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…

Addition of glutathione-rich inactivated yeasts to white musts: effects on wine composition and sensory quality

Glutathione plays a key role in preventing some oxidative processes during winemaking. This molecule limits the must enzymatic oxidation, reacts with caffeic acid and generates a colourless compound that prevents subsequent browning. It also has a protective effect on wine aroma, preventing the oxidation of the volatile compounds with a high sensory impact.

Read More

Evaluation of terroir suitability for vine cultivation in new areas using geographic multi-criteria decision support

Based on historical vine cultivation, the recent development of wine production in Drama wine region (Greece) has led to vine cultivation expansion of white and red varieties. The current cultivation of 500 ha of vineyards is expected to increase in the coming years. Natural terroir units (NTU) have been designed recently to support the production of high quality wines in the region [1]. The aim of this work is to evaluate the relevancy of the proposed NTUs regarding their suitability to produce wines of specific sensorial identity, and to provide guidelines for correct site selection for the expanding wine industry of the region.

Read More

Foliar application of urea improved the nitrogen composition of Chenin grapes

The nitrogen composition of the grapes directly affects the developments of alcoholic fermentation and influences the final aromatic composition of the wines. The aim of this study was to determine the effect and efficiency of foliar applications of urea on the nitrogen composition of grapes. This study was carried out during 2023 vintage and in the Chenin vineyard located in Estacion Experimental Mendoza (Argentina). Three urea concentrations 3, 6 and 9 Kg N/ha (C1, C2, and C3, respectively) and control (T) were applied in this vineyard at veraison.

Read More

Genetic variation among wild grapes native to Japan

Domesticated grapes are assumed to have originated in the Middle East. However, a considerable number of species are native in East Asian countries such as China, Korea and Japan as well. Evidence suggests that a total of seven species and eight varieties have been found to be native to Japan. A wide level variation in morphology, genetic and fruit composition exist in wild grape native to Japan.

Read More

New food trend ahead? Highlighting the nutritional benefits of grapevine leaves

The wine industry produces an enormous amount of waste every year. A wider inclusion of disregarded by-products in the human diet or its use as a source of bioactive compounds is a good strategy for reducing waste. It will not only introduce an added value to a waste product but also come upon the European Union and United Nations’ demands towards more sustainable agricultural approaches and circular economy.

Read More