基于转录组测序分析西门塔尔牛和安格斯牛脂肪沉积相关基因的差异表达

doi:10.3969/j.issn.1674-7968.2020.04.011

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Abstract The content and distribution of intramuscular fat (IMF) is the material basis for the formation of Bos taurus marbled meat. There is a difference in fat deposition capacity between Simmental cattle (B. taurus) and Angus cattle (B. taurus). The IMF content in Angus is significantly higher than that in Simmental cattle. In this study, high-throughput sequencing technology was used to screen the genes related to backfat deposition, in order to provide reference for the research on the mechanism of fat deposition in Simmental and Angus cattles. Three 15-month-old bulls from each breed were fattened and slaughtered to determine the meat quality of the carcass. Transcriptome sequencing and bioinformatics analysis were performed on the backfat fat tissues of the 2 breeds. The results showed that there were no significant differences in crude fat, water loss, ribeye area and pH between the 2 breeds, while the shear force of Simmental cattle was significantly higher than that of Angus cattle (P<0.01). Analysis of transcriptome data showed that there were 1 296 differentially expressed genes (DEGs) in the backfat tissue of the 2 breeds, which mainly enriched in metabolic process, growth and development etc. of 55 function items and lipid metabolism, carbohydrate metabolism, energy metabolism etc. of 44 metabolic pathways. According to the pathway and function analysis, 3 genes including pyruvate dehydrogenase kinase 4 (PDK4), nuclear receptor subfamily 4 group A member 1 (NR4A1) and prospero related homeobox (PROX1) were selected for gene expression analysis by quantitative real-time PCR. Quantitative results showed that the relative expression of PROX1 and PDK4 in the backfat of Angus cattle was 47% and 14% higher than that in the Simmental cattle (P<0.01), and the relative expression of NR4A1 in the Simmental cattle backfat was 30% higher than that in the Angus cattle (P<0.05). The differentially expressed genes obtained in this study could be used as candidate genes for the improvement of beef quality traits and provide basic information to further explore the genetic mechanism of backfat growth and development.

Key words： Cattle Transcriptome Meat quality trait Real-time quantitative PCR Candidate Gene

Received: 09 August 2019

ZTFLH:	S603.2
	S823.9

Corresponding Authors: * shuxingao@126.com

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	ZHAO Wei-Ming
	WU Hui-Guang
	WU Jiang-Hong
	WANG Guo-Fu
	GAO Shu-Xin

Cite this article:

ZHAO Wei-Ming,WU Hui-Guang,WU Jiang-Hong, et al. Analysis of Differentially Expressed Genes Related to Fat Deposition in Simmental and Angus Cattle (Bos taurus) Based on Transcriptome Sequencing[J]. 农业生物技术学报, 2020, 28(4): 693-701.

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http://journal05.magtech.org.cn/Jwk_ny/EN/10.3969/j.issn.1674-7968.2020.04.011 OR http://journal05.magtech.org.cn/Jwk_ny/EN/Y2020/V28/I4/693

