NRGene Delivers First Food Potato Genomes

Potato pangenome research drives cooperation between international public and private sectors

Published online: Dec 19, 2017 Articles
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NRGene, the worldwide leader in genomic assembly and analysis, is working with a team of researchers from Wageningen University & Research (WUR) in the Netherlands and leading commercial partners to create multi-genome mapping of commercial food potatoes.

Potatoes are the fourth-most consumed food crop in the world, reaching $13 billion in global trade.

The potato genome is complex. It’s an auto-tetraploid, which means that each potato cell contains four nearly identical copies of each chromosome and gene, making the assembly and phasing of the four copies extremely difficult for traditional technologies. 

NRGene has completed the phased assembly of three commercial potato varieties. The assembly is built of scaffolds with an N50 of 1.19 Mbp, less than 0.89 percent unfilled gaps, and BUSCO results of 96.25 percent, 86 percent of which are found in more than one copy.

The potato breeding and research community is continuously seeking improved genomic infrastructures to allow more efficient molecular breeding, and NRGene technologies provide the solution: DenovoMAGIC delivers the initial assemblies, while PanMAGIC compares the genomes all-to-all to get the best view of local differences and polymorphism such as SNPs, as well as global changes, such as gene PAVs and CNVs, translocations, and duplications of different sizes and whole chromosomic regions.

The potato pangenome will synergize the assembly information to contribute a comprehensive genomics view of the potato genome. The group, led by  WUR potato researchers Richard Finkers and Richard Visser, is seeking other researchers from academia and industry to join the project to enrich the pan-genome analysis and thus better characterize the natural genetic diversity of the species.

WUR plays an important role in supporting potato breeding in the EU. It focuses on gathering knowledge and stimulating cooperation between potato researchers and the potato industry throughout the production chain, creating an environment where research results are accessible and usable within the potato sector. 

“Potato research and breeding faced significant difficulties during the last 100 years,” says. “NRGene’s genomes and pan-genome analysis will allow us to map traits on the level of haplotypes, which was previously almost impossible.”

“NRGene has achieved a very prominent position in world agriculture right now, having delivered more than 300 crop genomes over the past two years,” says NRGene CEO Gil Ronen. “Many crops already have a single genome; a few have more than one. Simply by plugging in raw data from multiple varieties, researchers across all crops can get a broad genomics analysis of an entire species, allowing them to get a complete picture of what needs to be done to increase yields, reduce resource requirements and directly address food scarcity problems around the globe.”