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Plant J. 2016 Nov;88(4):648-661. doi: 10.1111/tpj.13274. Epub 2016 Sep 16.

Inter-varietal structural variation in grapevine genomes.

Author information

1
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.
2
Dipartimento di Biologia, Università degli Studi di Bari 'Aldo Moro', Bari, Italy.
3
Department of Computer Engineering, Bilkent University, Ankara, TR-06800, Turkey.
4
Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.

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.

KEYWORDS:

SRP009057; Vitis vinifera L.; candidate genes; copy number variation; genomic variation; high-throughput sequencing; single nucleotide polymorphism; table grape

PMID:
27419916
DOI:
10.1111/tpj.13274
[Indexed for MEDLINE]
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