Eagle Genomics, a Cambridge UK based bioinformatics company, and Rijk Zwaan, a breeder and producer of vegetable seeds, have completed an innovative research project that will help develop improved seeds for farmers and commercial producers of watermelon, cucumber and tomato.While many genomes have been annotated to a high quality, such as human, mouse, and fruit fly, there are numerous economically important crops whose genomes have been sequenced but not fully annotated.
Such annotation helps identify important genetic markers for traits that are of interest to plant breeders – such as disease resistance, taste, yield, and other factors.
The generation of these annotations usually requires expensive computational resources, so Rijk Zwaan engaged Eagle to build a more efficient automated analysis pipeline for the prediction of traits.
The pipeline was designed to help identify the regions within the genome known as regulatory units which control the effectiveness of the traits of interest. The pipeline will be applied to the genomes of newly-emerging crop species such as watermelon, cucumber and tomato as Rijk Zwaan’s research progresses.
Using the recently announced watermelon genome from The International Watermelon Genome Initiative (www.iwgi.org) as a test case, Eagle’s solution allowed Rijk Zwaan to analyse complete genome datasets for regulatory units within a few hours at a computational cost of approximately $100 per genome.
Eagle used flexible cloud-based bioinformatics resources coupled with their significant expertise in plant genomics which enabled Rijk Zwaan to obtain the results promptly and with confidence in their accuracy, thus avoiding any delay to ongoing research.
Rijk Zwaan’s Remco Ursem praised the quality of Eagle’s work: “With this pipeline Rijk Zwaan has a new, fast and flexible tool for studying the genetic basis of regulational mechanisms that influence crop and fruit characteristics.”
Will Spooner, Eagle’s chief technical officer, added.“Our approach combines best-of-breed tools developed in academia for well-studied organisms with Eagle’s expertise in applying these tools within commercial settings.
“With food security becoming an increasingly significant global issue, the results of this study show the value of using genomics to improve crops and ultimately help improve this.”