A multi species, low cost, genome wide genotyping platform for molecular breeding in small grains

IWGSC webinar 01/26/2023 Presenter: Jason Fiedler, Research Geneticist, USDA Agricultural Research Service, USA Outline: 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 the public. 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. Slides of the presentations can be downloaded here: https://tinyurl.com/2drvpv3p