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26 results on '"Di Vittori, Valerio"'

1. Author Correction: Adaptive gene loss in the common bean pan-genome during range expansion and domestication

Author

Cortinovis, Gaia, Vincenzi, Leonardo, Anderson, Robyn, Marturano, Giovanni, Marsh, Jacob Ian, Bayer, Philipp Emanuel, Rocchetti, Lorenzo, Frascarelli, Giulia, Lanzavecchia, Giovanna, Pieri, Alice, Benazzo, Andrea, Bellucci, Elisa, Di Vittori, Valerio, Nanni, Laura, Ferreira Fernández, Juan José, Rossato, Marzia, Aguilar, Orlando Mario, Morrell, Peter Laurent, Rodriguez, Monica, Gioia, Tania, Neumann, Kerstin, Alvarez Diaz, Juan Camilo, Gratias, Ariane, Klopp, Christophe, Bitocchi, Elena, Geffroy, Valérie, Delledonne, Massimo, Edwards, David, and Papa, Roberto

Published
2024
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2. Adaptive gene loss in the common bean pan-genome during range expansion and domestication

Author

Cortinovis, Gaia, Vincenzi, Leonardo, Anderson, Robyn, Marturano, Giovanni, Marsh, Jacob Ian, Bayer, Philipp Emanuel, Rocchetti, Lorenzo, Frascarelli, Giulia, Lanzavecchia, Giovanna, Pieri, Alice, Benazzo, Andrea, Bellucci, Elisa, Di Vittori, Valerio, Nanni, Laura, Ferreira Fernández, Juan José, Rossato, Marzia, Aguilar, Orlando Mario, Morrell, Peter Laurent, Rodriguez, Monica, Gioia, Tania, Neumann, Kerstin, Alvarez Diaz, Juan Camilo, Gratias, Ariane, Klopp, Christophe, Bitocchi, Elena, Geffroy, Valérie, Delledonne, Massimo, Edwards, David, and Papa, Roberto

Published
2024
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3. Selection and adaptive introgression guided the complex evolutionary history of the European common bean

Author

Bellucci, Elisa, Benazzo, Andrea, Xu, Chunming, Bitocchi, Elena, Rodriguez, Monica, Alseekh, Saleh, Di Vittori, Valerio, Gioia, Tania, Neumann, Kerstin, Cortinovis, Gaia, Frascarelli, Giulia, Murube, Ester, Trucchi, Emiliano, Nanni, Laura, Ariani, Andrea, Logozzo, Giuseppina, Shin, Jin Hee, Liu, Chaochih, Jiang, Liang, Ferreira, Juan José, Campa, Ana, Attene, Giovanna, Morrell, Peter L, Bertorelle, Giorgio, Graner, Andreas, Gepts, Paul, Fernie, Alisdair R, Jackson, Scott A, and Papa, Roberto

Subjects
Biological Sciences, Genetics, Human Genome, Humans, Phaseolus, Genetic Variation, Genotype, Biological Evolution, Hybridization, Genetic
Abstract

Domesticated crops have been disseminated by humans over vast geographic areas. Common bean (Phaseolus vulgaris L.) was introduced in Europe after 1492. Here, by combining whole-genome profiling, metabolic fingerprinting and phenotypic characterisation, we show that the first common bean cultigens successfully introduced into Europe were of Andean origin, after Francisco Pizarro's expedition to northern Peru in 1529. We reveal that hybridisation, selection and recombination have shaped the genomic diversity of the European common bean in parallel with political constraints. There is clear evidence of adaptive introgression into the Mesoamerican-derived European genotypes, with 44 Andean introgressed genomic segments shared by more than 90% of European accessions and distributed across all chromosomes except PvChr11. Genomic scans for signatures of selection highlight the role of genes relevant to flowering and environmental adaptation, suggesting that introgression has been crucial for the dissemination of this tropical crop to the temperate regions of Europe.

