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Sequencing the gene space of potato chromosome IV, comparative analysis with tomato and development of a genebased mapping platform (contribution to a BBSRC project) - IF0142

Description
This proposal will allow the UK to participate in an international collaboration to determine the DNA sequence of the 'gene-rich' regions of the potato genome, by sequencing chromosome IV. The other chromosomes are being sequenced by groups in other countries. Potato, the world's fourth most important food crop, is the most important member of the Solanaceae, which also includes tomato, pepper, aubergine and many medically relevant plants. The potato genome is very similar to tomato and, as the UK is also sequencing tomato chromosome IV, we will be able to perform a highly detailed comparative sequence analysis of these two crop species. Moreover, by studying gene and genome sequence data we will be able to create a 'genetic marker' system, based on small DNA variations between different varieties. This will allow us to readily examine a large number of genes and to see how they vary between varieties with different characteristics. This will be extremely useful for efforts to breed potato crops that can be grown in a more environmentally friendly and sustainable manner. All of the data generated will be placed in the public domain in a user ready format with the identification of putative genes and their function. The project will also be used to bring the UK research community working on Solanaceous plants together each year for the purposes of communicating the results of
their research.
Objective
Contribution to the international mission to sequence the potato genome. The Potato Genome Sequencing Consortium (PGSC) aims to complete the sequencing of the potato ‘gene space’ by the end of 2010.

1. Constructing a high density SNP-based gene map of potato that is anchored to the physical map.
2. Sequencing the gene-rich regions of potato chromosome IV via a BAC by BAC approach (c. 350 BACs in total, in collaboration with TEAGASC, Ireland).
3. Integrating comparative sequence resources for potato and tomato into ‘Solanaceae Knowledgebase’.
4. Annotating, curating and making publicly available the derived genomic sequence.
5. Conducting a detailed comparative sequence analysis of potato and tomato chromosome IV.
6. Disseminating information to Solanaceae Research Community-UK (SRC UK).
Time-Scale and Cost
From: 2008

To: 2011

Cost: £109,053
Contractor / Funded Organisations
Scottish Crop Research Institute, BBSRC Central Office
Keywords
Arable              
Crops              
Genetics              
Genomics              
Integrated Farming Systems              
Plant Genetic Resources              
Potatoes              
Sustainable Farming and Food Science              
Sustainable Farming Systems