Tanaka Keisuke, Hamaguchi Yu, Suzuki Shunji, Enoki Shinichi
NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan.
Laboratory of Fruit Genetic Engineering, The Institute of Enology and Viticulture, University of Yamanashi, Kofu, Japan.
Front Plant Sci. 2020 Nov 5;11:532211. doi: 10.3389/fpls.2020.532211. eCollection 2020.
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 α-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.
甲州葡萄（Vitis vinifera sp. cv. Koshu）原产于日本，用作鲜食葡萄和加工葡萄。它也是日本白葡萄酒酿造中的重要葡萄品种，在系统发育上与欧洲葡萄不同。为了解其基因组信息，我们通过基于短读长的重测序方法，将其小变异和结构变异与鲜食葡萄品种“汤普森无核”和欧洲酿酒葡萄品种“丹娜”的进行了比较。与这些品种相比，甲州葡萄基因组表现出较高的杂合性，这一特征在7号染色体上尤为突出。此外，在比较的葡萄品种中，甲州葡萄的结构变异在拷贝数变异方面包含的重复程度最高、范围最大，缺失程度最少、范围最小，缺失变异数量也最少。通过对小变异和结构变异的富集分析，推断出与细胞死亡相关的植物抗病性，这些细胞死亡与超敏反应以及环境胁迫反应有关，如缺水、氧化应激和细胞壁组织。甲州葡萄中的变异积累水平表明，苯丙烷类、黄酮类、谷胱甘肽和α-亚麻酸途径与多酚和风味成分有关。总之，这些甲州葡萄基因组信息为提高甲州葡萄酒的品质提供了基础，并可能促进将甲州葡萄用作遗传资源。
