|
|
Screening and Comparison of LncRNAs Related to Body Size Development in Debao Pony (Equus caballus) and Mongolian Horse |
FANG Jun, LING Yu, PAN Jing, CAO Yu, ZHOU Huan-Min, ZHANG Yan-Ru* |
College of Life Sciences, Inner Mongolia Agricultural University, Hohhot 010018, China |
|
|
Abstract Debao pony (Equus caballus) is an excellent horse breed in Guangxi of China. It has significant differences in body height compared with other breeds of horses in China. However, the regulation mechanism of body height growth of Debao pony is still poorly understood. This study was carried out from sampling and transcriptome sequencing of Mongolian horse and Debao pony childhood and adulthood pituitary and long bone epiphysis. There were 847 long-chain non coding RNAs (lncRNAs) differentially expressed at different stages of development, including 512 up-regulated and 335 down-regulated; and 1 633 lncRNAs were differentially expressed in different varieties, including 882 up-regulated and 751 down-regulated. In addition, there were 41 lncRNAs differentially expressed in pituitary tissue and 5 lncRNAs in long bone tissue during adult and juvenile development period of Debao pony; 41 lncRNAs were differentially expressed in pituitary tissue and 7 lncRNAs in long bone during the two development period of Mongolian horse. There were 59 lncRNAs differentially expressed in pituitary tissues and 34 lncRNAs in long bone tissues during juvenile period of Mongolian horse and Debao pony; 32 lncRNAs were differentially expressed in pituitary tissues and 35 lncRNAs in long bone tissue during adult period of the two horse breeds. KEGG and Gene Ontology (GO) analyses were performed on the corresponding target genes of these differentially expressed lncRNAs, and the results showed that they were mainly involved in the development of nervous system and endocrine system. According to the function enrichment, pathway enrichment and previous studies of key candidate genes, 20 protein coding genes were screened out, and 13 differentially expressed lncRNAs targeted growth hormone (GH) and insulin-like growth factor-1 (IGF-1) genes by trans action. The results of this study could provide a reference for the study on the mechanism of Debao pony body size development and the breeding of domestic animals targeting dwarfism.
|
Received: 08 January 2020
|
|
Corresponding Authors:
*yanru1964@163.com
|
|
|
|
[1] 曹宇,张东,芦杨等.2019.基于转录组测序的蒙古羊和杜泊羊骨骼肌热响应相关基因的筛选[J].农业生物技术学报,27(9):1614-1628.
(Cao Y,Zhang D,Lu Y,et al.2019.Heat response related genes screened in skeletal muscle of Mongolian sheep (Ovis aries) and Dorper sheep by RNA sequence[J].Journal of Agricultural Biotechnology,27(9):1614-1628.)
[2] 邓涛.2000.中国矮马与普氏野马的亲缘关系[J].畜牧兽医学,31(1):28-33.
(Deng T.2000.The relationship between Chinese pony and Pugh's wild horse[J].Animal Husbandry and Veterinary Science,31(1):28-33.)
[3] 房君.2019.转录组学揭示德保矮马体尺矮小的分子遗传机制[D].博士论文,内蒙古农业大学,导师:周欢敏,pp.4-5.
(Fang J.2019.Transciptome reveal the genetic molecular mechanism of small body size in Debao pony[D].Thesis for Ph.D.,Inner Mongolia Agricultural University,Supervisor:Zhou H M,pp.4-5.)
[4] 国家畜禽遗传资源委员.2011.中国畜禽遗传资源志:马驴驼志[M].中国农业出版社,北京,pp.26-243.
(China National Commission of Animal Genetic Resources.2011.China's Livestock and Poultry Genetic Resources Record:Horse Donkey Camel Record[M].China Agricultural Press,Beijing,pp.26-243.)
[5] 蒋钦杨,黄艳娜,韦英明等.2013.德保矮马生长激素受体基因PCR-SSCP分析[J].黑龙江畜牧兽医,(05):3-7.
(Jiang Q Y,Huang Y N,Wei Y M,et al.2013.PCR-SSCP analysis of growth hormone receptor gene of Debao pony[J].Heilongjiang Animal Husbandry and Veterinary,(05):3-7.)
[6] 蒋钦杨,韦英明,陈宝剑等.2009.马生长激素基因多态性与体尺指标之间的关联性分析[J].Genetics and Breeding,49(3):1-4.
(Jiang Q Y,Wei Y M,Chen B J,et al.2013.Analysis of the association between the polymorphism of horse growth hormone gene and body size index[J].Genetics and Breeding,49(3):1-4.)
[7] 蒋钦杨,韦英明,黄艳娜等.2009.德保矮马生长激素基因的克隆与序列分析[J].西南大学学报:自然科学版,(12):35-38.
(Jiang Q Y,Wei Y M,Huang Y N,et al.2009.Cloning and sequence analysis of growth hormone gene of Debao pony[J].Journal of Southwest University:Natural Science Edition,(12):35-38.)
