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…

Il piano regolatore delle citta’ del vino

Obiettivo generale di questo documenta è fornire un metodo di pianificazione che superi l’organizzazione delle aree rurali, ed in particolare vitate, finalizzata unicamente all’ot­timizzazione economico produttiva delle aziende, verso una pianificazione integrata degli spazi aperti.

Techniques to study graft union formation in grapevine 

Grapevines are grown grafting in most viticultural regions. Grapevine rootstocks are either hybrids or pure species of different American Vitis spp. (particularly V. berlandieri, V. rupestris and V. riparia), which are primarily used to provide root resistance to the insect pest Phylloxera. In addition to Phylloxera resistance, ideally grapevine rootstocks should be resistant to other soil borne pathogens and adapted to abiotic stress conditions. New rootstocks have the potential to adapt agriculture to climate change without changing the characteristics of the harvested product. However, high grafting success rates are an essential prerequisite.

Nitrogen requirements of table grape cultivars grown in the san Joaquin valley of California

Ground water in the interior valleys of California is contaminated with nitrates derived from agricultural activities, primarily the over-fertilization of crops.

Autochthonous yeasts: a microbiological tool to exalt the quality of the apulian sparkling wine

The selection, characterization, and recruitment of autochthonous yeast strains to drive the alcoholic fermentation process is a highly researched practice because it allows the differentiation of the organoleptic properties of wines, assuring process standardization, reducing fermentation times and improving the quality and safety of the final products [1, 2]. Sparkling wines are “special wines” obtained by secondary fermentation of the base wine. ​In the traditional method (Champenoise method), the re-fermentation takes place in the bottle after the addition to the base wine of the so-called tirage solution. This step, also known as prise de mousse, is followed by an aging period characterized by the release of compounds from the yeast cells that affect the organoleptic properties of the final product. The use of autochthonous yeasts as starter cultures for secondary fermentation is one of the recent innovations proposed to enhance and differentiate these wines’ sensory quality [3,4]. Apulia is the second Italian wine-producing region, and its productive chain is now going through a qualitative evolution by implementing the employment of innovative approaches to exalt the peculiar properties of regional wines.

Role of anthocyanins and copigmentation in flavonol solubility in red wines 

Over the last years, due to climate change, several red wines, such as the Sangiovese wines, have been often subjected to loss of clarity due to the formation of deposits of fine needle-shaped crystals. This phenomenon turned out to be due to an excess of quercetin (Q) and its glycosides (Q-Gs) in wines. These compounds are synthesized to a large extent when grapes are excessively exposed to UVB radiations in vineyards[1]. Unfortunately, it is not easy to predict the degree of Q precipitation because its solubility strongly depends on the wine and matrix composition[2].