Analyzes of pan-genome and resequencing atlas unveil the genetic basis of jujube domestication

Mingxin Guo (), Qun Lian, Ye Mei, Wangwang Yang, Suna Zhao, Siyuan Zhang, Xinfeng Xing, Haixiang Zhang, Keying Gao, Wentong He, Zhitong Wang, Huan Wang, Jun Zhou, Lin Cheng, Zhigui Bao, Sanwen Huang, Jianbin Yan () and Xusheng Zhao ()
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Mingxin Guo: Luoyang Normal University
Qun Lian: Chinese Academy of Agricultural Sciences
Ye Mei: Chinese Academy of Agricultural Sciences
Wangwang Yang: Luoyang Normal University
Suna Zhao: Luoyang Normal University
Siyuan Zhang: Luoyang Normal University
Xinfeng Xing: Luoyang Normal University
Haixiang Zhang: Luoyang Normal University
Keying Gao: Luoyang Normal University
Wentong He: Bureau of Natural Resources and Planning of Cangxian County
Zhitong Wang: Bureau of Natural Resources and Planning of Cangxian County
Huan Wang: Chinese Academy of Agricultural Sciences
Jun Zhou: North Minzu University
Lin Cheng: Chinese Academy of Agricultural Sciences
Zhigui Bao: Chinese Academy of Agricultural Sciences
Sanwen Huang: Chinese Academy of Agricultural Sciences
Jianbin Yan: Chinese Academy of Agricultural Sciences
Xusheng Zhao: Luoyang Normal University

Nature Communications, 2024, vol. 15, issue 1, 1-13

Abstract: Abstract 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.

Date: 2024
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DOI: 10.1038/s41467-024-53718-z

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