A genome-wide association study identify single nucleotide polymorphisms associated with milk fat percentage in buffaloes from Brazil.

The quality of buffalo milk contains considerably higher fat, protein, and mineral levels than bovine milk. This study aimed to identify SNPs possible associated with milk fat percentage (MFP) in river buffalo (Bubalus bubalis). A total of 384 females, born in 2007 and 2008, from Rio Grande do Norte and S?o Paulo states, Brazil were used in this study. The phenotypic trait associated with SNPs was MFP, with general mean equal to 4.26%?0.28. Samples of tail hair follicles were collected to DNA extraction and genomic DNA was extracted by the phenol-chloroform-isoamyl alcohol method. Genotyping was performed with the BovineHD BeadChip (Illumina), which contains 777,962 SNPs, using the Infinium(R) HD assay kit and the Illumina HiScan(TM) system, as described by the manufacturer. After the genotyping quality control, was generated a data file containing a total of 15,745 markers, which were used for genomic association study. The association analyses were carried out considering one by one marker by the maximum likelihood method, through the MACRO command and the MIXED procedure of SAS program. Student T-test was used at 1% level of significance (P<0.01) for each SNP. The fixed effects considered in the model were: SNPs (as linear covariable defined as 0 (AA); 1 (AB) and 2 (BB)), contemporary group (CG) and daily milking number (2 levels), while age of animals as considered covariables (linear and quadratic). After data consistency, a total of 358 animals were analyzed, resulting in 33 CG defined as: farm, year and season of calving (dry season - April to September; rainy season - October to March). Among a total of 15,745 SNPs, were observed 161 markers (P<0.01) associated with MFP. The BBU19 (BTA20) and BBU21 (BTA22) chromosomes present the greatest numbers of significant SNPs markers (P<0.01) for the MFP, with 31 SNPs identified in each one. These markers should be validated in a different population in order to validate the genetic associations observed in this study, before these SNPs can be used for assisted selection to improve the quality of milk and its derivatives.