利用RNA-seq技术筛选大白猪皮下和肌内脂肪
组织差异表达基因
收稿日期: 2017-02-09
修回日期: 2017-03-02
网络出版日期: 2017-04-13
基金资助
中央级公益性科研院所基本科研业务费专项资金项目(编号：2013ywf-yb-5, 2013ywf-zd-2),中国农业科学院农业科技创新项目(编号：ASTIP-IAS05),国家高技术研究发展计划项目(“863”计划)(编号：2008AA10Z140),中国农业科学院创新基金项目(2004-院-1)和国家重点基础研究发展计划项目(“973”计划)(编号：2015CB943100)资助[Supported by the Basic Research Fund for Central Public Research Institutes of CAAS (Nos. 2013ywf-yb-5, 2013ywf-zd-2), the Agricultural Science and Technology Innovation Program (No. ASTIPIAS05), the National High Technology Research Development Program of China (“863” Program) (No. 2008AA10Z140), the Innovation Research Foundation of CAAS (No.2004-CAAS-1) and the National Basic Research and Development Program of China (“973” Program)(No. 2015CB943100)];中央级公益性科研院所基本科研业务费专项资金项目(2013ywf-yb-5, 2013ywf-zd-2);中国农业科学院农业科技创新项目(ASTIP-IAS05);国家高技术研究发展计划项目(“863”计划)(2008AA10Z140);中国农业科学院创新基金项目(2004-院-1)(No.2004-CAAS-1);国家重点基础研究发展计划项目(“973”计划)(2015CB943100)
Identification of differentially expressed genes between subcutaneous and intramuscular adipose tissue of Large White pig using RNA-seq
Received date: 2017-02-09
Revised date: 2017-03-02
Online published: 2017-04-13
Supported by
the Basic Research Fund for Central Public Research Institutes of CAAS(2013ywf-yb-5, 2013ywf-zd-2);the Agricultural Science and Technology Innovation Program(ASTIP-IAS05);the National High Technology Research Development Program of China (“863” Program)(2008AA10Z140);the Innovation Research Foundation of CAAS(No.2004-CAAS-1);the National Basic Research and Development Program of China (“973” Program)(2015CB943100)
为了比较分析大白猪皮下和肌内脂肪组织的全转录组数据,探究调控脂肪沉积的分子机制,本文采用RNA-seq技术和生物信息学方法鉴定大白猪皮下和肌内脂肪组织基因表达谱,对差异表达基因进行GO(Gene Ontology)分析、信号通路富集分析以及蛋白互作网络分析。大白猪皮下和肌内脂肪组织中有180个基因差异表达,上调基因主要参与细胞增殖、脂质激酶活性和磷脂代谢等与脂质代谢相关的生物学过程正调控,下调基因显著富集于脂肪细胞分化中起重要调控作用的MAPK信号转导通路。差异表达基因主要通过参与脂质代谢及通过MAPK信号转导通路调控脂肪细胞成脂分化,进而影响大白猪皮下和肌内脂肪的沉积。
黄万龙,张秀秀,李嫒,苗向阳
. 利用RNA-seq技术筛选大白猪皮下和肌内脂肪
组织差异表达基因[J]. 遗传, 2017
, 39(6)
: 501
-511
.
DOI: 10.16288/j.yczz.17-038
To explore the molecular mechanisms of lipid accumulation in different types of adipose tissue, the transcriptomes of the subcutaneous and intramuscular adipose tissues from the Large White pig were determined using RNA-seq technology and bioinformatics methods. The differential gene expression profiles were identified and analyzed with the Gene Ontology, KEGG pathway and protein-protein interaction network strategies. There were 180 differentially expressed genes between the two adipose tissues. The genes up-regulated in the subcutaneous, as compared to intramuscular, adipose tissues were mainly involved in the biological processes related to lipid metabolism. The down-regulated genes were significantly enriched in MAPK signaling pathway, suggesting that this signaling pathway could have an important regulatory role(s) in adipocyte differentiation. In summary, differentially expressed genes between the subcutaneous and intramuscular adipose tissues were predominantly involved in lipid metabolism/accumulation and regulation of adipogenesis in the Large White pig.
