Dataset Information

Genomic Characterization of the Japanese Indigenous Wine Grape Vitis sp. cv. Koshu.

ABSTRACT: Vitis sp. cv. Koshu is indigenous to Japan and used as a table and processing grape. It also constitutes an important grape cultivar in Japanese white wine making and is phylogenetically distinct from European grapes. To understand its genomic information, we compared its small and structural variations with those of the table grape cultivar "Thompson seedless" and European wine grape cultivar "Tannat" via a short-read-based resequencing approach. The Koshu genome exhibited high heterozygosity compared to these cultivars, with this characteristic being particularly prominent on chromosome 7. Furthermore, Koshu structural variation encompassed the most and largest extent of duplications and the fewest and smallest extent of deletions with regard to copy number variation and the fewest absence variations among the compared grape cultivars. Plant disease resistance related to cell death associated with hypersensitive response and environmental stress response, such as water deprivation, oxidative stress, and cell wall organization, was inferred through enrichment analysis of small and structural variations. Variant accumulation levels in Koshu indicated that phenylpropanoid, flavonoid, glutathione, and ?-linolenic acid pathways were related to polyphenol and flavor components. Together, this Koshu genomic information provides a foundation for improving the quality of Koshu wine and may facilitate the use of Koshu as a genetic resource.

SUBMITTER: Tanaka K

PROVIDER: S-EPMC7720679 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Genomic Characterization of the Japanese Indigenous Wine Grape <i>Vitis</i> sp. cv. Koshu.

Tanaka Keisuke K Hamaguchi Yu Y Suzuki Shunji S Enoki Shinichi S

Frontiers in plant science 20201105

<i>Vitis</i> sp. cv. Koshu is indigenous to Japan and used as a table and processing grape. It also constitutes an important grape cultivar in Japanese white wine making and is phylogenetically distinct from European grapes. To understand its genomic information, we compared its small and structural variations with those of the table grape cultivar "Thompson seedless" and European wine grape cultivar "Tannat" via a short-read-based resequencing approach. The Koshu genome exhibited high heterozyg ...[more]

PMID: 33329619

Similar Datasets

Project description:Vitis vinifera cv. Koshu is an indigenous grape cultivar that has been cultivated for more than a thousand years in Japan and one of the most important cultivars in white winemaking. To improve Koshu wine quality, it is necessary to identify the metabolites in Koshu berry. We conducted a comprehensive and comparative lipidome analysis of Koshu and Pinot Noir berries cultivated in the same location in Japan using GC-MS/MS for fatty acids and LC-MS for glycerolipids and glycerophospholipids. Koshu skins and juices contained 22 and 19 fatty acids, respectively, whereas 23 and 20 fatty acids were detected in Pinot Noir skins and juices. C22:6n3 and C24:0 contents in Koshu skins were two and three times higher than those in Pinot Noir skins. C24:0 content in Koshu juices was also higher than that in Pinot Noir juices. Forty-nine lipid components (six digalactosyldiacylglycerols, one monogalactosyldiacylglycerol, 10 phosphatidylcholines, 12 phosphatidylethanolamines, and 20 triglycerides) were detected in Pinot Noir and Koshu skins. Strong peaks were observed for MGDG 36:6, DGDG 36:6, PC 34:2, PC 36:5, TG 54:6, TG 54:7, and TG 54:8 in Koshu skins. The contents of 36 of the 49 lipid components were significantly higher in Pinot Noir skins than Koshu skins. Pinot Noir skins contained more lipids whose alkyl chains have more than 18 carbons than Koshu skins. Further analysis of both lipid profiles revealed that the number of double bonds in a fatty acid molecule in Pinot Noir skins and juices was significantly larger than that in Koshu skins and juices. A strong relationship exists between the heat requirement of grapevine cultivars and the level of fatty acid desaturation. C18-fatty acids were the major components in Koshu and Pinot Noir berries. The expression levels of C18-fatty acid desaturases regulated the accumulation of C18-unsaturated fatty acids in berry skins. The loss of C18:3 in Koshu berries at the end of ripening was observed. Koshu might effectively convert C18:3 into (Z)-hex-3-enal for the production of C6-aroma compounds. These findings by the lipidome analysis are expected to contribute to the improvement of Koshu wine aroma and breeding strategies of cold-tolerant Koshu grapevines.

Project description:Rotundone is a sesquiterpene that gives grapes and wine a desirable 'peppery' aroma. Previous research has reported that growing grapevines in a cool climate is an important factor that drives rotundone accumulation in grape berries and wine. This study used historical data sets to investigate which weather parameters are mostly influencing rotundone concentration in grape berries and wine. For this purpose, wines produced from 15 vintages from the same Shiraz vineyard (The Old Block, Mount Langi Ghiran, Victoria, Australia) were analysed for rotundone concentration and compared to comprehensive weather data and minimal temperature information. Degree hours were obtained by interpolating available temperature information from the vineyard site using a simple piecewise cubic hermite interpolating polynomial method (PCHIP). Results showed that the highest concentrations of rotundone were consistently found in wines from cool and wet seasons. The Principal Component Analysis (PCA) showed that the concentration of rotundone in wine was negatively correlated with daily solar exposure and grape bunch zone temperature, and positively correlated with vineyard water balance. Finally, models were constructed based on the Gompertz function to describe the dynamics of rotundone concentration in berries through the ripening process according to phenological and thermal times. This characterisation is an important step forward to potentially predict the final quality of the resultant wines based on the evolution of specific compounds in berries according to critical environmental and micrometeorological variables. The modelling techniques described in this paper were able to describe the behaviour of rotundone concentration based on seasonal weather conditions and grapevine phenological stages, and could be potentially used to predict the final rotundone concentration early in future growing seasons. This could enable the adoption of precision irrigation and canopy management strategies to effectively mitigate adverse impacts related to climate change and microclimatic variability, such as heat waves, within a vineyard on wine quality.

Dataset Information

Genomic Characterization of the Japanese Indigenous Wine Grape Vitis sp. cv. Koshu.

Publications

Genomic Characterization of the Japanese Indigenous Wine Grape <i>Vitis</i> sp. cv. Koshu.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets