De novo Vitis champinii whole genome assembly allows rootstock-specific identification of potential candidate genes for drought and salt tolerance

Young white wines are typically released to the market a few months after harvest, to be consumed within a year, when their fresh fruity aromas are still dominant and appealing to modern consumers. Esters, particularly higher alcohol acetates (HAAs) and ethyl esters of fatty acids (EEFAs), play a central role in the fruity expression of young white wines [1]. However, these esters are known to undergo significant hydrolysis during the first months of aging [1, 2].

Vitis vinifera is the most grown grapevine species, which originated about 6 million years ago in the trans-caucasian area as the ancestral (wild) type v. Vinifera spp. Sylvestris. On the other hand, the human being (homo sapiens) is much younger since he originated about 300.000 years ago in north africa.

Vine diseases have a strong impact on vineyards sustainability, which in turns leads to strong economic consequences. Among those diseases, Flavescence dorée spreads quickly and is incurable, which led in France to the setup of a mandatory pest control implying the systematic use of pesticides and the prospection and uprooting of every infected plants. Remote sensing could be a very powerful tool to optimize prospection as it allows to produce quickly accurate maps over large areas. Recent studies have shown that high spatial resolution (10cm/pixel) multispectral images acquired from UAVs allow to map Flavescence dorée in vineyards using leaves discolorations [e.g. Albetis et al., Remote Sensing, 2017].

Different terroirs have been identified in Bolgheri area (a viticultural appellation in the Tirrenian coast of Tuscany) by the aid of pedological, landscape and agronomic observations in 1993. Numerous preliminary observations suggested that wines obtained from these different terroirs were unique.

Haplotype-resolved genome assemblies were produced for Chasselas and Ugni Blanc, two heterozygous real-field genetic pool Vitis vinifera cultivars by combining high-fidelity long-read sequencing (HiFi) and high‐throughput chromosome conformation capture (Hi-C). The telomere-to-telomere full coverage of the chromosomes allowed us to assemble separately the two haplo-genomes of both cultivars and revealed structural variations between the two haplotypes of a given cultivar.