characterization of a full-length cDNA and promoter of a globe artichoke p-coumaroyl ester 3'-hydroxylase (CYP98A49), which is involved in both chlorogenic acid and lignin biosynthesis. Phylogenetic analyses demonstrated that this gene belongs to the CYP98 family. CYP98A49 was also heterologously expressed in yeast, in order to perform an enzymatic assay with p-coumaroylshikimate and p-coumaroylquinate as substrates. Real Time quantitative PCR analysis revealed that CYP98A49 expression is induced upon exposure to UV-C radiation. A single nucleotide polymorphism in the CYP98A49 gene sequence of two globe artichoke varieties used for genetic mapping allowed the localization of this gene to linkage group 10 within the previously developed maps.
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Affiliation(s)
- Andrea Moglia
- DiVaPRA, Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095, Grugliasco (TO), Italy
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Acquadro A, Lanteri S, Scaglione D, Arens P, Vosman B, Portis E. Genetic mapping and annotation of genomic microsatellites isolated from globe artichoke. Theor Appl Genet 2009; 118:1573-87. [PMID: 19326092 DOI: 10.1007/s00122-009-1005-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2008] [Accepted: 03/08/2009] [Indexed: 05/14/2023]
Abstract
Cynara cardunculus includes three taxa, the globe artichoke (subsp. scolymus L. Hegi), the cultivated cardoon (var. altilis) and their progenitor, the wild cardoon (var. sylvestris). Globe artichoke is an important component of the Mediterranean rural economy, but its improvement through breeding has been rather limited and its genome organization remains largely unexplored. Here, we report the isolation of 61 new microsatellite loci which amplified a total of 208 alleles in a panel of 22 C. cardunculus genotypes. Of these, 51 were informative for linkage analysis and 39 were used to increase marker density in the available globe artichoke genetic maps. Sequence analysis of the 22 loci associated with genes showed that 9 are located within coding sequence, with the repetitive domain probably being involved in DNA binding or in protein-protein interactions. The expression of the genes associated with 9 of the 22 microsatellite loci was demonstrated by RT-PCR.
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Affiliation(s)
- Alberto Acquadro
- Di.Va.P.R.A. Plant Genetics and Breeding, University of Turin, via L. da Vinci 44, 10095, Grugliasco, Turin, Italy
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Comino C, Hehn A, Moglia A, Menin B, Bourgaud F, Lanteri S, Portis E. The isolation and mapping of a novel hydroxycinnamoyltransferase in the globe artichoke chlorogenic acid pathway. BMC Plant Biol 2009; 9:30. [PMID: 19292932 PMCID: PMC2664813 DOI: 10.1186/1471-2229-9-30] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2008] [Accepted: 03/18/2009] [Indexed: 05/19/2023]
Abstract
BACKGROUND The leaves of globe artichoke and cultivated cardoon (Cynara cardunculus L.) have significant pharmaceutical properties, which mainly result from their high content of polyphenolic compounds such as monocaffeoylquinic and dicaffeoylquinic acid (DCQ), and a range of flavonoid compounds. RESULTS Hydroxycinnamoyl-CoA:quinate hydroxycinnamoyltransferase (HQT) encoding genes have been isolated from both globe artichoke and cultivated cardoon (GenBank accessions DQ915589 and DQ915590, respectively) using CODEHOP and PCR-RACE. A phylogenetic analysis revealed that their sequences belong to one of the major acyltransferase groups (anthranilate N-hydroxycinnamoyl/benzoyltransferase). The heterologous expression of globe artichoke HQT in E. coli showed that this enzyme can catalyze the esterification of quinic acid with caffeoyl-CoA or p-coumaroyl-CoA to generate, respectively, chlorogenic acid (CGA) and p-coumaroyl quinate. Real time PCR experiments demonstrated an increase in the expression level of HQT in UV-C treated leaves, and established a correlation between the synthesis of phenolic acids and protection against damage due to abiotic stress. The HQT gene, together with a gene encoding hydroxycinnamoyl-CoA:shikimate/quinate hydroxycinnamoyltransferase (HCT) previously isolated from globe artichoke, have been incorporated within the developing globe artichoke linkage maps. CONCLUSION A novel acyltransferase involved in the biosynthesis of CGA in globe artichoke has been isolated, characterized and mapped. This is a good basis for our effort to understand the genetic basis of phenylpropanoid (PP) biosynthesis in C. cardunculus.
