Whole genome comparison between table and wine grapes reveals a comprehensive catalog of structural variants
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Fecha
2014-01
Profesor/a Guía
Facultad/escuela
Idioma
en
Título de la revista
ISSN de la revista
Título del volumen
Editor
BioMed Central Ltd.
Nombre de Curso
Licencia CC
Atribution 4.0 International (CC BY 4.0)
Licencia CC
https://creativecommons.org/licenses/by/4.0/deed.es
Resumen
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.
Notas
Indexación: Scopus.
Palabras clave
Sultanina Genome, Vitis Vinifera L, Structural Variants
Citación
BMC Plant Biology. Volume 14, Issue 1. 7 January 2014. Article number 7
DOI
10.1186/1471-2229-14-7