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…

Pre-breeding for developing heat stress resilient grape varieties to ensure yield 

Climate change has numerous detrimental consequences and creates new challenges for viticulture around the world. Transitory or constant high temperatures frequently associated with an excess of sunlight (UV) can cause a variety of physiological disorders, such as sunburn. Diverse environmental factors and the plant’s response mechanisms to stress determine the symptoms. Grapevine berry sunburn leads to a drastic reduction in yield, and may eventually decline berry quality. Consequently, this poses a significant risk to the winegrowers.

Effect of different plant fibers on the elimination of undesirable compounds in red wine. Correlation with its polysaccharide composition

The presence of undesirable compounds in wines, such as OTA, biogenic amines and pesticides residues, affects wine quality and can cause health problems for the consumer. The main tool that a winemaker has to reduce their content in the wine is fining. However, some of the fining agents commonly used in the winery can cause allergies or even increase the protein content in the wine, increasing the turbidity. To avoid these problems, the use of plant fibers may be an alternative, such as those from grape pomace[1] or other plant origins.

Sustainable management of grapevine trunk diseases

Grapevine trunk diseases (GTD) occur wherever grapes are grown and are considered the main biotic factor reducing yields and shortening vineyards’ lifespan. Currently, no product is available to eradicate GTD once grapevines are infected. Therefore, prophylactic strategies based on pruning wound protection and ‘remedial surgery’, the only eradication method based on the elimination of infected wood and renewal of the vine by means of new canes or suckers, are the only effective strategies available. The Canadian grape and wine industry focusses on a sustainable production and thus, looking for alternatives to chemicals for disease management is a top priority.

Combined use of leaf removal and natural shading to delay grape ripening in Manto negro (Vitis vinifera L.) under deficit irrigation 

The increasingly frequent heat waves during grape ripening pose challenges for premium wine grape production. This makes the development of irrigation and canopy management techniques of great importance to maximize yield and grape quality. A field experiment was carried out during 2021 and 2022 using Manto negro wine grapes to study the effect of two irrigation strategies and different light exposure levels on grape quality.

Molecularly imprinted polymers: an innovative strategy for harvesting polyphenoles from grape seed extracts

Multiple sclerosis (MS) is a multifactorial autoimmune disease associating demyelination and axonal degeneration developing in young adults and affecting 2–3 million people worldwide. Plant polyphenols endowed with many therapeutic benefits associated with anti-inflammatory and antioxidant properties represent highly interesting new potential therapeutic strategies. We recently showed the safety and high efficiency of grape seed extract (GSE), a complex mixture of polyphenolics compounds comprising notably flavonoids and proanthocyanidins, in an experimental autoimmune encephalomyelitis (EAE) mouse model of MS.