GENOMIC VARIATION AND CLONES GENTOYPING IN VITIS VINIFERA L. ?MALBEC?

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

Napoli

Congreso; LXIII SIGA ANNUAL CONGRESS; 2019

Italian Society of Agricultural Genetics

Somatic mutations are a major force introducing novel genetic variation; this role becomes enhanced in systems lacking of sexual reproduction. The later is the case of grapevines used in the wine industry. Even though clonal propagation is a normal practice in this industry, a remarkable phenotypic variation has been reported at the intra-cultivar level. However, less is known about the genetic variability among clones. Malbec is the main cultivar for the Argentine viticulture. This cultivar shows a notorious phenotypic variation on many traits of technological interest, for example on the biochemical composition of berries. Therefore, it turns relevant to develop a formal protocol to discriminate among clones with different properties. Here we performed a genomic analysis in order to test if the genetic variability is in agreement with the phenotypic variability, and also to develop a genetic-based tool for clone identification. For this aim we obtained Illumina reads at a 35x depth for four different Malbec clones (MB53, MB59, Cot143 and Cot225). Bioinformatic tools were employed to align reads to the reference genome (PN40024) and to perform variant calling analysis for single nucleotide variants (SNVs) discovery. Afterwards, strict quality and frequency filters were applied to obtain a set of reliable SNVs. We discovered 2 million of shared SNVs (i.e. all clones shared the same allele), therefore these variants distinguish Malbec from the reference genome. On the other, hand we identified 458 non-shared SNVs (i.e. at least one of the clones doesn?t have the variant), these were of particular interest to us because they allow for clone discrimination. From the latter list we picked 48 SNVs to validate them through Sanger sequencing. After validation we built a genotyping chip using the FLUIDGM platform. We genotyped 221 plants, including clones of known origin as well as mass selections, and we were able to find 8 different haplotypes. We showed that with a small but informative number of SNVs it is possible to separate clones of the same cultivar in an efficient and affordable manner.