College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China.
College of Agronomy Animal Husbandry and Bioengineering, Xing'an Vocational and Technical College, Ulanhot 137400, China.
Genes (Basel). 2023 Feb 16;14(2):504. doi: 10.3390/genes14020504.
Age is an important physiological factor that affects the metabolism and immune function of beef cattle. While there have been many studies using the blood transcriptome to study the effects of age on gene expression, few have been reported on beef cattle. To this end, we used the blood transcriptomes of Japanese black cattle at different ages as the study subjects and screened 1055, 345, and 1058 differential expressed genes (DEGs) in the calf vs. adult, adult vs. old, and calf vs. old comparison groups, respectively. The weighted co-expression network consisted of 1731 genes. Finally, blue, brown, and yellow age-specific modules were obtained, in which genes were enriched in signaling pathways related to growth and development and immune metabolic dysfunction, respectively. Protein-protein interaction (PPI) analysis showed gene interactions in each specific module, and 20 of the highest connectivity genes were chosen as potential hub genes. Finally, we identified 495, 244, and 1007 genes by exon-wide selection signature (EWSS) analysis of different comparison groups. Combining the results of hub genes, we found that VWF, PARVB, PRKCA, and TGFB1I1 could be used as candidate genes for growth and development stages of beef cattle. CORO2B and SDK1 could be used as candidate marker genes associated with aging. In conclusion, by comparing the blood transcriptome of calves, adult cattle, and old cattle, the candidate genes related to immunity and metabolism affected by age were identified, and the gene co-expression network of different age stages was constructed. It provides a data basis for exploring the growth, development, and aging of beef cattle.
年龄是影响肉牛代谢和免疫功能的重要生理因素。虽然已有许多使用血液转录组研究年龄对基因表达影响的研究，但在肉牛中报道较少。为此，我们以不同年龄的日本黑牛血液转录组为研究对象，分别在犊牛与成年牛、成年牛与老年牛、犊牛与老年牛的比较组中筛选到 1055、345 和 1058 个差异表达基因（DEGs）。加权共表达网络由 1731 个基因组成。最后，获得了蓝色、棕色和黄色三个具有年龄特异性的模块，其中基因分别富集在与生长发育和免疫代谢功能障碍相关的信号通路中。蛋白质-蛋白质相互作用（PPI）分析显示了每个特定模块中的基因相互作用，选择最高连接度的 20 个基因作为潜在的枢纽基因。最后，我们通过不同比较组的外显子范围选择特征（EWSS）分析分别鉴定到 495、244 和 1007 个基因。综合枢纽基因的结果，我们发现 VWF、PARVB、PRKCA 和 TGFB1I1 可以作为肉牛生长发育阶段的候选基因。CORO2B 和 SDK1 可以作为与衰老相关的候选标记基因。综上所述，通过比较犊牛、成年牛和老年牛的血液转录组，鉴定出了受年龄影响的免疫和代谢相关候选基因，并构建了不同年龄阶段的基因共表达网络。为探索肉牛的生长、发育和衰老提供了数据基础。
