A multi-species, low-cost, genome-wide genotyping platform to support molecular breeding in small grains

Sponsored IWGSC webinar

Join us for an Illumina-sponsored IWGSC (International Wheat Genome Sequencing Consortium) webinar on Thursday, January 26, 2023 at 8 AM (PT) / 11 AM (ET). 

In this webinar, you will learn:

• USDA developed a new multi-species platform based on the Illumina Infinium II array technology that targets approximately 3,000 SNPs in wheat, oat, and barley each.
• This platform is highly robust with a quick turnaround time for usable data.
• This platform will allow for more breeding programs to overcome recurrent and emerging threats to agricultural producers.

Presenter

Jason Fiedler
Research Geneticist
USDA Agriculture Research Service, USA

Full abstract

Molecular breeding applies genetic information to predict performance and is a powerful tool for the rapid development of new and improved small grain germplasm. For efficient deployment, a durable, robust, high-throughput genotyping platform—with a short turnaround time and low cost—is required to inform selections within breeding programs. 

To meet these needs, we have developed a new multi-species platform based on the Illumina Infinium II array technology that targets approximately 3,000 SNPs in wheat, oat and barley each. These markers are evenly spaced along each genome, have a high information content, and include many known-informative markers already used for selection in breeding programs.

Validation of this platform with ~10,000 previously genotyped wheat oat and barley lines highlighted very good technical performance and high concordance with most currently used platforms. At least 2,000 markers were informative within a given breeding program which is sufficient for the development of highly accurate genome prediction models. 

The platform is highly robust, requiring only 200 ng of DNA, with a short three-day turnaround time for usable data. The cereal grain content was added to a new 3,000 SNP Soy array and has been released as the USDA-SoyWheOatBar-3K, which is currently available for $14 per sample. This multi-species format also enables dual hybridization to decrease the per-sample cost. Line concordance between dual and single mode is over 95% for all SNPs and increases to over 98% with a subset of high-performing SNPs. 

This new platform will allow more breeding programs to use molecular tools in their pipeline and accelerate the release of varieties that can overcome the recurrent and emerging threats to our agricultural producers.