Thesis (Ph.D.) - Cairo University - Faculty of Agriculture - Department of Animal Production

The aim of this study was to perform a genome-wide association study (GWAS) to identify genomic loci and detect potentially candidate genes associated with seven milk production traits; daily milk yield (DMY), fat percentage (FP), fat yield (FY), protein percentage (PP), protein yield (PY), lactose percentage (LP) and lactose yield (LY) in Egyptian buffalo. The phenotypic dataset included 161,479 daily milk records from 1,670 animals and 60,318 monthly measures for other traits from 1481 animals. Adjustment for non-genetic effects has been made using univariate animal model by BLUPF90. A total number of 114 animals with high and low deviated performance were selected for genotyping with Axiom Buffalo Genotyping 90K Array. Adjusted phenotypes were used for GWAS in the way of SNP-by-SNP using a single marker regression. With 5% Bonferroni genome-wide threshold, 55 significant and 33 suggestive SNPs were detected for association with the tested traits and were distributed over 25 buffalo chromosomes (BBU). The 88 SNPs were two for DMY, three for FP, seven for FY, 21 for PP, 14 for PY, 39 for LP and two for LY. The identified genomic regions were coincided with previously reported QTL in buffalo and cattle populations. In addition, novel genomic loci were suggested. The identified SNPs are placed within or close to many promising candidate genes with biological roles associated with milk production traits, for example:, TPD52, ZBTB10, RALYL, and SNX16 on BBU15; ADGRD1 on BBU17; ESRRG on BBU5; and GRIP1 on BBU4. This is the first GWAS for milk quality traits in Egyptian buffalo

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