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

Abstract

Grapevine cultivars are clonally propagated to preserve their varietal attributes. However, genetic variations accumulate due to the occurrence of somatic mutations. This process is anthropically influenced through plant transportation, clonal propagation and selection. Malbec is a cultivar that is well-appreciated for the elaboration of red wine. It originated in Southwestern France and was introduced in Argentina during the 1850s. In order to study the clonal genetic diversity of Malbec grapevines, we generated whole-genome resequencing data for four accessions with different clonal propagation records. A stringent variant calling procedure was established to identify reliable polymorphisms 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.

Diploid genome assembly of the Malbec grapevine cultivar enables haplotype-aware analysis of transcriptomic differences underlying clonal phenotypic variation

“…3 and Fig S3A). According to a previous intra-cultivar genetic variation analysis, the four selected clones represent different derived genotypes from the same clonal genetic lineage (Group-Fr), with clones 595, 596, 136N and 505 belonging to genotypes I, B, H and E, respectively 35 . Clone 595 had reproducible higher levels of total polyphenols and anthocyanins berry content at harvest (Fig.…”

“…and 505 belonging to genotypes I, B, H and E, respectively 35 . Clone 595 had reproducible higher levels of total polyphenols and anthocyanins berry content at harvest (Fig.…”

“…Genome de novo assembly and annotation:Plant material: For genomic sequencing and assembly, samples were collected from the Malbec clone accession 136N, representing a clonal lineage with short propagation history in Argentina (i.e., Group-Fr)35 . Accession 136N is implanted at the Vivero Mercier Argentina experimental vineyard located at Lujan de Cuyo, Mendoza, Argentina (-33.09° S, -68.87° W).…”

DNA-Based Technologies for Grapevine Biodiversity Exploitation: State of the Art and Future Perspectives

“…This technique has been used for genotyping wild and cultivated grapevines [87,88]. In addition to RADSeq, another innovative and cost-effective RRS method is the genotyping by sequencing (GBS) technique developed by Elshire et al [89], which has been applied to several species, including Vitis [90][91][92][93][94]. It employs restriction enzymes and the next-generation sequencing of genomic libraries for de novo genotyping of SNPs.…”

“…It employs restriction enzymes and the next-generation sequencing of genomic libraries for de novo genotyping of SNPs. With this approach, Calderon et al [94] distinguished 14 different clonal genotypes within the Malbec cultivar. RRS approaches do not require the preselection of regions to be interrogated but need extensive sequencing.…”