Challenge to genomic selection in strawberry at four breeding stations in Japan

There are more than 30 strawberry breeding stations in Japan, which have developed various cultivars with high-quality fruits under heated conditions. Nonetheless, breeders have begun to feel the limitations of conventional breeding methods, and there is a need for more strategic breeding approaches based on genetic information. To address this problem, we developed a next-generation molecular breeding method to improve fruit firmness in strawberries using a combination of genomic selection (GS) and recurrent selection. This approach was developed in conjunction with four breeding stations operated at the National Agriculture and Food Research Organization Institute of Vegetable and Floriculture Science (NARO-IVFS) and Tochigi, Fukuoka and Chiba prefectures. Multiple parental populations were developed at the four breeding stations, and genotyping and phenotyping were performed for GS modelling. Simple sequence repeat (SSR) markers and single nucleotide polymorphisms (SNPs) previously mapped onto linkage maps were used for genotyping. Conventional GS requires genome-wide genotyping for both the training and breeding populations. To decrease the cost and time for genotyping in the breeding population, we used an Ensemble-based genetic and genomic search (EGGS) in order to generate a model with fewer DNA markers. Second-generation populations (G2) exhibiting reduced variation in fruit firmness compared with the original populations have already been developed. The frequencies of targeted genotypes were increased from the initial population (G0) to the second generation (G2). Though many issues remain to be addressed, we expect that our method will open a new avenue for strawberry breeding.