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.

How to handle high subgenome sequence similarity in allopolyploid Fragaria x ananassa: Linkage Disequilibrium Based Variant Filtering

“…This could be the case for chr_7B because a major gene for resistance to Phytophtora cactorum (FaRPc-2) is located on this chromosome [23]. To mitigate this, a larger diversity panel could be utilized, focusing on adding rare genetic variation instead of genetic variation already represented well in the original panel, for example by constructing a breeding core collection [24].…”