文献类型： 外文期刊

作者： Cheng, Lin ¹ ; Wang, Nan ¹ ; Bao, Zhigui ¹ ; Zhou, Qian ⁵ ; Guarracino, Andrea ⁶ ; Yang, Yuting ¹ ; Wang, Pei ¹ ; Zhang, Zhiyang ¹ ; Tang, Die ¹ ; Zhang, Pingxian ¹ ; Wu, Yaoyao ¹ ; Zhou, Yao ¹ ; Zheng, Yi ¹ ; Hu, Yong ¹ ; Lian, Qun ¹ ; Ma, Zhaoxu ¹ ; Lassois, Ludivine ² ; Zhang, Chunzhi ¹ ; Lucas, William J. ¹⁰ ; Garrison, Erik ⁶ ; Stein, Nils ¹¹ ; Staedler, Thomas ¹³ ; Zhou, Yongfeng ¹ ; Huang, Sanwen ¹ ;

作者机构： 1.Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Minist Agr & Rural Affairs,Shenzhen Branch, Natl Key Lab Trop Crop Breeding,Minist Agr & Rural, Shenzhen, Peoples R China

2.Univ Liege, TERRA Teaching & Res Ctr, Plant Genet & Rhizosphere Proc Lab, Gembloux Agrobio Tech, Gembloux, Belgium

3.Chinese Acad Trop Agr Sci, Natl Key Lab Trop Crop Breeding, Haikou, Peoples R China

4.Max Planck Inst Biol Tubingen, Dept Mol Biol, Tubingen, Germany

5.Sun Yat Sen Univ, Sch Agr & Biotechnol, Shenzhen, Peoples R China

6.Univ Tennessee, Hlth Sci Ctr, Dept Genet Genom & Informat, Memphis, TN USA

7.Yale Univ, Sch Med, Dept Genet, New Haven, CT USA

8.Nanjing Agr Univ, Coll Hort, Nanjing, Peoples R China

9.Univ Chinese Acad Sci, Chinese Acad Sci, Key Lab Plant Mol Physiol, Inst Bot, Beijing, Peoples R China

10.Univ Calif Davis, Coll Biol Sci, Dept Plant Biol, Davis, CA USA

11.Leibniz Inst Plant Genet & Crop Plant Res IPK, Gatersleben, Seeland, Germany

12.Martin Luther Univ Halle Wittenberg, Inst Agr & Nutr Sci, D-06120 Halle, Saale, Germany

13.Swiss Fed Inst Technol, Inst Integrat Biol, CH-8092 Zurich, Switzerland

14.Swiss Fed Inst Technol, Zurich Basel Plant Sci Ctr, Zurich, Switzerland

期刊名称：NATURE （ 影响因子：48.5； 五年影响因子：55.0 ）

ISSN： 0028-0836

年卷期： 2025 年 640 卷 8058 期

页码：

收录情况： SCI

摘要： The tetraploid genome and clonal propagation of the cultivated potato (Solanum tuberosum L.)1,2 dictate a slow, non-accumulative breeding mode of the most important tuber crop. Transitioning potato breeding to a seed-propagated hybrid system based on diploid inbred lines has the potential to greatly accelerate its improvement3. Crucially, the development of inbred lines is impeded by manifold deleterious variants; explaining their nature and finding ways to eliminate them is the current focus of hybrid potato research4, 5, 6, 7, 8, 9-10. However, most published diploid potato genomes are unphased, concealing crucial information on haplotype diversity and heterozygosity11, 12-13. Here we develop a phased potato pangenome graph of 60 haplotypes from cultivated diploids and the ancestral wild species, and find evidence for the prevalence of transposable elements in generating structural variants. Compared with the linear reference, the graph pangenome represents a broader diversity (3,076 Mb versus 742 Mb). Notably, we observe enhanced heterozygosity in cultivated diploids compared with wild ones (14.0% versus 9.5%), indicating extensive hybridization during potato domestication. Using conservative criteria, we identify 19,625 putatively deleterious structural variants (dSVs) and reveal a biased accumulation of deleterious single nucleotide polymorphisms (dSNPs) around dSVs in coupling phase. Based on the graph pangenome, we computationally design ideal potato haplotypes with minimal dSNPs and dSVs. These advances provide critical insights into the genomic basis of clonal propagation and will guide breeders to develop a suite of promising inbred lines.