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…

Building of a hierarchy of wines based on terroirs: an initiative from the producers of Muscadet

The Muscadet area is situated in the southeast of Nantes, close to the Atlantic coast. It constitutes the western extension
of the French vineyard “Loire Valley”. The Muscadet is renowned and often spontaneously linked to a white wine.
However it remains misconceived as an ordinary wine, lacking authenticity.

Read More

Light-struck taste in white wine: enological approach for its prevention

Light-struck taste is a defect prevalent in white wines bottled in clear glass light-exposed for a considerable amount of time leading to a loss of color and appearance of sulfur-like odors. The reaction involves riboflavin (RF), a highly photosensitive compound that undergoes to intermolecular photoreduction by the uptake of two electron equivalents from an external donor, the methionine. The reaction includes different steps forming methional which is extremely unstable and decomposes to methane thiol and acrolein. The reaction of two molecules of methane thiol yields dimethyl disulfide. Methane thiol is highly volatile, has a low perception threshold (2 to 10 µg/L in wine) and confers aroma-like rotten eggs or cabbage.

Read More

Dimethyl sulfide: a compound of interest from grape to wine glass

The overall quality of fine wines is linked to the development of “bouquet” during wine bottle ageing1. Several chemical reactions, occurring in atmosphere protected from oxygen, are favourable to the formation and preservation of sulphur compounds such as dimethyl sulfide (DMS). DMS accumulate in wines thanks to hydrolysis of its precursors (DMSp) mainly constituted by S-

Read More

A browser application for comprehensive 3-dimensional LC × LC × IM – MS data analysis to study grape and wine polyphenols

The analysis of structurally diverse proanthocyanidins in grapes and wine is challenging. Comprehensive two-dimensional liquid chromatography (LC×LC) and ion mobility spectrometry-mass spectrometry (IMS-MS) are increasingly used to address the challenges associated with the analysis of highly complex samples such as wine and grapes

Read More

isUP-AgrO European project – unlocking the potential for agricultural research on an EU outmost region: boosting ISOPlexis center

The isUP-AgrO project aims to enhance the capability of ISOPlexis – Centre of Sustainable Agriculture and Food Technology, a research unit from the University of Madeira, an outermost region of Portugal.

Read More