Whole-Genome Resequencing of Seven Eggplant (Solanum melongena) and One Wild Relative (S. incanum) Accessions Provides New Insights and Breeding Tools for Eggplant Enhancement

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dc.contributor.authorGramazio, Pietroen
dc.contributor.authorYan, Haidongen
dc.contributor.authorHasing, Tomasen
dc.contributor.authorVilanova, Santiagoen
dc.contributor.authorProhens, Jaimeen
dc.contributor.authorBombarely, Aurelianoen
dc.contributor.departmentSchool of Plant and Environmental Sciencesen
dc.date.accessioned2020-02-10T20:07:04Zen
dc.date.available2020-02-10T20:07:04Zen
dc.date.issued2019-10-08en
dc.description.abstractWhole-genome resequencing provides information of great relevance for crop genetics, evolution, and breeding. Here, we present the first whole-genome resequencing study using seven eggplant (Solanum melongena) and one wild relative (Solanum incanum) accessions. These eight accessions were selected for displaying a high phenotypic and genetic diversity and for being the founder parents of an eggplant multiparent advanced generation intercrosses population. By resequencing at an average depth of 19.8x and comparing to the high-quality reference genome "67/3" over 10 million high-reliable polymorphisms were discovered, of which over 9 million (84.5%) were single nucleotide polymorphisms and more than 700,000 (6.5%) InDels. However, while for the S. melongena accessions, the variants identified ranged from 0.8 to 1.3 million, over 9 million were detected for the wild S. incanum. This confirms the narrow genetic diversity of the domesticated eggplant and suggests that introgression breeding using wild relatives can efficiently contribute to broadening the genetic basis of this crop. Differences were observed among accessions for the enrichment in genes regulating important biological processes. By analyzing the distribution of the variants, we identified the potential footprints of old introgressions from wild relatives that can help to unravel the unclear domestication and breeding history. The comprehensive annotation of these eight genomes and the information provided in this study represents a landmark in eggplant genomics and allows the development of tools for eggplant genetics and breeding.en
dc.description.notesThis work has been funded by the European Union's Horizon 2020 Research and Innovation Programme under grant agreement no. 677379 (G2P-SOL project: Linking genetic resources, genomes, and phenotypes of Solanaceous crops), by the Spanish Ministerio de Economia, Industria y Competitividad and Fondo Europeo de Desarrollo Regional/European Regional Development Fund (grant AGL2015-64755-R), and by the Spanish Ministerio de Ciencia, Innovacion y Universidades (MCIU), Agencia Estatal de Investigacion (AEI), and Fondo Europeo de Desarrollo Regional/European Regional Development Fund (grant RTI2018-09592-B-100). PG is grateful to Universitat Politecnica de Valencia and to Japan Society for the Promotion of Science for their respective postdoctoral grants [PAID-10-18 and FY2019 JSPS Postdoctoral Fellowship for Research in Japan (Standard)].en
dc.description.sponsorshipEuropean UnionEuropean Union (EU) [677379]; Spanish Ministerio de Economia, Industria y Competitividad; Fondo Europeo de Desarrollo Regional/European Regional Development Fund [RTI2018-09592-B-100, AGL2015-64755-R]; Spanish Ministerio de Ciencia, Innovacion y Universidades (MCIU); Agencia Estatal de Investigacion (AEI); Japan Society for the Promotion of ScienceMinistry of Education, Culture, Sports, Science and Technology, Japan (MEXT)Japan Society for the Promotion of Science [PAID-10-18]; Universitat Politecnica de Valenciaen
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.3389/fpls.2019.01220en
dc.identifier.issn1664-462Xen
dc.identifier.other1220en
dc.identifier.pmid31649694en
dc.identifier.urihttp://hdl.handle.net/10919/96788en
dc.identifier.volume10en
dc.language.isoenen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectwhole-genome resequencingen
dc.subjectSolanum melongenaen
dc.subjectS. incanumen
dc.subjectpolymorphismsen
dc.subjectgenome characterizationen
dc.titleWhole-Genome Resequencing of Seven Eggplant (Solanum melongena) and One Wild Relative (S. incanum) Accessions Provides New Insights and Breeding Tools for Eggplant Enhancementen
dc.title.serialFrontiers in Plant Scienceen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
dc.type.dcmitypeStillImageen

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