中国农业科学院黄三文团队利用分阶段全基因组图谱进行杂交马铃薯的单倍型设计。2025年1月22日，《自然》杂志在线发表了这项成果。

研究人员开发了一个包含60个单倍型的分阶段马铃薯全基因组图谱，涵盖栽培二倍体和祖先野生种，并发现了转座元件在产生结构变异中的广泛存在。与线性参考基因组相比，该图谱全基因组代表了更广泛的多样性（3076Mb vs 742Mb）。值得注意的是，研究人员观察到栽培二倍体的杂合性高于野生种（14.0% vs 9.5%），这表明马铃薯在驯化过程中发生了广泛的杂交。使用保守标准，研究人员识别了19625个可能有害的结构变异（dSV），并揭示了有害的单核苷酸多态性（dSNP）在耦合阶段围绕dSV的偏向性积累。基于图谱全基因组，研究人员通过计算设计了理想的马铃薯单倍型，最小化dSNP和dSV。这些进展为克隆繁殖的基因组基础提供了重要见解，并将指导育种者开发一系列有前景的自交系。

据了解，栽培马铃薯（Solanum tuberosum L.）的四倍体基因组和克隆繁殖方式决定了这一重要块茎作物的缓慢、非累积性育种模式。将马铃薯育种转向基于二倍体自交系的种子繁殖杂交系统，具有显著加速其改良的潜力。关键是，自交系的开发受到多种有害变异的阻碍；解释这些变异的性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，大多数已发布的二倍体马铃薯基因组未进行分阶段处理，隐藏了有关单倍型多样性和杂合性的关键信息。

附：英文原文

Title: Leveraging a phased pangenome for haplotype design of hybrid potato

Author: Cheng, Lin, Wang, Nan, Bao, Zhigui, Zhou, Qian, Guarracino, Andrea, Yang, Yuting, Wang, Pei, Zhang, Zhiyang, Tang, Di, 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, Stdler, Thomas, Zhou, Yongfeng, Huang, Sanwen

Issue&Volume: 2025-01-22

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 research4,5,6,7,8,9,10. 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 (3,076Mb versus 742Mb). 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.

DOI: 10.1038/s41586-024-08476-9

Source: https://www.nature.com/articles/s41586-024-08476-9