基于转录组测序鉴定猪肌内脂肪沉积相关生物学通路及候选基因

doi:10.16431/j.cnki.1671-7236.2021.12.019

Abstract

Abstract: The aim of this study was using transcriptome to analyze the deposition mechanism of porcine intramuscular fat (IMF) content, in order to find the pathways and candidate genes related to IMF deposition.The whole sib individuals with large differences in IMF content were selected for double terminal chain specific transcriptome sequencing, and the related genes were screened by edgeR software.ClusterProfiler software was used to perform GO function enrich and KEGG pathway analysis on differential genes, and molecular module (MCODE) analysis was used to mine the intramuscular fat-related candidate genes.The results showed that a total of 474 differentially expressed genes were screened, of which 329 were significantly up-regulated and 145 were significantly down-regulated, enriched and involved in 20 biological processes.Combined with GO network analysis, a total of 15 IMF-related processes were screened, mainly including:Regulation of ion transmembrane transport, regulation of glucose transmembrane transport membrane potential and fatty acid metabolism.MCODE analysis results showed that the differentially expressed genes PPP1CB, CLCA1, COX4I1, SGK1, PAK, PC, KRAS, MAST1, VWC2, CACNG family genes, especially PPP1CB, CLCA1, COX4I1, KRAS and CACNG family genes, might be key genes for regulating IMF, and could be used as IMF candidate gene for further study.In conclusion, this study had identified some new pathways for the action of IMF and screened out candidate genes related to IMF content, which could provide materials for the study of IMF deposition mechanism and reference for the breeding of high-quality meat quality in pigs.

Key words: pigs; IMF; deposition; transcriptome sequencing

CLC Number:

S813.3

SUN Jingxi, PANG Shilong, SUN Jingchun, CHU Guiyan. Identification of Biological Pathways and Candidate Genes Related to Porcine Intramuscular Fat Deposition Using Transcriptome Sequencing[J]. China Animal Husbandry and Veterinary Medicine, 2021, 48(12): 4508-4519.

