不同性别滩羊背最长肌中肌肉发育相关LncRNA的筛选及分析

doi:10.7668/hbnxb.20194341

摘要/Abstract

摘要：

旨在从基因水平分析LncRNA对公母滩羊肌肉发育的影响,因肌肉的生长发育是养殖业经济效益的重要指标,而骨骼肌的发育与产肉性能显著相关。为初步揭示影响肌肉发育差异的分子机理,从而进行转录组测序分析,筛选与绵羊肌肉发育相关的LncRNA。通过对公母滩羊各3 头(8月龄)的背最长肌组织进行全转录组测序(RNA-seq)和分析,从而筛选出可能与滩羊肌肉发育相关的LncRNA。结果显示:鉴定到的8 513个LncRNAs中共筛选出45个组间差异表达LncRNAs,其中18个上调,27个下调。预测DELncRNA的co_location靶基因并进行GO功能富集分析结果显示:靶基因显著富集在268个GO条目中,其中有促生长激素分泌细胞分化、典型的Wnt受体信号通路参与对细胞凋亡过程的负向调节、对生长激素分泌的正向调节、cAMP介导的信号传递等条目;KEGG通路富集分析结果表明,DEGs富集在AMPK、NF-KB、PI3K-AKT、MAPK、cAMP、FOXO等信号通路,进一步筛选出TCONS_00017263、TCONS_00147966、TCONS_00163484、TCONS_00079802、TCONS_00079803这5个可能参与肌肉发育相关的LncRNA。对随机挑选的6个DELs进行实时荧光定量PCR验证,其结果的表达趋势与转录组测序结果趋势一致,进一步验证了测序结果的准确性。研究获得的这些DELncRNA可能造成了滩羊公母肌肉生长发育上的差异,同时这些相关LncRNA为调控肌肉发育提供了更多信息,并为今后宁夏地区不同性别滩羊肉用性能的分子育种提供了科学依据。

关键词: 滩羊, LncRNA, RNA-seq技术, 肌肉发育, qRT-PCR

Abstract:

This study aims to analyze the effects of LncRNA on muscle development of male and female Tan sheep from the gene level,because muscle growth and development is an important indicator of economic benefit in breeding industry,and skeletal muscle development is significantly correlated with meat production performance.In order to preliminarily reveal the molecular mechanism affecting the differences in muscle development,transcriptome sequencing analysis was conducted to screen the LncRNA related to sheep muscle development.Full transcriptome sequencing (RNA-seq) and analysis were performed on longissimus dorsi muscle tissues of 3 male and female sheeps (8 months old),so as to screen out LncRNAs that may be related to muscle development of Tan sheep.The results showed that among the 8 513 LncRNAs were identified,45 intergroup differentially expressed LncRNAs were selected,of which 18 were up-regulated and 27 down-regulated.Prediction of co_location target gene of DELncRNA and GO functional enrichment analysis showed that target genes were significantly enriched in 268 GO terms,including somato-secreting cell differentiation,typical Wnt receptor signaling pathway involved in negative regulation of apoptosis,positive regulation of growth hormone secretion,and cAMP-mediated signaling.KEGG pathway enrichment analysis showed that DEGs was enriched in AMPK,NF-KB,PI3K-AKT,MAPK,cAMP,FOXO and other signaling pathways.Five LncRNAs,namely,TCONS_00017263,TCONS_00147966,TCONS_00163484,TCONS_00079802,and TCONS_00079803,which may be involved in muscle development,were further screened.Real-time Fluorescence Quantitative PCR was performed on 6 randomly selected DELs,and the expression trend was consistent with the trend of transcriptome sequencing,which further verified the accuracy of the sequencing results.These DELncRNAs obtained in the study may cause the differences in muscle growth and development of Tan sheep between males and females,and these related LncRNAs may provide more information for regulating muscle development and provide scientific basis for molecular breeding of meat performance of Tan sheep of different genders in Ningxia in the future.

