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

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 

机构地区：[1]College of Horticulture,Qingdao Agricultural University,Qingdao 266109,China [2]State Key Laboratory of Tropical Crop Breeding,Shenzhen Branch,Guangdong Laboratory of Lingnan Modern Agriculture,Key Laboratory of Synthetic Biology,Ministry of Agriculture and Rural Affairs,Agricultural Genomics Institute at Shenzhen,Chinese Academy of Agricultural Sciences,Shenzhen 518120,China [3]Key Laboratory of Horticultural Plant Biology Ministry of Education,College of Horticulture and Forestry Sciences,Huazhong Agricultural University,Wuhan 430070,China [4]School of Agriculture and Food Science,University College Dublin,Belfield,Dublin 4,Ireland [5]National Demonstration Center for Experimental Plant Science Education,College of Agriculture,Guangxi University,Nanning 530004,China [6]State Key Laboratory of Resource Insects,Southwest University,Chongqing 400715,China [7]Institute of Horticulture Crops,Xinjiang Academy of Agricultural Sciences,Urumqi 830091,China [8]Beijing Key Laboratory of Grape Science and Enology,Institute of Botany,Chinese Academy of Sciences,Xiangshan,Beijing 100093,China [9]College of Enology,Northwest A&F University,Yangling 712100,China [10]SVQV,INRAE-University of Strasbourg,68000 Colmar,France [11]Genetics and Genomics of Plants,CeBiTec&Faculty of Biology,Bielefeld University,33615 Bielefeld,Germany [12]Unidad de Hortofruticultura,Centro de Investigación y Tecnología Agroalimentaria de Aragón(CITA),50059 Zaragoza,Spain [13]Institute for Integrative Systems Biology(I2SysBio),Systems Biotech Program,Universitat de València-CSIC,Paterna,46908,Valencia,Spain [14]Cold Spring Harbor Laboratory,Cold Spring Harbor,NY 11724,USA [15]USDA ARS NEA Robert W.Holley Center for Agriculture and Health,Agricultural Research Service,Ithaca,NY 14853,USA [16]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 U

出　　处：《Horticulture Research》2023年第5期207-219,共13页园艺研究（英文）

基　　金：This work was supported by the National Natural Science Fund for Excellent Young Scientists Fund Program(Overseas)to Y.Z.,the National Key Research and Development Program of China(grant 2019YFA0906200);the Agricultural Science and Technology Innovation Program(CAAS-ZDRW202101);the Shenzhen Science and Technology Program(grant KQTD2016113010482651);the BMBF-funded de.

摘　　要：Grapevine is one of the most economically important crops worldwide.However,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 regions.Here,we assembled a telomere-to-telomere(T2T)gap-free reference genome for the cultivar PN40024 using PacBio HiFi long reads.The T2T reference genome(PN_T2T)is 69 Mb longer with 9018 more genes identified than the 12X.v0 version.We annotated 67%repetitive sequences,19 centromeres and 36 telomeres,and incorporated gene annotations of previous versions into the PN_T2T assembly.We detected a total of 377 gene clusters,which showed associations with complex traits,such as aroma and disease resistance.Even 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 phosphorylation.The fully annotated complete reference genome therefore constitutes an important resource for grapevine genetic studies and breeding programs.

关 键 词：BREEDING CROPS CULTIVAR 

分 类 号：S663.1[农业科学—果树学]