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Open Access Highly Accessed Research article

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

Alex Di Genova12, Andrea Miyasaka Almeida14, Claudia Muñoz-Espinoza14, Paula Vizoso14, Dante Travisany12, Carol Moraga14, Manuel Pinto5, Patricio Hinrichsen5, Ariel Orellana14 and Alejandro Maass123*

Author Affiliations

1 Fondap Center for Genome Regulation, Av. Blanco Encalada 2085, 3rd floor, Santiago, Chile

2 Mathomics Bioinformatics Laboratory, Center for Mathematical Modeling and Center for Genome Regulation, University of Chile, Av. Blanco Encalada 2120, 7th floor, Santiago, Chile

3 Department of Mathematical Engineering, University of Chile, Av. Blanco Encalada 2120, 5th floor, Santiago, Chile

4 Centro de Biotecnología Vegetal, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Av. República 237, Santiago, Chile

5 Centro de Investigación La Platina, Instituto de Investigaciones Agropecuarias, Santa Rosa 11610, Santiago, La Pintana, Chile

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BMC Plant Biology 2014, 14:7  doi:10.1186/1471-2229-14-7

Published: 7 January 2014

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.

Keywords:
‘Sultanina’ genome; Vitis vinifera L; Structural variants