Construction of a strawberry breeding core collection to capture and exploit genetic variation

Abstract Genetic diversity is crucial for the success of plant breeding programs and core collections that capture this diversity are an important resource to exploit this. In this study, we present a method for constructing a core collection that integrates both genomic and pedigree information to capture maximum genetic variation in a minimum subset of genotypes within a strawberry breeding program, while also being future proof. Our stepwise approach starts with selecting the most important crossing parents of advanced selections and genotypes included for specific traits, to represent also future genetic variation. We then use pedigree-genomic-based relationship coefficients combined with the ‘accession to nearest entry’ criterion to complement the core collection and maximize its representativeness of the current breeding program. Combined pedigree-genomic-based relationship coefficients allow for accurate relationship estimation without the need to genotype every individual in the breeding program. The resulting core collection can for example be used to develop a haplotype reference panel for imputation-based genotyping methods.