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…

Relationships between vineyard soil physiochemical properties and under-vine soil cover as potential drivers of terroir in the Barossa

Aims: Soils are an intrinsic feature of the landscape and have influenced culturally and economically important terroir delineation in many wine-producing regions of the world. Soil physiochemical properties govern a wide array of ecosystem services, and can therefore affect grapevine health and fruit development. These physiochemical properties can reflect a combination of factors,

Read More

The effect of wine cork closures on volatile sulfur compounds during accelerated post-bottle ageing in Shiraz wines

Reduced off-flavour is an organoleptic defect due to an excess of volatile sulfur compounds (VSC) in wine and often happening in Shiraz wines. This off-flavour is a direct consequence of the lack of oxygen flow during winemaking and bottle storage. Therefore, wine closure could have a direct impact on the formation of VSC due to the oxygen transfer rate that can modulate their levels. Even if dimethylsulfide (DMS) contributes to reduced off-flavor, it is also a fruity note enhancer in wine and its evolution during wine ageing is not well understood.

Read More

Sensory evaluation of grape berries: predictive power for sensory properties of Sauvignon blanc, Riesling and Pinot noir wines

Sensory analysis of grape berries is a common tool to evaluate the degree of grape maturation and to make sound picking decisions.

Read More

Unraveling vineyard site from vintage contributions: Elemental composition of site-specific Pinot noir wines across multiple vintages

Understanding vineyard site contribution to elemental composition of wines has, historically, been limited due to lack of continuity across multiple vintages, as well as lack of uniformity in scion clone and lack of controlled pilot-scale winemaking conditions.  We recently completed our fifth vintage, and have elemental composition characterizing wines from four vintages (2015–2018)

Read More

METHYL SALICYLATE: A TRENDY COMPOUND MARKER OF ZELEN, A UNIQUE SLOVENIAN VARIETY

The wine market interest for autochthonous varieties, particularly from less known wine regions, has significantly raised in the past few years. In that context, Slovenia, a small country from central Europe with a long winemaking tradition, is getting more and more attention, particularly through its range of unique regional varieties. Among them, Zelen, meaning “green” in Slovene, can only be found in the Vipava valley region, located on the western side of the country, near the border with Italy. When they are young, Zelen wines display very singular aromas reminiscent of rosemary, sage and white fruit. Despite its uniqueness, Zelen wine aromatic typicality is poorly documented in the literature.

Read More