terclim by ICS banner
IVES 9 IVES Conference Series 9 International Congress on Grapevine and Wine Sciences 9 2ICGWS-2023 9 Differential gene expression and novel gene models in 110 Richter uncovered through RNA Sequencing of roots under stress

Differential gene expression and novel gene models in 110 Richter uncovered through RNA Sequencing of roots under stress

Abstract

The appearance of the Phylloxera pest in the 19th century in Europe caused dramatical damages in grapevine diversity. To mitigate these losses, grapevine growers resorted to using crosses of different Vitis species, such as 110 Richter (110R) (V. berlandieri x V. rupestris), which has been invaluable for studying adaptations to stress responses in vineyards. Recently, a high quality chromosome scale assembly of 110R was released, but the available gene models were predicted without using as evidence transcriptional sequences obtained from roots, that are crucial organs in rootstock, and they may express certain genes exclusively. Therefore, we employed RNA sequencing reads of 110R roots under different stress conditions to predict new gene models in each haplotype of 110R under different stresses. We discovered 1,174 and 1,245 new genes for the V. rupestris and V. berlandieri haplotype, respectively. We profiled gene expression on the newly generated transcriptome and identified differentially expressed genes (DEGs) under different stress conditions. Interestingly, among the DEGs we identified different functions on each haplotype, hinting at specific contributions from each parental genome, such as ion transportation or biological process involved in interspecies interaction between organisms. These results demonstrate the value of integrating expression data from more tissues to increase the detection of genes during genome annotations and highlight the value of diploid phased genome references to investigate the contributions of each parental genome in hybrid organisms.

Acknowledgements: Special acknowledgement to the Spanish government grant PRE2019-088446 and the project PID2021-125575OR-C21

References:

1)  Velt A. et al. (2023). An improved reference of the grapevine genome reasserts the origin of the PN40024 highly homozygous genotype. G3-GENES GENOM GENET, 13 (5) jkad067, DOI 10.1093/g3journal/jkad067

2)  Minio A. et al. (2022). HiFi chromosome-scale diploid assemblies of the grape rootstocks 110R, Kober 5BB, and 101–14 Mgt. Sci. Data., 9: 660, DOI 10.1038/s41597-022-01753-0

DOI:

Publication date: October 6, 2023

Issue: ICGWS 2023

Type: Poster

Authors

Alberto Rodriguez-Izquierdo1*, Sara Pascual-El Bobakri1, David Carrasco1, Rosa Arroyo-Garcia1*

1Center for Plant Biotechnology and Genomics (CBGP-UPM-INIA-CSIC)-Universidad Politécnica de Madrid, Campus Montegancedo UPM, Madrid, Spain

Contact the author*

Keywords

rootstock, transcriptome, haplotype, 110 Richter, curation, hybrid, DEG

Tags

2ICGWS | ICGWS | ICGWS 2023 | IVES Conference Series

Citation

Related articles…

Can yeast cells sense other yeasts beyond competition interactions?

The utilization of non-Saccharomyces yeasts in the wine industry has increased significantly in recent years. Alternative species need commonly be employed in combination with Saccharomyces cerevisiae to avoid stuck fermentation, or microbial spoilage. The employment of more than one yeast starter can lead to interactions between different species with an impact on the outcome of wine fermentation. Previous studies[1] demonstrated that S. cerevisiae elicits transcriptional responses with both shared and species-specific features in co-culture with other yeast species.

The evolution of the aromatic composition of carbonic maceration wines

The vinification by Carbonic maceration (CM) involves the process whereby the whole bunches are subjected to anaerobic conditions during several days. In this anaerobic condition, the grape endogenous enzymes begin an intracellular fermentation. This situation favors that whole grapes split open and release their juice into the tank, increasing the liquid phase that is fermented by yeasts [1]. Then, two types of wines are obtained; one from the free-run liquid in the tank (FCM) and other from the liquid after pressing the whole grape bunches (PCM). PCM wines are recognized as high quality young wines because their fruity and floral aromas[2] that although they are very intense at the end of the winemaking they gradually disappear during conservation.

New tool to evaluate color modifications during oxygen consumption in white and red wines

Measuring the effect of oxygen consumption on the color of wines as the level of dissolved oxygen decreases over time is very useful to know how much oxygen a wine can consume without significantly altering its color. The changes produced in wine after being exposed to high oxygen concentrations have been studied by different authors, but in all cases the wine has been analyzed once the oxygen consumption process has been completed. This work presents the results obtained with the use of an equipment designed and made to measure simultaneously the level of dissolved oxygen and the spectrum of the wine, during the oxygen consumption process from saturation levels with air to very low levels, which indicate the total consumption of the dosed oxygen[1,2].

Rootstock effect on Cabernet Sauvignon aromatic and chemical composition

Grape quality potential for wine production is strongly influenced by environmental parameters and agronomic factors. Several studies underline the rootstock effect on scions vegetative growth and berry composition [1] with an impact on wine quality. Rootstocks are promising agronomic tools for climate change adaptation and in most grape-growing regions the potential diversity of rootstocks is not fully used and only a few genotypes are planted. Moreover, little is known about the effect of rootstock genetic variability on the aromatic composition in wines.

Irrigation frequency in four grapevine red varieties in Spain. Effect on must volatile composition

The irrigation water management in the vineyard is a crucial aspect to obtain sustainable quality production over time. Previous studies have set the water requirements to be applied in the vineyard at 30 % of the reference evapotranspiration (ET0), although there are no studies that settle the effects of the frequency of irrigation application on red varieties in Spain. The present study contemplates the application of deficit irrigation (30 % ET0) applying a weekly dose in a single irrigation (T07) or in two irrigation events (T03) per week. The study has been carried out in 2021-2022 with four red varieties in different Spanish wine regions: Garnacha Tinta (Badajoz), Tempranillo (Valladolid), Syrah (Albacete) and Mencía (Lugo). The effects of irrigation frequency on must volatile composition have been evaluated through GC-MS.