Crop improvement is a long-term, expensive institutional endeavor. Genomic selection (GS), which uses single nucleotide polymorphism (SNP) information to estimate genomic breeding values, has proven efficient to increasing genetic gain by accelerating the breeding process in animal breeding programs. As for crop improvement, with few exceptions, GS applicability remains in the evaluation of algorithm performance. In this study, we examined factors related to GS applicability in line development stage for grain yield using a hard red winter wheat (Triticum aestivum L.) doubled-haploid population. The performance of GS was evaluated in two consecutive years to predict grain yield. In general, the semi-parametric reproducing kernel Hilbert space prediction algorithm outperformed parametric genomic best linear unbiased prediction. For both parametric and semi-parametric algorithms, an upward bias in predictability was apparent in within-year cross-validation, suggesting the prerequisite of cross-year validation for a more reliable prediction. Adjusting the training population's phenotype for genotype by environment effect had a positive impact on GS model's predictive ability. Possibly due to marker redundancy, a selected subset of SNPs at an absolute pairwise correlation coefficient threshold value of 0.4 produced comparable results and reduced the computational burden of considering the full SNP set. Finally, in the context of an ongoing breeding and selection effort, the present study has provided a measure of confidence based on the deviation of line selection from GS results, supporting the implementation of GS in wheat variety development.

Department of Biochemistry and Molecular Biology 246 Noble Research Center Stillwater OK 74078 USA

Department of Biochemistry and Molecular Biology Oklahoma State University Stillwater OK 74078 USA

Department of Genetics and Physiology of Forest Trees Faculty of Forestry and Wood Sciences Czech University of Life Sciences Kamycka 129 165 21 Prague 6 Czech Republic

Department of Plant and Soil Science Oklahoma State University 371 Agriculture Hall Stillwater OK 74078 USA

Forest and Conservation Sciences Faculty of Forestry The University of British Columbia 2424 Main Mall Vancouver BC V6T 1Z4 Canada

Present Address Scion 49 Sala Street Whakarewarewa Rotorua 3046 New Zealand

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