Prolonged lactation is common in yaks under grazing conditions with natural reproduction. To understand the differences in milk protein composition and mammary gland function between standard lactation yaks (TL yaks) and prolonged lactation yaks (HL yaks), milk samples from 15 TL and 15 HL yaks were collected from a yak pasture in the northwest highlands of China. The iTRAQ technique was used to analyze the skim milk proteins. The analysis revealed 202 differentially expressed proteins, with 109 up-regulated and 93 down-regulated in HL yak milk. Caseins, including κ-casein, αs1-casein, αs2-casein, and β-casein, were found to be overexpressed by more than 1.43-fold in HL yak milk. Gene Ontology (GO) function analysis indicated that the milk from HL yaks resembled that of a degeneration stage, similar to dairy cows. KEGG pathway enrichment showed that carbohydrate metabolism and amino acid biosynthesis were the most affected pathways. These results highlight significant differences in the skim milk proteins between TL and HL yaks and suggest that HL yaks' mammary glands are in a degeneration phase.
