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Genomic analyses of diverse wild and cultivated accessions provide insights into the evolutionary history of jujube

文献类型： 外文期刊

作者： Guo, Mingxin 1 ; Zhang, Zhongren 3 ; Li, Shipeng 1 ; Lian, Qun 4 ; Fu, Pengcheng 1 ; He, Yali 1 ; Qiao, Jinxin 1 ; Xu, Ke 1 ;

作者机构： 1.Luoyang Normal Univ, Coll Life Sci, Luoyang, Peoples R China

2.Luoyang Normal Univ, Jujube Res Ctr, Luoyang, Peoples R China

3.Novogene Bioinformat Inst, Beijing, Peoples R China

4.Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Minist Agr, Genome Anal Lab, Shenzhen, Peoples R China

5.Shanxi Acad Agr Sci, Pomol Inst, Taigu, Peoples R China

关键词： jujube; resequencing; evolutionary history; seed-setting rate; fruit weight

期刊名称：PLANT BIOTECHNOLOGY JOURNAL （ 影响因子：9.803； 五年影响因子：9.555 ）

ISSN： 1467-7644

年卷期：

页码：

收录情况： SCI

摘要： The Chinese jujube (Ziziphus jujubaMill.), a member of the Rhamnaceae family, is an important perennial fruit tree crop of substantial economic, ecological and nutritional value, and is also used as a traditional herbal medicine. Here, we report the resequencing of 493 jujube accessions, including 202 wild and 291 cultivated accessions at >16x depth. Our population genomic analyses revealed that the Shanxi-Shaanxi area of China was jujube's primary domestication centre and that jujube was then disseminated into East China before finally extending into South China. Divergence events analysis indicated thatZiziphus acidojujubaandZiziphus jujubadiverged around 2.7 Mya, suggesting the interesting possibility that a long pre-domestication period may have occurred prior to human intervention. Using the large genetic polymorphism data set, we identified a 15-bp tandem insertion in the promoter of the jujube ortholog of thePOLLEN DEFECTIVE IN GUIDANCE 1(POD1) gene, which was strongly associated with seed-setting rate. Integrating genome-wide association study (GWAS), transcriptome data, expression analysis and transgenic validation in tomato, we identified aDA3/UBIQUITIN-SPECIFIC PROTEASE 14(UBP14) ortholog, which negatively regulate fruit weight in jujube. We also identified candidate genes, which have likely influenced the selection of fruit sweetness and crispness texture traits among fresh and dry jujubes. Our study not only illuminates the genetic basis of jujube evolution and domestication and provides a deep and rich genomic resource to facilitate both crop improvement and hypothesis-driven basic research, but also identifies multiple agriculturally important genes for this unique perennial tree fruit species.

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