基于GEO数据库筛选与水牛肌内脂肪沉积相关的候选基因及生物信息学分析

doi:10.16431/j.cnki.1671-7236.2023.11.005

摘要/Abstract

摘要： 【目的】筛选与水牛肌内脂肪沉积相关的关键基因，为挖掘改善水牛肌内脂肪沉积的分子标记提供参考。【方法】通过GEO数据库下载GSE19586数据集，使用limma R语言程序包筛选广西水牛和青海牦牛36月龄背最长肌的差异表达基因（differentially expressed genes，DEGs），使用clusterProfiler R语言程序包分别对上调、下调的DEGs进行GO功能和KEGG通路富集分析，使用STRING在线软件对DEGs进行蛋白互作（PPI）网络分析，并使用Cytoscape 3.9.1软件对其结果进行可视化，筛选排名前二十的枢纽基因。【结果】本研究共筛选出254个DEGs，其中61个上调，193个下调。GO功能富集结果显示，上调DEGs主要富集于肌动蛋白-肌球蛋白细丝滑动、肌球蛋白复合体、肌球蛋白结合、甘油三酯代谢、酰基甘油代谢、中性脂代谢、细胞凋亡信号通路调控等过程；下调DEGs主要富集于短链脂肪酸代谢、不饱和脂肪酸代谢、细胞对酮的反应、细胞基质连接、脂蛋白合成及蛋白质的成熟、加工、聚合等过程。KEGG通路富集结果显示，上调DEGs主要参与代谢途径、脂肪细胞因子、胰岛素抵抗、磷酸腺苷活化蛋白激酶（AMPK）、甲状腺激素信号转导途径和碳水化合物消化吸收等信号通路；下调DEGs主要参与代谢途径、吞噬体、溶酶体、黏着斑和细胞凋亡等信号通路。PPI网络中共有116个节点和205条连线，其中上调蛋白26个，下调蛋白90个；筛选出的前20个枢纽基因分别为ACTB、PPARGC1、NR3C1、FOS、GOT2、SERPINE1、RAC1、LEP、STAT5B、HPRT1、DDC、FABP1、HDAC1、RHOA、EEF1A1、PCK1、SOD2、PRKCB、GPX1和CTGF。【结论】本研究共筛选出广西水牛和青海牦牛36月龄背最长肌DEGs 254个，挖掘到可能与水牛肌内脂肪沉积相关的候选基因MYH3、GPX1、LDLR、LEP和PCK1，为寻找改善水牛肌内脂肪沉积的分子标记提供了理论基础。

关键词: 水牛; 肌内脂肪沉积; 差异表达基因; 蛋白互作

Abstract: 【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.

Key words: buffaloes; intramuscular fat deposition; differentially expressed genes; protein-protein interaction

中图分类号:

梁莎莎, 于农淇, 卢瑛, 李厅厅, 鄢胜飞, 黄健, 谭正准, 黄荣春, 李辉, 潘伟军, 覃广胜. 基于GEO数据库筛选与水牛肌内脂肪沉积相关的候选基因及生物信息学分析[J]. 中国畜牧兽医, 2023, 50(11): 4359-4369.

LIANG Shasha, YU Nongqi, LU Ying, LI Tingting, YAN Shengfei, HUANG Jian, TAN Zhengzhun, HUANG Rongchun, LI Hui, PAN Weijun, QIN Guangsheng. Screening of Key Genes Related to Intramuscular Fat Deposition in Buffaloes Based on GEO Database and Bioinformatics Analysis[J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(11): 4359-4369.

