Leveraging a phased pangenome for haplotype design of hybrid potato

作者：Lin Zhang Cheng, Nan Wang, Zhigui Bao, Qian Zhou, Andrea Guarracino, Yuting Yang, Pei Wang, Zhiyang Zhang, Dié Tang, Pingxian Zhang, Yaoyao Wu, Yao Zhou, Yi Feng Zheng, Yong Hu, Qun Lian, Zhaoxu Ma, Ludivine Lassois, Chunzhi Zhang, William John Lucas, Erik P. Garrison, Nils Stein, Thomas C Stadler, Yongfeng Zhou, Sanwen Huang · 发表于：Nature · 年份：2025 · DOI：10.1038/s41586-024-08476-9 · 被引用次数：64 · 研究领域：Plant Pathogens and Resistance、Plant Disease Resistance and Genetics、Chromosomal and Genetic Variations

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 dSV...