Low-Coverage Whole-Genome Resequencing in Livestock and Poultry: Statistical Foundations, Applications and Future Directions

Low-coverage whole-genome resequencing (lcWGS) is emerging as a powerful population-scale genomic strategy for livestock and poultry research. By integrating sparse sequencing reads with genotype likelihoods, haplotype information and imputation models, lcWGS enables genome-wide variant discovery and genetic inference across large animal cohorts. This feature is particularly valuable for breeding populations, indigenous breeds and conservation resources, where broad sampling is essential for capturing population-specific variation and linking genomic diversity with economically and adaptively important traits. In this review, we synthesize the statistical foundations, analytical workflows and major applications of lcWGS in livestock and poultry genomics. We discuss how lcWGS supports genetic diversity assessment, population structure analysis, genome-wide association studies, genomic selection, selection-signature detection, environmental adaptation research and genetic resource conservation. We further highlight the importance of coordinated study design, including sequencing depth, sample size, reference-panel construction, imputation strategy, phenotype quality and downstream analytical models. Beyond its role as a cost-efficient genotyping approach, lcWGS provides a flexible framework for integrating population genomics with functional annotation, multi-omics resources, long-read assemblies, graph pan-genomes and interpretable prediction models. These developments are expanding the potential of lcWGS from variant discovery toward biological interpretation, precision breeding, climate-resilient animal production and the sustainable management of livestock and poultry genetic resources.