Leveraging a phased pangenome for haplotype design of hybrid potato

The tetraploid genome and clonal propagation of the cultivated potato (Solanum tuberosum L.)<sup>1,2</sup> 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<sup>3</sup>. 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<sup>4-10</sup>. However, most published diploid potato genomes are unphased, concealing crucial information on haplotype diversity and heterozygosity<sup>11-13</sup>. 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.

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Publication Details

Journal
Nature
Published
2025-01-22
DOI
https://doi.org/10.1038/s41586-024-08476-9
Citations
37
Primary Topic
Plant Pathogens and Resistance
Type
article
Field-Weighted Citation Impact
64.74

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article

Leveraging a phased pangenome for haplotype design of hybrid potato

Erik Garrison, Thomas Städler, Andrea Guarracino, Pingxian Zhang et al.
37 citations
Nature
Plant Pathogens and Resistance
64.74
article

Leveraging a phased pangenome for haplotype design of hybrid potato

Erik Garrison, Thomas Städler, Andrea Guarracino, Pingxian Zhang, Sanwen Huang, Zhigui Bao, Yong Hu, Yao Zhou, Nils Stein, Qian Zhou, Yi Zheng, William J. Lucas, Ludivine Lassois, Lin Cheng, Dié Tang, Yaoyao Wu, Chunzhi Zhang, Pei Wang, Zhiyang Zhang, Nan Wang, Qun Lian, Yuting Yang, Yongfeng Zhou, Zhaoxu Ma
article en
37 citations

Abstract

The tetraploid genome and clonal propagation of the cultivated potato (Solanum tuberosum L.)<sup>1,2</sup> 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<sup>3</sup>. 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<sup>4-10</sup>. However, most published diploid potato genomes are unphased, concealing crucial information on haplotype diversity and heterozygosity<sup>11-13</sup>. 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.

NatureVol. 640(8058)
Chinese Academy of Tropical Agricultural Sciences (CN), Nanjing Agricultural University (CN), University of Liège (BE), Sun Yat-sen University (CN), University of Tennessee Health Science Center (US), Gembloux Agro-Bio Tech (BE), Beijing Botanical Garden (CN), Yale University (US), ETH Zurich (CH), Agricultural Genomics Institute at Shenzhen (CN), Institute of Botany of the Slovak Academy of Sciences (SK), Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK) (DE), Chinese Academy of Agricultural Sciences (CN), Ministry of Agriculture and Rural Affairs (CN), Max Planck Institute for Biology (DE), Martin Luther University Halle-Wittenberg (DE), University of California, Davis (US)
National Natural Science Foundation of China, Chinese Academy of Agricultural Sciences, National Key Research and Development Program of China, Agricultural Science and Technology Innovation Program
Openalex Percentile: Top 0%
Plant Pathogens and Resistance
64.74
DOIOpen Access PDFOpenAlex
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