CSN2 A1/A2 Genotyping in Dairy Cattle: A Decision-Oriented Review of Molecular Methods and Practical Applications

This study presents a structured narrative review integrating methodological and decision-oriented perspectives. Milk proteins, particularly β-casein, have attracted increasing scientific and commercial attention due to their genetic variability and role in dairy production and product differentiation. Among β-casein variants, the A1 and A2 alleles of the CSN2 gene are of particular relevance, as their single-nucleotide difference has influenced breeding strategies and the expansion of A2-oriented dairy markets. Although multiple validated molecular genotyping approaches are available for CSN2 A1/A2 discrimination, guidance on their context-appropriate deployment in agricultural systems remains largely technique-centric. The present framework integrates analytical performance, sample complexity, and operational constraints to support the selection of fit-for-purpose methods across breeding, diagnostic, and dairy authentication contexts. Classical and advanced approaches, including polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP), allele-specific polymerase chain reaction (AS-PCR) and amplification refractory mutation system PCR (ARMS-PCR), high-resolution melting (HRM) analysis, sequencing-based methods, single nucleotide polymorphism (SNP) arrays, and digital polymerase chain reaction (dPCR), are comparatively evaluated not only in terms of sensitivity and throughput but also with respect to scalability, reproducibility, and decision risk. This framework provides a practical decision-support tool for aligning genotyping strategies with application-specific risk profiles, thereby improving reliability, transparency, and regulatory compliance in modern dairy systems.