宁乡猪皮下脂肪与肌内脂肪组织转录组差异分析

doi:10.16288/j.yczz.23-131

遗传 ›› 2023, Vol. 45 ›› Issue (12): 1147-1157.doi: 10.16288/j.yczz.23-131

宁乡猪皮下脂肪与肌内脂肪组织转录组差异分析

王芳^1,^2,³(), 张跃博^1,², 蒋谦^1,³, 印遇龙^1,^2,³, 谭碧娥^1,^2,³(), 陈家顺^1,^2,³()

1.湖南农业大学动物科学技术学院，动物营养基因组与种质创新研究中心，长沙 410128
2.农业农村部畜禽资源(猪)评价利用重点实验室，长沙 410128
3.畜禽产品品质调控湖南省重点实验室，长沙 410128

收稿日期:2023-05-09 修回日期:2023-08-16 出版日期:2023-12-20 发布日期:2023-09-18
通讯作者: 谭碧娥,陈家顺 E-mail:1264873344@qq.com.;bietan@hunau.edu.cn;jschen@hunau.edu.cn
作者简介:王芳，硕士研究生，专业方向：畜牧学。E-mail: 1264873344@qq.com.
基金资助:
国家重点研发计划项目(2021YFD1300403);国家自然科学基金项目(32302761);国家自然科学基金项目(U20A2054);湖南省自然科学基金项目(2022JJ40165);国家生猪产业技术体系建设专项(CARS-35);湖南省教育厅优秀青年基金项目(22B0206)

Analysis of transcriptome differences between subcutaneous and intramuscular adipose tissue of Ningxiang pigs

Fang Wang^1,^2,³(), Yuebo Zhang^1,², Qian Jiang^1,³, Yulong Yin^1,^2,³, Bi’e Tan^1,^2,³(), Jiashun Chen^1,^2,³()

1. Animal Nutrition Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
2. Key Laboratory of Evaluation and Utilization of Livestock and Poultry Resources (Pigs), Ministry of Agriculture and Rural Affairs, Changsha 410128, China
3. Hunan Provincial Key Laboratory of Quality Control of Livestock and Poultry Products, Changsha 410128, China

Received:2023-05-09 Revised:2023-08-16 Published:2023-12-20 Online:2023-09-18
Contact: Bi’e Tan,Jiashun Chen E-mail:1264873344@qq.com.;bietan@hunau.edu.cn;jschen@hunau.edu.cn
Supported by:
National Key Research and Development Program of China(2021YFD1300403);National Natural Science Foundation of China(32302761);National Natural Science Foundation of China(U20A2054);Youth Science Fund Project of the Natural Science Foundation of Hunan(2022JJ40165);Earmarked Fund for China Agriculture Research System(CARS-35);Excellent Youth Project of Hunan Provincial Department of Education(22B0206)

摘要/Abstract

摘要：

为了比较分析宁乡猪皮下脂肪(subcutaneous fat，SAF)和肌内脂肪(intramuscular fat，IMF)组织脂肪沉积的分子机制，本文利用RNA-seq技术鉴定和分析宁乡猪SAF和IMF组织中差异基因表达谱。选取6头250日龄健康状况良好、种内个体体重相近(约85 kg)的雄性宁乡猪为实验材料，采集SAF与IMF组织样品。通过对两个脂肪组织转录组测序并进行GO (Gene Ontology)功能注释及KEGG (Kyoto Encyclopedia of Genes and Genomes)信号通路富集分析，得到与脂肪沉积和脂质代谢相关的差异基因。为验证测序数据结果的可靠性，本研究随机选取6个差异基因进行qRT-PCR验证。结果表明，宁乡猪SAF和IMF组织中有2406个基因差异表达，其中1422个基因表达上调，984个基因表达下调。通过GO功能注释分析发现，差异表达基因主要通过参与类固醇生物合成、不饱和脂肪酸的生物合成、甘油磷脂代谢及自噬途径等与脂质代谢相关途径，调控宁乡猪SAF和IMF的沉积。KEGG通路富集结果显示，差异基因主要富集在脂质结合、脂肪酸代谢过程、甘油酯代谢过程、脂类生物合成等与脂质代谢相关的生物学过程。qRT-PCR结果与测序结果一致，表明测序结果可靠。通过对宁乡猪SAF与IMF组织进行转录组测序以及生物信息学分析，筛选到TCAP、NR4A1、ACACA、LPL、ELOVL6、DGAT1、PRKAA1、ATG101、TP53INP2、FDFT1、ACOX1和SCD等基因与脂质代谢相关，这些基因可能在宁乡猪SAF与IMF组织中脂肪沉积和代谢过程发挥重要调控作用，对进一步研究宁乡猪脂肪沉积机制具有重要意义。