Published
2023

5. Transcriptomic response to nitrogen availability reveals signatures of adaptive plasticity during tetraploid wheat domestication.

Author

Pieri, Alice, Beleggia, Romina, Gioia, Tania, Tong, Hao, Di Vittori, Valerio, Frascarelli, Giulia, Bitocchi, Elena, Nanni, Laura, Bellucci, Elisa, Fiorani, Fabio, Pecchioni, Nicola, Marzario, Stefania, De Quattro, Concetta, Limongi, Antonina Rita, De Vita, Pasquale, Rossato, Marzia, Schurr, Ulrich, David, Jacques L, Nikoloski, Zoran, and Papa, Roberto

Published
2024
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7. Genotype Combinations Drive Variability in the Microbiome Configuration of the Rhizosphere of Maize/Bean Intercropping System

Author

Lanzavecchia, Giovanna, primary, Frascarelli, Giulia, additional, Rocchetti, Lorenzo, additional, Bellucci, Elisa, additional, Bitocchi, Elena, additional, Di Vittori, Valerio, additional, Sillo, Fabiano, additional, Ferraris, Irene, additional, Carta, Giada, additional, Delledonne, Massimo, additional, Nanni, Laura, additional, and Papa, Roberto, additional

Published
2024
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8. Challenges and Opportunities behind the Use of Herbaria in Paleogenomics Studies

Author

Papalini, Simone, primary, Di Vittori, Valerio, additional, Pieri, Alice, additional, Allegrezza, Marina, additional, Frascarelli, Giulia, additional, Nanni, Laura, additional, Bitocchi, Elena, additional, Bellucci, Elisa, additional, Gioia, Tania, additional, Pereira, Luis Guasch, additional, Susek, Karolina, additional, Tenaillon, Maud, additional, Neumann, Kerstin, additional, and Papa, Roberto, additional

Published
2023
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9. Nitrogen availability during domestication shaped the divergence of tetraploid wheat

Author

Pieri, Alice, primary, Beleggia, Romina, additional, Gioia, Tania, additional, Tong, Hao, additional, Di Vittori, Valerio, additional, Frascarelli, Giulia, additional, Bitocchi, Elena, additional, Nanni, Laura, additional, Bellucci, Elisa, additional, Fiorani, Fabio, additional, Pecchioni, Nicola, additional, Marzario, Stefania, additional, De Quattro, Concetta, additional, Limongi, Antonina Rita, additional, De Vita, Pasquale, additional, Rossato, Marzia, additional, Schurr, Ulrich, additional, David, Jacques, additional, Nikoloski, Zoran, additional, and Papa, Roberto, additional

Published
2023
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10. Domestication and Crop History

Author

Di Vittori, Valerio, Bellucci, Elisa, Bitocchi, Elena, Rau, Domenico, Rodriguez, Monica, Murgia, Maria Leonarda, Nanni, Laura, Attene, Giovanna, Papa, Roberto, Kole, Chittaranjan, Series editor, Pérez de la Vega, Marcelino, editor, Santalla, Marta, editor, and Marsolais, Frédéric, editor

Published
2017
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11. The evolutionary history of the common bean (Phaseolus vulgaris) revealed by chloroplast and nuclear genomes

Author

Frascarelli, Giulia, primary, Galise, Teresa R., additional, D’Agostino, Nunzio, additional, Cafasso, Donata, additional, Cozzolino, Salvatore, additional, Cortinovis, Gaia, additional, Sparvoli, Francesca, additional, Bellucci, Elisa, additional, Di Vittori, Valerio, additional, Nanni, Laura, additional, Pieri, Alice, additional, Rossato, Marzia, additional, Vincenzi, Leonardo, additional, Benazzo, Andrea, additional, Delledonne, Massimo, additional, Bitocchi, Elena, additional, and Papa, Roberto, additional

Published
2023
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12. CRISPR-Cas9-based repeat depletion for the high-throughput genotyping of complex plant genomes

