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Screening of Key Genes Related to Intramuscular Fat Deposition in Buffaloes Based on GEO Database and Bioinformatics Analysis
- LIANG Shasha, YU Nongqi, LU Ying, LI Tingting, YAN Shengfei, HUANG Jian, TAN Zhengzhun, HUANG Rongchun, LI Hui, PAN Weijun, QIN Guangsheng
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2023, 50(11):
4359-4369.
doi:10.16431/j.cnki.1671-7236.2023.11.005
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Abstract
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【Objective】 This study was aimed to screen the key genes related to intramuscular fat (IMF) deposition, and provide reference for mining molecular markers to improve IMF deposition in buffaloes.【Method】 The GSE19586 dataset was downloaded from GEO database, the differentially expressed genes (DEGs) of longissimus dorsi muscle in Guangxi buffaloes and Qinghai yaks at 36 months of age were screened using limma R package, the up- and down-regulated DEGs were enriched for GO function and KEGG pathway using clusterProfiler R package, respectively, and the protein-protein interaction (PPI) network of DEGs were analyzed using STRING online.The results were visualized by Cytoscape 3.9.1, and the top 20 pivotal genes in terms were screened.【Result】 A total of 254 DEGs were screened in this study, including 61 up-regulated genes and 193 down-regulated genes.GO function enrichment analysis showed that up-regulated DEGs were mainly enriched in processes such as actin-myosin filament sliding, myosin complex, myosin binding, triglyceride metabolism, acylglycerol metabolism, neutral lipid metabolism, cell apoptosis signaling pathway regulation, etc.Down-regulated DEGs were mainly enriched in short-chain fatty acid metabolism, unsaturated fat metabolism, cell reaction to ketone, cell matrix connection, lipoprotein synthesis, protein maturation, processing, polymerization and other processes.KEGG pathway enrichment analysis showed that up-regulated DEGs were mainly involved in metabolic pathways, adipocytokines, insulin resistance, AMP-activated protein kinase (AMPK), thyroid hormone signaling pathways, carbohydrate digestion and absorption and other signal pathways.Down-regulated DEGs were mainly involved in metabolic pathway, phagosome, lysosome, adhesive spot, apoptosis and other signal pathways.There were 116 nodes and 205 links in PPI network, including 26 up-regulated proteins and 90 down-regulated proteins.The top 20 pivotal genes were ACTB, PPARGC1, NR3C1, FOS, GOT2, SERPINE1, RAC1, LEP, STAT5B, HPRT1, DDC, FABP1, HDAC1, RHOA, EEF1A1, PCK1, SOD2, PRKCB, GPX1 and CTGF.【Conclusion】 A total of 254 DEGs in longissimus dorsi muscle of Guangxi buffaloes and Qinghai yaks at 36 months of age were screened in this study.The candidate genes MYH3, GPX1, LDLR, LEP and PCK1 might be related to IMF deposition in buffaloes were mined, which provided a theoretical basis for finding molecular markers to improve the meat quality in buffaloes.