Seed World

Genome Insight: No Longer Just a Dream

Scientists at KeyGene in Wageningen, the Netherlands, together with their partners, work on sequencing, assembling, understanding and using genomes of a variety of economically important crops, including vegetables, field crops and ornamentals. With the unique combination of their skills and PromethION technology they offer real genome insight.

A significant focus in KeyGene’s research is crop improvement through breeding for traits such as pathogen resistance, longer shelf life, improved taste, color, easy packaging, and, more recently, the development of methods to select crop varieties that can grow under LED lighting in urban farming. Sequencing, assembling, understanding and using genome sequences opens up new possibilities for these crop innovations.

KeyGene’s scientists showed their capabilities in sequencing lettuce (Lactuca sativa) an important crop, with 74 billion of plants harvested globally every year. In order to further enhance lettuce-breeding efforts, the team at KeyGene performed whole genome sequencing of two lettuce lines using the high-yield, high-throughput PromethION platform of Oxford Nanopore Technology.

For lettuce KeyGene produced a breathtaking amount of some 600.000.000.000 bases (600 Gb), running the PromethION for just a few days.

‘At KeyGene we are able to isolate high quality DNA in very large chunks’ says lead scientist Alexander Wittenberg. ‘We are now able to produce high quality DNA in molecule sizes of 50.000 bases. With the combination of our performance in DNA isolation, the speed of the PromethION platform, and fast assembly-bioinformatics we have a unique offer. We give our partners a much better genome insight, a great basis for genes-for-trait discovery and improved breeding results.’

The team showcased their capabilities in lettuce recently. Earlier a reference genome was published for this crop, using ‘old’ sequencing technology and small chunks of DNA. Sequencing and assembly took several years. KeyGene now sequenced the genome of two lettuce breeding lines. It took them just two months after receiving leaf samples of the lines to get to two full genomes which were more complete, thus offering a much higher usability than the earlier published genome.

By combining the PromethION results with optical mapping of the lettuce genomes, the researchers were able to further improve the assembly. They managed to get to a so called near chromosome level, an important achievement.

Having better genome insight helps plant breeders to improve understanding of the genetics of important traits of their crops. It also enables plant breeders to set up a much more effective and efficient breeding program. Selecting for many traits at the same time is now at the breeders’ fingertips.

The lettuce research clearly shows the perspectives of whole genome sequencing using Nanopore technology at KeyGene. The speed of the analysis and data production, and the big chuncks of DNA analyzed, make the assembly of whole genomes more precise and complete, and much faster. Wittenberg: “It is amazingly easy and attractive now to sequence, assemble, understand and use the ‘genomes’ of full crop germplasm collections by breeding institutes and companies.”

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