Potato pangenome research drives cooperation between international public and private sectors
Ness Ziona, Israel – 19 December 2017 – 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 €11 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% unfilled gaps, and BUSCO results of 96.25%, 86% of which are found in more than one copy.
The potato breeding and research community, in which the Netherlands is leading, 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 potato researcher Richard Finkers, PhD, and Prof. Richard Visser, PhD, from WUR 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 EU potato breeding. 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 Dr. Finkers of WUR. “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 Gil Ronen, NRGene CEO. “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 analyses 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.”
Richard Finkers of WUR will present the potato genome research at the PAG XXVI conference, 1:30 PM – 3:40 PM, Tuesday, January 16, 2018, at the Garden Ballroom hall in San Diego.
NRGene is a genomic big data company delivering cutting-edge software and algorithms to reveal the complexity and diversity of humans, plants, and animals and support the most advanced and sophisticated breeding and research programs. NRGene tools have already been employed by some of the leading seed companies worldwide as well as the most influential research teams in academia. www.nrgene.com.
About Wageningen University & Research, the Netherlands
The mission of Wageningen University & Research is “To explore the potential of nature to improve the quality of life.” A staff of 6,500 and 10,000 students from over 100 countries work everywhere around the world in the domain of healthy food and living environment for governments and the business community-at-large.
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