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…

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.

Water and nutritional savings shape non-structural carbohydrates in grapevine (Vitis vinifera L.) cuttings

Global changes and sustainability challenge researchers in saving water and nutrients. The response of woody crops, which can be forced at facing more drought events during their life, is particularly important. Vitis vinifera can be an important model for its relevance in countries subjected to climate changes and its breeding, requiring cuttings plantation and strong pruning.

Do wine sulphites affect gut microbiota? An in vitro study of their digestion in the gastrointestinal tract

“Sulphites” and mainly sulphur dioxide (SO2) is by far the most widely used additive (E-220/INS 220) in winemaking and likely the most difficult to replace. The well-known antioxidant, antioxidasic and antimicrobial properties of SO2 make this molecule a practically essential tool, not only in winemaking, but also in the production of other food products. The current trend in winemaking is the reduction of this unfriendly additive due to its negative effects on health and environmental. In particular, it could cause headaches and intolerance/allergic reactions in sensitive individuals. Wine is considered one of the major contributors of exposure of SO2 in the adult population, when this beverage is included in the diet.

The weak role of organic mulches in shaping bacterial communities in grapevine

The interest in sustainable and ecologic agricultural practices in grapevine has grown significantly in recent years in the context of ecological transition. Organic mulches are treatments that support the circular economy and positively affect the soil and the plant. They are an alternative to herbicides and other conventional practices since they may influence soil moisture, erosion, structure and weed control. However, their effects on the soil and must microbiota remain unknown.

Culturable microbial communities associated with the grapevine soil in vineyards of La Rioja, Spain

The definition of soil health is complex due to the lack of agreement on adequate indicators and to the high variability of global soils. Nevertheless, it has been widely used as synonymous of soil quality for more than one decade, and there is a consensus warning of scientists that soil quality and biodiversity loss are occurring due to the traditional intensive agricultural practices.
In this work we monitored a set of soil parameters, both physicochemical and microbiological, in an experimental vineyard under three different management and land use systems: a) addition of external organic matter (EOM) to tilled soil; b) no tillage and plant cover between grapevine rows, and c) grapevines planted in rows running down the slope and tilled soil.