Russia in Potato Genome Sequencing Consortium





The international Potato Genome Sequencing Consortium (PGSC) is a collaboration between 16 research groups; Argentina, Brazil, China, Chile, India, Ireland, The Netherlands, New Zealand, Peru, Poland, Russia, the United Kingdom and the United States. PGSC had started its activity from the beginning of 2004. Russia became the member of PGSC from 2006.

The primary objective of the Potato Genome Sequencing Consortium (PGSC) is to elucidate the complete DNA sequence of the potato genome (850 Mbp) by the end of 2010.

List of institutes and members involved in the project:

  1. Beijing Genomics Institute, China

    Sanwen Huang and Xu Xun.

  2. Centre Bioengineering RAS, Russia

    Konstantin Skryabin and Boris Kuznetsov.

  3. Central Potato Research Institute, Shimla, India

    Swarup Chakrabarti, V.U. Patil, Shashi Rawat and S.K. Pandey

  4. Chinese Academy of Agricultural Sciences, China

    Zhonghua Zhang.

  5. Dundee University, United Kingdom

    Dan Bolser and David Martin.

  6. Institute of Biochemistry and Biophysics PAS, Poland

    Wlodzimierz Zagorski, Jacek Hennig, Pawel Szczesny, Piotr Zielenkiewicz and Robert Gromadka.

  7. Instituto Nacional de Tecnologia Agropecuaria, Argentina

    Sergio Feingold, Leandro Barreiro and Gabriela Massa.

  8. Instituto de Investigaciones Agropecuarias, Chile

    Boris Sagredo and Nilo Mejia.

  9. International Potato Center (CIP), Peru

    Merideth Bonierbale, Marc Ghislain and Reinhard Simon.

  10. Italian National Agency for New Technologies, Energy and Sustainable Development, Italy

    Giovanni Giuliano and Gaetano Perrotta.

  11. Michigan State University, USA

    Robin Buell, Steven Lundback and Brett Whitty.

  12. New Zealand Institute for Plant & Food Research, New Zealand

    Jeanne Jacobs, Mark Fiers and Susan Thomson.

  13. Scottish Crop Research Institute, United Kingdom

    Glenn Bryan, David Marshall, Robbie Waugh and Sanjeev Kumar Sharma.

  14. Teagasc Agriculture and Food Development Authority, Ireland

    Dan Milbourne, Istvan Nagy and Marialaura Destefanis.

  15. Universidad Peruana Cayetano Heredia, Peru

    Gisella Orjeda, Frank Guzman, Michael Torres, Tomas Miranda, German de la Cruz, Roberto Lozano and Olga Ponce.

  16. Virginia Polytechnic Institute & State University, USA

    Richard E. Veilleux.

  17. Wageningen University, The Netherlands

    Bas te Lintel Hekkert, Christian Bachem, Erwin Datema, Jan de Boer, Richard Visser, Roeland van Ham, Theo Borm and Xiaomin Tang.


To contact the Potato Genome Sequencing Consortium, please write to:

potato-genome-i@googlegroups.com

The PGSC originally started out with sequencing RH89-039-16 potato diploid variety. This part of the project builds on a diploid potato genomic bacterial artificial chromosome (BAC) clone library of 78,000 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 30,000 BACs are anchored to the Ultra High Density genetic map of potato, composed of 10,000 unique AFLPTM markers.

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 aim of Russia is the equencing of 12 chromosome.

More then 800 BACs were anchored on 12 chromosome. We had chosen BAC-by-BAC strategy of sequencing based on the anchoring data.

Physical map of 12 chromosome
Physical map of 12 chromosome. Coloured blocks correspond to the anchored BACs areas.

For 12 chromosome sequencing 2 basic approach were used Sanger sequencing of BAC subclones and 454 sequencing of BAC mixtures.

ABI 3730 capillar sequencer
ABI 3730 capillar sequencer.

Roche 454 FLX sequencer
Roche 454 FLX sequencer.

Up to date 248 BACs were sequenced using these two approaches 196 BACs by 454 sequencing and 52 BACs using 3730 sequencer. All the data obtained were published through PGSC web-site and are in PGSC database.





Financial support

According to PGSC status, each partner is performing their sequencing projects on funding from their own resources. Russian potato sequencing project was supported by the following Rosnauka and RFBR grants:

Partcipation on international conferences.

The sequencing progress and workplans are instantly discussed on the conferences wich were held twice a year.

PGSC Conference in Wageningen
5th PGSC Conference in Wageningen, Holland, 2007.

Contact

Boris Kuznetsov

Boris Kuznetsov,

PhD, Head of Molecular Diagnostics,

Bioengineering Centre, Russian Academy of Sciences, Moscow, 117312, Russia

Tel.:+7(499)135-1240