Genomic selection shows improved expected genetic gain over phenotypic selection of agronomic traits in allotetraploid white clover

Abstract Key message Genomic selection using white clover multi-year-multi-site data showed predicted genetic gains through integrating among-half-sibling-family phenotypic selection and within-family genomic selection were up to 89% greater than half-sibling-family phenotypic selection alone. Abstract Genomic selection, an effective breeding tool used widely in plants and animals for improving low-heritability traits, has only recently been applied to forages. We explored the feasibility of implementing genomic selection in white clover ( Trifolium repens L.), a key forage legume which has shown limited genetic improvement in dry matter yield (DMY) and persistence traits. We used data from a training population comprising 200 half-sibling (HS) families evaluated in a cattle-grazed field trial across three years and two locations. Combining phenotype and genotyping-by-sequencing (GBS) data, we assessed different two-stage genomic prediction models, including KGD-GBLUP developed for low-depth GBS data, on DMY, growth score, leaf size and stolon traits. Predictive abilities were similar among the models, ranging from −0.17 to 0.44 across traits, and remained stable for most traits when reducing model input to 100–120 HS families and 5500 markers, suggesting genomic selection is viable with fewer resources. Incorporating a correlated trait with a primary trait in multi-trait prediction models increased predictive ability by 28–124%. Deterministic modelling showed integrating among-HS-family phenotypic selection and within-family genomic selection at different selection pressures estimated up to 89% DMY genetic gain compared to phenotypic selection alone, despite a modest predictive ability of 0.3. This study demonstrates the potential benefits of combining genomic and phenotypic selection to boost genetic gains in white clover. Using cost-effective GBS paired with a prediction model optimized for low read-depth data, the approach can achieve prediction accuracies comparable to traditional models, providing a viable path for implementing genomic selection in white clover.