Decoding the secrets of Malbec genome by the analysis of the clonal genomic variation

CALDERÓN, LUCIANO; MAURI, N; MARTINEZ-ZAPATER, JM; LIJAVETZKY, D

Mendoza

Congreso; XVII CONGRESO LATINOAMERICANO DE GENÉTICA; 2019

ALAG

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 SNPs that distinguish cv. Malbec from the reference genome, and identified 458 SNVs explaining the genetic variation between the four Malbec genotypes, including 421 clone-specific SNVs. Using that information, we developed a Malbec ?Fluidigm? SNP chip that allowed us to found a notorious genetic variability in a large clone collection, as a consequence of somatic mutations accumulation.