Non-Synonymous Variants in Fat QTL Genes among High- and Low-Milk-Yielding Indigenous Breeds

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. SIMPLE SUMMARY: Milk fat is a crucial trait that varies significantly among cattle breeds and determines the milk quality and pricing value. Indigenous breeds have disparity in milk quantity and quality. Our study is one of a kind which helps to decipher the variations at the genetic level correlated with transcriptional level among high and low milk-yielding cattle breeds exploring the fat QTLs. We assessed and unveiled a few key differences between the high and low-milk-yield breeds. ABSTRACT: 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 GHR, TLR4, LPIN1, CACNA1C, ZBTB16, ITGA1, ANK1, and NTG5E and, vice versa, in the genes MFGE8, FGF2, TLR4, LPIN1, NUP98, PTK2, ZTB16, DDIT3, and NT5E. The identified SNPs were ratified by pyrosequencing to prove that key differences exist in fat QTLs between the high- and low-milk-yielding breeds.