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…

Plant fibers in comparison with other fining agents for the re-duction of pesticide residues and the effect on the volitile profile of Austrian white and red wines.

Pesticide residues in Austrian wines have so far been poorly documented. In 250 wines, 33 grape musts and 45 musts in fermentation, no limit values were exceeded, but in some cases high lev-els (>0.100 mg/l) of single residues were found, meaning that a reduction of these levels before bottling could make sense. In the course of this study, a white and a red wine were spiked with a mix of 23 pesticide residues from the group of fungicides (including botryticides), herbicides and insecticides. The influence of the following treatments on residue concentrations and volatile profiles were investigated: two activated charcoal products, a bentonite clay, two commer-cial mixed fining agents made of bentonite and charcoal, two yeast cell wall products, and a plant fiber-based novel filter additive. The results of this study show that all the agents tested reduced both residues and aromavolatile compounds in wine, with activated charcoal having the strongest effect and bentonite the weakest. The mixed agents and yeast wall products showed less aroma losses than charcoal products, but also lower residue reduction. Plant fibers showed good reduction of pesticides with moderate aroma damage, but these results need to be con-firmed under practical conditions.

The plantation frame as a measure of adaptation to climate change

The mechanization of vineyard work originally led to a reduction in planting densities due to the lack of machinery adapted to the vineyard. The current availability of specific machinery makes it possible to establish higher planting densities. In this work, three planting densities (1.40×0.80 m, 1.80×1 m and 2.20×1.20 m, corresponding to 8928, 5555 and 3787 plants/ha respectively) were studied with four varieties autochthonous of Galicia (northwestern Spain): Albariño and Treixadura (white), Sousón and Mencía (red). The vines were trained in a vertical shoot positioning system using a single Royat cordon, and pruned to spurs with two buds each. Agronomic data (yield, pruning wood weight, Ravaz index) and oenological data in must were collected. The higher planting density (1.40×0.80 m) had no significant effect on grape yield per vine in white varieties, although production per hectare was much higher due to the greater number of plants. In red varieties, this planting density resulted in a significantly lower production per vine, compensated by the greater number of plants. In addition, it significantly reduced the Brix degree in the must of the Albariño, Treixadura and Sousón varieties, and increased the total acidity in the latter two and Mencía. It also caused an increase in extractable and total anthocyanins and IPT in red grapes. The effects of high planting density on grapes are of great interest for the adaptation of varieties in the context of climate change. In the future, it could be advisable to modify the limits imposed by the appellations of origin on the planting density of these varieties in order to obtain more balanced wines.

Methodology for soil study and zoning

La caractérisation des sols en vue d’une étude de terroirs viticoles peut être réalisée à différents niveaux de complexité, suivant le nombre de variables pris en compte et suivant le fait que celles-ci sont spatialisées ou non

Parcours de découverte des terroirs viticoles

A partir des recherches conduites sur la caractérisation des terroirs viticoles par des chercheurs de l’Unité de Recherches Vigne et Vin (1, 2, 3, 4, 5) du Centre INRA d’Angers, Terre des Sciences, le Centre de Culture Scientifique et Technique d’Angers (CCSTA) a mis au point un parcours de découverte d’une journée dans le vignoble angevin avec une approche pluridisciplinaire.

Inhibition of Oenococcus oeni during alcoholic fermentation by a selected Lactiplantibacillus plantarum strain

The use of selected cultures of the species Lactiplantibacillus plantarum in Oenology has grown in prominence in recent years. While initial applications of this species centred very much around malolactic fermentation (MLF), there is strong evidence to show that certain strains can be harnessed for their bio-protective effects. Unwanted spontaneous MLF during alcoholic fermentation (AF), driven by rogue Oenococcus oeni, is a winemaking deviation that is very difficult to manage when it occurs. This work set out to determine the efficacy of one particular strain of Lactiplantibacillus plantarum(Viniflora® NoVA™ Protect), against this problem in Cabernet Sauvignon must. The work was carried out at commercial scale and in a winery environment and compared the bio-protective culture with the more traditional approach of reducing must pH by the addition of tartaric acid. The combination of both was also investigated. The concentration of both Oenococcus oeni and Lactiplantibacillus plantarum was determined using qPCR. The adventitious Oenococcus oeni showed the most growth during AF in the control wine, whereas in the wines treated with Lactiplantibacillus plantarum a bacteriostatic effect against this species was observed. This effect was comparable to the wines treated with tartaric acid. This has particular commercial relevance for controlling the flora in musts with high pH, or when the addition of tartaric acid is either not permitted or is prohibitive for other reasons.