Author

Rossato, Marzia, primary, Marcolungo, Luca, additional, De Antoni, Luca, additional, Lopatriello, Giulia, additional, Bellucci, Elisa, additional, Cortinovis, Gaia, additional, Frascarelli, Giulia, additional, Nanni, Laura, additional, Biotcchi, Elena, additional, Di Vittori, Valerio, additional, Vincenzi, Leonardo, additional, Lucchini, Filippo, additional, Bett, Kirstin E, additional, Remsay, Larissa, additional, Konkin, David, additional, Delledonne, Massimo, additional, and Papa, Roberto, additional

Published
2023
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14. Challenges and Opportunities behind the Use of Herbaria in Paleogenomics Studies

Author

European Commission, Ministero dell'Istruzione, dell'Università e della Ricerca, Papalini, Simone, Di Vittori, Valerio, Pieri, Alice, Allegrezza, Marina, Frascarelli, Giulia, Nanni, Laura, Bitocchi, Elena, Bellucci, Elisa, Gioia, Tania, Guasch, Luís, Susek, Karolina, Tenaillon, Maud, Neumann, Kerstin, Papa, Roberto, European Commission, Ministero dell'Istruzione, dell'Università e della Ricerca, Papalini, Simone, Di Vittori, Valerio, Pieri, Alice, Allegrezza, Marina, Frascarelli, Giulia, Nanni, Laura, Bitocchi, Elena, Bellucci, Elisa, Gioia, Tania, Guasch, Luís, Susek, Karolina, Tenaillon, Maud, Neumann, Kerstin, and Papa, Roberto

Abstract

Paleogenomics focuses on the recovery, manipulation, and analysis of ancient DNA (aDNA) from historical or long-dead organisms to reconstruct and analyze their genomes. The aDNA is commonly obtained from remains found in paleontological and archaeological sites, conserved in museums, and in other archival collections. Herbarium collections represent a great source of phenotypic and genotypic information, and their exploitation has allowed for inference and clarification of previously unsolved taxonomic and systematic relationships. Moreover, herbarium specimens offered a new source for studying phenological traits in plants and for disentangling biogeography and evolutionary scenarios of species. More recently, advances in molecular technologies went in parallel with the decreasing costs of next-generation sequencing (NGS) approaches, which paved the way to the utilization of aDNA for whole-genome studies. Although many studies have been carried out combining modern analytic techniques and ancient samples, such as herbarium specimens, this research field is still relatively unexplored due to the need for improving strategies for aDNA manipulation and exploitation from ancient samples. The higher susceptibility of aDNA to degradation and contamination during herbarium conservation and manipulation and the occurrence of biochemical postmortem damage can result in a more challenging reconstruction of the original DNA sequence. Here, we review the methodological approaches that have been developed for the exploitation of historical herbarium plant materials, such as best practices for aDNA extraction, amplification, and genotyping. We also focus on some strategies to overcome the main problems related to the utilization of herbarium specimens for their exploitation in plant evolutionary studies.

Published
2023

15. CRISPR/Cas9-Mediated Enrichment Coupled to Nanopore Sequencing Provides a Valuable Tool for the Precise Reconstruction of Large Genomic Target Regions

Author

Lopatriello, Giulia, primary, Maestri, Simone, additional, Alfano, Massimiliano, additional, Papa, Roberto, additional, Di Vittori, Valerio, additional, De Antoni, Luca, additional, Bellucci, Elisa, additional, Pieri, Alice, additional, Bitocchi, Elena, additional, Delledonne, Massimo, additional, and Rossato, Marzia, additional

Published
2023
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16. Domestication and Crop History

Author

Di Vittori, Valerio, primary, Bellucci, Elisa, additional, Bitocchi, Elena, additional, Rau, Domenico, additional, Rodriguez, Monica, additional, Murgia, Maria Leonarda, additional, Nanni, Laura, additional, Attene, Giovanna, additional, and Papa, Roberto, additional

