Predicting superior crosses in winter wheat using genomics: A retrospective study to assess accuracy

• Published in: Crop science Vol. 64; no. 4; pp. 2195 - 2211
• Main Authors: Ballén‐Taborda, Carolina, Lyerly, Jeanette, Smith, Jared, Howell, Kimberly, Brown‐Guedira, Gina, DeWitt, Noah, Ward, Brian, Babar, Md Ali, Harrison, Stephen A., Mason, Richard E., Mergoum, Mohamed, Murphy, J. Paul, Sutton, Russell, Griffey, Carl A., Boyles, Richard E.
• Format: Journal Article
• Language: English
• Published: 01.07.2024
• ISSN: 0011-183X; 1435-0653
• DOI: 10.1002/csc2.21266

In plant breeding, selecting cross‐combinations that are more likely to result in superior lines for cultivar development is critical. This step, however, is subjective with decisions being based on available genomic and phenotypic data for prospective parents. Genomic prediction (GP) provides new opportunities to accelerate genetic gain for a target trait by identifying superior crosses through simulation of progeny performance. In this context, this study deployed GP using the phenotype and genotype of potential parents to predict the progeny genetic variance (VG) and means of overall, inferior 10%, and superior 10% (μ, μip, and μsp, respectively). This retrospective experimental design investigated whether the crosses that produced superior soft red winter wheat breeding lines would have been made if progeny simulations had guided crossing decisions of breeding programs. Here, data from historical wheat breeding lines were used to train GP models and predict VG and means for yield, test weight, heading date, and plant height for all combinations of 217 parents. Predicted and observed data for 670 lines derived from biparental crosses were compared to assess the accuracy of progeny simulations, and low‐to‐moderate prediction accuracy was observed for the four traits (0.25–0.52). Of the pedigrees that produced lines that were selected and advanced into later stage nurseries, 76% were predicted to give rise to progeny with above‐average yield. The moderate correlation found between predicted progeny means and observed line per se performance justifies using cross‐combination prediction as a tool to reduce crossing number and focus on segregating populations that harbor future cultivars. Core Ideas In plant breeding, selecting parents to be crossed is critical for developing superior progeny. Historical winter wheat data were used to assess the usefulness of genomic prediction for parental selection. Predicted yield and SunGrains breeders’ assessment and selection largely agreed. Simulated progeny performance could allow breeders to focus on the most promising crosses.