[en] Jujube (Ziziphus jujuba Mill.), belonging to the Rhamnaceae family, is gaining increasing prominence as a perennial fruit crop with significant economic and medicinal values. Here, we conduct de novo assembly of four reference-grade genomes, encompassing one wild and three cultivated jujube accessions. We present insights into the population structure, genetic diversity, and genomic variations within a diverse collection of 1059 jujube accessions. Analyzes of the jujube pan-genome, based on our four assemblies and four previously released genomes, reveal extensive genomic variations within domestication-associated regions, potentially leading to the discovery of a candidate gene that regulates flowering and fruit ripening. By leveraging the pan-genome and a large-scale resequencing population, we identify two candidate genes involved in domestication traits, including the seed-setting rate, the bearing-shoot length and the leaf size in jujube. These genomic resources will accelerate evolutionary and functional genomics studies of jujube.
Disciplines :
Agriculture & agronomy
Author, co-author :
Guo, Mingxin ; College of Life Sciences, Luoyang Normal University, Luoyang, China. mxguolynu@126.com
Lian, Qun; 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 ; School of Biology & Environmental Science, University College Dublin, Belfield, Dublin, Ireland
Mei, Ye ; 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
Yang, Wangwang ; College of Life Sciences, Luoyang Normal University, Luoyang, China
Zhao, Suna ; College of Life Sciences, Luoyang Normal University, Luoyang, China
Zhang, Siyuan ; College of Life Sciences, Luoyang Normal University, Luoyang, China
Xing, Xinfeng ; College of Life Sciences, Luoyang Normal University, Luoyang, China
Zhang, Haixiang ; College of Life Sciences, Luoyang Normal University, Luoyang, China
Gao, Keying ; College of Life Sciences, Luoyang Normal University, Luoyang, China
He, Wentong; National Foundation for Improved Cultivar of Chinese Jujube, Bureau of Natural Resources and Planning of Cangxian County, Cangzhou, China
Wang, Zhitong; National Foundation for Improved Cultivar of Chinese Jujube, Bureau of Natural Resources and Planning of Cangxian County, Cangzhou, China
Wang, Huan ; 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
Zhou, Jun; School of Biological Science and Engineering, North Minzu University, Yinchuan, China
Cheng, Lin ; Université de Liège - ULiège > TERRA Research Centre ; 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
Bao, Zhigui ; 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
Huang, Sanwen ; 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
Yan, Jianbin ; 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. jianbinlab@caas.cn
Zhao, Xusheng ; College of Life Sciences, Luoyang Normal University, Luoyang, China. xszhaolynu@126.com
This work was supported by the National Key R&D Program of China (2023YFA0915800 and 2023ZD04076 to J.Y.); the National Natural Science Foundation of China (32271928 to M.G.); the Luoyang Key Science and Technology Innovation Program (2101016 A to X.Z.); the Tianchi Talent in Xinjiang of China (to X.Z.), the Innovation Program of Chinese Academy of Agricultural Sciences and the Elite Young Scientists Program of CAAS (to J.Y.). We thank Decang Kong (National Foundation for Improved Cultivar of Chinese Jujube, Bureau of Natural Resources and Planning of Cangxian County) and Yongkang Wang (National Jujube Germplasm Repository, Shanxi Agricultural University) for assisting for sampling.This work was supported by the National Key R&D Program of China (2023YFA0915800 and 2023ZD04076 to J.Y.); the National Natural Science Foundation of China (32271928 to M.G.); the Luoyang Key Science and Technology Innovation Program (2101016\u2009A to X.Z.); the Tianchi Talent in Xinjiang of China (to X.Z.), the Innovation Program of Chinese Academy of Agricultural Sciences and the Elite Young Scientists Program of CAAS (to J.Y.). We thank Decang Kong (National Foundation for Improved Cultivar of Chinese Jujube, Bureau of Natural Resources and Planning of Cangxian County) and Yongkang Wang (National Jujube Germplasm Repository, Shanxi Agricultural University) for assisting for sampling.
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