Inter‐varietal structural variation in grapevine genomes. (16th September 2016)

• Record Type: Journal Article
• Authors: Cardone, Maria Francesca; D'Addabbo, Pietro; Alkan, Can; Bergamini, Carlo; Catacchio, Claudia Rita; Anaclerio, Fabio; Chiatante, Giorgia; Marra, Annamaria; Giannuzzi, Giuliana; Perniola, Rocco; Ventura, Mario; Antonacci, Donato
• Is Part Of: Plant journal. Volume 88:Number 4(2016:Nov.)
• Page Start: 648
• Page End: 661
• Publication Date: 2016-09-16
• Subjects: Vitis vinifera L. -- table grape -- high‐throughput sequencing -- genomic variation -- copy number variation -- single nucleotide polymorphism -- SRP009057 -- candidate genes; Plant molecular biology -- Periodicals; Plant cells and tissues -- Periodicals; Botany -- Periodicals; 580
• DOI: 10.1111/tpj.13274
• Languages: English
• ISSNs: 0960-7412

Abstract

Summary: 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. Significance Statement: Grapes are important for both fruit and wine production. To help identify genomic variations underlying phenotypic differences, we present an inter‐varietal atlas of structural variations and single nucleotide variants. Using comparative analyses, we correlated such genomic variations to agronomically relevant phenotypes.