References

[1] FORTIN A,ROBERTSON W M,TONG A K.The eating quality of Canadian pork and its relationship with intramuscular fat[J].Meat Science,2005,69(2):297-305.
[2] HUANG W,ZHANG X,LI A,et al.Genome-wide analysis of mRNAs and lncRNAs of intramuscular fat related to lipid metabolism in two pig breeds[J].Cellular Physiology and Biochemistry,2018,50(6):2406-2422.
[3] WANG L,ZHOU Z,ZHANG T,et al.IRLnc:A novel functional noncoding RNA contributes to intramuscular fat deposition[J].BMC Genomics,2021,22(1):95.
[4] SUN Y,CHEN X,QIN J,et al.Comparative analysis of long noncoding RNAs expressed during intramuscular adipocytes adipogenesis in fat-type and lean-type pigs[J].Journal of Agricultural and Food Chemistry,2018,66(45):12122-12130.
[5] PIÓRKOWSKA K,MAŁOPOLSKA M,ROPKA-MOLIK K,et al.Evaluation of SCD,ACACA and FASN mutations:Effects on pork quality and other production traits in pigs selected based on RNA-seq results[J].Animals (Basel),2020,10(1):123.
[6] LI Q,HUANG Z,ZHAO W,et al.Transcriptome analysis reveals long intergenic non-coding rnas contributed to intramuscular fat content differences between Yorkshire and Wei pigs[J].International Journal of Molecular Sciences,2020,21(5):1732.
[7] SODHI S S,PARK W C,GHOSH M,et al.Comparative transcriptomic analysis to identify differentially expressed genes in fat tissue of adult Berkshire and Jejunative pig using RNA-seq[J].Molecular Biology Reports,2014,41(9):6305-6315.
[8] MUOZ M,GARCÍA-CASCO J M,CARABALLO C,et al.Identification of candidate genes and regulatory factors underlying intramuscular fat content through longissimus dorsi transcriptome analyses in heavy Iberian pigs[J].Frontiers in Genetics,2018,9:608.
[9] ZOU C,LI L,CHENG X,et al.Identification and functional analysis of long intergenic non-coding RNAs underlying intramuscular fat content in pigs[J].Frontiers in Genetics,2018,9:102.
[10] PARKHOMCHUK D,BORODINA T,AMSTISLAVSKIY V,et al.Transcriptome analysis by strand-specific sequencing of complementary DNA[J].Nucleic Acids Research,2009,37(18):e123.
[11] KIM D,LANGMEAD B,SALZBERG S L.HISAT:A fast spliced aligner with low memory requirements[J].Nature Methods,2015,12(4):357-360.
[12] PERTEA M,KIM D,PERTEA G M,et al.Transcript-level expression analysis of RNA-seq experiments with HISAT,StringTie and Ballgown[J].Nature Protocols,2016,11(9):1650-1667.
[13] TRAPNELL C,ROBERTS A,GOFF L,et al.Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks[J].Nature Protocols,2012,7(3):562-578.
[14] ROBINSON M D,MCCARTHY D J,SMYTH G K.EdgeR:A Bioconductor package for differential expression analysis of digital gene expression data[J].Bioinformatics,2010,26(1):139-140.
[15] YU G C,WANG L G,HAN Y Y,et al.clusterProfiler:An R package for comparing biological themes among gene clusters[J].Omics,2012,16(5):284-287.
[16] ZHOU Y,ZHOU B,PACHE L,et al.Metascape provides a biologist-oriented resource for the analysis of systems-level datasets[J].Nature Communication,2019,10(1):1523.
[17] PENA R N,ROS-FREIXEDES R,TOR M,et al.Genetic marker discovery in complex traits:A field example on fat content and composition in pigs[J].International Journal of Molecular Sciences,2016,17(12):2100.
[18] 吕亚宁,贺琛昕,兰旅涛.猪肌内脂肪与肉品质的关系及其影响因素的研究进展[J].中国畜牧兽医,2020,47(2):554-563. LYU Y N,HE C X,LAN L T.A research advances on the relationship between intramuscular fat and meat quality and influence factor of intramuscular fat in pigs[J].China Animal Husbandry & Veterinary Medicine,2020,47(2):554-563.(in Chinese)
[19] CHO Y L,MIN J K,ROH K M,et al.Phosphoprotein phosphatase 1CB (PPP1CB),a novel adipogenic activator,promotes 3T3-L1 adipogenesis[J].Biochemical Biophysical Research Communications,2015,467(2):211-217.
[20] HOU X,LIU Q,MENG Q,et al.TMT-based quantitative proteomic analysis of porcine muscle associated with postmortem meat quality[J].Food Chemistry,2020,328:127133.
[21] DECARA J,ARRABAL S,BEIROA D,et al.Antiobesity efficacy of GLP-1 receptor agonist liraglutide is associated with peripheral tissue-specific modulation of lipid metabolic regulators[J].Biofactors,2016,42(6):600-611.
[22] BINDER N K,SHEEDY J R,HANNAN N J,et al.Male obesity is associated with changed spermatozoa Cox4I1 mRNA level and altered seminal vesicle fluid composition in a mouse model[J].Molecular Human Reproduction,2015,21(5):424-434.
