[1]张蕾,任嵩,杨娴婧,等.基于RNA-Seq挖掘玫瑰冠鸡与科宝鸡胚胎期胸肌组织差异表达基因[J].江苏农业学报,2020,(05):1237-1246.[doi:doi:10.3969/j.issn.1000-4440.2020.05.022]
　ZHANG Lei,REN Song,YANG Xian-jing,et al.Identification of differentially expressed genes in embryonic breast muscle tissue of Rose-crowned chicken and Cobb broilers based on RNA-Seq[J].,2020,(05):1237-1246.[doi:doi:10.3969/j.issn.1000-4440.2020.05.022]
点击复制

基于RNA-Seq挖掘玫瑰冠鸡与科宝鸡胚胎期胸肌组织差异表达基因()
分享到：

江苏农业学报[ISSN:1006-6977/CN:61-1281/TN]

卷:
期数:
2020年05期
页码:
1237-1246
栏目:
畜牧兽医·水产养殖
出版日期:
2020-10-31

文章信息/Info

Title:
Identification of differentially expressed genes in embryonic breast muscle tissue of Rose-crowned chicken and Cobb broilers based on RNA-Seq
作者:
张蕾; 任嵩; 杨娴婧; 孙杰; 廖和荣
(石河子大学动物科技学院，新疆石河子832000)
Author(s):
ZHANG Lei; REN Song; YANG Xian-jing; SUN Jie; LIAO He-rong
（College of Animal Science and Technology, Shihezi University， Shihezi 832000, China）
关键词:
玫瑰冠鸡; 科宝鸡; 胚胎期; 胸肌; 差异表达基因; RNA-Seq
Keywords:
Rose-crowned chicken; Cobb broilers; embryonic period; breast muscle; differentially expressed genes; RNA-Seq
分类号:
S831.2
DOI:
doi:10.3969/j.issn.1000-4440.2020.05.022
文献标志码:
A
摘要:
本研究旨在挖掘玫瑰冠鸡与科宝鸡胚胎期胸肌组织中差异表达基因，探讨2种鸡肌肉发育及肌内脂肪（IMF）沉积的分子遗传机理。本研究利用RNA-Seq技术对玫瑰冠鸡和科宝鸡胚胎期胸肌组织中差异表达基因（Differentially expressed genes, DEGs）进行筛选，通过GO富集和KEGG数据库对DEGs的功能进行注释与分析。结果显示：4个文库共鉴定到4 643个差异表达基因，其中玫瑰冠公鸡胸肌和科宝公鸡胸肌中有1 909个显著表达的基因，以科宝鸡为参照，929个上调，980个下调；玫瑰冠母鸡胸肌和科宝母鸡胸肌中有2 734个显著表达的基因，其中1 444个上调，1 290个下调。经荧光定量PCR验证，选取的12个差异基因的表达趋势与测序结果一致。GO富集结果表明，MYL2调控骨骼肌的生长发育，MYOG参与肌细胞的形成与分化；ACACA、ACOX2和ACOX3参与脂肪酸代谢过程；Notch1参与了胚胎发育及脂肪分化相关过程。此外，KEGG通路分析结果显示，能量代谢相关的信号通路(mTOR)与肌肉发育相关的信号通路相互作用影响肌纤维的发育。细胞连接相关通路（局部粘附、ECM-受体互作）参与了肌肉脂肪代谢过程。本研究结果为进一步解析鸡优质肉质性状相关的遗传机制奠定了基础。
Abstract:
This study aimed to identify differentially expressed genes (DEGs) in the embryonic breast muscle tissue of Rose-crowned chicken and Cobb broilers, and to explore the molecular genetic mechanism in muscle development and intramuscular fat (IMF) deposition. RNA-Seq technology was used to screen differentially expressed genes in the embryonic breast muscle tissues of Rose-crowned chicken and Cobb broilers. GO enrichment and KEGG database were used to annotate the functions of DEGs. The results showed that a total of 4 643 differentially expressed genes were identified in the four libraries. Among them, 1 909 genes were significantly expressed in the breast muscle of Rose-crowned cocks and Cobb cocks. Taking Cobb broilers as reference, 929 genes were up-regulated and 980 genes were down-regulated. There were 2 734 significantly expressed genes in the breast muscle of Rose-crouned henes and Cobb hens, 1 444 genes were up-regulated and 1 290 genes were down-regulated. The results of real-time PCR indicated that the expression trend of 12 differential genes was consistent with the sequencing results. Go enrichment analysis results showed that MYL2 regulated the growth and development of skeletal muscle. MYOG was involved in the formation and differentiation of muscle cells. ACACA, ACOX2 and ACOX3 were involved in the fatty acid metabolism. Notch1 was involved in embryo development and adipogenesis-related processes. In addition, KEGG pathway analysis results indicated that the interaction between the energy metabolism-related signaling pathway (mTOR) and muscle development-related signaling pathways affected the development of muscle fibers. Cell junction-related pathways (focal adhesion, ECM-receptor interaction) were involved in IMF metabolism. The results of this study lay the foundation for further analysis of genetic mechanisms associated with high-quality meat quality traits in chickens.