Key words: Tan sheep, LncRNA, RNA-seq technology, Muscle development, qRT-PCR

宋昀静, 田彦梅, 孟科, 尤科梅, 冯登侦. 不同性别滩羊背最长肌中肌肉发育相关LncRNA的筛选及分析[J]. 华北农学报, 2024, 39(1): 219-227. doi: 10.7668/hbnxb.20194341.

SONG Yunjing, TIAN Yanmei, MENG Ke, YOU Kemei, FENG Dengzhen. Screening and Analysis of LncRNA Related to Muscle Development in Longissimus Dorsi Muscle of Different Sex Tan Sheep[J]. Acta Agriculturae Boreali-Sinica, 2024, 39(1): 219-227. doi: 10.7668/hbnxb.20194341.

http://www.hbnxb.net/CN/Y2024/V39/I1/219

图/表 10

表1 设计的引物序列

Tab.1 Sequences of the primers

引物名称 Primer name	引物序列(5'—3') Primer sequence(5'—3')
TCONS_00147966	F: TGTGGAGATGCCTTTGAGAAGTG R: CTGATTGGAGCACACGGATACTG
ENSOART00000027545	F: GAGAGGGAGTGCTTGGGTGAG R: GGGCGGCTTGGTTTCTTTGG
TCONS_00199205	F: TCACAGGAATCGGAGATGAGCAG R: AGCAGTTAGGACACCACCAGAG
TCONS_00069075	F: GCCGCCGCTTCCTCTCTC R: TCAGTGACTGGACCCAGGTATTC
ENSOART00000028239	F: GCACTCACAGCAGCCAAAGG R: TCAGTCAGCACCGCATCTCC
ENSOART00000028920	F: GGGCTAGGGTGGGATGACTTC R: AACCTGGACTGGAGATTCATTTCAC
GADPH	F: TCGGAGTGAACGGATTCGG R: TGATGACGAGCTTCCCGTTC

表2 肌肉发育性能差异分析

Tab.2 Differential analysis of muscle development performance

指标 Indexes	滩羊Tan sheep
指标 Indexes	公羊(TX) Ram	母羊(T) Ewe
胴体质量/kg Carcass weight	12.77±0.41a	10.17±0.19b
活体质量/kg Live weight	26.03±1.19a	22.20±0.31b
净肉率/% Net meat percentage	33.22±3.19a	32.94±1.79a
净肉质量/kg Net meat weight	8.92±0.51a	7.18±0.30b

表3 测序数据质量评估

Tab.3 Sequencing data quality assessment

样品 Sample	原始序列 Raw reads	有效序列/% Clean reads	错误率/% Error rate	Q20 /%	Q30 /%	GC含量/% GC content	总对比数据 Total mapped	比对率/% Mapped ratio
T2X	93 427 110	92 950 110	0.03	97.86	94.08	50.97	82 633 919	88.90
T3X	81 058 112	80 854 296	0.03	97.55	93.04	48.40	72 082 560	89.15
T4X	91 217 782	90 807 628	0.02	98.04	94.26	49.15	82 525 090	90.88
T50	89 605 464	89 190 166	0.02	98.25	94.85	48.99	80 837 548	90.64
T60	86 259 834	85 850 880	0.02	98.04	94.38	49.31	77 110 013	89.82
T70	88 543 880	88 113 542	0.02	98.01	94.31	49.33	79 352 964	90.06

图1 各样本转录本的表达水平分布每个区域的盒形图对应5个统计量(自上而下分别为最大值、上四分位数、中值、下四分位数和最小值) 。

Fig.1 Distribution of expression levels of transcripts in each sample The box plot for each region corresponds to five statistics (maximum,upper quartile,median,lower quartile and minimum respectively from top to bottom).

图2 LncRNA类型分布

Fig.2 Distribution of LncRNA type

图3 DELs的筛选与统计左图为差异表达的LncRNA的总体分布火山图,图中红色点表示有显著性差异表达的上调基因,绿色点表示有显著性差异表达的下调基因;右图为鉴定到的LncRNA的维恩图。

Fig.3 Screening and statistics of DELs The left figure shows the overall distribution of differentially expressed LncRNAs,in the figure,red dots represent significantly differentially expressed up-regulated genes, and green dots represent significantly differentially expressed down-regulated genes;the diagram on the right shows the Venn diagram of the identified LncRNAs.