关键词: 宁乡猪, 肌内脂肪, 皮下脂肪, RNA-seq, 差异表达基因

Abstract:

To compare and analyze the molecular mechanisms of adipose deposition in subcutaneous fat (SAF)and intramuscular fat (IMF) tissues in Ningxiang pigs, differential gene expression profiles in SAF and IMF tissues of Ningxiang pigs were identified and analysed using RNA-seq technology. Six healthy 250-day-old male Ningxiang pigs with similar body weights (approximately 85 kg) of intraspecific individuals were selected as experimental material and samples of SAF and IMF tissues were collected. Differential genes associated with fat deposition and lipid metabolism were obtained by sequencing two adipose tissue transcriptomes and performing GO (Gene Ontology) functional annotation and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis. To verify the reliability of the sequencing results, six differential genes were randomly selected to validate using qRT-PCR. The results showed that we identified 2406 DEGs, with 1422 up-regulated and 984 down-regulated genes in two tissues. GO functional annotation analysis revealed that the differentially expressed genes were mainly involved in lipid metabolism related pathways, such as steroid biosynthesis, unsaturated fatty acid biosynthesis, glycerophospholipid metabolism and autophagy pathway. KEGG pathway enrichment showed that the differentially expressed genes were mainly enriched in the biological processes related to lipid binding, fatty acid metabolism, glycol ester metabolism, lipid biosynthesis and other biological processes related to lipid metabolism. Genes related to lipid metabolism, such as TCAP, NR4A1, ACACA, LPL, ELOVL6, DGAT1, PRKAA1, ATG101, TP53INP2, FDFT1, ACOX1 and SCD were identified by bioinformatic analyses and verified by qRT-PCR. Our results indicated that these genes may play important roles in the regulation of fat deposition and metabolism in the SAF and IMF tissue, providing the further mechanistic investigation of fat deposition in Ningxiang pigs.

Key words: Ningxiang pig, intramuscular fat, subcutaneous fat, RNA-seq, differentially expressed gene

王芳, 张跃博, 蒋谦, 印遇龙, 谭碧娥, 陈家顺. 宁乡猪皮下脂肪与肌内脂肪组织转录组差异分析[J]. 遗传, 2023, 45(12): 1147-1157.

Fang Wang, Yuebo Zhang, Qian Jiang, Yulong Yin, Bi’e Tan, Jiashun Chen. Analysis of transcriptome differences between subcutaneous and intramuscular adipose tissue of Ningxiang pigs[J]. Hereditas(Beijing), 2023, 45(12): 1147-1157.

