Genomic Analysis and Prediction within a US Public Collaborative Winter Wheat Regional Testing Nursery

Plant breeding programs exert considerable effort evaluating new breeding lines across many locations to identify superior performing candidates for release as new varieties. For this evaluation in wheat, regional testing networks have developed in the U.S. to provide additional information to breeders on the performance of their lines. Previously, the information collected in these trials, was only applicable on the line per se. With the development of inexpensive, high-density genetic markers, whole-genome profiles can be obtained for every experimental line and can transition to allele based breeding with genomic selection prediction models that take into account alleles common between lines.  With this approach, models can then be used to predict phenotypes and pre-select new lines based on ideal allelic combinations. The Southern Regional Performance Nursery is an 84-year-old nursery established by the USDA-ARS to characterize performance and quality of near-release wheat varieties from breeding programs in the central plains at more than 30 locations each year. Genetic gain is measured across years by including multiple long-term check cultivars for comparison. Whole genome profiles have been generated using genotyping-by-sequencing on entries dating back to 1992. Diversity was analyzed on a per program basis and preliminary genomic selection models have outperformed phenotypic correlations. Further work will determine the most suitable training population structure and derive a more accurate assessment on reported genetic gain of wheat across the Midwest. This research will refine GS models that have the ability to leverage preexisting regional testing networks for increased genetic gain.