Study helps elucidate Malbec grape genome

An international team of researchers has achieved a significant milestone in grapevine genomics with the publication of the first diploid Malbec grape genome. The study helps to understand genetic diversity and clonal variation, crucial aspects for wine quality.

Grapevine genomes are notoriously known for their high heterozygosity, making genomic assembly a complex challenge. Traditional approaches often focus on nearly homozygous lines, which do not capture the full genetic diversity of complex cultivars like Malbec. This limitation prevents full understanding of the genetic mechanisms that drive clonal variation, which has a direct impact on wine quality.

To face these challenges, the team of researchers from the Instituto de Biología Agrícola de Mendoza, Instituto de Ciencias de la Vid y del Vino and Max Planck Institute for Biology Tübingen, among others, used advanced sequencing technologies to carry out the first diploid genomic assembly of Malbec. This assembly was possible thanks to the use of advanced PacBio long-read sequencing and trio binning techniques, which allowed the separation and assembly of the two haplotypes inherited from Malbec's parental cultivars, Prunelard and Magdeleine Noire des Charentes.

Genomic assembly revealed significant polymorphic regions and provided detailed gene model annotations for both haplotypes. Transcriptomic analyzes of Malbec clonal variants uncovered differences in gene expression, especially highlighting the higher anthocyanin content in certain clones. This increase was associated with elevated responses to abscisic acid, leading to overexpression of genes involved in phenylpropanoid metabolism and abiotic stress responses.

These findings underscore the critical role of haplotype-resolved assemblies in understanding the genetic basis of clonal variation and its impact on traits essential to wine quality and vine adaptability. Luciano Calderón, one of the lead researchers, stated that "the genomic assembly not only enhances our understanding of Malbec's genetic diversity, but also provides a valuable resource for studying the molecular mechanisms underlying clonal variation. It opens up new possibilities for breeding and improvement of vine cultivars”.

The assembled Malbec genome provides a comprehensive reference for future genetic studies and breeding programs aimed at improving grapevine cultivars. By understanding the genetic basis of traits such as berry composition and stress responses, researchers can develop more resilient, high-quality vines, benefiting the wine industry and addressing the challenges posed by climate change.

Article published from the research received the following summary:

"To preserve their varietal attributes, established vine cultivars (Vitis vinifera L. ssp. vinifera) must be propagated clonally, due to their highly heterozygous genomes. Malbec is a cultivar of French origin appreciated for producing high quality wines and is a daughter of the Prunelard and Magdeleine Noire des Charentes cultivars. Here, we constructed a diploid assembly of the Malbec genome after PacBio's binning trio long-read the two haploid complements inherited from either parent. After deduplication and haplotype recognition corrections, complete assemblies for both haplophases were obtained with a very low haplotype exchange error rate (<0,025). Haplophase alignment identified >25% of polymorphic regions.

Gene annotation, including RNA-seq transcriptome assembly and ab initio prediction evidence, resulted in similar numbers of genetic models for both haplophases. The annotated diploid assembly was exploited in the transcriptomic comparison of four Malbec clonal accessions that exhibited variation in fruit composition characteristics. Transcriptome analysis of the maturing pericarp using either haplophase as a reference produced similar results, although some differences were observed. Particularly, among the differentially expressed genes identified only with the inherited Magdeleine haplotype as a reference, we observed an overrepresentation of hypothetically hemizygous genes. The higher anthocyanin content of the berry from clonal accession 595 was associated with increased responses to abscisic acid, possibly leading to the observed overexpression of phenylpropanoid metabolism genes and dysregulation of genes associated with the abiotic stress response.

Overall, the results highlight the importance of producing diploid assemblies to fully represent the genomic diversity of highly heterozygous woody crop cultivars and unravel the molecular basis of clonal phenotypic variation.”

More information can be found at doi.org/10.1093/hr/uhae080