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Genome-wide regression models considering general and specific combining ability predict hybrid performance in oilseed rape with similar accuracy regardless of trait architecture

Werner, ChristianR., Qian, Lunwen, Voss-Fels, KaiP., Abbadi, Amine, Leckband, Gunhild, Frisch, Matthias, Snowdon, RodJ.
Theoretical and applied genetics 2018 v.131 no.2 pp. 299-317
Brassica napus, agronomic traits, breeding programs, crossing, doubled haploids, field experimentation, genomics, genotype, genotyping, heterosis, hybrids, marker-assisted selection, parents, prediction, regression analysis, single nucleotide polymorphism, specific combining ability, statistical models
KEY MESSAGE : Genomic prediction using the Brassica 60 k genotyping array is efficient in oilseed rape hybrids. Prediction accuracy is more dependent on trait complexity than on the prediction model. In oilseed rape breeding programs, performance prediction of parental combinations is of fundamental importance. Due to the phenomenon of heterosis, per se performance is not a reliable indicator for F₁-hybrid performance, and selection of well-paired parents requires the testing of large quantities of hybrid combinations in extensive field trials. However, the number of potential hybrids, in general, dramatically exceeds breeding capacity and budget. Integration of genomic selection (GS) could substantially increase the number of potential combinations that can be evaluated. GS models can be used to predict the performance of untested individuals based only on their genotypic profiles, using marker effects previously predicted in a training population. This allows for a preselection of promising genotypes, enabling a more efficient allocation of resources. In this study, we evaluated the usefulness of the Illumina Brassica 60 k SNP array for genomic prediction and compared three alternative approaches based on a homoscedastic ridge regression BLUP and three Bayesian prediction models that considered general and specific combining ability (GCA and SCA, respectively). A total of 448 hybrids were produced in a commercial breeding program from unbalanced crosses between 220 paternal doubled haploid lines and five male-sterile testers. Predictive ability was evaluated for seven agronomic traits. We demonstrate that the Brassica 60 k genotyping array is an adequate and highly valuable platform to implement genomic prediction of hybrid performance in oilseed rape. Furthermore, we present first insights into the application of established statistical models for prediction of important agronomical traits with contrasting patterns of polygenic control.