Defining gene regulation and co-regulation at single cell resolution in grapevine

Remote sensing applications in viticulture have been a research theme now for nearly two decades, becoming a valuable tool for vineyard management. Metrics produced using remotely sensed images of vineyards have yielded relationships with grape quality and yield that can help optimise vineyard performance

Context and purpose of the study. Climate change scenarios predict ever increasing frequency of drought events and coupled with disease outbreaks poses survival risks to perennial fruit crops such as grapevine.

Vitis champinii cultivars Ramsey and Dog-ridge are main choices for rootstocks to adapt viticulture in semi-arid and arid regions thanks to their distinctive tolerance to drought and salinity. However, genetic studies on non-vinifera rootstocks have heavily relied on the grapevine (Vitis vinifera) reference genome, which difficulted the assessment of the genetic variation between rootstock species and grapevines. In the present study, this limitation is addressed by introducing a novo phased genome assembly and annotation of Vitis champinii. This new Vitis champinii genome was employed as reference for mapping RNA-seq reads from the same species under drought and salt stresses, and for comparison the same reads were also mapped to the Vitis vinifera PN40024.V4 reference genome. A significant increase in alignment rate was gained when mapping Vitis champinii RNA-seq reads to its own genome, compared to the Vitis vinifera PN40024.V4 reference genome, thus revealing the expression levels of genes specific to Vitis champinii. Moreover, differences in coding sequences were observed in ortholog genes between Vitis champinii and Vitis vinifera, which therefore challenges previous differential expression analyses performed between contrasting Vitis genotypes on the same gene from the Vitis vinifera genome. Genes with possible implications in drought and salt tolerance have been identified across the genome of Vitis champinii, and the same genomic data can potentially guide the discovery of candidate genes specific from Vitis champinii for other traits of interest, therefore becoming a valuable resource for rootstock breeding designs, specially towards increased drought and salinity due to climate change.

Grapevine (Vitis spp.) is greatly influenced by climatic conditions and its economic value is therefore directly linked to environmental factors. Among these factors, temperature plays a critical role in vine phenology and fruit composition. In such conditions, elucidating the mechanisms employed by the vine to cope with heat waves becomes urgent. For the past few years, our research team has been producing molecular and metabolic data to highlight the molecular players involved in the response of the vine and the fruit to high temperatures [1]. Some of these temperature-sensitive genes are currently undergoing characterization using transgenesis approaches coupled or not with genome editing, taking advantage of the Microvine genotype [2].

In April 2024, the French official catalog includes 449 grape varieties and rootstocks. In 10 years it has been enriched with 70 varieties. It is an indisputable marker of the interest of professionals in genetic resources of all origins and the expectations they have to prepare the viticulture of the future. The scientific community has now put all irons in the fire and is not neglecting any avenue of adaptation. The regular decline in the use of phytosanitary products and the already marked effects of climate change are the targets of varietal improvement.