Utilizing genomic prediction to boost hybrid performance in a sweet corn breeding program

Front Plant Sci. 2024 Apr 25:15:1293307. doi: 10.3389/fpls.2024.1293307. eCollection 2024.


Sweet corn breeding programs, like field corn, focus on the development of elite inbred lines to produce commercial hybrids. For this reason, genomic selection models can help the in silico prediction of hybrid crosses from the elite lines, which is hypothesized to improve the test cross scheme, leading to higher genetic gain in a breeding program. This study aimed to explore the potential of implementing genomic selection in a sweet corn breeding program through hybrid prediction in a within-site across-year and across-site framework. A total of 506 hybrids were evaluated in six environments (California, Florida, and Wisconsin, in the years 2020 and 2021). A total of 20 traits from three different groups were measured (plant-, ear-, and flavor-related traits) across the six environments. Eight statistical models were considered for prediction, as the combination of two genomic prediction models (GBLUP and RKHS) with two different kernels (additive and additive + dominance), and in a single- and multi-trait framework. Also, three different cross-validation schemes were tested (CV1, CV0, and CV00). The different models were then compared based on the correlation between the estimated breeding values/total genetic values and phenotypic measurements. Overall, heritabilities and correlations varied among the traits. The models implemented showed good accuracies for trait prediction. The GBLUP implementation outperformed RKHS in all cross-validation schemes and models. Models with additive plus dominance kernels presented a slight improvement over the models with only additive kernels for some of the models examined. In addition, models for within-site across-year and across-site performed better in the CV0 than the CV00 scheme, on average. Hence, GBLUP should be considered as a standard model for sweet corn hybrid prediction. In addition, we found that the implementation of genomic prediction in a sweet corn breeding program presented reliable results, which can improve the testcross stage by identifying the top candidates that will reach advanced field-testing stages.

Keywords: G×E interaction; RKHS model; cross-validation schemes; hybrid prediction; non-additive effects.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was supported by the National Institute of Food and Agriculture SCRI 2018-51181-28419, AFRI 2019-05410, and USDA-NIFA 2022-51181-38333 to MR). We also thank the financial support from the Brazilian Government through the National Council for Scientific and Technological Development (CNPq) and the Coordination for the Improvement of Higher Education Personnel (CAPES) through the CAPES-PrInt scholarship. This study was financed in part by the CAPES - Finance Code 001.