Causal variants in animal genomes: approaches to identification, phenotypic impact, and implications for selective breeding

This review provides a comprehensive analysis of causal variants as the most informative genetic markers in livestock breeding, highlighting their potential to enhance the precision and efficiency of animal selection strategies. It discusses the types and classifications of genetic variants arising in animal genomes, addresses complex issues related to genetic variant terminology, and evaluates their prevalence and significance in phenotypic variability and evolution. The review explores the molecular mechanisms underlying genetic causality, detailing how variants in both regulatory and coding regions can influence gene expression regulation and the structural and functional properties of transcripts and proteins. It also outlines the diversity of methodological approaches used to identify causal variants and assess their functional impact, incorporating both experimental techniques and bioinformatic tools. Prominent examples of causal variants identified in the genomes of mammals and birds are presented, demonstrating their influence on traits such as growth rate, body conformation, milk and meat production and quality, reproductive performance, coat color, and disease resistance. In addition, the review describes current strategies and future prospects for the use of causal variants as genetic markers to improve animal productivity traits within marker-assisted and genomic selection frameworks. Finally, it addresses the conceptual and practical challenges in distinguishing truly causal variants from those merely statistically associated with traits, emphasizing the need for more rigorous criteria and methodological standards in this area of research.