Abstract : Highlights What are the main findings? Differentially expressed milk fat QTL genes explored with whole genome se-quencing for variant analysis. Identified non-synonymous SNPs for hub and bottleneck QTL genes associated with milk fat traits. What is the implication of the main finding? Identified differential pattern(s) of SNPs in fat QTLs between high and low milk yield breeds. Impact of the identified SNP pattern(s) on milk fat traits can be further explored.