Cheng Lin, Wang Nan, Bao Zhigui, Zhou Qian, Guarracino Andrea, Yang Yuting, Wang Pei, Zhang Zhiyang, Tang Dié, Zhang Pingxian, Wu Yaoyao, Zhou Yao, Zheng Yi, Hu Yong, Lian Qun, Ma Zhaoxu, Lassois Ludivine, Zhang Chunzhi, Lucas William J, Garrison Erik, Stein Nils, Städler Thomas, Zhou Yongfeng, Huang Sanwen
National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
Plant Genetics and Rhizosphere Processes Laboratory, TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium.
Nature. 2025 Apr;640(8058):408-417. doi: 10.1038/s41586-024-08476-9. Epub 2025 Jan 22.
The tetraploid genome and clonal propagation of the cultivated potato (Solanum tuberosum L.) 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 improvement. 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 research. However, most published diploid potato genomes are unphased, concealing crucial information on haplotype diversity and heterozygosity. 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.
栽培马铃薯（Solanum tuberosum L.）的四倍体基因组和克隆繁殖决定了这种最重要块茎作物缓慢、非累积性的育种模式。将马铃薯育种转变为基于二倍体自交系的种子繁殖杂交系统，有可能极大地加速其改良进程。至关重要的是，自交系的发育受到多种有害变异的阻碍；解释这些变异的本质并找到消除它们的方法是当前杂交马铃薯研究的重点。然而，大多数已发表的二倍体马铃薯基因组是未分型的，掩盖了关于单倍型多样性和杂合性的关键信息。在这里，我们构建了一个包含60个单倍型的分型马铃薯泛基因组图谱，这些单倍型来自栽培二倍体和原始野生种，并发现了转座元件在产生结构变异中普遍存在的证据。与线性参考基因组相比，图谱泛基因组代表了更广泛的多样性（3076 Mb对742 Mb）。值得注意的是，我们观察到栽培二倍体的杂合性高于野生二倍体（14.0%对9.5%），这表明马铃薯驯化过程中发生了广泛的杂交。使用保守标准，我们鉴定出19625个推定的有害结构变异（dSVs），并揭示了处于耦合阶段的dSVs周围有害单核苷酸多态性（dSNPs）的偏向性积累。基于图谱泛基因组，我们通过计算设计出具有最小dSNPs和dSVs的理想马铃薯单倍型。这些进展为克隆繁殖的基因组基础提供了关键见解，并将指导育种者培育出一系列有前景的自交系。