参考文献/References:

[1]WANG Y, HUI X, WANG H, et al. Association of H-FABP gene polymorphisms with intramuscular fat content in Three-yellow chickens and Hetian-black chickens[J]. Journal of Animal Science and Biotechnology, 2016, 7(1): 9.
[2]WU G, SHI X, ZHOU J, et al. Differential expression of meat quality and intramuscular fat deposition related genes in Hanjiang black pigs[J]. Acta Biochim Biophys Sin, 2014, 46(12): 1087-1090.
[3]BONNY S P, HOCQUETTE J F, PETHICK D W, et al. The variation in the eating quality of beef from different sexes and breed classes cannot be completely explained by carcass measurements[J]. Animal, 2016，10(6): 987-995.
[4]LIU R, WANG H, LIU J, et al. Uncovering the embryonic development-related proteome and metabolome signatures in breast muscle and intramuscular fat of fast-and slow-growing chickens[J]. BMC Genomics, 2017, 18(1): 816.
[5]SMITH J H. Relation of body size to muscle cell size and number in the chicken[J]. Poultry Science, 1963, 42(2): 283-290.
[6]SPORER K R B, TEMPELMAN R J, ERNST C W, et al. Transcriptional profiling identifies differentially expressed genes in developing turkey skeletal muscle[J]. BMC Genomics, 2011, 12(1): 143.
[7]AL-MUSAWI S L, STICKLAND N C, BAYOL S A M. In ovo temperature manipulation differentially influences limb musculoskeletal development in two lines of chick embryos selected for divergent growth rates[J]. Journal of Experimental Biology, 2012, 215(9): 1594-1604.
[8]廖菁. 鸡肌纤维生长发育规律及Pax基因遗传效应的研究[D].扬州：扬州大学,2010.
[9]任嵩,张蕾,杨娴婧,等. 鸡胚发育早期肌肉中脂肪沉积规律的研究[J]. 中国家禽, 2019（23）: 9-14.
[10]YAN X, ZHU M J, DODSON M V, et al. Developmental programming of fetal skeletal muscle and adipose tissue development[J]. Journal of Genomics, 2013, 1: 29.
[11]VELLEMAN S G. Muscle development in the embryo and hatchling[J]. Poultry Science, 2007, 86(5): 1050-1054.
[12]CHARTRIN P, BERNADET M D, GUY G, et al. Do age and feeding levels have comparable effects on fat deposition in breast muscle of mule ducks?[J]. Animal, 2007, 1(1): 113-123.
[13]秦玉梅,任嵩,李佳玉,等. 鸡FSHβ、ESRα基因多态性及其合并基因型与产蛋性能的关联性分析[J]. 江苏农业学报, 2017,33(4): 854-862.
[14]杨娴婧,韩雨轩,王海亮,等. 不同品种鸡肌肉营养价值及风味的研究[J]. 中国家禽, 2018（2）: 9-14.
[15]ZHANG M, LI F, MA X, et al. Identification of differentially expressed genes and pathways between intramuscular and abdominal fat-derived preadipocyte differentiation of chickens in vitro[J]. BMC Genomics, 2019, 20(1): 1-15.
[16]束婧婷,章明,宋迟,等. 基于表达谱芯片挖掘清远麻鸡和科宝肉鸡比目鱼肌差异表达基因[J]. 畜牧兽医学报, 2016, 47(1): 25-33.
