Sequencing the 'gene space' of potato chromosome IV comparative analysis with tomato and development of a gene-based mapping platform

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.

We propose to sequence and annotate the euchromatic regions of potato chromosome 4 as part of a global effort to sequence the potato genome. PGSC aims to release a draft anchored physical map and 'minimum tiling path' (MTP) in 2007. The first phase of this project will be to prioritise, validate and sequence ~150 BAC clones from the chromosome 4 MTP. These BACs will provide a framework for alignment with tomato chromosome 4, currently being sequenced through a BBSRC/DEFRA/SEERAD funded project, destined for completion by October 2008. We aim to complete the potato chromosome 4 physical map by: a) screening the BAC library used for physical map construction with gene-based markers generated in this project with a new multiplex SNP mapping platform, b) using existing potato BAC-end sequence (BES) data to detect overlaps with the existing sequences. This will enhance the quality of the physical map, prioritise BACs for a second phase of sequencing and maximise the coverage and volume of comparative sequence data. To better define the target regions for sequencing we will exploit the extensive BAC FISH localisation data generated by the ITSP to delineate the transition between eu- and hetero-chromatin. Chromosome 4 sequencing will be conducted to HTGS phase 2 using a BAC by BAC approach. Based on size estimates for tomato and potato we have set a target of sequencing ~250 BACs (av. size 120kb at 30%-40% overlap, ~18-21 Mb of unique sequence). We are partnered in this venture by TEAGASC (Ireland), who will sequence an additional 120 BACs. BAC sequence data will be annotated individually using established automated pipelines tuned for Solanaceous genome sequence. Annotated sequences will be integrated into public databases.