基于差异可变剪接的德保矮马垂体内体高相关基因的筛选

doi:10.3969/j.issn.1674-7968.2019.08.009

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Abstract Variable splicing enables a single gene to produce multiple mRNAs, thereby enhancing protein diversity, which is closely related to the growth and development of organisms. Among the abundant horse (Equus caballus) breed resources in China, Debao pony and Mongolian horse have obvious height differences. In this study, 137 449 alternative splicing events were detected by RNA-seq and bioinformatics analysis using hypophysis tissue which closely related to horse size. There were 4 main types of alternative splicing including intron retention (IntronR), alternative 3' splice site (A3SS), alternative 5' splice site (A5SS) and exon skipping (ES). In different horse breeds and different development durations, 37 genes presented differential alternative splicing, including 23 differentially alternative splicing genes between immature Debao pony and immature Mongolian horse, 1 differentially alternative splicing gene between adult Debao pony and adult Mongolian horse, 5 differentially alternative splicing genes between immature Debao pony and adult Debao pony, and 8 differentially alternative splicing genes between immature Mongolian horse and adult Mongolian horse. In alternative splicing types of hypophysis, cassette exon splicing of WDR35 gene and ES splicing of OSBPL6 gene in immature Debao pony were identified as important factors affecting dwarfism of Debao pony. Moreover, in the developing hypophysis of Debao pony and Mongolian horse, 13 genes including CPEB1, TCF12, CCDC28B, KIT, FAM129A, PTPRF, EPHA5, OGDH, USP28, EMID1, ANKHD1, KIDINS220 and INF2 were selected as candidate genes targeting dwarf trait by comparing differential alternative splicing types of immature and adult horses. Above dwarf-related genes provide basic information for further molecular breeding targeting horse height.

Key words： Alternative splicing Debao pony Mongolian horse Dwarfism

Received: 29 November 2018

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Corresponding Authors: * , zhouhuanminim@163.com; yanru1964@163.com

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	Articles by authors
	PAN Jing
	FANG Jun
	LIU Chun-Xia
	CAO Jun-Wei
	XING Yan-Ping
	ZHOU Huan-Min
	ZHANG Yan-Ru

Cite this article:

PAN Jing,FANG Jun,LIU Chun-Xia, et al. Height-related Genes Screening in Hypophysis of Debao Pony (Equus caballus) by Differential Alternative Splicing[J]. 农业生物技术学报, 2019, 27(8): 1410-1422.

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http://journal05.magtech.org.cn/Jwk_ny/EN/10.3969/j.issn.1674-7968.2019.08.009 OR http://journal05.magtech.org.cn/Jwk_ny/EN/Y2019/V27/I8/1410