Published
2017
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17. An Arabidopsis root phloem pole cell atlas reveals PINEAPPLE genes as transitioners to autotrophy

Author

Otero, Sofia, primary, Sevilem, Iris, additional, Roszak, Pawel, additional, Lu, Yipeng, additional, Di Vittori, Valerio, additional, Bourdon, Matthieu, additional, Kalmbach, Lothar, additional, Blob, Bernhard, additional, Heo, Jung-ok, additional, Peruzzo, Federico, additional, Laux, Thomas, additional, Fernie, Alisdair R, additional, Tavares, Hugo, additional, and Helariutta, Yka, additional

Published
2021
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18. CRISPR-Cas9-based repeat depletion for high-throughput genotyping of complex plant genomes

Author

Rossato, Marzia, Marcolungo, Luca, De Antoni, Luca, Lopatriello, Giulia, Bellucci, Elisa, Cortinovis, Gaia, Frascarelli, Giulia, Nanni, Laura, Bitocchi, Elena, Di Vittori, Valerio, Vincenzi, Leonardo, Lucchini, Filippo, Bett, Kirstin E., Ramsay, Larissa, Konkin, David James, Delledonne, Massimo, and Papa, Roberto

Abstract

High-throughput genotyping enables the large-scale analysis of genetic diversity in population genomics and genome-wide association studies that combine the genotypic and phenotypic characterization of large collections of accessions. Sequencing-based approaches for genotyping are progressively replacing traditional genotyping methods because of the lower ascertainment bias. However, genome-wide genotyping based on sequencing becomes expensive in species with large genomes and a high proportion of repetitive DNA. Here we describe the use of CRISPR-Cas9 technology to deplete repetitive elements in the 3.76-Gb genome of lentil (Lens culinaris), 84% consisting of repeats, thus concentrating the sequencing data on coding and regulatory regions (single-copy regions). We designed a custom set of 566,766 gRNAs targeting 2.9 Gbp of repeats and excluding repetitive regions overlapping annotated genes and putative regulatory elements based on ATAC-seq data. The novel depletion method removed ∼40% of reads mapping to repeats, increasing those mapping to single-copy regions by ∼2.6-fold. When analyzing 25 million fragments, this repeat-to-single-copy shift in the sequencing data increased the number of genotyped bases of ∼10-fold compared to nondepleted libraries. In the same condition, we were also able to identify ∼12-fold more genetic variants in the single-copy regions and increased the genotyping accuracy by rescuing thousands of heterozygous variants that otherwise would be missed because of low coverage. The method performed similarly regardless of the multiplexing level, type of library or genotypes, including different cultivars and a closely related species (L. orientalis). Our results showed that CRISPR-Cas9-driven repeat depletion focuses sequencing data on single-copy regions, thus improving high-density and genome-wide genotyping in large and repetitive genomes.

Published
2023
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19. Pod indehiscence in common bean is associated with the fine regulation ofPvMYB26

Author

Di Vittori, Valerio, primary, Bitocchi, Elena, additional, Rodriguez, Monica, additional, Alseekh, Saleh, additional, Bellucci, Elisa, additional, Nanni, Laura, additional, Gioia, Tania, additional, Marzario, Stefania, additional, Logozzo, Giuseppina, additional, Rossato, Marzia, additional, De Quattro, Concetta, additional, Murgia, Maria L, additional, Ferreira, Juan José, additional, Campa, Ana, additional, Xu, Chunming, additional, Fiorani, Fabio, additional, Sampathkumar, Arun, additional, Fröhlich, Anja, additional, Attene, Giovanna, additional, Delledonne, Massimo, additional, Usadel, Björn, additional, Fernie, Alisdair R, additional, Rau, Domenico, additional, and Papa, Roberto, additional

Published
2020
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20. Genetic Diversity, Population Structure, and Andean Introgression in Brazilian Common Bean Cultivars after Half a Century of Genetic Breeding

