Single nucleotide polymorphism in BuLA-DQB gene influencing milk yield and composition traits in Murrah buffaloes

The concentration of fat, protein and total solids reflect in the high economic value of buffalo milk. Thus, the study of genes associated with host defense mechanisms play a critical role to avoid diseases that cause damage to milk yield and its constituents. The aim of this study was to identify SNPs in the exon 2 of the BuLA-DQB gene in 185 Murrah buffaloes by PCR and sequencing techniques and verify their associations with milk yield, fat and protein yields and percentages. The PCR primers were designed based on the BuLA-DQB sequence (GenBank number NW_005784025.1) using Primer3Plus software. DNA sequences were analyzed with CodonCode Aligner 6.0.2 software for SNPs identification. Statistical analyzes were performed using PROC MIXED of SAS 9.2 software to verify the association analysis between polymorphisms and traits using the following statistical model: Yijkl=?+CGi+Sj+Mk+?1(Iijkl-I?)+?2(Iijkl-I?)+eijkl where: Yijkl is the milk yield, fat and protein percentages of milk at 270 days; ? is the constant inherent to all observations; CGi is the fixed effect of contemporary group (animals from the same farm, year and birth season); Sj is the random effect of sire; Mk is the fixed effect of genotype for SNP; ?1 is the regression coefficient of trait Yijkl in relation to the age of the cow at measurement; ?2 is the quadratic regression coefficient of trait Yijkl in relation to the age of the cow in the measurement; Iijkl is the age of the cow evaluated at measurement; I? is the average age of the cows evaluated at measurement and eijkl is the residual random effects associated with the trait Yijkl with mean 0 and variance ?s 2. We identify the SNP g.1,802A>G (synonymous substitution) and the SNP g.1,906G>A (Arg102Gln nonsynonymous substitution), named according to reference gene sequence (NW_005784025.1), in a sequenced fragment of 295 bp containing the entire exon 2 of the BuLA-DQB gene. These SNPs were significantly associated (P < 0.05) with total milk yield, milk yield at 270 days of lactation, fat and protein yield. This is the first description of BuLA-DQB polymorphisms associated with milk yield and composition traits in Murrah buffaloes.