CSN1S1 and CSN3 genetic variants affect milk quality traits in the buffalo population in Serbia

The Mediterranean water buffalo breed is the most common in Europe. Caseins are major milk proteins whose gene variants can affect milk yield, composition, and processing characteristics. The most prevalent type of milk protein, αS1 casein, has been associated with milk quality traits. κ casein has been associated with traits crucial for cheese manufacturing. Small-scale households in Serbia raise buffaloes primarily for their use to make milk and butter. This study aimed to assess the association of <italic>CSN1S1 </italic>and <italic>CSN3</italic> genetic variants, solely and in haplotype, with milk quality traits in the water buffalo population in Serbia. The study involved 130 water buffaloes from Serbia. <italic>CSN1S1</italic> and <italic>CSN3</italic> genotypes were determined using sequencing analysis on an ABI PRISM 3130 Genetic Analyzer. A subgroup of 42 animals was analyzed for the composition of raw buffalo milk. Statistical analyses were performed using Statistica 8 software and Thesias software for haplotype analysis. We found that <italic>CSN1S1</italic> 472G&gt;C was associated with higher protein and casein levels in milk. Haplotype analysis of variants <italic>CSN1S1 </italic>472G&gt;C and<italic> CSN3 </italic>467C&gt;T showed that haplotype 1C3C had significantly higher casein levels<italic> (p</italic>=0.00002) and protein levels<italic> (p</italic>=0.0004) in comparison with the reference haplotype, 1G3C. Our results showed that genetic variants <italic>CSN1S1 </italic>472G&gt;C and<italic> CSN3</italic> 467C&gt;T in haplotype significantly impact casein levels in buffalo milk and suggest that their haplotype analysis provides greater significance in association with milk casein level than individual analysis.