| Summary: | The effect of breed on milk components—fat, protein, lactose, and water—has been observed to be significant. As fat is one of the major price-determining factors for milk, exploring the variations in fat QTLs across breeds would shed light on the variable fat content in their milk. Here, on whole-genome sequencing, 25 differentially expressed hub or bottleneck fat QTLs were explored for variations across indigenous breeds. Out of these, 20 genes were identified as having nonsynonymous substitutions. A fixed SNP pattern in high-milk-yielding breeds in comparison to low-milk-yielding breeds was identified in the genes <i>GHR, TLR4, LPIN1, CACNA1C, ZBTB16, ITGA1, ANK1,</i> and <i>NTG5E</i> and, vice versa, in the genes <i>MFGE8, FGF2, TLR4, LPIN1, NUP98, PTK2, ZTB16, DDIT3</i>, and <i>NT5E</i>. The identified SNPs were ratified by pyrosequencing to prove that key differences exist in fat QTLs between the high- and low-milk-yielding breeds.
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