A genome-structure adaptive framework for ROH-based inbreeding estimation in Penaeus vannamei

Reliable genomic inbreeding estimation in aquaculture species is challenged by genome fragmentation, high heterozygosity and unoptimized parameters. This study developed a genome-structure adaptive framework for optimizing Runs of Homozygosity (ROH) detection parameters, using Penaeus vannamei as a model. Taking advantage of whole-genome resequencing of five inbred families and two reference genomes with distinct continuity, we established an empirical set of non-overlapping genomic windows in PLINK to capture genomic features like SNP density. Genome coverage served as a key metric for evaluating the robustness of parameters in ROH analysis, while LD half-decay separated LD-driven homozygosity from true IBD signals. This approach identified three genome-sensitive parameters as critical to detection accuracy: SNP density, maximum inter-marker gap and minimum ROH length. Despite divergent optimal thresholds (high-contiguity: 0.5–0.8 SNP/kb, 80–100 kb gap, 30 kb minimum length; fragmented: 4 SNP/kb, 20 kb gap, 10 kb minimum length), FROH values remained consistent (r = 0.953) and matched pedigree expectations (FPED = 0.25), demonstrating scalability and reproducibility. This represents the first ROH parameter optimization method tailored to crustacean genomes, providing a foundation for accurate FROH calculation and enhanced cross-study comparability in shrimp and other aquaculture species.