Whole genome comparison between table and wine grapes reveals a comprehensive catalog of structural variants

Alex Di Genova, Andrea M. Almeida, Claudia Muñoz-Espinoza, Paula Vizoso, Dante Travisany, Carol Moraga, Manuel Pinto, Patricio Hinrichsen, Ariel Orellana, Alejandro Maass

Research output: Contribution to journalArticlepeer-review

67 Citations (Scopus)

Abstract

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.

Original languageEnglish
Article number7
JournalBMC Plant Biology
Volume14
Issue number1
DOIs
Publication statusPublished - 7 Jan 2014

Keywords

  • 'Sultanina' genome
  • Structural variants
  • Vitis vinifera L

ASJC Scopus subject areas

  • Plant Science

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