[1] 常洪, 韩国才, 毛永红, 等. 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. 43-65.
(Chang H, Han G C, Mao Y H, et al.2011. Animal genetic resources in China: Horse, donkeys, camels[M]. China Agriculture Press, Beijing. pp. 43-65.)
[2] 郭家中, 陶海溪, 李鹏飞, 等. 2018. 简州大耳羊早期胎儿到新出生阶段背最长肌中可变剪接的鉴定与分析[J]. 西北农业学报, 27(3): 316-325.
(Guo J Z, Tao H X, Li P F, et al.2018. Identification and analysis of alternative splicing in longissimus dorsi of Jianzhou da'er goat from an early embryo stage to a neonatal stage[J]. Acta Agriculturae Boreali-occidentalis Sinica, 27(3): 316-325.)
[3] 冉茂良, 陈斌, 李智, 等. 2016. 基于RNA-seq测序数据鉴定和分析猪基因组可变剪接事件[J]. 中国科学: 生命科学, 46(3): 274-284.
(Ran M L, Chen B, Li Z, et al.2016. Identification and analysis of alternative splicing events in Sus scrofa using RNA-Seq data[J]. Scientia Sinica (Vitae), 46(3): 274-284.)
[4] 徐铁山, 顾丽红, 侯水生, 等. 2016. 应用RNA-seq数据开展鸭基因组可变剪接的鉴定与分析[J]. 中国家禽, 38(17): 10-16.
(Xu T S, Gu L H, Hou S S, et al.2016. Identification and analysis of alternative splicing in duck genome using RNA-seq data[J]. China Poultry, 38(17): 10-16.)
[5] Alatzoglou K S, Kular D, Dattani M T.2015. Autosomal dominant osteopetrosis type Ⅱ[J]. Journal of Back and Musculoskeletal Rehabilitation, 12(4): 347-55.
[6] Amar M J, Sutphen R, Kousseff B G.1997. Expanded phenotype of cranioectodermal dysplasia (Sensenbrenner syndrome)[J]. American Journal of Medical Genetics Part A, 70(4): 349-352.
[7] Baralle F E, Giudice J.2017. Alternative splicing as a regulator of development and tissue identity[J]. Nature Reviews Molecular Cell Biology, 18(7): 437-451.
[8] Chabot B. Shkreta L.2016. Defective control of pre-messenger RNA splicing in human disease[J]. Journal of Cell Biology, 212(1): 13-27.
[9] Córdova-Fletes C, Becerra-Solano L E, Rangel-Sosa M M, et al.2018. Uncommon runs of homozygosity disclose homozygous missense mutations in two ciliopathy-related genes (SPAG17 and WDR35) in a patient with multiple brain and skeletal anomalies[J]. European Journal of Medical Genetics, 61(3): 161-167.
[10] Crijns C P, Bree H J V, Broeckx B J G, et al.2017. The influence of the size, age and sex on the computed tomographic measured size of the pituitary gland in normal horses[J]. Anatomia Histologia Embryologia, 46(3): 267-273.
[11] Fan J H, Feng G G, Huang L, et al.2012. Role of naofen in apoptosis of hepatocytes induced by lipopolysaccharide through mitochondrial signaling in rats[J]. Hepatology Research, 42(7): 696-705.
[12] Graveley B R.2001. Alternative splicing: Increasing diversity in the proteomic world[J]. Trends in Genetics, 17(2): 100-107.
[13] Graveley B R, Brooks A N, Carlson J W, et al.2010. The developmental transcriptome of Drosophila melanogaster[J]. Nature, 471(7339): 473-479.
[14] Huang L, Kondo F, Gosho M, et al.2014. Enhanced expression of WD repeat-containing protein 35 via CaMKK/AMPK activation in bupivacaine-treated Neuro2a cells[J]. PLOS ONE, 9(5): e98185.
[15] Jeong C, Lee J Y, Kim J, et al.2014. Novel COL9A3 mutation in a family diagnosed with multiple epiphyseal dysplasia: A case report[J]. BMC Musculoskeletal Disorders, 15: 371.
[16] Kamilar J M, Tecot S R.2015. Connecting proximate mechanisms and evolutionary patterns: Pituitary gland size and mammalian life history[J]. Journal of Evolutionary Biology, 28(11): 1997-2008.
[17] 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): R36.
[18] Konstantinidou A E, Helen F, Stavros S, et al.2009. Cranioectodermal dysplasia: A probable ciliopathy[J]. American Journal of Medical Genetics Part A, 149A(10): 2206-2211.
[19] Lanning N J, Carter-Su C.2006. Recent advances in growth hormone signaling[J]. Reviews in Endocrine and Metabolic Disorders, 7(4): 225-235.
[20] Levin L S, Perrin J C, Ose L, et al.1977. A heritable syndrome of craniosynostosis, short thin hair, dental abnormalities, and short limbs: Cranioectodermal dysplasia[J]. Journal of Pediatrics, 90(1): 55-61.
[21] Marquez Y, Brown J W S, Simpson C, et al.2012. Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis[J]. Genome Research, 22(6): 1184-1195.
[22] Online Mendelian Inheritance in Man, OMIM (TM)[DB].2006. Johns Hopkins University, Baltimore, MD.MIM Number: {218330}: {12/21/2006}.
[23] Ouimet M, Hennessy E J, van Solingen C, et al.2016. miRNA targeting of oxysterol-binding protein-like 6 regulates cholesterol trafficking and efflux[J]. Arteriosclerosis, Thrombosis, and Vascular Biology, 36(5): 942-951.
[24] Pan Q, Shai O, Lee L J, et al.2008. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing[J]. Nature Genetics, 40(12): 1413-1415.
[25] Ramani A K, Calarco J A, Pan Q, et al.2011. Genome-wide analysis of alternative splicing in Caenorhabditis elegans[J]. Genome Research, 21(2): 342-348.
[26] Sato Y, Feng G G, Huang L, et al.2010. Enhanced expression of naofen in kidney of streptozotocin-induced diabetic rats: Possible correlation to apoptosis of tubular epithelial cells[J]. Clinical and Experimental Nephrology, 14(3): 205-212.
[27] Scotti M M, Swanson M S.2016. RNA mis-splicing in disease[J]. Nature Reviews Genetics, 17(1): 19-32.
[28] Sensenbrenner J A, Dorst J P, Owens R P.1975. New syndrome of skeletal, dental and hair anomalies[J]. Birth Defects Original Article Series, 11(2): 372-379.
[29] Singh R K, Cooper T A.2012. Pre-mRNA splicing in disease and therapeutics[J]. Trends in Molecular Medicine, 18(8): 472-482.
[30] Tsunekawa K, Kondo F, Okada T, et al.2013. Enhanced expression of WD repeat-containing protein 35 (WDR35) stimulated by domoic acid in rat hippocampus: Involvement of reactive oxygen species generation and p38 mitogen-activated protein kinase activation[J]. BMC Neuroscience, 14: 4.
[31] Wang E T, Sandberg R, Luo S, et al.2008. Alternative isoform regulation in human tissue transcriptomes[J]. Nature, 456(7221): 470-476.
[32] Wit J M, van Duyvenvoorde H A, van Klinken J B, et al.2014. Copy number variants in short children born small for gestational age[J]. Hormone Research in Paediatrics, 82(5): 310-318.
[33] Xie C, Mao X, Huang J, et al.2011. KOBAS 2.0: A web server for annotation and identification of enriched pathways and diseases[J]. Nucleic Acids Research, 39(2): W316-22.
[34] 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.