The genome sequence for the potato cyst nematode Globodera pallida and its utilisation for improved control

The aim of this project is to define bases for novel control and enhanced pest management of the potato cyst nematode, Globodera pallida by obtaining and utilising the full genome sequence. The British Potato Council estimates the UK potato production, processing and retail markets to be worth c. £3 billion p.a. and the potato cyst nematodes (PCN), Globodera rostochiensis and G. pallida, are the most economically important nematode problems of this industry. They occur in 65% of UK potato land with G. pallida present at 92% of these sites. PCN impose an annual cost in excess of £50 million on UK potato growers and threaten the future of the crop for many growers. Breeding for resistance since the mid 1950s has produced few commercially acceptable varieties with resistance to G. pallida. Currently used chemical control methods are under increasing pressure due to cost, environmental and health concerns and there are no benign alternatives to the currently used compounds. Control of G. pallida is an essential requirement to maintain the competitiveness of U.K. production. For example, the consumer demand for food with no pesticide residues has resulted in Waitrose sourcing all its potatoes from crops that have not received a nematicide treatment (www.waitrose.com). This requires imports from countries with a lower PCN incidence or requires a more extensive agricultural system in the UK. Consumer support is likely for UK produce that avoids pesticide residues or environmental harm and is soundly based on a sustainable approach. This proposal underpins the innovation needed to reach that outcome. Over the next 5 years, Wellcome Trust Sanger Institute will undertake a major genome sequencing programme aimed at nematodes and other helminths that are human or veterinary-important parasites. WTSI is willing to sequence this plant parasitic nematode for comparative genomic studies. Gene identification will be carried out ab initio and by experimental analysis. The scientific outputs of the proposed work will be of relevance to plant nematologists and to the wider scientific community. A G. pallida genome sequence will allow the UK plant nematology community to remain internationally competitive and will enable new collaborative links to be built with researchers working in other fields including plant development, molecular plant pathology and evolution of resistance. The proposal has broad support. The British Potato Council will independently support CASE awards for postgraduate students that will be aligned with the project. Other support is evident from the letters of support from both industry and the scientific community.

The aim of this project is to define bases for novel control and enhanced pest management of the potato cyst nematode, Globodera pallida, by obtaining the full genome sequence. The UK potato production, processing and retail markets are worth c. £3 billion p.a. and the potato cyst nematodes (PCN), Globodera rostochiensis and G. pallida, are the most economically important nematode problems of this industry. They occur in 65% of UK potato land with G. pallida present at 92% of these sites. Breeding for resistance has produced few commercially acceptable varieties with resistance to G. pallida. Currently used chemical control methods are under increasing pressure due to cost, environmental and health concerns. Control of G. pallida is an essential requirement to maintain the competitiveness of U.K. production. The sequencing strategy can be considered as comprising several stages: (1) 1.9 million whole genome shotgun sequencing reads (~8x coverage), 20000 BAC end and 50000 fosmid end reads will be produced (2) initial assembly into contigs (3) generation of larger scaffolds (linked contigs) by automated resequencing (50,000 reads) from selected shotgun clones to extend the length of contigs that were truncated by the presence of GC-rich sequences, secondary structure, etc (4) assembly refinement and annotation. Gene identification will be carried out ab initio and by experimental analysis using tiling arrays.