Leveraging a phased pangenome for haplotype design of hybrid potato

Lin Cheng, Nan Wang, Zhigui Bao, Qian Zhou, Andrea Guarracino, Yuting Yang, Pei Wang, Zhiyang Zhang, Dié Tang, Pingxian Zhang, Yaoyao Wu, Yao Zhou, Yi Zheng, Yong Hu, Qun Lian, Zhaoxu Ma, Ludivine Lassois, Chunzhi Zhang, William J. Lucas, Erik Garrison, Nils Stein, Thomas Städler, Yongfeng Zhou and Sanwen Huang ()
Additional contact information
Lin Cheng: Chinese Academy of Agricultural Sciences
Nan Wang: Chinese Academy of Agricultural Sciences
Zhigui Bao: Chinese Academy of Agricultural Sciences
Qian Zhou: Sun Yat-Sen University
Andrea Guarracino: University of Tennessee Health Science Center
Yuting Yang: Chinese Academy of Agricultural Sciences
Pei Wang: Chinese Academy of Agricultural Sciences
Zhiyang Zhang: Chinese Academy of Agricultural Sciences
Dié Tang: Chinese Academy of Agricultural Sciences
Pingxian Zhang: Chinese Academy of Agricultural Sciences
Yaoyao Wu: Chinese Academy of Agricultural Sciences
Yao Zhou: Chinese Academy of Agricultural Sciences
Yi Zheng: Chinese Academy of Agricultural Sciences
Yong Hu: Chinese Academy of Agricultural Sciences
Qun Lian: Chinese Academy of Agricultural Sciences
Zhaoxu Ma: Chinese Academy of Agricultural Sciences
Ludivine Lassois: University of Liège
Chunzhi Zhang: Chinese Academy of Agricultural Sciences
William J. Lucas: University of California, Davis
Erik Garrison: University of Tennessee Health Science Center
Nils Stein: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Thomas Städler: ETH Zurich
Yongfeng Zhou: Chinese Academy of Agricultural Sciences
Sanwen Huang: Chinese Academy of Agricultural Sciences

Nature, 2025, vol. 640, issue 8058, 408-417

Abstract: Abstract 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 research4–10. However, most published diploid potato genomes are unphased, concealing crucial information on haplotype diversity and heterozygosity11–13. 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.

Date: 2025
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DOI: 10.1038/s41586-024-08476-9

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