[17]刘瑞莉,吴磊,袁玮,等. MYL2基因在肌肉生长过程中的研究[J]. 黑龙江畜牧兽医, 2018 (3): 10-14.
[18]CUI H X, LIU R R, ZHAO G P, et al. Identification of differentially expressed genes and pathways for intramuscular fat deposition in pectoralis major tissues of fast-and slow-growing chickens[J]. BMC Genomics, 2012, 13(1): 213.
[19]WRIGHT W E, SASSOON D A, LIN V K. Myogenin, a factor regulating myogenesis, has a domain homologous to MyoD[J]. Cell, 1989, 56(4): 607-617.
[20]BERGSTROM D A, TAPSCOTT S J. Molecular distinction between specification and differentiation in the myogenic basic helix-loop-helix transcription factor family[J]. Molecular and Cellular Biology, 2001, 21(7): 2404-2412.
[21]宫克城. mTOR 信号转导通路在运动后骨骼肌的生长代谢中的作用[J]. 首都体育学院学报, 2009 (4): 449-453.
[22]肖俊,华国洪,李华,等. 海康鸡屠宰性能及肉质特性分析[J]. 江苏农业科学,2019,47(17):196-200.
[23]陆宇哲，潘红平，王帅，等. 3种不同来源中华乌塘鳢成鱼肉质比较分析[J]. 南方农业学报，2018,49(10):2047-2054.
[24]邝良德,谢晓红,郭志强,等. 鲜喂饲用苎麻对肉兔生产性能、肉质及经济效益的影响[J]. 江苏农业科学,2018,46(19):174-176.
[25]BARBER M C, PRICE N T, TRAVERS M T. Structure and regulation of acetyl-CoA carboxylase genes of metazoa[J]. Biochimica et Biophysica Acta (BBA)-Molecular and Cell Biology of Lipids, 2005, 1733(1): 1-28.
[26]JOHANSSON , CURRAN J E, JOHNSON M P, et al. Identification of ACOX2 as a shared genetic risk factor for preeclampsia and cardiovascular disease[J]. European Journal of Human Genetics, 2011, 19(7): 796.
[27]VAN VELDHOVEN P P, VANHOVE G, ASSSELBERGHS S, et al. Substrate specificities of rat liver peroxisomal acyl-CoA oxidases: palmitoyl-CoA oxidase (inducible acyl-CoA oxidase), pristanoyl-CoA oxidase (non-inducible acyl-CoA oxidase), and trihydroxycoprostanoyl-CoA oxidase[J]. Journal of Biological Chemistry, 1992, 267(28): 20065-20074.
[28]袁伟,李作农,曾瑞霞,等. Notch 信号在人脂肪源间充质干细胞成脂中的作用[J]. 解剖科学进展, 2017, 23(6): 626-629.
[29]CUI H, ZHENG M, ZHAO G, et al. Identification of differentially expressed genes and pathways for intramuscular fat metabolism between breast and thigh tissues of chickens[J]. BMC Genomics, 2018, 19(1): 55.

相似文献/References:

[1]秦玉梅,任嵩,李佳玉,等.鸡FSHβ、ESRα基因多态性及其合并基因型与产蛋性能的关联性分析[J].江苏农业学报,2017,(04):854.[doi:doi:10.3969/j.issn.1000-4440.2017.04.020]
　QIN Yu-mei,REN Song,LI Jia-yu,et al.Effects of single and combined genotypes of FSHβ and ESRα genes on laying performance in chicken[J].,2017,(05):854.[doi:doi:10.3969/j.issn.1000-4440.2017.04.020]

备注/Memo

备注/Memo:
收稿日期：2020-03-12基金项目：国家自然科学基金项目（31660654、31860641）作者简介：张蕾(1994-)，女，新疆昌吉人，硕士研究生，主要从事动物遗传育种。（E-mail）595173387@qq.com通讯作者：孙杰，（E-mail）sunjie_shzu@126.com
更新日期/Last Update: 2020-11-16