Towards the definition of a detailed transcriptomic map of grape berry development

Grapevine leafroll associated virus (GLRaV) infections deteriorate vine physiological performance and cause high losses of yield and fruit quality

Climate change results in increasing water stress due to co-effects of rising evapotranspiration (ET) and decreased precipitation over the past 65 years (Spinoni et al. 2019).

The South African Table grape industry has to expand to new markets with high quality niche products, but limited water availability threatens sustainable production. To overcome this challenge and to obtain high-quality products for the new markets, require constant technological advancement. Currently, limited available scientific information about growth balances and physiology and especially grape quality parameters, hinders technological advancement and thus efficient regulatory management of the morphological, chemical, and pathological status of table grapes, especially in response to abiotic factors.

Evidence for a specific effect of soil mineral composition on wine character is largely anecdotal. However, soil potassium supply to the vine must be properly balanced between deficiency and excess for good fruit quality.

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.