Genomic Prediction and the Practical Breeding of 12 Quantitative-Inherited Traits in Cucumber (Cucumis sativus L.)

Abstract

Genomic prediction is an effective way for predicting complex traits, and it is becoming more essential in horticultural crop breeding. In this study, we applied genomic prediction in the breeding of cucumber plants. Eighty-one cucumber inbred lines were genotyped and 16,662 markers were identified to represent the genetic background of cucumber. Two populations, namely, diallel cross population and North Carolina II population, having 268 combinations in total were constructed from 81 inbred lines. Twelve cucumber commercial traits of these two populations in autumn 2018, spring 2019, and spring 2020 were collected for model training. General combining ability (GCA) models under five-fold cross-validation and cross-population validation were applied to model validation. Finally, the GCA performance of 81 inbred lines was estimated. Our results showed that the predictive ability for 12 traits ranged from 0.38 to 0.95 under the cross-validation strategy and ranged from −0.38 to 0.88 under the cross-population strategy. Besides, GCA models containing non-additive effects had significantly better performance than the pure additive GCA model for most of the investigated traits. Furthermore, there were a relatively higher proportion of additive-by-additive genetic variance components estimated by the full GCA model, especially for lower heritability traits, but the proportion of dominant genetic variance components was relatively small and stable. Our findings concluded that a genomic prediction protocol based on the GCA model theoretical framework can be applied to cucumber breeding, and it can also provide a reference for the single-cross breeding system of other crops.