Whole genome resequencing and custom genotyping unveil clonal lineages in ‘Malbec’ grapevines (Vitis vinifera L.)

CALDERÓN, LUCIANO; MAURI, NURIA; MUÑOZ, CLAUDIO; CARBONELL-BEJERANO, PABLO; BREE, LAURA; BERGAMIN, DANIEL; SOLA, CRISTOBAL; GOMEZ-TALQUENCA, SEBASTIAN; ROYO, CAROLINA; IBÁÑEZ, JAVIER; MARTÍNEZ-ZAPATER, JOSÉ MIGUEL; LIJAVETZKY, DIEGO

Scientific Reports

Springer Nature

Lugar: Basingstoke; Año: 2021 vol. 11

Grapevine cultivars are clonally propagated to preserve their varietal attributes. However, geneticvariations accumulate due to the occurrence of somatic mutations. This process is anthropicallyinfluenced through plant transportation, clonal propagation and selection. Malbec is a cultivar thatis well-appreciated for the elaboration of red wine. It originated in Southwestern France and wasintroduced in Argentina during the 1850s. In order to study the clonal genetic diversity of Malbecgrapevines, we generated whole-genome resequencing data for four accessions with differentclonal propagation records. A stringent variant calling procedure was established to identify reliablepolymorphisms among the analyzed accessions. The latter procedure retrieved 941 single nucleotide variants (SNVs). A reduced set of the detected SNVs was corroborated through Sanger sequencing, and employed to custom-design a genotyping experiment. We successfully genotyped 214 Malbec accessions using 41 SNVs, and identified 14 genotypes that clustered in two genetically divergent clonal lineages. These lineages were associated with the time span of clonal propagation of the analyzed accessions in Argentina and Europe. Our results show the usefulness of this approach for the study of the scarce intra-cultivar genetic diversity in grapevines. We also provide evidence on how human actions might have driven the accumulation of different somatic mutations, ultimately shaping the Malbec genetic diversity pattern.