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…

Energy partitioning and functionality of photosystem II in water-stressed grapevines during heatwaves revealed by continuous measurements of chlorophyll fluorescence

The increased intensity and frequency of heatwaves, coupled with prolonged periods of drought, are a significant threat to viticulture worldwide. During these conditions the more exposed leaves can show visible symptoms of heat damage. We monitored the functionality of photosystem II (PSII) in the field to better understand the impact of heatwaves on canopy performance. A factorial experiment was established in summer 2023 using Shiraz grapevines in the Barossa valley of South Australia, involving water-stressed and well-watered vines.

The surprising role of VvLYK6 in grapevine immune responses triggered by chitin oligomers

For sustainable viticulture, the substitution of chemical inputs with biocontrol products has become one of the most considered strategies. This strategy is based on elicitor-triggered immunity that requires a deep understanding of the molecular mechanisms involved in plant defense activation. Plant immune responses are triggered through the perception of conserved microbe-associated molecular patterns (MAMPs) which are recognized by pattern recognition receptors (PRRs) at the plasma membrane.

Influence of polysaccharide extracts from wine by-products on the volatile composition of sparkling white wines

In the production of sparkling wines, during the second fermentation, mannoproteins are released by yeast autolysis, which affect the quality of the wines. The effect of mannoproteins has been extensively studied, and may affect aroma and foam quality. However, there are no studies on the effect of other polysaccharides such as those from grapes. Considering the large production of waste from the wine industry, it was proposed to obtain polysaccharide-rich extracts from some of these by-products[1].

Comparison of the effects of hormone- and natural-based elicitors on key metabolic pathways in cv. Tempranillo

One of the most important effects of climate change in wine-growing areas is the advance of phenological stages, especially concerning early berry ripening. In the hottest seasons, this results in a lack of synchrony between sugar and phenolic ripeness. In order to cope with this fact, a general effort is being made by researchers and growers aiming at delaying ripening through different strategies. One of the proposed approaches is the application of elicitors. This study aims to assess the effect at the transcriptomic level of application of three elicitors (Vitalfit, Fruitel, and Protone) in Tempranillo.

Application of an in vitro digestion model to study the bioaccessibility and the effect of the intestinal microbiota on the red wine proanthocyanidins 

Proanthocyanidins are important phenolic fraction for wine quality, contributing to astringency, bitterness and color. Their metabolism begins in the mouth and continues throughout the gastrointestinal tract; however, most of them are accumulated in the colon where are metabolized by the intestinal microbiota, giving rise to a whole series of phenolic acids that may have greater activity at physiological level than the precursors[1]. This study aimed to evaluate in vitro the bioaccessibility of proanthocyanidins in a red wine developed by Bodegas Pradorey, as well as to evaluate the potential effect of intestinal microbiota on polyphenols metabolism identifying and quantifying secondary metabolites.