Skip to main content
ARS Home » Plains Area » Fargo, North Dakota » Edward T. Schafer Agricultural Research Center » Cereal Crops Improvement Research » Research » Publications at this Location » Publication #411777
Research Project: Improvement of Disease and Pest Resistance in Barley, Durum, Oat, and Wheat Using Genetics and Genomics

Location: Cereal Crops Improvement Research

Title: The USDA-SoyWheOatBar-3K: a rapid, inexpensive genotyping platform to enable genomics-assisted breeding of small grains

Author
item Fiedler, Jason
item BRAULT, CHARLOTTE - University Of Minnesota
item CONLEY, EMILY - University Of Minnesota
item BEAUBIEN, KAREN - University Of Minnesota
item BAZZER, SUMANDEEP - South Dakota State University
item CAFFE, MELAINE - South Dakota State University
item SMITH, KEVIN - University Of Minnesota
item ANDERSON, JIM - University Of Minnesota

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 1/15/2024
Publication Date: 1/15/2024
Citation: Fiedler, J.D., Brault, C., Conley, E., Beaubien, K., Bazzer, S., Caffe, M., Smith, K., Anderson, J. 2024. The USDA-SoyWheOatBar-3K: a rapid, inexpensive genotyping platform to enable genomics-assisted breeding of small grains. Meeting Abstract. Poster No. PO0345.

Interpretive Summary:

Technical Abstract: Molecular breeding is the use of genetic information to predict performance and can assist in quickly developing new and improved small grain germplasm. For large scale implementation of these tools, durable, robust, low-cost molecular markers - with a rapid turnaround time - are required to inform selections within breeding programs. To meet these needs, we have developed a new genotyping platform based on the Illumina Infinium II array technology that targets approximately 3,000 SNPs in wheat, oat, and barley. The markers are evenly spaced along each genome, have a high information content, and include many known-informative markers already used in selection. Validation of this platform with ~10,000 previously genotyped lines demonstrated very good technical performance, high concordance with other platforms, and ability to be upgraded to higher density sets through imputation. At least 2,000 markers were informative within a given breeding program and are sufficient for the development of highly accurate genome prediction models. The platform is highly robust with a turnaround time of only three days for usable data. The small grains content was added to a new 3,000 Soy array and has been released as the USDA-SoyWheOatBar-3K for $14 a sample. This multi-species format also enables dual- and tri- hybridization to decrease the per-sample cost. Concordance between multi- and single-mode is ~95% for all SNPs and increases to ~99% on a high-performing subset. This new platform will enable many programs to utilize powerful molecular breeding tools to develop improved crop varieties.