Advancing red clover breeding through genomic selection methods

Red clover is a major forage legume and a highly valuable crop for Northern Europe due to its high protein value and multiple ecological services. It is an important crop for both the ruminant industry and ecological farming. As growing conditions change due to rapid climate change, the demand for red clover breeding has increased. In this thesis, the potential for accelerating genetic gain through improved red clover breeding was studied. First, since the response to selection is a function of genetic variation, the success of genomic selection depends on available genetic resources. Hence, red clover genetic resources available at the Nordic Genetic Resource Center (NordGen) gene bank and the Swedish seed company Lantmännen were used to evaluate the crop’s genetic diversity and population structure. Red clover accessions currently used for breeding have low values for measures of inbreeding, which suggests a lower risk of inbreeding depression. However, their genetic diversity was low, relative to available wild populations and landraces, which can increase the risk of inbreeding depression. Hence, the progression of breeding could be limited by the gene pool. In this thesis, red clover populations with the potential to be used in red clover breeding to increase genetic diversity were identified. Second, genetic gain in red clover can be rapidly increased by the introduction of genomic prediction models that minimize the need for time-consuming field trials. Both genome-wide association study (GWAS) and genomic prediction (GP) were tested for dry matter yield and forage quality traits based on data generated through multi-environment field trials and genotyping-by-sequencing. The results showed that dry matter yield and forage quality are affected by genes regulating responses to environmental inputs and stresses. This thesis showed that, by increasing genetic diversity and implementing GP in red clover breeding, genetic gain can be accelerated.