terclim by ICS banner
IVES 9 IVES Conference Series 9 Harnessing whole genome sequencing data to predict protein structure and function variation in grapevine

Harnessing whole genome sequencing data to predict protein structure and function variation in grapevine

Abstract

Grapevine (Vitis vinifera) is amongst the world’s most cultivated fruit crops, and of global and economic significance, producing a wide variety of grape-derived products, including wine, and table grapes. The genus Vitis, encompassing approximately 70 naturally occurring inter-fertile species, exhibits extensive genetic and phenotypic diversity, highlighted by the global cultivation of thousands of predominantly Vitis vinifera cultivars. Despite the importance of harnessing its naturally occurring genetic diversity to pursue traits of interest, especially considering the continued and growing demand for sustainable high-quality grape production, the systematic characterization of available functional genetic variants remains limited. Such characterizations hold the potential not only as a critical tool for directed breeding, including the identification of molecular markers for genetic selection, but would also enable the functional characterization of genes that may exert influence over key functional traits. This project aims to comprehensively analyze global genetic variation in grapevine cultivars, emphasizing the development of methodologies for large-scale prediction of the impact of genomic sequence variations on protein structure and function. To this end, a curated bioinformatics pipeline was designed to enable the detection of sequence variation present within the coding regions of previously reported Vitis Whole-Genome Sequencing (WGS) datasets. Validation of this pipeline included utilizing genomic regions with known Insertions and Deletions (InDels) and Single Nucleotide Polymorphisms (SNPs) to quantify its efficiency. Lastly, comparative analyses and recording of coding region sequence variation among grapevine cultivars were conducted to facilitate future predictions regarding the impact of genetic variations on protein structure and function.

Download the abstract

DOI:

Publication date: June 14, 2024

Issue: Open GPB 2024

Type: Poster

Authors

Dylan Grobler1*, Justin Lashbrooke1, Pablo Carbonell-Bejerano2

1 Department of Genetics, Stellenbosch University. (7600) Stellenbosch, South Africa
2 Instituto de Ciencias de la Vid y del Vino, ICVV, CSIC – Universidad de La Rioja – Gobierno de La Rioja. (26007) La Rioja, Logroño, Spain

Contact the author*

Keywords

grapevine, genetic resources, genetic variation, protein prediction

Tags

IVES Conference Series | Open GPB | Open GPB 2024

Citation

Related articles…

Copper reduction strategy for sangiovese in organic viticulture

Organic viticulture requires copper based treatments for bunch protection even though an intensive employment is no longer admitted because of its low leaching and phytotoxicity in the soil. UE Reg. 1981/2018 set copper employment to 4 kg/ha for year or 28 during 7 years with an absolute level allowed of 6 Kg/ha although those limits were decreased frequently.

Read More

Using the fraction of transpirable soil water to estimate grapevine leaf water potential: comparing the classical statistical regression approach to machine learning algorithms

Weather uncertainty is forcing Mediterranean winegrowers to adopt new irrigation strategies to cope with water scarcity while ensuring a sustainable yield and improved berry and wine quality standards. Therefore, more accurate and high-resolution monitoring of soil water content and vine water status is a major concern. Leaf water potential measured at pre-dawn (PD) is considered to be in equilibrium with soil water potential and is highly correlated with soil water content at the soil depth where roots extract water.

Read More

Characterization of a unique mannan from Starmerella bacillaris for protein stabilization in white wine

Yeast cell wall components are valuable biotechnological tools with applications in oenology and beyond [1], [2].

Read More

Partial rootzone drying (PRD): strategic irrigation management as viticultural tool affecting plant physiology and berry quality

Partial rootzone drying (PRD) is an irrigation management technique designed to reduce water use in grapevines without a decline in yield, thereby increasing water use efficiency (WUE). The principle of PRD is to keep part of the root system at a constant drying rate to produce soil derived signals to above-ground plant organs to induce a

Read More

PREVALENCE OF OAK-RELATED AROMA COMPOUNDS IN PREMIUM WINES

Barrel fermentation and barrel-ageing of wine are commonly utilised practices in premium wine production. The wine aroma compounds related to barrel contact are varied and can enhance a range of wine aromas and flavours, such as ‘struck flint’, ‘caramel’, ‘red berry’, ‘toasty’ and ‘nutty’, as well as conventional oaky characters such as ‘vanilla’, ‘spice’, ‘smoky’ and ‘coconut’. A survey of commercially produced premium Shiraz, Cabernet Sauvignon, Pinot Noir and Chardonnay wines was conducted, assessing the prevalence of compounds that have been proposed as barrel-ageing markers¹ including oak lactones, volatile phenols, furanones, aldehydes, thiazoles2,3, phenylmethanethiol⁴ and 2-furylmethanethiol.⁵

Read More