Genotype imputation from low-coverage WGS using haplotype reference panels in cultivated strawberry

These findings demonstrate that constructing a large, genetically diverse haplotype reference panel improves genotype dosage imputation from low-coverage sequencing data. However, high accuracy is still achievable with limited resources, making this a cost-efficient alternative to SNP arrays when adopting WGS-based genotyping in breeding programs. The strategy is broadly applicable to other crops where dense genotyping is needed but resources are limited. In such cases, sequencing approximately 70 genetically representative samples at ≥ 25× depth was sufficient in our study to build a reference panel suitable for imputation.