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

Abstract

Low-coverage whole-genome sequencing (lcWGS) allows reading a small portion of each animal’s DNA across the entire genome at low cost. When combined with computational methods, this approach can accurately reconstruct full genetic profiles. This review shows that lcWGS is effective for cattle genomics: it captures rare and breed-specific genetic variants better than standard SNP chips, supports accurate genomic predictions, and becomes cost-competitive. Key factors affecting its performance include sequencing depth (typically 0.5–2×), the size and composition of the reference panel, and the choice of imputation software. While challenges remain—such as optimizing protocols for crossbred animals and complex genomic regions—lcWGS is a practical and scalable tool for modern cattle breeding programs. Keywords: cattle, low-pass sequencing, lcWGS, imputation