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.

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…

Characterizing graft union formation in different scion/rootstock combinations of grapevine 

In most viticultural regions, grapevines are cultivated grafted, employing either hybrid or pure species of various American Vitis spp., such as V. berlandieri, V. rupestris, and V. riparia, as grapevine rootstocks. These rootstocks play a crucial role in providing resistance to the Phylloxera insect pest. Beyond Phylloxera resistance, it is desirable for grapevine rootstocks to exhibit resistance to other soil-borne pathogens and adaptability to abiotic stress conditions. The introduction of new rootstocks holds promise for adapting agriculture to climate change without altering the characteristics of the final harvested product.

Phenolic extraction and mechanical properties of skins and seeds during maceration of four main italian red wine grape varieties

AIM: Red grape varieties are characterized by different phenolic contents (prominently tannins and anthocyanins) found in skins and seeds.

Evaluation of consumer behaviour, acceptance and willingness to return of faulty wines

The analysis of consumer attitudes towards wine, especially towards wines perceived as faulty, is an aspect that requires more research than has been carried out so far [1]. This study aims to analyse consumer behaviour in situations involving the consumption of faulty wines and to assess the level of acceptance of such wines.

Effet de l’ombrage respectif des ceps et des grappes de Muscat sur leurs teneurs en composés volatils libres et glycosyles et en précurseurs d’aromes carotenoïdiques

Le Muscat de Frontignan est bien connu pour ses fortes teneurs en composés terpéniques et par l’odeur florale et fruitée que ces composés confèrent aux vins qui en sont issus (1,2).

Recent advances in measuring, estimating, and forecasting grapevine yield and quality

Grapevine yield and fruit quality are two major drivers of input allocation and, ultimately, revenue for grape producers. Because yield and fruit quality vary substantially from year-to-year and within a single block, opportunities exist for optimization via precision management activities that could lead to more profitable and sustainable grape production. Here, we review recent advances in the techniques and technology used to measure, estimate, and forecast grapevine yield and fruit quality. First, we discuss direct “measurement” of yield and quality (i.e. ground-truth data generation), with an emphasis on potential for scalability and automation. Second, we discuss technology and techniques that do not directly measure yield and quality, but use correlated measurements for their estimation.