Differences in skin and hair phenotypes between the scapular and ventral regions of yaks (Bos grunniens) are obvious and become more prominent with age. However, the genetic mechanism that causes differences in yak skin at different ages has not been reported. In this study, we investigated the transcriptomic profile of yak skin across different ages (0.5 years, 2.5 years, and 4.5 years) and body sites (scapular and ventral regions). Differential gene expression analysis was initially conducted to explore the transcriptomic differences in skin at different ages and different body sites. Subsequently, weighted gene co-expression network analysis (WGCNA) was employed to analyze the transcriptomic data comprehensively. The results showed that, among all comparison groups, the Y2.5_S vs. Y2.5_V group (regional comparison) exhibited the highest number of DEGs, with 491 genes (179 upregulated and 312 downregulated), followed by the Y2.5_V vs. Y0.5_V group (age comparison), which had 370 DEGs (103 upregulated and 267 downregulated). DEGs such as IGF2BP3, ADCY8, FOSL1, and S100A8 were found in all comparison groups of different ages, and multiple members of the HOX gene family including HOXC10, HOXA9, HOXA6, HOXB9, and HOXB6 were differentially expressed in comparison groups at different sites. Functional enrichment analysis showed that there were more obvious differences in immune function between different ages of skin and more obvious differences in endocrine function between different parts of skin. WGCNA revealed that genes related with immunity such as GLYATL2, ACSL5, and SPDEF were the core genes of the co-expression module associated with the scapula region, and multiple genes related to hair follicle development such as FOXN1, OVOL1, DLX3, HOXC13, and TCHH were found to be the hub genes of the co-expression module associated with the ventral region. Overall, our study provides valuable insights into the transcriptomic complexity of yak skin across different ages and body sites. The differential gene expression patterns and co-expression network modules identified in this study lay the foundation for further research on skin biology and adaptation mechanisms in yaks.

(1) Background: Hair growth can function as an indicator of an animal’s health and nutritional status, furnishing a valuable means for early diagnosis and timely modifications to management practices, and is influenced by hormones, the immune system, and the levels of minerals within the animal’s body. (2) Methods: In this study, a total of 81 yaks were selected and divided into three groups according to their ages (1–2 years, 3–4 years, 5–6 years), and the concentrations of melatonin, dihydrotestosterone, IgA, IgG, and IgM in their blood serum and the levels of Ca, Mg, Zn, Fe, and P in both their blood serum and hair were detected. (3) Results: The levels of melatonin and dihydrotestosterone in yaks aged 1–2 years were significantly higher than those of other age groups (p < 0.001). In addition, the concentration of melatonin in male yaks was markedly greater than that in female yaks (p < 0.05). When it came to immunoglobulins, the IgA level in 1–2-year-old yaks was strikingly higher than those in yaks aged 3–4 years and 5–6 years (p < 0.05). In terms of mineral elements, the concentrations of calcium, magnesium, zinc, and iron in the blood serum of 1–2-year-old and 5–6-year-old yaks were significantly elevated compared to those in 3–4-year-old yaks. However, there was no notable difference between the 1–2-year-old and 5–6-year-old groups. The correlation analysis showed that there was a significant correlation between DHT and the levels of melatonin and IgA in yaks. Additionally, a significant correlation was observed between IgA and IgG, as well as between IgA and the levels of Fe, Mg, and Ca. It is likely that they jointly regulate the hair growth and immune processes of yaks. (4) Conclusions: There are positive correlations among melatonin, dihydrotestosterone, and IgA in the blood serum and the content of Fe and Mg in the hair to varying degrees, implying these indicators may jointly regulate yak hair growth and immune status. These research findings provide data support for applied research into evaluating the overall health status of yaks through the growth status of hair or by measuring the mineral content in hair in a non-invasive way.