Sequencing the Potato genome: Outline and first results to come from the Elucidation of the sequence of the world's third most important food crop

Richard G.F. Visser, Christian W.B. Bachem, Jan M. de Boer, Glenn J. Bryan, Swarup K. Chakrabati, Sergio Feingold, Robert Gromadka, Roeland C.H.J. van Ham, Sanwen Huang, Jeanne M.E. Jacobs, Boris Kuznetsov, Paulo E. de Melo, Dan Milbourne, Gisella Orjeda, Boris Sagredo, Xiaomin Tang

Research output: Contribution to journalReview articlepeer-review

61 Scopus citations

Abstract

Potato is a member of the Solanaceae, a plant family that includes several other economically important species, such as tomato, eggplant, petunia, tobacco and pepper. The Potato Genome Sequencing Consortium (PGSC) aims to elucidate the complete genome sequence of potato, the third most important food crop in the world. The PGSC is a collaboration between 13 research groups from China, India, Poland, Russia, the Netherlands, Ireland, Argentina, Brazil, Chile, Peru, USA, New Zealand and the UK. The potato genome consists of 12 chromosomes and has a (haploid) length of approximately 840 million base pairs, making it a medium-sized plant genome. The sequencing project builds on a diploid potato genomic bacterial artificial chromosome (BAC) clone library of 78000 clones, which has been fingerprinted and aligned into ~7000 physical map contigs. In addition, the BAC-ends have been sequenced and are publicly available. Approximately 30000 BACs are anchored to the Ultra High Density genetic map of potato, composed of 10000 unique AFLPTM markers. From this integrated genetic-physical map, between 50 to 150 seed BACs have currently been identified for every chromosome. Fluorescent in situ hybridization experiments on selected BAC clones confirm these anchor points. The seed clones provide the starting point for a BAC-by-BAC sequencing strategy. This strategy is being complemented by whole genome shotgun sequencing approaches using both 454 GS FLX and Illumina GA2 instruments. Assembly and annotation of the sequence data will be performed using publicly available and tailor-made tools. The availability of the annotated data will help to characterize germplasm collections based on allelic variance and to assist potato breeders to more fully exploit the genetic potential of potato.

Original languageEnglish
Pages (from-to)417-429
Number of pages13
JournalAmerican Journal of Potato Research
Volume86
Issue number6
DOIs
StatePublished - Nov 2009

Bibliographical note

Funding Information:
The PGSC-Indian component is financed entirely by the Indian Council of Agricultural Research, New Delhi, India The PGSC-South America (Argentina, Brazil, Chile and Peru) was funded by grants from FEMCIDI from the Organization of American States (SEDI/AE-305 /07), the Programa Cooperativo para el Desarrollo Tecnológico Agroalimentario y Agroindustrial del Cono Sur (PROCISUR), the Perez Guerrero Trust Fund (PGTF) and the Brazilian Corporation for Agricultural Research (Embrapa).

Funding Information:
The PGSC-NZ team is funded by The New Zealand Institute for Plant & Food Research Ltd. as a Strategic Science Initiative. Susan Thomson and Mark Fiers are greatly acknowledged for their contribution.

Funding Information:
The PGSC-China was funded by Ministry of Science and Technology (2007DFB30080), Ministry of Agriculture (‘948’ Program: 2007-Z5) and National Natural Science Foundation (30671319).

Funding Information:
The PGSC-Peruvian team was funded by grants from the Peruvian Fund for Innovation in Science and Technology (FINCYT), the Peruvian Ministry of Agriculture (MINAG) and the Peruvian Council of Science and Technology (Concytec). Additional support was received from Universidad Peruana Cayetano Heredia, Universidad Nacional San Cristobal de Huamanga and the Peruvian Ministry of foreign affairs. The PGSC-Chilean initiative has been supported by National Commission of Scientific and Technologic Research (CON-ICYT) and the Foundation for the Innovation in Agriculture (FIA).

Funding Information:
We are indebted to the US groups for their contribution to the potato genome sequencing project and would also particularly like to thank Dr. Robin Buell her input and for the critical reading of the manuscript The Polish part of the PGSC was supported by a grant from the Polish Ministry of Science and Higher Education with contract no. 47/ PGS/2006/01.

Funding Information:
Glenn J Bryan would like to acknowledge the financial support of Scottish Government Rural and Environment Research and Analysis Directorate (RERAD), Department for Environment Food and Rural Affairs (DEFRA) and the Potato Council. Dan Milbourne is supported by Teagasc (The Agriculture and Food Development Authority of Ireland).

Funding Information:
funded by grants from the Netherlands Technology Foundation (STW), the Fund for Economic Structural Support (FES), the Netherlands Genomics initiative (NGI) and additional support from the Board of Wageningen University and Research Centre, The Netherlands Ministries of Economic Affairs (EZ) and Agriculture (LNV). Background data making the project possible was kindly provided by the Centre for BioSystems Genomics (CBSG) and an EU-project (APOPHYS EU-QLRT-2001-01849).

Funding Information:
The Centre for Bioengineering RAS, Moscow, Russia was funded by grants from Federal Agency on Science and innovations (state contracts 02.451.11.7013, 02.512.11.2099, 02 552 11 7010, 02 552 11 7045).

Copyright:
Copyright 2009 Elsevier B.V., All rights reserved.

Keywords

  • AFLP
  • Cytogenetics
  • Genetics
  • Next generation sequencing
  • Potato genome sequencing consortium

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