terclim by ICS banner
IVES 9 IVES Conference Series 9 De novo Vitis champinii whole genome assembly allows rootstock-specific identification of potential candidate genes for drought and salt tolerance

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

Abstract

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 stressesand 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.

DOI:

Publication date: May 31, 2022

Issue: Terclim 2022

Type: Poster

Authors

Andres Zhou-Tsang1,2, Grant R. Cramer5, Cristobal A. Onetto3, Amanda R. Walker4, Anthony R. Borneman3,1 and Matthew Gilliham2,1

1Australian Research Council Training Centre for Innovative Wine Production, The University of Adelaide, Glen Osmond SA, Australia
2The Waite Research Institute, and The School of Agriculture, Food and Wine, Faculty of Sciences, The University of Adelaide, Glen Osmond SA, Australia
3The Australian Wine Research Institute, Glen Osmond SA, Australia
4CSIRO Agriculture and Food, Glen Osmond SA, Australia
5Department of Biochemistry and Molecular Biology, University of Nevada, Reno NV, USA

Contact the author

Keywords

Ramsey, Dogridge, rootstock, genome, drought, salt, ortholog, RNAseq

Tags

IVES Conference Series | Terclim 2022

Citation

Related articles…

Analysis of voltammetric fingerprints of different white grape musts reveals genotype-related oxidation patterns

Must oxidation is a complex process involving multiple enzymatic transformations, including the oxidation of phenolics containing an ortho-diphenol function. The latter process has a primary influence on wine aroma characteristics and stability, due to the central role of ortho-diphenols in the non-enzymatic oxidative reactions taking place during winemaking and in finished wine. Although oxidation of must is traditionally avoided, in recent years its contribution to wine quality has been revisited, and in some cases improvements to wine aroma have been observed with the application of controlled must oxidation. Nowadays there is a great interest in the wine industry towards the identification of specific markers or patterns to characterize and classify the response of grape must to oxidation.

Climate change and economic challenge – strategies for vinegrowers, winemakers and wine estates

For wine areas around the world, nature and climate are becoming factors of production whose endowment becomes a stake beyond the traditional economic factors: labor, capital, land. They strongly influence agricultural and environmental conditions for production.

Risposte enologiche del Nero d’Avola su suoli a diverso grado di salinità

Vengono riportati i risultati enologici di uno studio condotto sul Nero d’Avola in un tipico ambiente viticolo siciliano, in cui insistono suoli che presentano un diverso grado di salinità.

Enhancement of the terroir

The terroir is today the most important factor of production and development in the wine sector. In a context where the commercial challenge is taking place all over the place, the distinction between traditional and “new” producing countries is not only a geographical, cultural and technical counter position but also, and above all, a legal one. Indeed, the system of standards present in the “old world” (plantation rights, production decrees, yields per hectare, etc.) which may represent, in the short term on the global market, constraints to development and product innovation must become an opportunity. But threats become opportunities, if we work, from the vine to the market, via communication, more on the elements of difference than on those of affinity.

Effects of soil water content and environmental conditions on vine water status and gas exchange of Vitis vinifera L. cv. chardonnay

Vine water status has a significant influence on vineyard yield and berry composition (Williams and Matthews, 1990; Williams et al., 1994). It has been hypothesized that the response of plants to soil water deficits may be due to some sort of “root signal” (Davies and Zhang, 1991). This signal probably arises due to the roots sensing a reduction in soil water content or an increase in the mecanical impedance as the soil dries out.