图4 LncRNA差异表达聚类分析

Fig.4 Cluster analysis of LncRNA differential expression

图5 LncRNA差异表达显著富集的前30个GO条目 1.细胞内钙激活氯离子通道活性;2.天冬氨酸型内肽酶的活性;3.天冬氨酸型肽酶的活性;4.5'-脱氧核糖-5-磷酸裂解酶活性;5.外显子-外显子连接复合体;6.蛋白质在核包膜上的定位;7.核包膜组织;8.组蛋白精氨酸甲基化;9.刷状缘;10.细胞器核糖体;11.线粒体核糖体;12.内皮细胞分化的正向调节;13.黑色素体膜;14.壳质体;15.原醇代谢过程;16.DNA结合;17.序列特异性DNA结合;18.细胞基部;19.氯离子通道活性;20.内皮细胞分化的调控;21.蛋白酶体泛素依赖性蛋白分解代谢过程的正调控;22.蛋白插入膜;23.X染色体失活的剂量补偿;24.骨骼肌细胞分化的调控;25.微绒毛组装;26.细胞骨架的结构成分;27.氯离子传输;28.核外膜;29.ATP酶激活剂活性;30.初级代谢过程的调节。

Fig.5 Top 30 GO terms with significant enrichment in LncRNA differential expression 1.Intracellular calcium activated chloride channel activity;2.Aspartic-type endopeptidase activity;3.Aspartic-type peptidase activity;4.5'-deoxyribose-5-phosphate lyase activity;5.Exon-exon junction complex;6.Protein localization to nuclear envelope;7.Nuclear envelope organization;8.Histone arginine methylation;9.Brush border;10.Organellar ribosome;11.Mitochondrial ribosome;12.Positive regulation of endothelial cell differentiation;13.Melanosome membrane;14.Chitosome;15.Primary alcohol metabolic process;16.DNA binding;17.Sequence-specific DNA binding;18.Basal part of cell;19.Chloride channel activity;20.Regulation of endothelial cell differentiation;21.Positive regulation of proteasomal ubiquitin-dependent protein catabolic process;22.Protein insertion into membrane;23.Dosage compensation by inactivation of X chromosome;24.Regulation of skeletal muscle cell differentiation;25.Microvillus assembly;26.Structural constituent of cytoskeleton;27.Chloride transport;28.Nuclear outer membrane;29.ATPase activator activity;30.Regulation of primary metabolic process.

图6 DELncRNA靶基因KEGG富集排名前20的通路富集气泡图 1.胆汁分泌;2.剪接体;3.初级胆汁酸生物合成;4.胰岛素信号传导途径;5.病毒致癌;6.化学致癌作用;7.FOXO信号传导途径;8.非同源端接;9.细胞色素P450对异类物质的代谢;10.甲状腺激素信号传导途径;11.胰腺分泌物;12.核苷酸切除修复;13.单纯疱疹感染;14.ErbB信号传导途径;15.Fc gamma R介导的吞噬作用;16.癌症途径;17.AMPK信号传导途径;18.蛋白质的消化和吸收;19.鞘磷脂代谢;20.抗原处理和呈现。

Fig.6 Significantly enriched top 20 KEGG pathways with DELncRNA target genes 1.Bile secretion;2.Spliceosome;3.Primary bile acid biosynthesis;4.Insulin signaling pathway;5.Viral carcinogenesis;6.Chemical carcinogenesis;7.FOXO signaling pathway;8.Non-homologous end-joining;9.Metabolism of xenobiotics by cytochrome P450;10.Thyroid hormone signaling pathway;11.Pancreatic secretion;12.Nucleotide excision repair;13.Herpes simplex infection;14.ErbB signaling pathway;15.Fc gamma R-mediated phagocytosis;16.Pathways in cancer;17.AMPK signaling pathway;18.Protein digestion and absorption;19.Sphingolipid metabolism;20.Antigen processing and presentation.

图7 6个DELncRNAs的qRT-PCR验证

Fig.7 qRT-PCR validation of 6 DELncRNAs

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