Candidate Genes and Gene Networks Change with Age in Japanese Black Cattle by Blood Transcriptome Analysis

• Published in: Genes Vol. 14; no. 2; p. 504
• Main Authors: Chang, Chencheng, Yang, Yanda, Zhou, Le, Baiyin, Batu, Liu, Zaixia, Guo, Lili, Ma, Fengying, Wang, Jie, Chai, Yuan, Shi, Caixia, Zhang, Wenguang
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 16.02.2023; MDPI
• Subjects: Age; Aging; Beef; Beef cattle; Blood; blood transcriptome; co-expression network; Data analysis; Developmental stages; DNA testing; Gene expression; Genetic aspects; Genetic transcription; Genomes; growth; Immune response; Influence; Japanese black cattle; Laboratory animals; Metabolism; Methods; Protein interaction; Proteins; Transcriptomes; China; blood transcriptome; growth; aging; Japanese black cattle; co-expression network
• ISSN: 2073-4425; 2073-4425
• 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.