From vine to wine: Decoding Malbec's genetic diversity for clonal excellence

In a pioneering venture, scientists have completed the diploid genome assembly of the Malbec grapevine, illuminating the genetic factors that endow it with the capacity to yield exceptional wines. This study meticulously explores the transcriptomic variances among clones, providing crucial knowledge for conserving the distinctive qualities of this esteemed cultivar.

Grapevine genomes, known for their high heterozygosity, present significant challenges for accurate assembly. Traditional approaches often focus on nearly homozygous lines, which fail to capture the full genetic diversity of complex cultivars like Malbec. Understanding clonal phenotypic variation, which significantly impacts wine quality, adds to this complexity. To address these challenges, a detailed and accurate genomic assembly is essential for comprehending the genetic mechanisms driving clonal variation and contributing to the unique attributes of the Malbec grapevine.

A 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, have published a study (DOI: 10.1093/hr/uhae080) in the journal Horticulture Research on March 14, 2024. This study presents the first diploid genome assembly of the Malbec grapevine, leveraging advanced sequencing technologies to resolve the two haplotypes inherited from its parental cultivars.

The study achieved a high-quality genome assembly of the Malbec grapevine using advanced PacBio long-read sequencing and trio binning techniques. This method enabled the separation and assembly of the two haplotypes inherited from Malbec's parent cultivars, Prunelard and Magdeleine Noire des Charentes. The assembled genome revealed significant polymorphic regions and provided detailed gene model annotations for both haplotypes. Transcriptomic analysis of Malbec clonal variants uncovered differences in gene expression, particularly highlighting the higher anthocyanin content in certain clones. This increased anthocyanin content was associated with heightened abscisic acid responses, leading to the 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 for wine quality and grapevine adaptability.

Dr. Luciano Calderón, one of the lead researchers, stated, "This genome 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 improving grapevine cultivars."

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

###

References

DOI

10.1093/hr/uhae080

Original Source URL

https://doi.org/10.1093/hr/uhae080

Funding information

This work was supported by Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT): PICT2018-02381, MINCyT/ANPCyT (FONTAR)-CDTI IBEROGEN; CONICET (Bilateral PCB-II, CONICET-CSIC, MINECO BIO2017-86375-R, and the project PID2020-120183RB-I00 funded by MCIN/AEI/10.13039/501100011033), and the Max Planck Society. L.C. was supported by a CONICET travel grant for a short-term stay at the Max Planck (Tübingen). We are grateful to Ilja Bezrukov for answering bioinformatics question and Silvina van Houten for collaboration with field work. We thank Olivier Yobregat (Institut Français de la Vigne et du Vin, IFV) for providing plant material from Malbec parental cultivars. This project received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 797460. This study benefited from the networking activities and resources produced within the COST action Integrape (CA17111) and COST innovators grant Grapedia (IG17111).

About Horticulture Research

Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2022. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.