With the aim of characterizing the genetic background of Egyptian buffalo and identifying genomic regions and potential causative mutations associated with milk yield, we performed a Genome-Wide Association Study (GWAS) in Egyptian buffalo using Axiom Buffalo Genotyping Array 90 K. This study was carried out with 250 buffalo cows using 89,069 daily milk records. After quality control, a total of 42,269 single nucleotide polymorphisms ( SNPs) remained for further analysis. Genome-wide analysis was performed in the way of SNP-by-SNP, through regressing the observations of an average daily milk yield deviations on SNP alleles. Several genomic regions were detected with suggestive signals of association on chromosomes BTA1, BTA5, BTA6, and BTA27. The most significant SNP (Affx-79526274) was located on chromosome BTA27. The convincingly associated SNPs were located within or close to several candidate genes. A GO analysis ranked immune response at the top of all biological process associated with those genes. This is the first GWAS in Egyptian buffalo. Although a small sample size was used in this study, several suggestive genomic loci associated with daily milk production were detected. Further work is required on a larger sample size with fine mapping of identified QTL to detect potential candidate regions.