参考文献

[1] ZHANG F, HANIF Q, LUO X, et al.Muscle transcriptome analysis reveal candidate genes and pathways related to fat and lipid metabolism in Yunling cattle[J].Animal Biotechnology, 2023, 34(4):1022-1029.
[2] ZHANG C, WANG G, WANG J, et al.Analysis of differential gene expression and novel transcript units of ovine muscle transcriptomes[J].PLoS One, 2014, 9(2):e89817.
[3] WANG Y, JIA X, HSIEH J, et al.Transcriptome response of liver and muscle in heat-stressed laying hens[J].Genes (Basel), 2021, 12(2):255.
[4] WOOD J D, ENSER M, FISHER A V, et al.Fat deposition, fatty acid composition and meat quality:A review[J].Meat Science, 2008, 78(4):343-358.
[5] JEREMIAH L E, DUGAN M E, AALHUS J L, et al.Assessment of the relationship between chemical components and palatability of major beef muscles and muscle groups[J].Meat Science, 2003, 65(3):1013-1019.
[6] PARK S J, BEAK S H, JUNG D, et al.Genetic, management, and nutritional factors affecting intramuscular fat deposition in beef cattle:A review[J].Asian-Australasian Journal of Animal Sciences, 2018, 31(7):1043-1061.
[7] 李广祯.青海牦牛全基因组遗传多样性与选择信号研究[D].西宁:青海大学, 2022. LI G Z.Genome-wide genetic diversity and selection signature of Qinghai yak[D].Xining:Qinghai University, 2022.(in Chinese)
[8] 杨曼, 刘海, 张润, 等.北京黑猪MYH3和MYH13基因多态性与肉质性状的关联分析[J].中国畜牧兽医, 2022, 49(9):3428-3437. YANG M, LIU H, ZHANG R, et al.Association analysis of polymorphism of MYH3 and MYH13 genes with meat quality traits in Beijing Black pigs[J]. China Animal Husbandry & Veterinary Medicine, 2022, 49(9):3428-3437.(in Chinese)
[9] ALLAIS S, LEVEZIEL H, PAYET-DUPRAT N, et al.The two mutations, Q204X and nt821, of the myostatin gene affect carcass and meat quality in young heterozygous bulls of French beef breeds[J].Journal of Animal Science, 2010, 88(2):446-454.
[10] 代宇星, 盛志康, 楚菡, 等. MYH3基因在动物肌肉发育、能量代谢及生产性能中的研究进展[J].中国畜牧兽医, 2020, 47(10):3270-3277. DAI Y X, SHENG Z K, CHU H, et al.Research progression MYH3 gene in animal muscle development, energy metabolism and production performance[J]. China Animal Husbandry & Veterinary Medicine, 2020, 47(10):3270-3277.(in Chinese)
[11] CLARK D L, BOLER D D, KUTZLER L W, et al.Muscle gene expression associated with increased marbling in beef cattle[J]. Animal Biotechnology, 2011, 22(2):51-63.
[12] MCCLUNG J P, RONEKER C A, MU W, et al.Development of insulin resistance and obesity in mice overexpressing cellular glutathione peroxidase[J].Proceedings of the National Academy of Sciences of the United States of America, 2004, 101(24):8852-8857.
[13] GO G W, MANI A.Low-density lipoprotein receptor (LDLR) family orchestrates cholesterol homeostasis[J].The Yale Journal of Biology and Medicine, 2012, 85(1):19-28.
[14] 王光辉, 杨连玉, 宫世平, 等.肉牛肌内脂肪的沉积机制及其营养调控的研究进展[J].中国畜牧杂志, 2021, 57(6):25-30. WANG G H, YANG L Y, GONG S P, et al.The mechanism of intramuscular fat deposition and nutritional factors affecting its deposition in beef muscle[J].Chinese Journal of Animal Science, 2021, 57(6):25-30.(in Chinese)
[15] ATZMONY L, UGWU N, ZAKI T D, et al.Post-zygotic ACTB mutations underlie congenital smooth muscle hamartomas[J].Journal of Cutaneous Pathology, 2020, 47(8):681-685.
[16] 吕亚宁, 叶文文, 兰旅涛.牛肌内脂肪沉积影响因素及相关基因研究进展[J].中国草食动物科学, 2019, 39(4):55-57. LYU Y N, YE W W, LAN L T.Research progress on influencing factors and related genes of fat deposition in bovine muscle[J].China Herbivore Science, 2019, 39(4):55-57.(in Chinese)
[17] 熊讯, 阮涌, 许厚强.基于转录组分析干扰FABP1基因对猪肌内脂肪沉积的影响[J].南方农业学报, 2023, 54(3):724-734. XIONG X, RUAN Y, XU H Q.Transcriptome-based analysis of the effect of interference with the FABP1 gene on intramuscular fat deposition in pigs[J].Journal of Southern Agriculture, 2023, 54(3):724-734.(in Chinese)
[18] GIRMAY S, AHMAD H I, ZAHRA Q A.A simulation analysis and screening of deleterious nonsynonymous single nucleotide polymorphisms (nsSNPs) in sheep LEP gene[J].BioMed Research International, 2022, 2022:7736485.
[19] 徐炜琳.松辽黑猪四种基因多态性与背膘厚的关联分析[D].长春:吉林农业大学, 2017. XU W L.The association of polymorphisms of four genes with the backfat in Songliao Black swine[D].Changchun:Jilin Agricultural University, 2017.(in Chinese)
[20] 黄英, 杨明华, 孔令富, 等.Leptin介导AMPK信号通路对猪皮下前脂肪细胞脂类代谢调控的研究[J].生物技术通报, 2016, 32(2):211-218. HUANG Y, YANG M H, KONG L F, et al.The regulation of leptin-mediated AMPK signal pathway on lipid metabolism in porcine subcutaneous preadipocyte[J].Biotechnology Bulletin, 2016, 32(2):211-218.(in Chinese)
[21] LATORRE P, BURGOS C, HIDALGO J, et al.c.A2456C-substitution in Pck1 changes the enzyme kinetic and functional properties modifying fat distribution in pigs[J].Scientific Reports, 2016, 6:19617.
[22] DUAN J, SHAO F, SHAO Y, et al.Androgen inhibits abdominal fat accumulation and negatively regulates the PCK1 gene in male chickens[J].PLoS One, 2013, 8(3):e59636.
[23] HAKIMI P, YANG J, CASADESUS G, et al.Overexpression of the cytosolic form of phosphoenolpyruvate carboxykinase (GTP) in skeletal muscle repatterns energy metabolism in the mouse[J].Journal of Biological Chemistry, 2007, 282(45):32844-32855.
[24] WANG W, XUE W, JIN B, et al.Candidate gene expression affects intramuscular fat content and fatty acid composition in pigs[J].Journal of Applied Genetics, 2013, 54(1):113-118.
[25] HUANG J, FENG X, ZHU R, et al.Comparative transcriptome analysis reveals that PCK1 is a potential gene affecting IMF deposition in buffalo[J].BMC Genomics, 2020, 21(1):710.