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检测项目	样本名称
检测项目	原始测序数据的总条目数	质控后测序数据的总条目数	未测出的碱基比例 (%)	Q30 含量 (%)	GC含量 (%)
皮下脂肪1 (SAF1)	49,396,546	48,973,078	0.0242	94.95	51.82
皮下脂肪2 (SAF2)	44,730,178	44,346,492	0.0244	94.75	51.73
皮下脂肪3 (SAF3)	46,987,396	46,567,282	0.0244	94.82	51.70
皮下脂肪4 (SAF4)	44,732,785	44,345,424	0.0244	94.71	51.74
皮下脂肪5 (SAF5)	44,731,457	44,342,457	0.0244	94.78	51.76
皮下脂肪6 (SAF6)	46,986,125	46,563,457	0.0243	94.81	51.72
肌内脂肪1 (IMF1)	64,384,494	63,418,906	0.0254	93.76	56.01
肌内脂肪2 (IMF2)	60,812,492	59,754,558	0.0253	93.96	56.35
肌内脂肪3 (IMF3)	63,264,472	62,206,332	0.0254	93.80	56.43
肌内脂肪4 (IMF4)	64,383,456	63,417,524	0.0254	93.82	56.51
肌内脂肪6 (IMF5)	60,815,458	59,755,642	0.0253	93.95	56.35
肌内脂肪6 (IMF6)	63,266,257	62,207,524	0.0252	93.87	56.42

通路编号	通路描述	P值	IMF组织中差异表达基因
map00100	类固醇生物合成	0.004	表达上调：FDFT1、HACD、FADS、SCD
map00100	类固醇生物合成	0.004	表达下调：CYP51A1、DHCR7、LIPA、SQLE、LSS、SOAT、ACOT4、ELOVL6、ACOX1
map01040	不饱和脂肪酸的生物合成	0.005	表达上调：ENSSSCG00000031299、FADS2、HACD1 表达下调：ACOT4、DEPDC1B、ELOVL5、HACD2、HACD3、HACD4、HSD17B12、HSD17B7、HSD17B4、ACAA1、ACOT4、ACOX1
map00564	甘油磷脂代谢	0.007	表达上调：ACHE、AGPAT2、GNPAT、GPD1、GPD2、LCLAT1、LPCAT3、LYPLA2、MAFG、PCYT1B、PISD、PLA2G4E、PLPP4、PNPLA7、PTDSS1、PTDSS2、TAZ、ACHE、AGPAT2、GNPAT、GPD1、GPD2 表达下调：ADPRM、AGPAT1、CDS1、CDS2、CHKA、CHPT1、DGKB、DGKE、DGKH、ETNK1、GPAM、GPCPD1、ACHE、AGPAT2、GNPAT、GPD1、GPD2、LCLAT1、LPCAT3、LYPLA2、MAFG、PCYT1、PISD、PLA2G4E、PLPP4、PNPLA7、PTDSS1、PTDSS2、TAZ、ACHE、AGPAT2、GNPAT、GPD1、GPD2
map04140	自噬-动物	0.001	表达上调：TP53INP2、ULK1、AKT1S1、ATG101、ATG16L1、ATG4D、BNIP3、DDIT4、DEPTOR、GABARAPL2、HRAS、IRS1、MAP2K1、MAP2K2、MTMR3、MTOR、PPP2CA、PPP2CB、PRKAA2、PRKACA、PRKCQ、RAB7A、RAF1、RHEB 表达下调：AKT3、ATG10、ATG12、ATG4C、C9ORF72、CFLAR、CTSD、CTSL、EIF2AK3、EIF2AK4、HIF1A、IRS2、KRAS、MAP3K7、MRAS、NRAS、NRBF2、PIK3C3、PIK3CB、PIK3CD、PIK3R1、PRKAA1、PRKCD、RAB1A、RAB33B

基因	差异倍数	P值	表达模式(IMF组织)
TCAP	252,288.857	<0.05	上调
NR4A1	66.277	<0.05	上调
ACACA	2.632	<0.05	下调
LPL	3.080	<0.05	下调
ELOVL6	2.125	<0.05	下调
DGAT1	4.465	<0.05	下调
PRKAA1	2.458	<0.05	下调
ATG101	4.680	<0.05	上调
TP53INP2	3.703	<0.05	上调
FDFT1	2.829	<0.05	上调
ACOX1	9.487	<0.05	下调
SCD	2.032	<0.05	下调

宁乡猪皮下脂肪与肌内脂肪组织转录组差异分析

Analysis of transcriptome differences between subcutaneous and intramuscular adipose tissue of Ningxiang pigs

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