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

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

doi:10.1186/1471-2229-14-7

Abstract

BackgroundGrapevine (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.ResultsOur 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.ConclusionsThis 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.

Highlights

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
Our results show that there are a number of structural variants with respect to the grapevine reference genome, including genome fragment translocations, insertions and deletions (INDELs) and transposable elements relocalization
The main challenge of the de novo assembly relied on its high heterozygosity ([1,12,14,15])

Summary

Introduction

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. As up to now no genomic sequence from a typical table grape variety has been released, it is not yet possible to establish at a genomic level how different are the two main groups of grapevine genotypes. This is a key aspect to increase the knowledge of the genome of the species and for helping the breeding programs. Even though there is a reference genome from a wine variety, the genetic diversity observed in this species does not allow taking full advantage of this genomic tool

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Conclusion