Roche Nimblegen arrays have been used in research relating to potato blight.
A team of researchers has published the 240-megabase DNA sequence of phytophthora infestans, a parasitic water mould responsible for the Irish potato famine of the 1840s, in Nature.
Breeders have not been able to produce potato cultivars that remain resistant to this blight, known as plant (phyto) destroyer (phthora).
This fungal-like pathogen is an oomycete: an eukaryote related to algae and diatoms that is transferred by wind-borne spores that spread rapidly and germinate on wet leaves, killing entire fields of potatoes, tomatoes and other plants within a few weeks.
The sequencing of this mould and subsequent genomic analyses will help reveal details of its biologic and pathogenic processes, allowing the more rapid development of reliable, environmentally benign and economically feasible management tactics as well as insight into new breeding strategies.
Yearly potato production (300Mt) substantially contributes to worldwide food security, surpassed only by wheat (630Mt) and rice (608Mt).
While it is important to identify the problem genes responsible for infection, it is equally important to identify the genes that develop resistance, according to the company.
Brian J Haas, a primary contributor from the Broad Institute of MIT and Harvard, said: 'Nimblegen services generated the data that made it possible for us to identify key genes in pathogenesis, as described in our recent Nature publication on the potato blight genome.
'In particular, we identified a large number of so-called effector genes that are critical to pathogenesis that had been previously unknown and are extremely challenging to predict because of their small size and unusual structure,' he added.
The authors capitalised on Roche Nimblegen's flexible array design capability to use the data from the newly sequenced genome to build a custom gene expression microarray, which helped measure gene level changes between the vegetative stage and the infection stage.
Nearly three per cent of approximately 18,000 genes analysed on the Nimblegen Gene Expression microarray are induced at least twofold during infection.
Some of the induced genes belong to gene families with functions previously known to be involved in infection, such as RXLR genes, which may maintain virulence by suppressing host cell death.
Understanding the P infestans genes responsible for potato blight, and having discovering its genetic code, will lead to methods for controlling the infection to improve food production and reduce the impact on worldwide crop losses.
