绿壳蛋鸡与白来航蛋鸡microRNA变异及其靶基因预测分析

doi:10.16431/j.cnki.1671-7236.2016.06.003

›› 2016, Vol. 43 ›› Issue (6): 1413-1421.doi: 10.16431/j.cnki.1671-7236.2016.06.003

绿壳蛋鸡与白来航蛋鸡microRNA变异及其靶基因预测分析

管毓渝^1,2, 廖荣荣^1,3, 王振^1,2, 赵静^1,2, 陈振亮^1,2, 张哲^1,2, 肖倩^1,2, 孙浩^1,2, 王起山^1,2, 张向喆^1,2, 杨长锁^1,3, 潘玉春^1,2

1. 上海交通大学农业与生物学院, 上海 200240;
2. 上海市兽医生物技术重点实验室, 上海 200240;
3. 上海市农业科学院畜牧兽医研究所, 上海 201106

收稿日期:2015-11-19 出版日期:2016-06-20 发布日期:2016-07-11
通讯作者: 潘玉春 E-mail:panyuchun1963@aliyun.com
作者简介:管毓渝(1991-),男,浙江丽水人,硕士生,研究方向:统计基因组学与生物信息学,E-mail:guanyuyu1991@163.com
基金资助:
国家自然基金:运用高通量富集测序技术研究绿壳蛋鸡繁殖性状和蛋品质的遗传机制(31101706);农业部948项目:基于基因组简化与二代测序的基因判型技术引进及猪、牛、鸡相应技术的创新研发(2012-Z26);现代农业产业技术体系建设专项资金(CARS-41)

Analysis on Target Genes with Mutation in microRNA of Blue-shelled Chicken and White Leghorn

GUAN Yu-yu^1,2, LIAO Rong-rong^1,3, WANG Zhen^1,2, ZHAO Jing^1,2, CHEN Zhen-liang^1,2, ZHANG Zhe^1,2, XIAO Qian^1,2, SUN Hao^1,2, WANG Qi-shan^1,2, ZHANG Xiang-zhe^1,2, YANG Chang-suo^1,3, PAN Yu-chun^1,2

1. School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China;
2. Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai 200240, China;
3. Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China

Received:2015-11-19 Online:2016-06-20 Published:2016-07-11

摘要/Abstract

摘要： 本研究旨在分析绿壳蛋鸡与白来航蛋鸡microRNA变异及其靶基因,将已鉴定的microRNA与预测microRNA组成全基因组的microRNA,并通过与GGRS得到的两种鸡群体SNP位点进行映射,挖掘含SNP的microRNA。利用生物信息学的方法,对含SNP的microRNA进行靶基因预测,并对直接含有SNP的mature-microRNA进行聚焦。将这些靶基因进行富集,一共得到22个GO分类和10条KEGG信号通路与3个主要IPA调控网络,发现其在与生长相关的mTOR信号通路、Wnt信号通路、生长激素受体网络、胰岛素样生长因子Ⅰ受体网络得到了富集,与产蛋性状相关的卵母细胞减数分裂信号通路、黄体酮卵母细胞成熟信号通路得到了富集。此研究方法和结果可以给后期研究提供参考。

关键词: 绿壳蛋鸡; 白来航蛋鸡; microRNA; SNP; 靶基因预测; 富集分析

Abstract: The study was conducted to explore the potential different characters between Blue-shelled chicken and White leghorn.Global genome microRNA was combined the identified microRNA with complementary lab-predicted microRNA.Then the two breed chicken's SNP data got by GGRS were mapped to the microRNA and focused on SNP that deliberately located in mature-microRNA.Bioinformatics method was adopted for target prediction on microRNA which had SNPs.By further gene enrichment analysis,the study found these genes enriched in 22 GO terms,10 KEGG pathways,and 3 IPA important networks.And they enriched in traits which associated with growth,such as mTOR signaling pathways,Wnt signaling pathways,growth hormone receptor networks and insulin-like growth factor Ⅰ receptor networks.And they also enriched in some laying traits,such as oocyte meiotic signaling pathways and progesterone mature oocytes signaling pathways.The methods and the results might provide references for further studies.

Key words: Blue-shelled chicken; White leghorn; microRNA; SNP; target genes prediction; enrichment analysis

中图分类号:

S831

管毓渝, 廖荣荣, 王振, 赵静, 陈振亮, 张哲, 肖倩, 孙浩, 王起山, 张向喆, 杨长锁, 潘玉春. 绿壳蛋鸡与白来航蛋鸡microRNA变异及其靶基因预测分析[J]. , 2016, 43(6): 1413-1421.

GUAN Yu-yu, LIAO Rong-rong, WANG Zhen, ZHAO Jing, CHEN Zhen-liang, ZHANG Zhe, XIAO Qian, SUN Hao, WANG Qi-shan, ZHANG Xiang-zhe, YANG Chang-suo, PAN Yu-chun. Analysis on Target Genes with Mutation in microRNA of Blue-shelled Chicken and White Leghorn[J]. , 2016, 43(6): 1413-1421.

