Transcriptomic profiling of milk fat globules in cows with different β-casein genotypes

The A2 β-casein milk variant has attracted increasing scientific interest due to its potential health benefits. This has led to a growing trend in certain countries toward breeding A2A2 genotype cows to produce milk containing only A2 β-casein. However, it is unknown whether the β-casein genotype (A1A1 vs A2A2) is associated with gene expression differences in the mammary gland, potentially affecting milk synthesis or composition. Therefore, this study aimed to compare the milk fat globule (MFG) transcriptome of cows with different β-casein genotypes (A1A1 vs. A2A2) using RNA-seq (n = 14). The functional enrichment analysis of highly expressed genes in MFG revealed a strong representation of genes involved in protein synthesis, milk fat secretion and cellular energy metabolism, key processes essential for lactation. The genes encoding α-S1-casein (CSN1S1), β-lactoglobulin (PAEP/BLG), β-casein (CSN2), glycosylation-dependent cell adhesion molecule-1 (GLYCAM1), cytochrome c oxidase subunits I and III (COX1 and COX3), and κ-casein (CSN3) were found as the most abundant transcripts in MFG, with mean values of 90,401, 71,022, 53,579, 49,494, 38,551, 33,584, and 30,791 FPKM, respectively. Differential expression analysis between the two experimental groups revealed minimal differences at the gene level, with only two genes identified significantly different out of the 11,180 and 11,257 genes expressed in MFG (identified with DESeq2 and EdgeR packages, respectively). Both methods identified NADH dehydrogenase subunit 6 (ND6) as down-regulated in A2A2 cows, with DESeq2 additionally detecting down-regulation of 16S mitochondrial rRNA (16S Mt-rRNA). ND6 and 16S Mt-rRNA are mitochondrial genes involved in oxidative phosphorylation and energy production, and their reduced expression may suggest slightly impaired mitochondrial activity in A2A2 animals. Overall, these findings suggest that the β-casein genotype (A1A1 vs. A2A2) is not strongly associated with gene-level transcriptomic differences in the mammary gland, which could be of interest in the context of current selective breeding strategies for A2A2 genotype. However, other aspects such as post-transcriptional regulatory mechanisms should be further analysed.