Author

Almeida, Caléo Panhoca de, primary, Paulino, Jean Fausto de Carvalho, additional, Morais Carbonell, Sérgio Augusto, additional, Chiorato, Alisson Fernando, additional, Song, Qijian, additional, Di Vittori, Valerio, additional, Rodriguez, Monica, additional, Papa, Roberto, additional, and Benchimol-Reis, Luciana Lasry, additional

Published
2020
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21. The Development of a European and Mediterranean Chickpea Association Panel (EMCAP)

Author

Rocchetti, Lorenzo, primary, Bellucci, Elisa, additional, Cortinovis, Gaia, additional, Di Vittori, Valerio, additional, Lanzavecchia, Giovanna, additional, Frascarelli, Giulia, additional, Nanni, Laura, additional, Del Gatto, Andrea, additional, Pieri, Sandro, additional, Mangoni, Lorella, additional, Bitocchi, Elena, additional, and Papa, Roberto, additional

Published
2020
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23. Pod indehiscence in common bean is associated to the fine regulation ofPvMYB26and a non-functional abscission layer

Author

Di Vittori, Valerio, primary, Bitocchi, Elena, additional, Rodriguez, Monica, additional, Alseekh, Saleh, additional, Bellucci, Elisa, additional, Nanni, Laura, additional, Gioia, Tania, additional, Marzario, Stefania, additional, Logozzo, Giuseppina, additional, Rossato, Marzia, additional, De Quattro, Concetta, additional, Murgia, Maria L., additional, José Ferreira, Juan, additional, Campa, Ana, additional, Xu, Chunming, additional, Fiorani, Fabio, additional, Sampathkumar, Arun, additional, Fröhlich, Anja, additional, Attene, Giovanna, additional, Delledonne, Massimo, additional, Usadel, Björn, additional, Fernie, Alisdair R., additional, Rau, Domenico, additional, and Papa, Roberto, additional

Published
2020
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25. Convergent Evolution of the Seed Shattering Trait

Author

Di Vittori, Valerio, primary, Gioia, Tania, additional, Rodriguez, Monica, additional, Bellucci, Elisa, additional, Bitocchi, Elena, additional, Nanni, Laura, additional, Attene, Giovanna, additional, Rau, Domenico, additional, and Papa, Roberto, additional

Published
2019
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26. Pod indehiscence in common bean is associated with the fine regulation of PvMYB26.

Author

Di Vittori V, Bitocchi E, Rodriguez M, Alseekh S, Bellucci E, Nanni L, Gioia T, Marzario S, Logozzo G, Rossato M, De Quattro C, Murgia ML, Ferreira JJ, Campa A, Xu C, Fiorani F, Sampathkumar A, Fröhlich A, Attene G, Delledonne M, Usadel B, Fernie AR, Rau D, and Papa R

Subjects
Quantitative Trait Loci, Seeds, Phaseolus genetics
Abstract

In legumes, pod shattering occurs when mature pods dehisce along the sutures, and detachment of the valves promotes seed dispersal. In Phaseolus vulgaris (L)., the major locus qPD5.1-Pv for pod indehiscence was identified recently. We developed a BC4/F4 introgression line population and narrowed the major locus down to a 22.5 kb region. Here, gene expression and a parallel histological analysis of dehiscent and indehiscent pods identified an AtMYB26 orthologue as the best candidate for loss of pod shattering, on a genomic region ~11 kb downstream of the highest associated peak. Based on mapping and expression data, we propose early and fine up-regulation of PvMYB26 in dehiscent pods. Detailed histological analysis establishes that pod indehiscence is associated with the lack of a functional abscission layer in the ventral sheath, and that the key anatomical modifications associated with pod shattering in common bean occur early during pod development. We finally propose that loss of pod shattering in legumes resulted from histological convergent evolution and that it is the result of selection at orthologous loci., (© The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Experimental Biology.)

Published
2021
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