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Inter‐varietal structural variation in grapevine genomes
Author(s) -
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
Publication year - 2016
Publication title -
the plant journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.058
H-Index - 269
eISSN - 1365-313X
pISSN - 0960-7412
DOI - 10.1111/tpj.13274
Subject(s) - biology , genome , vitis vinifera , copy number variation , structural variation , indel , genetics , comparative genomic hybridization , gene , computational biology , botany , single nucleotide polymorphism , genotype
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 ( SNV s) for the grapevine genome analyzing four economically and genetically relevant table grapevine varieties. We found 4.8 million SNV s 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.