Identification of the hub genes related to adipose tissue metabolism of bovine

Abstract

Due to the demand for high-quality animal protein, there has been consistent interest in how to obtain more high-quality beef. As well-known, the adipose content of beef has a close connection with the taste and quality of beef, and cattle with different energy or protein diet have corresponding effects on the lipid metabolism of beef. Thus, we performed weighted gene co-expression network analysis (WGCNA) with subcutaneous adipose genes from Norwegian red heifers fed different diets to identify hub genes regulating bovine lipid metabolism. For this purpose, the RNA sequencing data of subcutaneous adipose tissue of 12-month-old Norwegian red heifers (n = 48) with different energy or protein levels were selected from the GEO database, and 7,630 genes with the largest variation were selected for WGCNA analysis. Then, three modules were selected as hub genes candidate modules according to the correlation between modules and phenotypes, including pink, magenta and grey60 modules. GO and KEGG enrichment analysis showed that genes were related to metabolism, and participated in Rap, MAPK, AMPK, VEGF signaling pathways, and so forth. Combined gene interaction network analysis using Cytoscape software, eight hub genes of lipid metabolism were identified, including TIA1, LOC516108, SNAPC4, CPSF2, ZNF574, CLASRP, MED15 and U2AF2. Further, the expression levels of hub genes in the cattle tissue were also measured to verify the results, and we found hub genes in higher expression in muscle and adipose tissue in adult cattle. In summary, we predicted the key genes of lipid metabolism in the subcutaneous adipose tissue that were affected by the intake of various energy diets to find the hub genes that coordinate lipid metabolism, which provide a theoretical basis for regulating beef quality.

Whole‐genome resequencing deciphers patterns of genetic diversity, phylogeny, and evolutionary dynamics in Kashmir cattle

“…Among the top signaling genes, PRNP , GBP4 , BOLA‐DQA5 and BOLA‐DQB are related to immunity (Cao et al., 2018; Fukunaga et al., 2020; Gurgul & Słota, 2007; Kosińska‐Selbi et al., 2020). In addition, some genes related to reproduction ( ABCE1 and ADAM3 ) (Chen et al., 2022; Jiao et al., 2017), growth and development and high‐altitude adaptation ( STUB1 , CLASRP and CLCA2 ; GX et al., 2019; Terefe et al., 2022; Wang et al., 2022) were also screened (Figures 4b and 5c,f; Table 1; Tables S11–S17).…”

Selective Sweeps in Cattle Genomes in Response to the Influence of Urbanization and Environmental Contamination

“…In genomic studies, specific variants of SLC24A4 were significantly associated with milk urea concentration [37], body conformation [38], reproduction [39], and production [40] traits in cattle. Likewise, gene CPSF2, with effects on the RNA binding activity, was significantly associated with lipid metabolism in cattle [41]. When assessing the selection sweeps and annotated genes for group comparisons including the mixed region, SLC24A4 and RIN3 were shared genes for both the urban_vs_mixed and rural_vs_mixed comparisons.…”