Graph-based pangenome provides insights into structural variations and genetic basis of metabolic traits in potato
文献类型： 外文期刊
作者： Zhu, Xiaoling 1 ; Yang, Rui 1 ; Liang, Qiqi 1 ; Yu, Yuye 1 ; Wang, Tingting 1 ; Meng, Li 1 ; Wang, Ping 1 ; Wang, Shaoyang 1 ; Li, Xianping 4 ; Yang, Qiongfen 4 ; Guo, Huachun 5 ; Sui, Qijun 4 ; Wang, Qiang 6 ; Du, Hai 7 ; Chen, Qin 8 ; Liang, Zhe 9 ; Wu, Xuewei 1 ; Zeng, Qian 1 ; Huang, Binquan 1 ;
作者机构： 1.Yunnan Univ, Sch Agr, State Key Lab Conservat & Utilizat Bioresources Yu, Kunming 650540, Peoples R China
2.Southwest United Grad Sch, Kunming 650500, Peoples R China
3.Huazhong Agr Univ, Hubei Hongshan Lab, Wuhan 430070, Peoples R China
4.Yunnan Acad Agr Sci, Ind Crops Res Inst, Kunming 650200, Peoples R China
5.Yunnan Agr Univ, Coll Agron & Biotechnol, Kunming 650201, Peoples R China
6.Sichuan Agr Univ, Coll Agron, Chengdu 611130, Peoples R China
7.Southwest Univ, Coll Agron & Biotechnol, Chongqing Engn Res Ctr Rapeseed, Chongqing 400716, Peoples R China
8.Northwest A&F Univ, Coll Agron, State Key Lab Crop Stress Biol Arid Areas, Yangling 712100, Peoples R China
9.Chinese Acad Agr Sci, Biotechnol Res Inst, Beijing 100081, Peoples R China
关键词： Genome assembly; structural variants; graph-based pangenome; PAV-based metabolomics-GWAS
期刊名称：MOLECULAR PLANT （ 影响因子：24.1； 五年影响因子：25.8 ）
ISSN： 1674-2052
年卷期： 2025 年 18 卷 4 期
页码：
收录情况： SCI
摘要： Potato is the world's most important nongrain crop. In this study, to assess genetic diversity within the Petota section, 29 genomes from Petota and Etuberosum sections were newly de novo assembled and 248 accessions of wild potatoes, landraces, and modern cultivars were re-sequenced at >25x depth. Subsequently, a graph-based pangenome was constructed using DM8.1 as the backbone, integrating194,330 nonredundant structural variants. To characterize the metabolome of tubers and illuminate the genomic basis of metabolic traits, LC-MS/MS was employed to obtain the metabolome of 157 accessions, and 9,321 structural variants (SVs) were detected to be significantly associated with 1,258 distinct metabolites via PAV (presence and absence variations)-based metabolomics-GWAS analysis, including metabolites of flavonoids, phenolic acids, and phospholipids. To facilitate the utilization of pangenome resources, a comprehensive platform, the Potato Pangenome Database (PPDB), was developed. Our study provides a comprehensive genomic resource for dissecting the genomic basis of agronomic and metabolic traits in potato, which will accelerate functional genomics studies and genetic improvements in potato.
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