Characterizing the intra-varietal genomic and phenotypic variation in Vitis vinifera L. cv. Malbec

CRISTOBAL SOLA; LAURA BREE; DIEGO LIJAVETZKY; CALDERÓN LUCIANO; CAROLINA ROYO; CLAUDIO MUÑOZ; JOSÉ MIGUEL MARTÍNEZ-ZAPATER; PABLO CARBONELL-BEJERANO; NURIA PANADERO

Bordeaux

Conferencia; XII International Conference on GRAPEVINE BREEDING and GENETICS; 2018

INRA

Grapevines for wine production are clonally propagated through asexual cuttings. Nonetheless anotorious phenotypic variability has been reported at the intra-varietal level for several cultivars,which is attributed mainly to the effect of somatic mutations. Here we studied the case of Malbec(synonym name for the French cultivar Cot), which is the main cultivar for Argentine viticulture.We aimed to characterize the existing genomic and phenotypic variation among Malbec clones,with the further objective of developing a molecular-based workflow to classify clones showingphenotypes of interest. To assess the genomic variation of this cultivar we re-sequenced fourMalbec clones at a ca. 35x depth. We employed bioinformatic algorithms to align our sequencesto the reference genome (PN40024), perform variant calling for single nucleotide variations(SNVs) discovery and apply quality filters to determine a set of reliable SNVs. We discovered ca.2.6 million SNVs, that distinguish cv. Malbec from the reference genome. We also identifiedbetween 22 and 29 thousand SNVs that are unique for each sequenced clone. After assessing thepredicted effect on gene expression of the identified clone-specific SNVs, we observed thatnearly 60% occurred in non-coding regions. However, 40% of the clone-specific variationsoccurred both in regulatory and exonic regions, therefore affecting genic expression at someextent. In order to assess the phenotypic variation, we performed biochemical analyses to tracethe ripening process and also to quantify berries? polyphenolic content on 27 clones (three plantsper clone were analyzed). The latter revealed great variation among clones, at the timing to arriveto the technological maturity (24º Brix for Malbec) and also on the anthocyanin concentration ofberries? skins, differences of nearly 50% were found. Therefore, in agreement with the observedfor other cultivars, the high degree of phenotypic variation is in concordance with the discoveredgenome-wide variation