title: Inter-varietal structural variation in grapevine genomes.
abstract: Grapevine (Vitis vinifera L.) is one of the world's most important crop plants, which is of large economic value for fruit and wine production. There is much interest in identifying genomic variations and their functional effects on inter-varietal, phenotypic differences. Using an approach developed for the analysis of human and mammalian genomes, which combines high-throughput sequencing, array comparative genomic hybridization, fluorescent in situ hybridization and quantitative PCR, we created an inter-varietal atlas of structural variations and single nucleotide variants (SNVs) for the grapevine genome analyzing four economically and genetically relevant table grapevine varieties. We found 4.8 million SNVs and detected 8% of the grapevine genome to be affected by genomic variations. We identified more than 700 copy number variation (CNV) regions and more than 2000 genes subjected to CNV as potential candidates for phenotypic differences between varieties.
authors.affiliation: Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA)-Unità di ricerca per l'uva da tavola e la vitivinicoltura in ambiente mediterraneo, Research Unit for viticulture and enology in Southern Italy, Turi (BA), Italy.
authors.forename: Maria Francesca
authors.initials: MF
authors.lastname: Cardone
authors.affiliation: Dipartimento di Biologia, Università degli Studi di Bari 'Aldo Moro', Bari, Italy.
authors.forename: Pietro
authors.initials: P
authors.lastname: D'Addabbo
authors.affiliation: Department of Computer Engineering, Bilkent University, Ankara, TR-06800, Turkey.
authors.forename: Can
authors.initials: C
authors.lastname: Alkan
authors.affiliation: Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA)-Unità di ricerca per l'uva da tavola e la vitivinicoltura in ambiente mediterraneo, Research Unit for viticulture and enology in Southern Italy, Turi (BA), Italy.
authors.forename: Carlo
authors.initials: C
authors.lastname: Bergamini
authors.affiliation: Dipartimento di Biologia, Università degli Studi di Bari 'Aldo Moro', Bari, Italy.
authors.forename: Claudia Rita
authors.initials: CR
authors.lastname: Catacchio
authors.affiliation: Dipartimento di Biologia, Università degli Studi di Bari 'Aldo Moro', Bari, Italy.
authors.forename: Fabio
authors.initials: F
authors.lastname: Anaclerio
authors.affiliation: Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA)-Unità di ricerca per l'uva da tavola e la vitivinicoltura in ambiente mediterraneo, Research Unit for viticulture and enology in Southern Italy, Turi (BA), Italy.|Dipartimento di Biologia, Università degli Studi di Bari 'Aldo Moro', Bari, Italy.
authors.forename: Giorgia
authors.initials: G
authors.lastname: Chiatante
authors.affiliation: Dipartimento di Biologia, Università degli Studi di Bari 'Aldo Moro', Bari, Italy.
authors.forename: Annamaria
authors.initials: A
authors.lastname: Marra
authors.affiliation: Dipartimento di Biologia, Università degli Studi di Bari 'Aldo Moro', Bari, Italy.|Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.
authors.forename: Giuliana
authors.initials: G
authors.lastname: Giannuzzi
authors.affiliation: Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA)-Unità di ricerca per l'uva da tavola e la vitivinicoltura in ambiente mediterraneo, Research Unit for viticulture and enology in Southern Italy, Turi (BA), Italy.
authors.forename: Rocco
authors.initials: R
authors.lastname: Perniola
authors.affiliation: Dipartimento di Biologia, Università degli Studi di Bari 'Aldo Moro', Bari, Italy.
authors.forename: Mario
authors.initials: M
authors.lastname: Ventura
authors.affiliation: Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA)-Unità di ricerca per l'uva da tavola e la vitivinicoltura in ambiente mediterraneo, Research Unit for viticulture and enology in Southern Italy, Turi (BA), Italy.
authors.forename: Donato
authors.initials: D
authors.lastname: Antonacci
mesh_terms: D055028:Comparative Genomic Hybridization / Q000379:methods; D056915:DNA Copy Number Variations / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D017404:In Situ Hybridization, Fluorescence; D016133:Polymerase Chain Reaction; D027843:Vitis / Q000235:genetics*
keywords: SRP009057; Vitis vinifera L.; candidate genes; copy number variation; genomic variation; high-throughput sequencing; single nucleotide polymorphism; table grape