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Affiliation(s)
- Cinzia Comino
- DiVaPRA Plant Genetics and Breeding, University of Torino 10095, Grugliasco (Torino), Italy
| | - Alain Hehn
- UMR 1121 Nancy Université (INPL)-INRA, Agronomie Environnement Nancy-Colmar 2 avenue de la Forêt de Haye 54505 Vandoeuvre-lès-Nancy, France
| | - Andrea Moglia
- DiVaPRA Plant Genetics and Breeding, University of Torino 10095, Grugliasco (Torino), Italy
| | - Barbara Menin
- DiVaPRA Plant Genetics and Breeding, University of Torino 10095, Grugliasco (Torino), Italy
| | - Frédéric Bourgaud
- UMR 1121 Nancy Université (INPL)-INRA, Agronomie Environnement Nancy-Colmar 2 avenue de la Forêt de Haye 54505 Vandoeuvre-lès-Nancy, France
| | - Sergio Lanteri
- DiVaPRA Plant Genetics and Breeding, University of Torino 10095, Grugliasco (Torino), Italy
| | - Ezio Portis
- DiVaPRA Plant Genetics and Breeding, University of Torino 10095, Grugliasco (Torino), Italy
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Sweeney M, Watts J, Portis E, Lucas M, Nutsch R, Meeuwse D, Bade D, Oliver V, Morck DW, Shinabarger D, Poppe S, Peterson M, Sweeney D, Knechtel M, Zurenko G. Identification of Porphyromonas levii isolated from clinical cases of bovine interdigital necrobacillosis by 16S rRNA sequencing. Vet Ther 2009; 10:E1-E10. [PMID: 20425726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Laboratories use pigmentation, antibiotic susceptibility, and biochemical tests to identify anaerobic organisms that play a role in bovine interdigital necrobacillosis (bovine foot rot). In this study, 16S rRNA gene sequencing was used to identify strains to the species level that were originally classified as Prevotella or Porphyromonas spp by conventional phenotype assessment methods. Of 264 qualified strains from ceftiofur clinical trials, 241 isolates were definitively identified by 16S rRNA sequencing as Porphyromonas levii. Similarly, of 275 qualified strains from tulathromycin clinical trials, 156 isolates were definitively identified by 16S rRNA sequencing as P. levii. The predominance of P. levii in this study supports the role of this organism as an associative agent of bovine foot rot and may have implications for routine laboratory diagnosis.
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Affiliation(s)
- M Sweeney
- Pfizer Animal Health, Kalamazoo, MI 49007, USA
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Spadaro D, Sabetta W, Acquadro A, Portis E, Garibaldi A, Gullino ML. Use of AFLP for differentiation of Metschnikowia pulcherrima strains for postharvest disease biological control. Microbiol Res 2008; 163:523-30. [PMID: 17428647 DOI: 10.1016/j.micres.2007.01.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2006] [Revised: 12/01/2006] [Accepted: 01/17/2007] [Indexed: 11/30/2022]
Abstract
Metschnikowia pulcherrima occurs naturally on fruits, buds and floral parts of apple trees. Some strains are effective as biocontrol agents against postharvest decay of apples and other fruits. The usefulness of the amplified fragment length polymorphism (AFLP) technique was evaluated for the genetic analysis of 26 strains of M. pulcherrima, isolated from different sources in different geographical regions. With six AFLP primer pairs, 729 polymorphic bands were scored. The technique showed a high discriminatory power. Genetic relationships between strains were also estimated using AFLP. All the isolates from the carposphere of apple, previously tested as biocontrol agents, were grouped in a single cluster with a high bootstrap value (97), indicating robustness and reproducibility. AFLP patterns could clearly distinguish the different strains and research is in progress to use some putative specific bands for single tag sequence (STS) conversion to develop isolate-specific markers.
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Affiliation(s)
- D Spadaro
- Di.Va.P.R.A - Plant Pathology, Università di Torino, I-10095 Grugliasco, Italy.
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