Genetic association study of polymorphisms in the DQB gene with protein and fat percentages in buffalo milk

To identify high-quality genetic material for animal improvement programs, researchers have used molecular genetics techniques to identify genes and alleles responsible for phenotypic variation associated with economic important traits. Thus, the aim of this study was to identify single nucleotide polymorphisms (SNPs) in the DQB gene affecting milk production and quality traits in Murrah buffaloes. Hair follicle samples of the 185 animals were collected for DNA extraction, PCR and sequencing to SNPs identification. Statistical analyzes were performed using PROC MIXED of SAS 9.2 software in order to verify the genetic association analysis between polymorphisms and studied 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; Sj is the random effect of sire, with mean 0 and variance ?s 2; 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. The contemporary group was considered the concatenation of farm, year and birth season. A total of four SNPs were identified in the exon 2 region of DQB gene sequence, which was employed for subsequent statistical analyzes. The SNP g.283A > G and SNP g.286G > T showed significantly association (P < 0.01) with fat percentage, while SNP g.118C > G and SNP g.154C > T presented significantly association (P < 0.05) with protein percentage in milk. This is the first description of DQB gene polymorphisms in buffalo associated with milk quality traits. These results suggest the use of these SNPs as molecular markers for economically important traits related to milk quality.