Background: The importance to detect the genetic polymorphism for milk protein genes in dairy cattle populations is the relationship of these genes with cheese yield, rennet time, and curd firmness. Mexican dairy cattle populations have been developed from genetic resources from around the world. It has incorporated a wide base of milk protein genes. The objectives were to estimate the allelic and genotypic frequencies, genetic diversity and polymorphic information content for the β-casein, κ-casein and β-lactoglobulin genes in Mexican Jersey populations.

Results: The β-casein allele with the highest frequency was A² (0.71), followed by A¹ (0.19), A³ (0.05), B (0.04), and C (0.01). The B allele of κ-casein had higher frequency (0.69) than the A (0.26) and E (0.05). For β-lactoglobulin, the most frequent allele was B (0.72), followed by A (0.26) and C alleles (0.02). The average genetic diversity (H_e) was 0.53. The average locus effective allele number was 1.79.

Conclusions: There is a high allelic diversity for κ-caseín, β-casein, and β-lactoglobulin in the population studied. It could be included in breeding programs aimed to improve the milk quality traits of economic importance.