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…

Evaluation of physiological properties of grapevine clones of ‘Tempranillo’ and ‘Graciano’ in DOCa Rioja (Spain)

In order to avoid the loss of grapevine intra-varietal diversity of DOCa Rioja grape varieties, Regional Government of La Rioja established a germplasm bank with more than 1.600 accessions, whose origin lies in the prospecting and sampling of ancient vineyards located throughout the whole region. 30 clones of Tempranillo and 13 clones of Graciano were preselected and multiplied in a new vineyard for further observations. The aim of this work is to describe the first results from the physiological characterization by an optical sensor of these preselected clones, which constitute the base of a new clonal selection that aims to increase the range of available certified clones and to improve the adaptation of these varieties to future objectives and environmental conditions.

Characterization of non-cultivated wild grapevines in Extremadura (Spain) 

Several Eurasian wild grapevine populations were found along Extremadura region (southwestern Spain). For conservation and study, one individual from four different populations (named L1, L2, L5 and L6) was vegetatively propagated and planted at Instituto de Investigaciones Agrarias Finca La Orden (CICYTEX), Badajoz. The aim of the present work was to characterize those conserved individuals from four different populations based on both an ampelographic description and a molecular analysis. Three vines per individual were studied.

Yeast mannoprotein characterization and their effect on Oenococcus oeni and malolactic fermentation

Mannoproteins are released at the end of alcoholic fermentation due to yeast autolysis [1]. It has been described a positive effect of these molecules on lactic acid bacteria growth [2]. The main objective of this work was the characterization of different mannoproteins extracted from active dry yeast (ADY) and the assessment of their effect on Oenococcus oeni and malolactic fermentation (MLF).

The characterization of Vitis vinifera L cv. Cabernet sauvignon: the contribution of Ecklonia maxima seaweed extract

Biostimulants and biofertilizers are considered environmentally friendly and cost-effective alternatives to synthetic fertilizers, plant growth regulators and crop improvement products. Broadly, plant biostimulants are expected to improve nutrient use efficiency, tolerance to abiotic stress, quality traits and availability of nutrients in the soil or rhizosphere. Currently, seaweed extracts account for more than 33% of the total plant biostimulant market. Within this category, Ascophyllum nodosum (AN), is the most widely studied and applied in biostimulant formulations.

Phenolic composition and chromatic characteristics of blends of cv. Tempranillo wines from vines grown with different viticultural techniques in a semi-arid area

The quality and color stability of red wines are directly related to content and distribution of phenolic compounds. However, the climate change produces the asynchrony between the dates of technological and maturity of grapes. The crop-forcing technique (CF) restores the coupling between phenolic and technological ripeness while limits vineyard yields. Blending of wines is frequently used to equilibriate composition of wines and to increase their stability, color and quality. The aim of the present work is to study the phenolic composition and color of wine blends made with FW (wines from vines subjected to CF) and CW (wines for vines under the usual cultivation practices).