Key words： intramuscular fat; subcutaneous fat; lipid metabolism; MAPK signaling pathway; pig; RNA-seq
| [1] | Dodson MV, Jiang ZH, Chen J, Hausman GJ, Guan LL, Novakofski J, Thompson DP, Lorenzen CL, Fernyhough ME, Mir PS, Reecy JM. Allied industry approaches to alter intramuscular fat content and composition in beef animals. J Food Sci, 2010, 75(1): R1-R8. |
| [2] | Listrat A, Lebret B, Louveau I, Astruc T, Bonnet M, Lefaucheur L, Picard B, Bugeon J. How muscle structure and composition influence meat and flesh quality. Sci World J, 2016, 2016: 3182746. |
| [3] | Kl?ting N, Blüher M. Adipocyte dysfunction, inflammation and metabolic syndrome. Rev Endocr Metab Disord, 2014, 15(4): 277-287. |
| [4] | Suzuki K, Irie M, Kadowaki H, Shibata T, Kumagai M, Nishida A. Genetic parameter estimates of meat quality traits in Duroc pigs selected for average daily gain, longissimus muscle area, backfat thickness, and intramuscular fat content. J Anim Sci, 2005, 83(9): 2058-2065. |
| [5] | Wood JD. Meat quality and the designer pig//Lyons TP, Coles DJA. Concepts of Meat Science. Nottingham, England: Nottingham Nutrition International, 2001. |
| [6] | Gao QX, Li J, Liu HL, Wang LY, Xu YX. Comparative study on lipogenic and lipolytic gene expression in intramuscular fat tissue between growing Erhualian and large white pigs. Acta Genet Sinica, 2004, 31(11): 1218-1225. |
| [6] | 高勤学, 李俊, 刘红林, 王林云, 徐银学. 二花脸猪与大约克猪生长期肌内脂肪合成与水解基因表达特征的比较研究. 遗传学报, 2004, 31(11): 1218-1225. |
| [7] | Qian Y, Zeng YQ, Du JF, Cui JX, Li H, Chen QM, Song YP, Chen W. CDS cloning and relationship between intramuscular fat content and mRNA expression of PID1 gene in pig. Hereditas (Beijing), 2010, 32(11): 1153-1158. |
| [7] | 钱源, 曾勇庆, 杜金芳, 崔景香, 李华, 陈其美, 宋一萍, 陈伟. 猪PID1基因CDS区的克隆及其mRNA表达与肌内脂肪沉积关系. 遗传, 2010, 32(11): 1153-1158. |
| [8] | Zhou GX, Wang SB, Wang ZG, Zhu XT, Shu G, Liao WY, Yu KF, Gao P, Xi QY, Wang XQ, Zhang YL, Yuan L, Jiang QY. Global comparison of gene expression profiles between intramuscular and subcutaneous adipocytes of neonatal landrace pig using microarray. Meat Sci, 2010, 86(2): 440-450. |
| [9] | Sun WX, Wang HH, Jiang BC, Zhao YY, Xie ZR, Xiong K, Chen J. Global comparison of gene expression between subcutaneous and intramuscular adipose tissue of mature Erhualian pig. Genet Mol Res, 2013, 12(4): 5085-5101. |
| [10] | Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods, 2008, 5(7): 621-628. |
| [11] | Qi YX, Liu YB, Rong WH. RNA-Seq and its applications: a new technology for transcriptomics. Hereditas (Beijing), 2011, 33(11): 1191-1202. |
| [11] | 祁云霞, 刘永斌, 荣威恒. 转录组研究新技术: RNA-Seq及其应用. 遗传, 2011, 33(11): 1191-1202. |