遗传 ›› 2023, Vol. 45 ›› Issue (12): 1147-1157.doi: 10.16288/j.yczz.23-131
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(
)
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: 基金资助:
Fang Wang1,2,3(), Yuebo Zhang1,2, Qian Jiang1,3, Yulong Yin1,2,3, Bi’e Tan1,2,3(
), Jiashun Chen1,2,3(
)
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:
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。
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.
表1
宁乡猪SAF和IMF转录组数据分析结果"
检测项目 | 样本名称 | ||||
---|---|---|---|---|---|
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 |
表2
可能与脂质代谢相关的富集通路(差异倍数FC>2)"
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 |
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 |
表3
脂质代谢显著差异表达基因"
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 |
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