Whole genome comparison between table and wine grapes reveals a comprehensive catalog of structural variants
Author
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Di Genova, Alex
Author
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Miyasaka Almeida, Andrea
es_CL
Author
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Muñoz Espinoza, Claudia
es_CL
Author
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Vizoso, Paula
es_CL
Author
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Travisany, Dante
es_CL
Author
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Moraga, Carol
es_CL
Author
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Pinto Contreras, Manuel
es_CL
Author
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Hinrichsen, Patricio
es_CL
Author
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Orellana López, Ariel
es_CL
Author
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Maass Sepúlveda, Alejandro
es_CL
Admission date
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2015-01-08T18:34:02Z
Available date
dc.date.available
2015-01-08T18:34:02Z
Publication date
dc.date.issued
2014
Cita de ítem
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BMC Plant Biology 2014, 14:7
en_US
Identifier
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doi:10.1186/1471-2229-14-7
Identifier
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https://repositorio.uchile.cl/handle/2250/127014
General note
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Artículo de publicación ISI
en_US
Abstract
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Background: Grapevine (Vitis vinifera L.) is the most important Mediterranean fruit crop, used to produce both
wine and spirits as well as table grape and raisins. Wine and table grape cultivars represent two divergent
germplasm pools with different origins and domestication history, as well as differential characteristics for berry size,
cluster architecture and berry chemical profile, among others. ‘Sultanina’ plays a pivotal role in modern table grape
breeding providing the main source of seedlessness. This cultivar is also one of the most planted for fresh
consumption and raisins production. Given its importance, we sequenced it and implemented a novel strategy for
the de novo assembly of its highly heterozygous genome.
Results: Our approach produced a draft genome of 466 Mb, recovering 82% of the genes present in the grapevine
reference genome; in addition, we identified 240 novel genes. A large number of structural variants and SNPs were
identified. Among them, 45 (21 SNPs and 24 INDELs) were experimentally confirmed in ‘Sultanina’ and six SNPs in
other 23 table grape varieties. Transposable elements corresponded to ca. 80% of the repetitive sequences involved
in structural variants and more than 2,000 genes were affected in their structure by these variants. Some of these
genes are likely involved in embryo development, suggesting that they may contribute to seedlessness, a key trait
for table grapes.
Conclusions: This work produced the first structural variants and SNPs catalog for grapevine, constituting a novel
and very powerful tool for genomic studies in this key fruit crop, particularly useful to support marker assisted
breeding in table grapes.
en_US
Patrocinador
dc.description.sponsorship
This project was supported by grants: Fondap 1509007, Basal programs
PFB-03 and PFB-16, Genoma-Chile Fondef G07I-1002, CIRIC-INRIA Chile
(line Natural Ressources) and Millennium Nucleus ICM-P10-062-F.