Leveraging a phased pangenome for haplotype design of hybrid potato

  1. Cheng, Lin
  2. Wang, Nan
  3. Bao, Zhigui ORCID logo
  4. Zhou, Qian
  5. Guarracino, Andrea ORCID logo
  6. Yang, Yuting
  7. Wang, Pei
  8. zhang, zhiyang ORCID logo
  9. Tang, Die
  10. Zhang, Pingxian ORCID logo
  11. Wu, Yaoyao
  12. Zhou, Yao ORCID logo
  13. Zheng, Yi
  14. Hu, Yong
  15. Lian, Qun
  16. ma, zhaoxu ORCID logo
  17. Lassois, Ludivine
  18. Zhang, Chunzhi
  19. Lucas, William J
  20. Garrison, Erik ORCID logo
  21. Stein, Nils ORCID logo
  22. Städler, Thomas
  23. Zhou, Yongfeng ORCID logo
  24. Huang, Sanwen ORCID logo

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WeightNameValue
1000 Titel
  • Leveraging a phased pangenome for haplotype design of hybrid potato
1000 Autor/in
  1. Cheng, Lin |
  2. Wang, Nan |
  3. Bao, Zhigui |
  4. Zhou, Qian |
  5. Guarracino, Andrea |
  6. Yang, Yuting |
  7. Wang, Pei |
  8. zhang, zhiyang |
  9. Tang, Die |
  10. Zhang, Pingxian |
  11. Wu, Yaoyao |
  12. Zhou, Yao |
  13. Zheng, Yi |
  14. Hu, Yong |
  15. Lian, Qun |
  16. ma, zhaoxu |
  17. Lassois, Ludivine |
  18. Zhang, Chunzhi |
  19. Lucas, William J |
  20. Garrison, Erik |
  21. Stein, Nils |
  22. Städler, Thomas |
  23. Zhou, Yongfeng |
  24. Huang, Sanwen |
1000 Erscheinungsjahr 2025
1000 LeibnizOpen
1000 Publikationstyp
  1. Artikel |
1000 Online veröffentlicht
  • 2025-01-22
1000 Erschienen in
1000 Quellenangabe
  • 640(8058):408-417
1000 FRL-Sammlung
1000 Lizenz
1000 Verlagsversion
  • https://dx.doi.org/10.1038/s41586-024-08476-9 |
  • https://pmc.ncbi.nlm.nih.gov/articles/PMC11981936/ |
1000 Ergänzendes Material
  • https://dx.doi.org/10.1038/s41586-024-08476-9 |
1000 Publikationsstatus
1000 Begutachtungsstatus
1000 Sprache der Publikation
1000 Abstract/Summary
  • 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 improvement(3). 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(4-10). However, most published diploid potato genomes are unphased, concealing crucial information on haplotype diversity and heterozygosity(11-13). 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.
1000 Sacherschließung
lokal agricultural genetics
lokal genomics
lokal structural variation
lokal plant breeding
lokal plant domestication
1000 Fächerklassifikation (DDC)
1000 Liste der Beteiligten
  1. https://frl.publisso.de/adhoc/uri/Q2hlbmcsIExpbiA=|https://frl.publisso.de/adhoc/uri/V2FuZywgTmFu|https://orcid.org/0000-0003-3601-460X|https://frl.publisso.de/adhoc/uri/WmhvdSwgUWlhbg==|https://orcid.org/0000-0001-9744-131X|https://frl.publisso.de/adhoc/uri/WWFuZywgWXV0aW5n|https://frl.publisso.de/adhoc/uri/V2FuZywgUGVp|https://orcid.org/0000-0002-9466-9439|https://frl.publisso.de/adhoc/uri/VGFuZywgRGll|https://orcid.org/0000-0001-6305-1006|https://frl.publisso.de/adhoc/uri/V3UsIFlhb3lhbw==|https://orcid.org/0000-0001-9791-7664|https://frl.publisso.de/adhoc/uri/WmhlbmcsIFlpIA==|https://frl.publisso.de/adhoc/uri/SHUsIFlvbmcg|https://frl.publisso.de/adhoc/uri/TGlhbiwgUXVuIA==|https://orcid.org/0009-0005-4787-2329|https://frl.publisso.de/adhoc/uri/TGFzc29pcywgTHVkaXZpbmUg|https://frl.publisso.de/adhoc/uri/WmhhbmcsIENodW56aGkg|https://frl.publisso.de/adhoc/uri/THVjYXMsIFdpbGxpYW0gSg==|https://orcid.org/0000-0003-3821-631X|https://orcid.org/0000-0003-3011-8731|https://frl.publisso.de/adhoc/uri/U3TDpGRsZXIsIFRob21hcw==|https://orcid.org/0000-0003-0780-2973|https://orcid.org/0000-0002-8547-5309
1000 Label
1000 Förderer
  1. https://doi.org/10.13039/501100001809 |
  2. https://doi.org/10.13039/501100012166 |
  3. https://doi.org/10.13039/501100012421 |
  4. Shenzhen Outstanding Talents Training Fund |
  5. Guangdong Major Project of Basic and Applied Basic Research |
1000 Fördernummer
  1. 32488302;32422079
  2. 2019FA0906200
  3. CAAS- ZDRW202404
  4. -
  5. 2021B03C1030004
1000 Förderprogramm
  1. -
  2. -
  3. -
  4. -
  5. -
1000 Dateien
  1. Leveraging a phased pangenome for haplotype design of hybrid potato
    Leveraging a phased pangenome for haplotype design of hybrid potato
1000 Förderung
  1. 1000 joinedFunding-child
    1000 Förderer https://doi.org/10.13039/501100001809 |
    1000 Förderprogramm -
    1000 Fördernummer 32488302;32422079
  2. 1000 joinedFunding-child
    1000 Förderer https://doi.org/10.13039/501100012166 |
    1000 Förderprogramm -
    1000 Fördernummer 2019FA0906200
  3. 1000 joinedFunding-child
    1000 Förderer https://doi.org/10.13039/501100012421 |
    1000 Förderprogramm -
    1000 Fördernummer CAAS- ZDRW202404
  4. 1000 joinedFunding-child
    1000 Förderer Shenzhen Outstanding Talents Training Fund |
    1000 Förderprogramm -
    1000 Fördernummer -
  5. 1000 joinedFunding-child
    1000 Förderer Guangdong Major Project of Basic and Applied Basic Research |
    1000 Förderprogramm -
    1000 Fördernummer 2021B03C1030004
1000 Objektart article
1000 Beschrieben durch
1000 @id frl:6511004.rdf
1000 Erstellt am 2025-04-11T14:51:16.341+0200
1000 Erstellt von 325
1000 beschreibt frl:6511004
1000 Bearbeitet von 317
1000 Zuletzt bearbeitet 2025-06-04T11:30:38.188+0200
1000 Objekt bearb. Wed Jun 04 11:30:27 CEST 2025
1000 Vgl. frl:6511004
1000 Oai Id
  1. oai:frl.publisso.de:frl:6511004 |
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