Optimising Genome-Wide Detection of Runs of Homozygosity: Impacts of Reference Genome Quality and Sequencing Parameters on Inbreeding Assessment.

ABSTRACT: Inbreeding and inbreeding depression pose a critical challenge to the persistence of small and isolated populations, driving the need for precise assessment of genomic metrics. Genome-wide runs of homozygosity (ROH) have been widely used for evaluating contemporary inbreeding levels and tracing historical events, circumventing the limitations of methods based on pedigree records. However, the reliability of ROH detection is contingent upon the quality of both the reference genome and resequencing data. Here, we employed a simulation-based approach, generating an inbred population with individuals exhibiting varying inbreeding coefficients and 13 reference genomes with differing levels of contiguity. This framework enabled us to systematically investigate the effects of sequencing depth, re

SUBMITTER: Shi M 

PROVIDER: S-EPMC12661482 | biostudies-literature | 2026 Jan

REPOSITORIES: biostudies-literature