Genome sequence and analysis of the tuber crop potato

Xun Xu, Shengkai Pan, Shifeng Cheng, Bo Zhang, Desheng Mu, Peixiang Ni, Gengyun Zhang, Shuang Yang, Ruiqiang Li, Jun Wang, Gisella Orjeda, Frank Guzman, Michael Torres, Roberto Lozano, Olga Ponce, Diana Martinez, Germán De La Cruz, S. K. Chakrabarti, Virupaksh U. Patil, G. SkryabinBoris B. Kuznetsov, Nikolai V. Ravin, Tatjana V. Kolganova, Alexey V. Beletsky, Andrei V. Mardanov, Alex Di Genova, Daniel M. Bolser, David M.A. Martin, Guangcun Li, Yu Yang, Hanhui Kuang, Qun Hu, Xingyao Xiong, Gerard J. Bishop, Boris Sagredo, Nilo Mejía, Wlodzimierz Zagorski, Robert Gromadka, Jan Gawor, Pawel Szczesny, Sanwen Huang, Zhonghua Zhang, Chunbo Liang, Jun He, Ying Li, Ying He, Jianfei Xu, Youjun Zhang, Binyan Xie, Yongchen Du, Dongyu Qu, Merideth Bonierbale, Marc Ghislain, Maria Del Rosario Herrera, Giovanni Giuliano, Marco Pietrella, Gaetano Perrotta, Paolo Facella, Kimberly O'Brien, Sergio E. Feingold, Leandro E. Barreiro, Gabriela A. Massa, Luis Diambra, Brett R. Whitty, Brieanne Vaillancourt, Haining Lin, Alicia N. Massa, Michael Geoffroy, Steven Lundback, Dean DellaPenna, C. Robin Buell, Sanjeev Kumar Sharma, David F. Marshall, Robbie Waugh, Glenn J. Bryan, Marialaura Destefanis, Istvan Nagy, Dan Milbourne, Susan J. Thomson, Mark Fiers, Jeanne M.E. Jacobs, Kare L. Nielsen, Mads Sønderkær, Marina Iovene, Giovana A. Torres, Jiming Jiang, Richard E. Veilleux, Christian W.B. Bachem, Jan De Boer, Theo Borm, Bjorn Kloosterman, Herman Van Eck, Erwin Datema, Baste Lintel Hekkert, Aska Goverse, Roeland C.H.J. Van Ham, Richard G.F. Visser

Research output: Contribution to journalArticlepeer-review

1231 Scopus citations

Abstract

Potato (Solanum tuberosum L.) is the world's most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop.

Original languageEnglish
Pages (from-to)189-195
Number of pages7
JournalNature
Volume475
Issue number7355
DOIs
StatePublished - 14 Jul 2011

Bibliographical note

Funding Information:
Acknowledgements We acknowledge the assistance of W. Amoros, B. Babinska, R. V. Baslerov, B. K. Bumazhkin, M. F. Carboni, T. Conner, J. Coombs, L. Daddiego, J. M. D’Ambrosio, G. Diretto, S. B. Divito, D. Douches, M. Filipiak, G. Gianese, R. Hutten, E. Jacobsen, E. Kalinska, S. Kamoun, D. Kells, H. Kossowska, L. Lopez, M. Magallanes-Lundback, T. Miranda, P. S. Naik, A. N. Panteleeva, D. Pattanayak, E. O. Patutina, M. Portantier, S. Rawat, R. Simon, B. P. Singh, B. Singh, W. Stiekema, M. V. Sukhacheva and C. Town in providing plant material, generating data, annotation, analyses, and discussions. We are indebted to additional faculty and staff of the BGI-Shenzhen,J CraigVenter Institute,andMSU ResearchTechnologySupportFacility who contributed tothis project.Backgroundandpreliminary data were providedbythe Centre for BioSystems Genomics (CBSG), EU-project (APOPHYS EU-QLRT-2001-01849) and US Department of Agriculture National Institute of Food and Agriculture SolCAP project (2008-55300-04757 and 2009-85606-05673). We acknowledge the funding made available by the ‘‘863’’ National High Tech Research Development PrograminChina(2006AA100107), ‘‘973’’NationalKey Basic Research Program in China (2006CB101904, 2007CB815703, 2007CB815705, 2009CB119000), Board of Wageningen University and Research Centre, CAPES - Brazilian Ministry of Education, Chinese Academy of Agricultural Sciences (seed grant to S.H.), Chinese Ministry of Agriculture (The ‘‘948’’ Program), Chinese Ministry of Finance (1251610601001), Chinese Ministry of Science and Technology (2007DFB30080), China Postdoctoral Science Foundation (20070420446 to Z.Z.), CONICET (Argentina), DAFF Research Stimulus Fund (07-567), CONICYT-Chile (PBCT-PSD-03), Danish Council for Strategic Research Programme Commission on Health, Food and Welfare (2101-07-0116), Danish Council for Strategic Research Programme Commission on Strategic Growth Technologies (Grant 2106-07-0021), FINCyT ((099-FINCyT-EQUIP-2009)/(076-FINCyT-PIN-2008), Préstamo BID no. 1663/OC-PE, FONDAP and BASAL-CMM), Fund for Economic Structural Support (FES), HarvestPlus Challenge Program, Indian Council of Agricultural Research, INIA-Ministry of Agriculture of Chile, Instituto Nacional de Innovacion Agraria-Ministry of Agriculture of Peru, Instituto Nacional de Tecnología Agropecuaria (INTA), Italian Ministry of Research (Special Fund for Basic Research), International Potato Center (CIP-CGIAR core funds), LBMG of Center for Genome Regulation and Center for Mathematical Modeling, Universidad de Chile (UMI 2807 CNRS), Ministry of Education and Science of Russia (contract02.552.11.7073), National Nature Science Foundation of China (30671319, 30725008, 30890032, 30971995), Natural Science Foundation of Shandong Province in China (Y2006D21), Netherlands Technology Foundation (STW), Netherlands Genomics Initiative (NGI), Netherlands Ministries of Economic Affairs (EZ) and Agriculture (LNV), New Zealand Institute for Crop & Food Research Ltd

Funding Information:
Strategic Science Initiative, Perez Guerrero Fund, Peruvian Ministry of Agriculture-Technical Secretariat of coordination with the CGIAR, Peruvian National Council of Science and Technology (CONCYTEC),Polish Ministry of Science andHigher Education (47/PGS/2006/01), Programa Cooperativo para el Desarrollo Tecnológico Agroalimentario y Agroindustrial del Cono Sur (PROCISUR), Project Programa Bicentenario de Ciencia y Tecnología - Conicyt, PBCT - Conicyt PSD-03, Russian Foundation for Basic Research (09-04-12275), Secretaría de Ciencia y Tecnología (SECyT) actual Ministerio de Ciencia y Tecnología (MINCyT), Argentina, Shenzhen Municipal Government of China (CXB200903110066A, ZYC200903240077A, ZYC200903240076A), Solexa project (272-07-0196), Special Multilateral Fund of the Inter-American Council for Integral Development (FEMCIDI), Teagasc, Teagasc Walsh Fellowship Scheme, The New Zealand Institute for Plant & Food Research Ltd Capability Fund, UK Potato Genome Sequencing grant (Scottish Government Rural and Environment Research and Analysis Directorate (RERAD), Department for Environment, Food and Rural Affairs (DEFRA), Agriculture and Horticulture Development Board - Potato Council), UK Biotechnology and Biological Sciences Research Council (Grant BB/F012640), US National Science Foundation Plant Genome Research Program (DBI-0604907 /DBI-0834044), Virginia Agricultural Experiment Station USDA Hatch Funds (135853), and Wellcome Trust Strategic award (WT 083481).

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