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Single Primer Enrichment Technology (SPET) for High-Throughput Genotyping in Tomato and Eggplant Germplasm

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Single Primer Enrichment Technology (SPET) for High-Throughput Genotyping in Tomato and Eggplant Germplasm

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dc.contributor.author Barchi, L. es_ES
dc.contributor.author Acquadro, A. es_ES
dc.contributor.author Alonso-Martín, David es_ES
dc.contributor.author Aprea, G. es_ES
dc.contributor.author Bassolino, L. es_ES
dc.contributor.author Demurtas, O.C. es_ES
dc.contributor.author Ferrante, P. es_ES
dc.contributor.author Gramazio, Pietro es_ES
dc.contributor.author Mini, P. es_ES
dc.contributor.author Portis, Ezio es_ES
dc.contributor.author Scaglione, D. es_ES
dc.contributor.author Toppino, L. es_ES
dc.contributor.author Vilanova Navarro, Santiago es_ES
dc.contributor.author Díez Niclós, Mª José Teresa De Jesús es_ES
dc.contributor.author Rotino, G.L. es_ES
dc.contributor.author Prohens Tomás, Jaime es_ES
dc.date.accessioned 2020-05-20T03:01:42Z
dc.date.available 2020-05-20T03:01:42Z
dc.date.issued 2019-08-07 es_ES
dc.identifier.uri http://hdl.handle.net/10251/143786
dc.description.abstract [EN] 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. es_ES
dc.description.sponsorship This work has been funded by the European Union's Horizon 2020 Research and Innovation Programme under the grant agreement number 677379 (G2P-SOL project: Linking genetic resources, genomes, and phenotypes of solanaceous crops). es_ES
dc.language Inglés es_ES
dc.publisher Frontiers Media SA es_ES
dc.relation.ispartof Frontiers in Plant Science es_ES
dc.rights Reconocimiento (by) es_ES
dc.subject SPET es_ES
dc.subject Genotyping es_ES
dc.subject Tomato es_ES
dc.subject Eggplant es_ES
dc.subject Germplasm es_ES
dc.subject.classification GENETICA es_ES
dc.title Single Primer Enrichment Technology (SPET) for High-Throughput Genotyping in Tomato and Eggplant Germplasm es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.3389/fpls.2019.01005 es_ES
dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/677379/EU/Linking genetic resources, genomes and phenotypes of Solanaceous crops/ es_ES
dc.rights.accessRights Abierto es_ES
dc.contributor.affiliation Universitat Politècnica de València. Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana - Institut Universitari de Conservació i Millora de l'Agrodiversitat Valenciana es_ES
dc.contributor.affiliation Universitat Politècnica de València. Departamento de Biotecnología - Departament de Biotecnologia es_ES
dc.description.bibliographicCitation Barchi, L.; Acquadro, A.; Alonso-Martín, D.; Aprea, G.; Bassolino, L.; Demurtas, O.; Ferrante, P.... (2019). Single Primer Enrichment Technology (SPET) for High-Throughput Genotyping in Tomato and Eggplant Germplasm. Frontiers in Plant Science. 10:1-17. https://doi.org/10.3389/fpls.2019.01005 es_ES
dc.description.accrualMethod S es_ES
dc.relation.publisherversion https://doi.org/10.3389/fpls.2019.01005 es_ES
dc.description.upvformatpinicio 1 es_ES
dc.description.upvformatpfin 17 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 10 es_ES
dc.identifier.eissn 1664-462X es_ES
dc.identifier.pmid 31440267 es_ES
dc.identifier.pmcid PMC6693525 es_ES
dc.relation.pasarela S\407111 es_ES
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