An association study with dairy traits confirms the importance of three SNPs for the assisted selection in the Mediterranean river buffalo

The search for DNA polymorphisms enhancing dairy animal genetics spans over 40 years, notably in cattle, identifying key alleles in casein and DGAT1 genes for milk traits improvement. Despite advanced genomic tools and precise phenotypic records, similar signs of progress have not been made in river buffaloes yet. This study aimed to explore the effects of four SNPs in CSN1S1 (AJ005430:c.578C>T), CSN3 (HQ677596:c.536C>T), SCD (FM876222:g.133A>C), and LPL (AWWX01438720.1:g14229A>G) genes on six milk traits (daily milk yield, dMY; protein yield, dPY; fat yields, dFY; fat %, dFP; and protein %, dPP; somatic cell score, SCS; and urea, MU) in a representative buffalo population. Genotyping was conducted on 800 buffaloes, and milk traits were recorded monthly from 2010 to 2021. Associations between SNPs and milk traits were analyzed using 15,742 milk test day records from 680 buffalo cows. Three out of four SNPs showed associations with various traits. CSN1S1 was associated with increased dMY (p=0.022), dPY (p=0.014), dFY (p=0.029), and SCS (p=0.032). CSN3 positively correlated with SCS (p=0.005) and milk urea (p=0.04). LPL demonstrated favourable effects on dMY (p=0.028), dFP (p=0.027) and dPP (p=0.050). Conversely, SCD showed no associations. This study represents the first confirmation of the importance of these genes in Mediterranean river buffalo breeding programs, providing valuable insights for preselecting young bulls for breeding.