参考文献

[1] 宋华慧,袁超,张晓昀,等.新杨绿壳蛋鸡蛋氨酸需要量的研究[J].动物营养学报,2014,26(9):2574-2581.
[2] 廖荣荣,张向喆,陈强,等.新杨绿壳蛋鸡和白来航鸡快慢羽品系产蛋性能比较[J].中国家禽,2014,36(4):6-8.
[3] Bolormaa S,Pryce J,Hayes B,et al.Multivariate analysis of a genome-wide association study in dairy cattle[J].Journal of Dairy Science,2010,93(8):3818-3833.
[4] Wang Z,Chen Q,Yang Y,et al.A genome-wide scan for selection signatures in Yorkshire and Landrace pigs based on sequencing data[J].Animal Genetics,2014,45(6):808-816.
[5] Wang Z,He K,Wang Q,et al.The prediction of the porcine pre-microRNAs in genome-wide based on support vector machine (SVM) and homology searching[J].BMC Genomics,2012,13(1):729-736.
[6] 焦晶凯,莫蓓红,高红艳.microRNA功能研究新进展[J].中国畜牧兽医,2013,40(2):45-49.
[7] Glazov E A,Cottee P A,Barris W C,et al.A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach[J].Genome Research,2008,18(6):957-964.
[8] 何川,赵乐乐,翟正晓,等.雌雄鸡胚性腺microRNA表达检测及靶基因预测分析[J].上海交通大学学报(农业科学版),2012,30(5):72-77.
[9] Hicks J A,Tembhurne P A,Liu H C.Identification of microRNA in the developing chick immune organs[J].Immunogenetics,2009,61(3):231-240.
[10] 耿立英,张传生,杜立新.鸡基因组pre-microRNA SNP多态性[J].生物多样性,2009,17(3):248-256.
[11] 孙桂荣,王蒋,王康.鸡miR-1816前体区单核苷酸多态性(SNP)与鸡经济性状关联分析[J].农业生物技术学报,2015,23(10):1293-1300.
[12] Liao R,Wang Z,Chen Q,et al.An efficient genotyping method in chicken based on genome reducing and sequencing[J].PLoS One,2015,10(8):e0137010.
[13] Griffiths-Jones S,Grocock R J,Van Dongen S,et al.miRBase:microRNA sequences,targets and gene nomenclature[J].Nucleic Acids Research,2006,34 (suppl 1):D140-D144.
[14] Griffiths-Jones S,Saini H K,van Dongen S,et al.miRBase:Tools for microRNA genomics[J].Nucleic Acids Research,2008,36 (suppl 1):D154-D158.
[15] Chang C C,Lin C J.LIBSVM:A library for support vector machines[J].ACM Transactions on Intelligent Systems and Technology (TIST),2011,2(3):27.
[16] Leclercq M,Diallo A B,Blanchette M.Computational prediction of the localization of microRNAs within their pre-miRNA[J].Nucleic Acids Research,2013,41(15):7200-7211.
[17] Li H,Durbin R.Fast and accurate short read alignment with Burrows-Wheeler transform[J].Bioinformatics,2009,25(14):1754-1760.
[18] Wong N,Wang X.miRDB:An online resource for microRNA target prediction and functional annotations[J].Nucleic Acids Research,2015,43:D146-D152.
[19] Enright A J,John B,Gaul U,et al.microRNA targets in drosophila[J].Genome Biology,2004,5(1):R1-R1.
[20] Lewis B P,Shih I H,Jones-Rhoades M W,et al.Prediction of mammalian microRNA targets[J].Cell,2003,115 (7):787-798.
[21] Krek A,Grün D,Poy M N,et al.Combinatorial microRNA target predictions[J].Nature Genetics,2005,37(5):495-500.
[22] Maragkakis M,Alexiou P,Papadopoulos G L,et al.Accurate microRNA target prediction correlates with protein repression levels[J].BMC Bioinformatics,2009,10(1):295-304.
[23] 王克华,窦套存,曲亮,等.七个鸡种蛋品质比较分析[J].中国家禽,2012,34(5):23-27.
[24] Luan X,Liu D,Cao Z,et al.Transcriptome profiling identifies differentially expressed genes in Huoyan goose ovaries between the laying period and ceased period[J].PLoS One,2014,9(11):e113211.
[25] 綦松智,吴登俊,张中显.mTOR对信号通路调控的研究进展[J].中国畜牧杂志,2010,1:57-60.
[26] Fingar D C,Blenis J.Target of rapamycin (TOR):An integrator of nutrient and growth factor signals and coordinator of cell growth and cell cycle progression[J].Oncogene,2004,23(18):3151-3171.
[27] 尹定子,宋海云.Wnt信号通路:调控机理和生物学意义[J].中国细胞生物学学报,2011,33(2):103-111.
[28] 陈思旭.Wnt/β-catenin 信号通路及Osterix在调控骨量和骨生长中的作用及机制研究[D].重庆:第三军医大学,2014.
[29] Hrabia A.Growth hormone production and role in the reproductive system of female chicken[J].General and Comparative Endocrinology,2015,220:112-118.
[30] 崔梓扬,杨洪雁,张宜强,等.绿壳蛋鸡 IGF-Ⅰ基因SNPs分析及其与末期产蛋性能的相关性研究[J].中国畜牧兽医,2012,39(12):125-128.

绿壳蛋鸡与白来航蛋鸡microRNA变异及其靶基因预测分析

Analysis on Target Genes with Mutation in microRNA of Blue-shelled Chicken and White Leghorn

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