Next generation molecular breeding in strawberry: using whole-genome sequencing based haplotypes

Molecular breeding in allo-octoploid cultivated strawberry (Fragaria × ananassa) faces challenges due to high subgenome similarity, which complicates variant calling in whole-genome sequencing (WGS). This thesis establishes a robust framework to implement WGS-based genotyping in a practical strawberry breeding program.

We first selected a representative core collection to capture germplasm diversity. Next, we developed a filtering method using linkage disequilibrium and allele balance to remove erroneous SNPs caused by subgenome similarity. Using these high-confidence SNPs, we built haplotype reference panels that allowed accurate imputation of low-coverage sequencing data. We then used these haplotypes to characterize genetic diversity and selection footprints across breeding populations and over time.

Overall, this work turns WGS into a flexible genotyping tool that supports day to day breeding decisions and long term management of genetic diversity in strawberry, and provides a blueprint that can be translated to other crops with minor adjustments.