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The complete reference genome for grapevine (Vitis vinifera L.) genetics and breeding

Horticulture Research 2023年第5期10卷 207-219页

作者： Xiaoya Shi Shuo Cao Xu Wang Siyang Huang Yue Wang Zhongjie Liu Wenwen Liu Xiangpeng Leng Yanling Peng Nan Wang Yiwen Wang Zhiyao Ma Xiaodong Xu Fan Zhang Hui Xue Haixia Zhong Yi Wang Kekun Zhang Amandine Velt Komlan Avia Daniela Holtgräwe Jérôme Grimplet JoséTomás Matus Doreen Ware Xinyu Wu Haibo Wang Chonghuai Liu Yuling Fang camille rustenholz Zongming Cheng Hua Xiao Yongfeng Zhou College of Horticulture Qingdao Agricultural UniversityQingdao 266109China State Key Laboratory of Tropical Crop Breeding Shenzhen BranchGuangdong Laboratory of Lingnan Modern AgricultureKey Laboratory of Synthetic BiologyMinistry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China Key Laboratory of Horticultural Plant Biology Ministry of Education College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhan 430070China School of Agriculture and Food Science University College DublinBelfieldDublin 4Ireland National Demonstration Center for Experimental Plant Science Education College of AgricultureGuangxi UniversityNanning 530004China State Key Laboratory of Resource Insects Southwest UniversityChongqing 400715China Institute of Horticulture Crops Xinjiang Academy of Agricultural SciencesUrumqi 830091China Beijing Key Laboratory of Grape Science and Enology Institute of BotanyChinese Academy of SciencesXiangshanBeijing 100093China College of Enology Northwest A&F UniversityYangling 712100China SVQV INRAE-University of Strasbourg68000 ColmarFrance Genetics and Genomics of Plants CeBiTec&Faculty of BiologyBielefeld University33615 BielefeldGermany Unidad de Hortofruticultura Centro de Investigación y Tecnología Agroalimentaria de Aragón(CITA)50059 ZaragozaSpain Institute for Integrative Systems Biology(I2SysBio) Systems Biotech ProgramUniversitat de València-CSICPaterna46908ValenciaSpain Cold Spring Harbor Laboratory Cold Spring HarborNY 11724USA USDA ARS NEA Robert W.Holley Center for Agriculture and Health Agricultural Research ServiceIthacaNY 14853USA Fruit Research Institute Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops(Germplasm Resources Utilization)Ministry of Agriculture/Key Laboratory of Mineral Nutrition and Fertilizers Efficient Utilization of Deciduous Fruit TreeLiaoning ProvinceXingch

Grapevine is one of the most economically important crops ***,the previous versions of the grapevine reference genome tipically consist of thousands of fragments with missing centromeres and telomeres,limiting the accessibility of the repetitive sequences,the centromeric and telomeric regions,and the study of inheritance of important agronomic traits in these ***,we assembled a telomere-to-telomere(T2T)gap-free reference genome for the cultivar PN40024 using PacBio HiFi long *** T2T reference genome(PN_T2T)is 69 Mb longer with 9018 more genes identified than the 12X.v0 *** annotated 67%repetitive sequences,19 centromeres and 36 telomeres,and incorporated gene annotations of previous versions into the PN_T2T *** detected a total of 377 gene clusters,which showed associations with complex traits,such as aroma and disease *** though PN40024 derives from nine generations of selfing,we still found nine genomic hotspots of heterozygous sites associated with biological processes,such as the oxidation–reduction process and protein *** fully annotated complete reference genome therefore constitutes an important resource for grapevine genetic studies and breeding programs.

关键词： breeding crops cultivar

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