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. 2025 Sep 18;188(19):5249-5265.e15.
doi: 10.1016/j.cell.2025.06.034. Epub 2025 Jul 31.

Ancient hybridization underlies tuberization and radiation of the potato lineage

Zhiyang Zhang  1 , Pingxian Zhang  1 , Yiyuan Ding  2 , Zefu Wang  3 , Zhaoxu Ma  4 , Edeline Gagnon  5 , Yuxin Jia  6 , Lin Cheng  1 , Zhigui Bao  7 , Zinan Liu  1 , Yaoyao Wu  8 , Yong Hu  1 , Qun Lian  1 , Weichao Lin  1 , Nan Wang  1 , Keyi Ye  1 , Hongru Wang  1 , Jinzhe Zhang  9 , Yongfeng Zhou  1 , Liang Liu  10 , Suhua Li  1 , William J Lucas  11 , Tiina Särkinen  12 , Sandra Knapp  13 , Loren H Rieseberg  14 , Jianquan Liu  15 , Sanwen Huang  16
Affiliations

Affiliations

  • 1 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, Guangdong 518120, China.
  • 2 Huazhong Agricultural University, Wuhan, Hubei 430070, China.
  • 3 State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Ecology and Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China.
  • 4 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, Guangdong 518120, China; Huazhong Agricultural University, Wuhan, Hubei 430070, China.
  • 5 Department of Integrative Biology, College of Biological Science, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
  • 6 The AGISCAAS-YNNU Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, Yunnan 650500, China.
  • 7 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, Guangdong 518120, China; Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen 72076, Germany.
  • 8 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, Guangdong 518120, China; State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
  • 9 State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
  • 10 Department of Statistics, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.
  • 11 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, Guangdong 518120, China; Department of Plant Biology, College of Biological Sciences, University of California, Davis, Davis, CA 95616, USA.
  • 12 Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, UK.
  • 13 Natural History Museum, London SW7 5BD, UK. Electronic address: s.knapp@nhm.ac.uk.
  • 14 Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada. Electronic address: loren.rieseberg@botany.ubc.ca.
  • 15 Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China; State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, Gansu 730000, China. Electronic address: liujq@nwipb.cas.cn.
  • 16 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, Guangdong 518120, China; National Key Laboratory of Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China. Electronic address: huangsanwen@caas.cn.
Free article

Ancient hybridization underlies tuberization and radiation of the potato lineage

Zhiyang Zhang et al. Cell. .
Free article
. 2025 Sep 18;188(19):5249-5265.e15.
doi: 10.1016/j.cell.2025.06.034. Epub 2025 Jul 31.

Authors

Zhiyang Zhang  1 , Pingxian Zhang  1 , Yiyuan Ding  2 , Zefu Wang  3 , Zhaoxu Ma  4 , Edeline Gagnon  5 , Yuxin Jia  6 , Lin Cheng  1 , Zhigui Bao  7 , Zinan Liu  1 , Yaoyao Wu  8 , Yong Hu  1 , Qun Lian  1 , Weichao Lin  1 , Nan Wang  1 , Keyi Ye  1 , Hongru Wang  1 , Jinzhe Zhang  9 , Yongfeng Zhou  1 , Liang Liu  10 , Suhua Li  1 , William J Lucas  11 , Tiina Särkinen  12 , Sandra Knapp  13 , Loren H Rieseberg  14 , Jianquan Liu  15 , Sanwen Huang  16

Affiliations

  • 1 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, Guangdong 518120, China.
  • 2 Huazhong Agricultural University, Wuhan, Hubei 430070, China.
  • 3 State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Ecology and Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China.
  • 4 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, Guangdong 518120, China; Huazhong Agricultural University, Wuhan, Hubei 430070, China.
  • 5 Department of Integrative Biology, College of Biological Science, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
  • 6 The AGISCAAS-YNNU Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, Yunnan 650500, China.
  • 7 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, Guangdong 518120, China; Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen 72076, Germany.
  • 8 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, Guangdong 518120, China; State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
  • 9 State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
  • 10 Department of Statistics, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.
  • 11 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, Guangdong 518120, China; Department of Plant Biology, College of Biological Sciences, University of California, Davis, Davis, CA 95616, USA.
  • 12 Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, UK.
  • 13 Natural History Museum, London SW7 5BD, UK. Electronic address: s.knapp@nhm.ac.uk.
  • 14 Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada. Electronic address: loren.rieseberg@botany.ubc.ca.
  • 15 Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China; State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, Gansu 730000, China. Electronic address: liujq@nwipb.cas.cn.
  • 16 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, Guangdong 518120, China; National Key Laboratory of Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China. Electronic address: huangsanwen@caas.cn.

Abstract

Interspecific hybridization may trigger species radiation by creating allele combinations and traits. Cultivated potato and its 107 wild relatives from the Petota lineage all share the distinctive trait of underground tubers, but the underlying mechanisms for tuberization and its relationship to extensive species diversification remain unclear. Through analyses of 128 genomes, including 88 haplotype-resolved genomes, we revealed that Petota is of ancient hybrid origin, with all members exhibiting stable mixed genomic ancestry, derived from the Etuberosum and Tomato lineages ca. 8-9 million years ago. Our functional experiments further validated the crucial roles of parental genes in tuberization, indicating that interspecific hybridization is a key driver of this innovative trait. This trait, along with the sorting and recombination of hybridization-derived polymorphisms, likely triggered the explosive species diversification of Petota by enabling occupation of broader ecological niches. These findings highlight how ancient hybridization fosters key innovation and drives subsequent species radiation.

Keywords: hybrid origin; potato lineage; radiation evolution; tuber formation.

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Conflict of interest statement

Declaration of interests The Agricultural Genomics Institute at Shenzhen has one pending patent application based on this study. S.H. is a member of the Cell advisory board.

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