Seed World

DuPont Pioneer Discusses Building Research-Ready Reference Genomes with Bionano Genomics


DuPont Pioneer Research Scientist Kevin Fengler shared Pioneer’s strategy for quickly building high-quality reference genomes for use in gene discovery and product development at the 2017 Plant Genomics & Gene Editing Congress in Philadelphia, PA. Fengler revealed that using a combination of genomics platforms, including Saphyr from Bionano Genomics, can yield a chromosome-scale reference genome in as little as two weeks post-data generation.

Bionano maps have been a part of DuPont Pioneer’s strategy for genome assembly improvements since 2015 when they adopted Irys, Bionano’s first generation system for optical genome mapping. Upon the release of Saphyr last year, Bionano’s most advanced system to date, DuPont Pioneer purchased the first one sold in the United States. The new platform offered increased throughput, lower cost per genome and greater ease-of-use. Saphyr now enables DuPont Pioneer to go from sample to fully assembled de novo genome map in only five days, even for large genomes such as maize.

To capture better the high levels of sequence diversity in a key crop like maize, multiple diverse maize reference genomes are assembled to a comprehensive pan genome view. On the challenge of quickly building these multiple high-quality de novo references using the current crop of sequencing tools, Fengler says it is “possible to readily generate assemblies with a contig N50 exceeding 1Mb, but going from contigs to chromosomes can still be a challenge.”

DuPont Pioneer finds that improvements to Bionano’s workflow (2-enzyme hybrid scaffolding) coupled with Saphyr’s much higher throughput help overcome the obstacles that typically bog down the transition from contigs to chromosome. Reference genomes are part of the foundation for the advanced breeding efforts at DuPont Pioneer and Fengler says, “In addition to increasing the contiguity of an assembly to chromosome scale scaffolds, the added benefits of mis-assembly resolution and gap characterization from this workflow set the table for high throughput reference genomes.”

Dr. Erik Holmlin, CEO of Bionano Genomics says, “We are very pleased to count DuPont Pioneer as part of the successful Saphyr launch and to have shipped them the first system sold in the United States. It’s really thrilling to hear how quickly the system has been integrated into a workflow for rapidly creating reference genomes that are ready to be used in advanced breeding applications.”