Genomic Selection in Animal Breeding: Principles, Applications, and Future Perspectives

Abstract

Genomic selection (GS) has transformed modern animal breeding by enabling the prediction of genetic merit using dense genome-wide molecular markers rather than relying solely on pedigree and phenotypic information. Since its conceptual introduction in 2001, GS has become a cornerstone of genetic improvement programs in livestock species, particularly dairy cattle, and has subsequently expanded to beef cattle, sheep, goats, swine, poultry, and aquaculture. The integration of high-density single nucleotide polymorphism (SNP) genotyping with advanced statistical prediction models has substantially increased the accuracy of breeding value estimation, shortened generation intervals, and accelerated rates of genetic gain. Compared with conventional best linear unbiased prediction (BLUP) and marker-assisted selection (MAS), genomic selection captures the combined effects of thousands of loci distributed throughout the genome, making it highly effective for complex quantitative traits governed by many genes of small effect. Recent advances, including single-step genomic BLUP, Bayesian prediction methods, whole-genome sequence analysis, functional genomics, multi-omics integration, artificial intelligence, and precision livestock farming technologies, have further enhanced the scope and efficiency of genomic prediction. These innovations are facilitating simultaneous improvement in productivity, fertility, feed efficiency, disease resistance, animal welfare, and environmental sustainability. Moreover, genomic information is increasingly being integrated with genome editing technologies such as CRISPR to support precision breeding strategies. This review summarizes the historical evolution, fundamental principles, methodological developments, and practical applications of genomic selection in livestock breeding while highlighting emerging innovations and future research directions that are expected to shape next-generation animal improvement programs.