Inter clonal genomic variation in Vitis vinifera L. cv. Malbec

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

Foz do Iguazú

Congreso; International congress of genetics 2018; 2018

International genetics federation

Somatic mutations are a major force introducing novel genetic variation; this role becomes enhanced in systems lacking of sexual reproduction. This is the case of grapevines used in the wine industry. Here clonal propagation through asexual cuttings is the regular practice, in order to preserve quality traits of productive relevance. Nonetheless, a remarkable phenotypic variation has been reported among clones within cultivars. However, less is known about the intra-cultivar genetic variability and its potential impact on the phenotype. Here we characterize the clonal genetic variability of Vitis vinifera L. cv. Malbec, which is the main cultivar for Argentine viticulture. We performed a genome wide analysis of four Malbec clones, obtaining Illumina reads at a 35x depth for each clone. Bioinformatic tools were employed to align our sequences to the reference genome (genotype PN40024). We implemented variant calling pipelines for single nucleotide variations (SNVs) discovery, and applied strict quality filters to determine a set of reliable SNVs. We discovered ca. 2.6 million SNVs that distinguish cv. Malbec from the reference genome, and identified between 22 and 29 thousand SNVs that are unique for each of the four sequenced clones. The predicted effect on gene expression of the clone-specific SNVs indicated that 60% occurred in non-coding regions; however, 40% occurred both in regulatory and exonic regions. We found a notorious clonal genetic variability, consequence of somatic mutations accumulation. Moreover, our in silico analyses showed that some clone-specific SNVs could be affecting gene expression, possibly explaining part of the phenotypic variation reported for Malbec