Unlocking the Grapevine Genome: Insights from Malbec's Diploid Assembly and Clonal Variation

Submitted by aolson on Sun, 09/01/2024 - 00:04

The grapevine cultivar Malbec, the offspring of Prunelard and Magdeleine Noire des Charentes, is known for its high-quality wine production. Due to grapevine's highly heterozygous genomes, clonal propagation is essential. Researchers from Argentina, Spain and Germany used PacBio long reads and trio binning to assemble the diploid genome, identifying polymorphic regions and obtaining comprehensive assemblies of the haplotypes. The resultant diploid assembly was highly contiguous with a contig N50 ~7Mb.  

Analysis of transcriptomic differences among four clonal Malbec accessions with varying berry compositions showed consistency in phenotypic and transcriptomic variations. Clone 595 exhibited higher berry anthocyanin content, linked to increased abscisic acid responses, upregulation of secondary metabolism genes, and deregulation of abiotic stress response genes.

Phasing haplotypes aided in identifying haplotype-specific gene expression, emphasizing the importance of diploid genome assemblies in understanding genomic diversity and unraveling molecular bases for clonal phenotypic variation in highly heterozygous cultivars like Malbec. The study provides insights into the genetic and transcriptomic factors contributing to the distinct traits observed in different Malbec clones, shedding light on the complexity of grapevine phenotypes.

Gramene examples:

Figure 1: Phylogram view of the Myb gene(determinant of berry color development in cultivated grape) in the two haplophases Vv. vinifera. Malbec Prunelard & Vv. vinifera. Malbec Magdeleine in relation to other Vitis varieties

Figure 2: Synteny between Vitis vinifera subsp. vinifera. Malbec Magdeleine chromosome 1 and Solanum lycopersicum

The Argentine members of the international team responsible for the sequencing and assembly of the Malbec genome. From left to right: Walter Tulle, Sebastian Gómez Talquenca, Cristobal Sola, Daniel Bergamin, Laura Bree, Luciano Calderón, Claudio Muñoz, and Diego Lijavetzky. Photo credit Roxana Gonzalez (@Vivero Mercier Argentina).

Reference:

Calderón L, Carbonell-Bejerano P, Muñoz C, Bree L, Sola C, Bergamin D, Tulle W, Gomez-Talquenca S, Lanz C, Royo C, Ibáñez J, Martinez-Zapater JM, Weigel D, Lijavetzky D. Diploid genome assembly of the Malbec grapevine cultivar enables haplotype-aware analysis of transcriptomic differences underlying clonal phenotypic variation. Hortic Res. 2024 Mar 14;11(5):uhae080. PMID: 38766532. doi: 10.1093/hr/uhae080.