Format: ORAL

Hua Xiao1, Zhongjie Liu1, Nan Wang1, Ying Su1, Qiming Long1, Yanling Peng1, Lingfei Shangguan2, Fan Zhang1, Shuo Cao1, Xu Wang1, Mengqin Ge2, Hui Xue1, Zhiyao Ma1, Wenwen Liu1, Xiaodong Xu1, Chaochao Li1, 8, Xuejing Cao1, Bilal Ahmad1, Xiangnian Su1, Yuting Liu1, Guizhou Huang1, Mengrui Du1, Zhenya Liu1, Yu Gan1, Lei Sun4, XiucaiFan4,Chuan Zhang3, Haixia Zhong3, Xiangpeng Leng5, Yanhua Ren2, Tianyu Dong2, Dan Pei2, Xinyu Wu3, Zhongxin Jin1, 8, Yiwen Wang1, Chonghuai Liu4, Jinfeng Chen6, Brandon Gaut7, Sanwen Huang1,8, Summaira Riaz9, Andrew M. Walker9,Jinggui Fang2,5, and Yongfeng Zhou1, 8, *Hua Xiao1, Zhongjie Liu1, Nan Wang1, Ying Su1, Qiming Long1, Yanling Peng1, Lingfei Shangguan2, Fan Zhang1, Shuo Cao1, Xu Wang1, Mengqin Ge2, Hui Xue1, Zhiyao Ma1, Wenwen Liu1, Xiaodong Xu1, Chaochao Li1, 8, Xuejing Cao1, Bilal Ahmad1, Xiangnian Su1, Yuting Liu1, Guizhou Huang1, Mengrui Du1, Zhenya Liu1, Yu Gan1, Lei Sun4, XiucaiFan4,Chuan Zhang3, Haixia Zhong3, Xiangpeng Leng5, Yanhua Ren2, Tianyu Dong2, Dan Pei2, Xinyu Wu3, Zhongxin Jin1, 8, Yiwen Wang1, Chonghuai Liu4, Jinfeng Chen6, Brandon Gaut7, Sanwen Huang1,8, Summaira Riaz9, Andrew M. Walker9,Jinggui Fang2,5, and Yongfeng Zhou1, 8, *

1 National 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, China 2 College of Horticulture, Nanjing Agricultural University, Nanjing, China 3 Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China 4 Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China 5 College of Horticulture, Qingdao Agricultural University, Qingdao, China 6 State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China 7 Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA 8 National Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China 9 Department of Viticulture and Enology, University of California, Davis, Davis, CA, USA

Grapevine is among the first domesticated crops.However, its breeding is impeded by the investigations of the genetic basis of important agronomic traits. Based on population genetics combining multiple new analytic methods, such as pan-genome and machine learning, we identified many important trait-related quantitative trait loci (QTLs), and revealed the importance of introgression in shaping the current texture of grapes. We constructed a variant map by interrogating resequencing data from grapevine cultivars based on pan-genome including 18 newly generated telomere-to-telomere gap-free haplotype-resolved assemblies and performed genome-wide association studies (GWAS) related to 29 traits. 148 significantly related QTLs were identified, and 8.1% QTLs of 12 traits were identified as significant contributions by structure variations (SVs). We also found some QTLs were located in regions of divergent selection between wine and table grapes. Given the previous studies showing genomic signals of introgression from wild to wine grapes in Europe, based on machine learning-based population genetic analyses, we predicted the time, mode, genomic pattern, and biological effects of these introgression events, and found that continuous gene flow between European wild grapes (EU) and cultivated grapes over the past ~2000 years, especially from EU to wine grapes, suggesting EU wild grapes were an important resource for improving the flavor of wine grapes. We further found that introgression may be a historically important process for improving clonal systems like domesticated grapes. Despite the potential benefits of introgression in grape improvement, the introgressed fragments introduced a higher deleterious burden, and most of these deleterious variants were in a heterozygous state in grapes. In general, our study facilitates the breeding of superior cultivars via genomic selection of multiple traitsandtheunderstandingof beneficial and harmful effects of introgression is critical for genomic breeding of grapevine to take advantage of wild resources.