Implementation of Genomic and Marker-Assisted Selection for Improving Winter Wheat: Insights from the University of Nebraska-Lincoln Breeding Program.

Development of a wheat variety requires ~12 years. Each year breeding lines are selected and advanced using a “breeder’s selection palette”, which is comprised of key phenotypic traits. Phenotype-based selections (PBSs) can be affected by biotic and abiotic stresses, and unforeseen changes in weather such as excess rain or damage due to hail. Further, PBS fails to capture the ability of a line to perform well in multiple growing-years under varied environmental conditions. Augmenting selection-palette with genomic information can aid in making better selections and overcome above limitations. We will demonstrate the use of marker-assisted selection (MAS) for traits with well-known, large effect loci and genomic selection (GS) for grain yield. The study comprised of 1,328 entries from five independent F_3:6 nurseries evaluated each year from 2012-2016 across 8 to 10 locations in Nebraska and two F_3:5 nurseries containing ~3,000 entries grown in 2015 and 2016 at Lincoln, Nebraska. Mixed models incorporating spatial variation provided better estimates of the phenotypic data. Genotype-by-sequencing, quality control and imputations provided ~100,000 SNP markers. Genome-wide association analysis identified SNPs in linkage disequilibrium with markers tagging known locus for viral and fungal disease resistance, height and grain quality, and were used for MAS. Genomic selection for yield was performed using 10-fold cross validations for each of the years, and the prediction abilities ranged from ~0.20 to ~0.50. Prediction ability for an entire new trial ranged from 0.154 to 0.376. Additionally, tracking entries advanced from 2012-2015 nurseries until 2016 indicated lines with “above average genomic estimate breeding value (GEBV) and observed phenotypic value (OPV)” are retained for longer times in the breeding program. Thus, selections in 2016 were based on a combination of GEBV and OPV. Overall, GS and MAS have supplemented the “breeder’s eye” and our results will assist breeding programs of other autogamous crops.