Identification of Differential Genes of Longissimus Dorsi Muscle of Songliao Black Pig and Landrace Pig Based on High-throughput Sequencing Technology

doi:10.7668/hbnxb.20193162

Abstract

Abstract:

This study aims to use high-throughput sequencing technology to perform mRNA sequencing and differential analysis of longissimus dorsi muscle tissue samples from Songliao black pigs and Landrace pigs,and screen out key genes that affect pig muscle growth,meat quality and fat deposition,so as to provide pork quality research provides new reference information.The longissimus dorsi muscle tissue samples of 6 Songliao black pigs and 6 Landrace pigs were collected,their RNA was extracted,and the mRNA was sequenced by Illumina HiSeq 2500 high-throughput sequencing technology,and the obtained reads were compared,annotated and differentiated.For expression analysis,NOISeq was used to screen out differentially expressed genes and perform enrichment analysis of related biological functions.The results showed that 664 differentially expressed genes were screened from the two pig species,of which 364 genes were highly expressed in Songliao black pigs and 300 genes were highly expressed in Landrace pigs.Through the biological function analysis of differentially expressed genes,LPIN1,FADS1,FADS2,PLIN2,PPARGC1A,PRKAG2 and ACSL1 were screened to participate in the regulation of lipid metabolism and muscle development.The related pathways were fatty acid metabolism,PPAR signaling pathway,AMPK signaling pathway,insulin signaling pathway and adipocytokine signaling pathway and so on.

Key words: Songliao black pig, Landrace pig, High-throughput sequencing, Longissimus dorsi muscle, Differential genes

SHI Yumei, CHEN Shaokang, XING Kai, ZHAO Yanhui, YUAN Jiani, SHENG Xihui, QI Xiaolong, NI Hemin, GUO Yong, WANG Chuduan. Identification of Differential Genes of Longissimus Dorsi Muscle of Songliao Black Pig and Landrace Pig Based on High-throughput Sequencing Technology[J]. Acta Agriculturae Boreali-Sinica, 2022, 37(5): 222-229. doi: 10.7668/hbnxb.20193162.

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Figures/Tables 7

Tab.1 Statistics of sample comparison results

样本 Sample	分组 Grouping	总读长 Total reads	比对率/% Comparison rate	样本 Sample	分组 Grouping	总读长 Total reads	比对率/% Comparison rate
SL1	松辽	10 295 863	88.53	L1	长白	9 152 284	90.49
SL2	松辽	9 800 893	88.08	L2	长白	11 620 495	88.87
SL3	松辽	10 984 670	88.19	L3	长白	9 395 823	88.28
SL4	松辽	12 227 762	88.14	L4	长白	10 226 545	86.66
SL5	松辽	10 516 442	87.66	L5	长白	12 804 405	87.70
SL6	松辽	10 332 247	88.58	L6	长白	10 644 773	87.37

Fig.1 Global analysis of gene expression A is the dynamic expression range map,which shows the distribution of differentially expressed genes with CPM values over 0 in each sample;B map reflects the proportion of low-expressed genes in total transcripts.

Fig.2 Biotype distribution(per sample)

x ¯

healty/

x ¯

tumoral),while the ordinate represents the value of D=

x ¯

healty-

x ¯

tumoral,the black point represents the(M,D)value,where(|M|>1),the red point represents differentially expressed genes.

Fig.3 Transcriptome differential analysis results Panel A represents the overall graph of the expression values of the two breeds of pigs,in which the red dots represent the differentially expressed genes.The abscissa represents the expression level of the gene in Landrace pigs,and the ordinate represents the expression level of the gene in Songliao Black pigs.Panel B represents(M,D)values and summary plots of differentially expressed genes.The abscissa represents the value of M=log₂( $x ¯$ healty/ $x ¯$ tumoral),while the ordinate represents the value of D= $x ¯$ healty- $x ¯$ tumoral,the black point represents the(M,D)value,where(|M|>1),the red point represents differentially expressed genes.

Fig.4 GO enrichment analysis 1.Cellular process; 2.Biological regulation; 3.Regulation of biological process; 4.Response to stimulus; 5.Metabolic process; 6.Multicellular organismal process; 7.Positive regulation of biological process; 8.Signaling; 9.Developmental process; 10.Localization; 11.Cellular component organization or biogenesis; 12.Negative regulation of biological process; 13.Immune system process; 14.Locomotion; 15.Multi-organism process; 16.Cell proliferation; 17.Biological adhesion; 18.Reproduction; 19.Reproductive process; 20.Behavior; 21.Growth; 22.Cell killing; 23.Rhythmic process; 24.Detoxification; 25.Pigmentation; 26.Cell aggregation; 27.Cell; 28.Cell part; 29.Organelle; 30.Membrane; 31.Membrane part; 32.Organelle part; 33.Extracellular region; 34.Protein-containing complex; 35.Extracellular region part; 36.Membrane-enclosed lumen; 37.Synapse; 38.Supramolecular complex; 39.Cell junction; 40.Synapse part; 41.Binding; 42.Catalytic activity; 43.Molecular function regulator; 44.Molecular transducer activity; 45.Transporter activity; 46.Structural molecule activity; 47.Transcription regulator activity; 48.Antioxidant activity; 49.Cargo receptor activity; 50.Protein tag; 51.Molecular carrier activity; 52.Translation regulator activity.

Fig.5 KEGG pathway enrichment analysis

Tab.2 Lipid metabolism-related KEGG pathway

基因名 Gene name	中文名 Chinese name	基因号 Gene number	富集通路 Enrichment pathway
LPIN1	脂质1基因	ENSSSCG00000008624	mTOR信号通路
FADS1	脂肪酸去饱和酶1基因	ENSSSCG00000024015	脂肪酸代谢
FADS2	脂肪酸去饱和酶2基因	ENSSSCG00000013072	PPAR信号通路
			脂肪酸代谢
PLIN2	脂滴包被蛋白2基因	ENSSSCG00000035863	PPAR信号通路
PPARGC1A	过氧化物酶体增殖物激活受体γ	ENSSSCG00000029275	AMPK信号通路
	辅助激活因子1α基因		胰岛素抵抗
			脂肪细胞因子信号通路
			胰岛素信号通路
PRKAG2	蛋白激酶腺嘌呤核糖核苷酸	ENSSSCG00000016432	AMPK信号通路
	激活的非催化亚基γ2基因		长寿调节途径-多物种
			紧密连接
			胰岛素抵抗
			脂肪细胞因子信号通路
			胰岛素信号通路
			昼夜节律
			肥厚型心肌病
ACSL1	酰基辅酶A合成酶长链家	ENSSSCG00000015784	PPAR信号通路
	族成员1基因		脂肪酸代谢
			脂肪细胞因子信号通路

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