[8] Benonisdottir S,Oddsson A,Helgason A,et al.2016.Epigenetic and genetic components of height regulation[J].Nature Communication,7:13490
[9] Berg J M,Lee C,Chen L,et al.2015.JAKMIP1,a novel regulator of neuronal translation,modulates synaptic function and autistic-like behaviors in mouse[J].Neuron,88(6):1173-1191.
[10] Canevelli M,Piscopo P,Talarico G,et al.2014.Familial Alzheimer's disease sustained by presenilin 2 mutations:Systematic review of literature and genotype-phenotype correlation[J].Neuroscience and Biobehavioral Reviews,(42):170-179.
[11] Essakow J L,Lauterpacht A,Lilos P,et al.2016.Genetic mutations,birth lengths,weights and head circumferences of children with IGF-I receptor defects.comparison with other congenital defects in the GH/IGF-I axis[J].Pediatric Endocrinology Reviews,14(1):19-26.
[12] Jeffcott L,Field J,Mclean J,et al.1986.Glucose tolerance and insulin sensitivity in ponies and Standardbred horses[J].Journal of Equine Veterinary Science,18(2):97-101.
[13] Kader A,Li Y,Dong K,et al.2015.Population variation reveals independent selection toward small body size in Chinese Debao pony[J].Genome Biology and Evolution,8(1):42-50.
[14] Kader A,Liu X,Dong K,et al.2016.Identification of copy number variations in three Chinese horse breeds using 70K single nucleotide polymorphism bead chip array[J].Animal Genetics,47(5):560-569.
[15] Kim D,Pertea G,Trapnell C,et al.2013.TopHat2:Accurate alignment of transcriptomes in the presence of insertions,deletions and gene fusions[J].Genome Biology,14(4):R3.
[16] 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.
[17] Kopp F,Mendell J T.2018.Functional classification and experimental dissection of long noncoding RNAs[J].Cell,172(3):393-407.
[18] Koyama T,Mirth C K.2016.Growth-blocking peptides as nutrition-sensitive signals for insulin secretion and body size regulation[J].PLOS Biology,14(2):e1002392
[19] Liang S,Luo H,Bu D,et al.2011.Utilizing sequence intrinsic composition to classify protein-coding and long noncoding transcripts[J].Nucleic Acids Research,41(17):e166.
[20] Liu X X,Pan J F,Zhao Q J,et al.2018.Detecting selection signatures on the X chromosome of the Chinese Debao pony[J].Journal of Animal Breeding and Genetics,135(1):84-92.
[21] Mao X,Cai T,Olyarchuk J G,et al.2005.Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary[J].Bioinformatics,21(19):3787-3793.
[22] Moser S C,van der Eerden B C J.2019.Osteocalcin-a versatile bone-derived hormone[J].Frontiers in Endocrinology,9:794.
[23] Perkel J M.2013.Visiting 'noncodarnia'[J].Biotechniques,54(6):301-304.
[24] Punta M,Coggill P C,Eberhardt R Y,et al.2011.The Pfam protein families database[J].Nucleic Acids Research,40(D1):D290-D301.
[25] Robles M,Peugnet P M,Valentino S A,et al.2018.Placental structure and function in different breeds in horses[J].Theriogenology,108:136-145.
[26] Switkowski K M,Jacques P F,Must A,et al.2019.Associations of protein intake in early childhood with body composition,height,and insulin-like growth factor Ⅰ in mid-childhood and early adolescence[J].The American Journal of Clinical Nutrition,109(4):1154-1163.
[27] Trapnell C,Williams B A,Pertea G,et al.2010.Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation[J].Nature Biotechnology,28(5):511-515.
[28] van de Pol C,van Oldruitenborgh-Oosterbaan M M S.2007.Measuring the height of ponies at the withers:Influence of time of day,water and feed withdrawal,weight-carrying,exercise and sedation[J].The Veterinary Journal,174:69-76.
[29] Zhang Y,Chen B,Li D,Zhou X,Chen Z.2019.LncRNA NEAT1/miR-29b-3p/BMP1 axis promotes osteogenic differentiation in human bone marrow-derived mesenchymal stem cells[J].Pathology Research and Practice,215(3):525-531.
[30] Young M D,Wakefield M J,Smyth G K,et al.2010.Gene ontology analysis for RNA-seq:Accounting for selection bias[J].Genome Biology,11(2):R14. |
[1] |
FU Lin, REN Hang-Xing, WANG Gao-Fu, JIANG Jing, LI Jie, SUN Xiao-Yan, LIU Liang-Jia, ZHOU Peng, ZHANG Li. Tissue Expression of LncRNA XLOC_15448 in Youzhou Dark Goat (Capra hircus) and Prediction of Its Interaction Molecules in Melanoma Pathogenesis[J]. 农业生物技术学报, 2020, 28(8): 1441-1449. |
|
|
|
|