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

ABSTRACT:

Background

To implement high-throughput sequencing-based genotyping in a strawberry (Fragaria × ananassa) breeding program, we aimed to construct a haplotype reference panel and explore its utility through genotype dosage imputation of low-coverage (1×) sequencing data. Although genotyping by whole genome sequencing (WGS) provides high SNP density, its cost remains a limitation for large-scale application. Imputation from low coverage data using a reference panel offers a cost effective alternative, but this approach has not yet been optimized for allo-octoploid strawberry.

Results

To reduce genotyping errors that limit phasing accuracy, we combined high sequencing depth (> 15×) with variant filtering based on average allele balance (AAB), linkage disequilibrium (LD), and Me

SUBMITTER: Koorevaar T 

PROVIDER: S-EPMC12629074 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature