Low-Coverage Whole-Genome Sequencing (lcWGS) in Cattle: Analysis of Potential and Prospects for Application

Whole-genome studies in cattle play a key role in exploring both individual and population-level genetic variability. Recently, low-coverage whole-genome sequencing (0.5-2×) has been considered as an alternative to traditional approaches. Low-coverage whole-genome sequencing (lcWGS), which provides uniform coverage of the entire genome at relatively low cost, combined with subsequent imputation, enables the reconstruction of genotypes with high accuracy and density. lcWGS enables detection of rare and functionally important variants and provides exploratory potential for structural variation analysis; however, accurate SV imputation still presents significant challenges. The aim of this review is to analyze the potential and prospects of lcWGS as a tool for genomic selection and genetic studies in cattle. The review systematizes current advances in the application of lcWGS in cattle, focusing on imputation accuracy, factors affecting it, and the comparative efficiency of different software solutions. A literature survey was conducted using PubMed and Google Scholar databases, with preference given to original studies, systematic reviews, and large-scale projects addressing imputation accuracy, reference panel composition and size, cost-effectiveness, and practical applications of lcWGS in cattle genomics. Key factors influencing efficiency include sequencing depth, reference panel size and composition, as well as the choice of imputation algorithm. lcWGS represents a cost-effective and powerful alternative to traditional genome-wide approaches, capable of capturing rare and breed-specific variants; however, its application to structural variation still requires methodological improvement and integration with high-resolution reference pangenomes or long-read sequencing. Despite significant progress and the high potential of lcWGS in cattle genomics, several challenges and limitations remain, requiring further investigation and resolution to fully realize the advantages of this technology. Addressing these challenges will enable more efficient use of lcWGS for genetic research and accelerate genetic progress in cattle breeding.