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 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.

Download the PDF

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…

Rapid optical method for tannins estimation in red wines

In this work, an innovative analytical method has been proposed for fast and reliable in-line analysis of tannins in wines; the method is fast, does not require sample preparation and is based on the selective reactivity of tannins in a mixture containing proteinaceous matter (i.e. gelatin), under pH 3.5, resulting in the formation of white cloudiness.

Read More

Effect of different pH values on the interaction between yeast mannoproteins and grape seed flavanols

The consequences of the global climate change in the vitiviniculture are revealed as a gap between phenolic and technological grape maturities, higher grape sugar concentration that leads to high wine alcohols levels, lower acidities and high pH values, among others. The unbalanced phenolic maturity caused in this scenario leads to harsh astringency and to instable colour of wines. Previous studies have reported that the addition of yeast mannoproteins (MPs) to wines may have positive effects on these two organoleptic properties due to their capability to interact with wine polyphenols [1]; however, studies about the effect of the pH on these interactions have not been carried out so far.

Read More

Territoires et zones viticoles. Aspects climatiques, pédologiques, agronomiques. Caractérisation des terroirs viticoles: une étude systémique

On assiste actuellement à l’émergence d’une demande sociale forte à l’égard de fonctions par ailleurs traditionnelles de l’agriculture, qui concernent la gestion des ressources du milieu, le maintien d’un tissu social rural, la valorisation des territoires ruraux et l’entretien des paysages.

Read More

Application of uv-led in wine as an alternative to sulphur dioxide

Sulfites (SO2) are commonly used in the wine industry to preserve products during storage for antiseptic and antioxidant purposes (Oliveira et al., 2011).

Read More

Effect of foliar application of urea and nano-urea on the cell wall of Monastrell grape skins

The foliar application of urea has been shown to be able to satisfy the specific nutritional needs of the vine as well as to increase the nitrogen composition of the must. On the other hand, the use of nanotechnology could be of great interest in viticulture as it would help to slow down the release of urea and protect it against possible degradation. Several studies indicate that cell wall synthesis and remodeling are affected by nitrogen availability.

Read More