[1] 付言峰, 李兰, 赵为民, 等. 2018. 转录组测序分析猪胚胎附植的中期和后期卵巢差异表达基因[J]. 畜牧兽医学报, 49(09): 1879-1888.
(Fu Y F, Li L, Zhao W M, et al.2018. Differentially expressed genes analysis between mid-implantation and post-implantation in porcine ovary by RNA sequencing[J]. Journal of Animal Husbandry and Veterinary Medicine, 49(09): 1879-1888.)
[2] 贺美玲, 王纯洁, 贾知锋, 等2018. 高通量测序分析Nisin对腹泻小鼠肠道菌群的影响[J]. 畜牧兽医学报, 49(09): 2015-2024.
(He M L, Wang C J, Jia Z F, et al.2018. The effect of nisin on intestinal flora in diarrheal mice analyzed by high-throughput sequencing[J]. Journal of Animal Husbandry and Veterinary Medicine, 49(09): 2015-2024.)
[3] 焦斐. 2012. 牦牛PRKAG3、FAS基因多态性与肉质相关性研究[D]. 硕士学位论文, 甘肃农业大学, 导师: 杨富民, pp. 20-30.
(Jiao F.2012. Study on the correlation between PRKAG3 and FAS gene polymorphism and meat quality in yak[D]. Thesis for M.S., Gansu Agricultural University, Supervisor: Yang F M, pp. 20-30.)
[4] 刘畅, 罗玉龙, 李文博, 等. 2019. 性别对巴美肉羊品质特性的影响[J/OL]. 食品工业科技.
(Liu C, Luo Y L, Li W B, et al.2019. Effect of gender on quality characteristics of Bamei sheep[J/OL]. Science and Technology of Food Industry. DOI:10.13386/j.issn1002-0306.2020.05.001.
[5] 秦丹丹, 王向东. 2018. NR4A1对糖脂代谢的调控作用[J]. 中国科学: 生命科学, 48(11): 1229-1237.
(Qin D D, Wang X D.2018. The regulation of NR4A1 on glucolipid metabolism[J]. Chinese Science: Life Sciences, 48(11): 1229-1237. )
[6] 汤冬, 张国森, 赵晓芳. 2019. 基于二代测序技术的转录组测序生物信息分析[J]. 河南大学学报(医学版), 38(01): 67-76.
(Tang D, Zhang G S, Zhao X F.2019. Bioinformatics analysis of transcriptome sequencing based on next generation sequencing[J]. Journal of Henan University (Medical Science), 38(01): 67-76. )
[7] 夏广军, 严昌国, 金海国. 等. 2014. 延边黄牛TG基因多态性与胴体和肉质性状相关性分析[J]. 中国兽医学报, 34(3): 500-504.
(Xia G J, Yan C G, Jin H G, et al.2014. Association between the polymorphism of TG gene and meat quality traits in Yanbian yellow cattles[J]. Chinese Journal of Veterinary Medicine, 34(3): 500-504. )
[8] 周芳, 岳华, 张斌, 等. 2016. 牦牛轮状病毒VP6基因序列分析及RT-PCR检测方法的建立与应用[J]. 畜牧兽医学报, 47(07): 1465-1473.
(Zhou F, Yue H, Zhang B, et al.2016. Establishment and application of an RT-PCR assay for yak rotavirus based on the sequence analysis of yak rotavirus VP6 gene[J]. Journal of Animal Husbandry and Veterinary Medicine, 47(07): 1465-1473.)
[9] 朱青, 刁飞扬, 刘嘉茵. 2017. 孤核受体NR4A1通过线粒体机制调控细胞凋亡[J]. 国际生殖健康/计划生育杂志, 36(06): 488-491, 513.
(Zhu Q, Diao F Y, Liu J Y.2017. Orphan nuclear receptor NR4A1 regulating apoptosis via mitochondria-related mechanisms[J]. International Journal of Reproductive Health/Family Planning, 36(06): 488-491, 513.)
[10] 张国梁, 刘基伟, 胡成华, 等. 2007. 西门塔尔, 夏洛来, 安格斯杂交牛不同营养水平的育肥效果分析[J]. 中国畜牧兽医, (07): 10-12.
(Zhang G L, Liu J W, Hu C H, et al. 2007. Analysis on fattening effect of different nutrient levels in Simmental, Charolais, and Angus hybrid cattle[J] Chinese Animal Husbandry Veterinarian, (07): 10-12.)
[11] Guo H F, Raza S H A, Schreurs N M, et al.2018. Genetic variants in the promoter region of the KLF3 gene associated with fat deposition in Qinchuan cattle[J]. Gene, 2018(672): 50-55.
[12] Haugas M, Tikker L, Achim K, et al.2016. Gata2 and Gata3 regulate the differentiation of serotonergic and glutamatergic neuron subtypes of the dorsal raphe[J]. Development, 143(23): 4495-4508.
[13] Kim D, Langmead B, Salzberg S L.2015. HISAT: A fast spliced aligner with low memory requirements[J]. Nature Methods, 12(4): 357-360.
[14] Kong L, Zhang Y, Ye Z Q, et al.2007. CPC: Assess the protein-coding potential of transcripts using sequence features and support vector machine[J]. Nucleic Acids Research, 35(Web Server issue): W345-W349.
[15] Laitinen A, Böckelman C, Hagström J, et al.2017. High PROX1 expression in gastric cancer predicts better survival[J]. PLOS ONE: e0183868.
[16] Lecompte S, Pasquetti G, Hermant X, et al.2013. Genetic and molecular insights into the role of PROX1 in glucose metabolism[J]. Diabetes, 62(5): 1738-1745.
[17] Li B, Dewey C N.2011. RSEM: Accurate transcript quantification from RNA-Seq data with or without a reference genome[J]. BMC Bioinformatics, 12: 323
[18] Li P, Bai Y, Zhao X, et al.2018. NR4A1 contributes to high-fat associated endothelial dysfunction by promoting CaMKII-Parkin-mitophagy pathways[J]. Cell Stress & Chaperones, 23(4): 749-761.
[19] Livak K J, Schmittgen T D.2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2^-ΔΔ^Ct method[J]. Methods, 25(4): 402-408.
[20] Nahle Z, Hsieh M, Pietka T, et al.2008. CD36-dependent regulation of muscle FoxO1 and PDK4 in the PPARγ-mediated adaptation to metabolic stress[J]. Journal of Biological Chemistry, 283(21): 14317-14326.
[21] Pei H, Chen L, Liao Q M, et al.2018. SUMO-specific protease 2 (SENP2) functions as a tumor suppressor in osteosarcoma via SOX9 degradation[J]. Experimental and Therapeutic Medicine, 16: 5359-5365.
[22] Pertea M, Pertea G M, Antonescu C M, et al.2015. String tie enables improved reconstruction of a transcriptome from RNA-seq reads[J]. Nature Biotechnology, 33(3): 290-295.
[23] Qin D D, Yang Y F, Pu Z Q, et al.2018. NR4A1 retards adipocyte differentiation or maturation via enhancing GATA2 and p53 expression[J]. Journal of Cellular & Molecular Medicine, 22(10): 4709-4720.
[24] Rahman M H, Jha M K, Kim J H, et al.2016. Pyruvate dehydrogenase kinase-mediated glycolytic metabolic shift in the dorsal root ganglion drives painful diabetic neuropathy[J]. Journal of Biological Chemistry, 291(11): 6011-6025.
[25] Sun S, Liu J, Zhao M, et al.2017. Loss of the novel mitochondrial protein FAM210B promotes metastasis via PDK4-dependent metabolic reprogramming[J]. Cell Death and Disease, 8(6): e2870.
[26] Trapnell C, Roberts A, Goff L, et al.2012. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks[J]. Nature Protocols (Print), 7(3): 562-578.
[27] Vailati Riboni M, Meier S, Priest N V, et al.2015. Adipose and liver gene expression profiles in response to treatment with a nonsteroidal antiinflammatory drug after calving in grazing dairy cows[J]. Journal of Dairy Science, 98(5): 3079-3085.
[28] Wu H, Bi J, Peng Y, et al.2017. Nuclear receptor NR4A1 is a tumor suppressor down-regulated in triple-negative breast cancer[J]. Oncotarget, 8(33): 54364-54377.
[29] Wu J, Zhao Y, Park Y K, et al.2018. Loss of PDK4 switches the hepatic NF-κB/TNF pathway from pro-survival to pro-apoptosis[J]. Hepatology, 68(3): 1111-1124.
[30] Xie X, Song X, Yuan S, et al.2015. Histone acetylation regulates orphan nuclear receptor NR4A1 expression in hypercholesterolaemia[J]. Clinical Science, 129(12): 1151-1161.
[31] Yun J Y, Jin H G, Cao Y, et al.2018. RNA-Seq analysis reveals a positive role of HTR2A in adipogenesis in Yan Yellow cattle[J]. International Journal of Molecular Sciences, 19(6): E1760.
[32] Zhang Y, Zhang C, Li H, et al.2017. Down-regulation of vascular PPAR-γ contributes to endothelial dysfunction in high-fat diet-induced obese mice exposed to chronic intermittent hypoxia[J]. Biochemical and Biophysical Research Communications, 492(2): 243-248.
[33] Zhou B, Si W, Su Z, et al.2013. Transcriptional activation of the PROX1 gene by HIF-1α and HIF-2α in response to hypoxia[J]. FEBS Letters, 587(6): 724-731.
[34] Zhou H, Du W, Li Y, et al.2017. Effects of melatonin on fatty liver disease: The role of NR4A1/DNA-PKcs/p53 pathway, mitochondrial fission and mitophagy[J]. Journal of Pineal Research, 64(1). DOI: 10.1111/jpi.12450.