[23] ZHAO X,HU H,LIN H,et al.Muscle transcriptome analysis reveals potential candidate genes and pathways affecting intramuscular fat content in pigs[J].Frontiers in Genetics,2020,11:877.
[24] DING R,YANG M,QUAN J,et al.Single-locus and multi-locus genome-wide association studies for intramuscular fat in Duroc pigs[J].Frontiers in Genetics,2019,10:619.
[25] CUI H,ZHENG M,ZHAO G,et al.Identification of differentially expressed genes and pathways for intramuscular fat metabolism between breast and thigh tissues of chickens[J].BMC Genomics,2018,19(1):55.
[26] SHENG X,NI H,LIU Y,et al.RNA-seq analysis of bovine intramuscular,subcutaneous and perirenal adipose tissues[J].Molecular Biology Reports,2014,41(3):1631-1637.
[27] 欧秀琼,李睿,张晓春,等.猪肌纤维性状形成和肌内脂肪沉积的遗传机制[J].中国畜牧兽医,2021,48(3):925-931. OU X Q,LI R,ZHANG X C,et al.Genetic mechanism of pig muscle fiber property formation and intramuscular fat deposition[J].China Animal Husbandry & Veterinary Medicine,2021,48(3):925-931.(in Chinese)
[28] HIROSE K,ITO T,FUKAWA K A,et al.Evaluation of effects of multiple candidate genes (LEP,LEPR,MC4R,PIK3C3,and VRTN) on production traits in Duroc pigs[J].Animal Science Journal,2014,85(3):198-206.
[29] DE LAS HERAS-SALDANA S,CHUNG K Y,KIM H,et al.Differential gene expression in longissimus dorsi muscle of hanwoo steers——New insight in genes involved in marbling development at younger ages[J].Genes (Basel),2020,11(11):1381.
[30] DEMEURE O,LIAUBET L,RIQUET J,et al.Determination of PRKAG1 coding sequence and mapping of PRKAG1 and PRKAG2 relatively to porcine back fat thickness QTL[J].Animal Genetics,2004,35(2):123-125.
[31] ZHANG Y,ZHANG J,GONG H,et al.Genetic correlation of fatty acid composition with growth,carcass,fat deposition and meat quality traits based on GWAS data in six pig populations[J].Meat Science,2019,150:47-55.
[32] GRZES M,SADKOWSKI S,RZEWUSKA K,et al.Pig fatness in relation to FASN and INSIG2 genes polymorphism and their transcript level[J].Molecular Biology Reports,2016,43(5):381-389.
[33] MAZUR I I,DROZDOVSKA S,ANDRIEIEVA O,et al.PPARGC1A gene polymorphism is associated with exercise-induced fat loss[J].Molecular Biology Reports,2020,47(10):7451-7457.
[34] MU X,CUI X,LIU R,et al.Identification of differentially expressed genes and pathways for abdominal fat deposition in ovariectomized and sham-operated chickens[J].Genes (Basel),2019,10(2):155.
[35] WANG Y,JIA M,LIANG C,et al.Anterior gradient 2 increases long-chain fatty acid uptake via stabilizing FABP1 and facilitates lipid accumulation[J].International Journal of Biological Sciences,2021,17(3):834-847.
[36] PARK J C,KIM S C,LEE S D,et al.Effects of dietary fat types on growth performance,pork quality,and gene expression in growing-finishing pigs[J].Asian-Australasian Journal of Animal Science,2012,25(12):1759-1767.
[37] FONTANESI L,SCHIAVO G,GALIMBERTI G,et al.A genome-wide association study for a proxy of intermuscular fat level in the Italian Large White breed identifies genomic regions affecting an important quality parameter for dry-cured hams[J].Animal Genetics,2017,48(4):459-465.

Identification of Biological Pathways and Candidate Genes Related to Porcine Intramuscular Fat Deposition Using Transcriptome Sequencing

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	CHEN Kaiwen, ZHAO Yunjiao, WANG Lei, ZHANG Jianbo, MA Yuhong, WU Guofang. Transcriptome Analysis of Porcine Leydig Cells Under Different Oxygen Concentrations [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(6): 2185-2195.
[2]	WEI Mingbang, BIANBA Qiongda, XIAO Qingqing, DUAN Mengqi, CHAMBA Yangzom, SHANG Peng. Cloning,Bioinformatics and Expression Analysis of CDKN1B Gene in Tibetan Pigs [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(6): 2196-2206.
[3]	SHI Jingu, HUANG Shanshan, HUANG Jiwei, CHEN Kunhai, HU Dasheng, ZHU Zhixiong, HAN Shuyu. Comparative Transcriptome Analysis of Streptococcus agalactiae from Tilapia Under High Temperature Stress [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(6): 2207-2216.
[4]	ZHANG Fangwei, ZHANG Qi, LEI Liangliang, SUN Wusheng, ZHANG Di, ZHANG Yunpeng, ZHANG Jingbo, WANG Xiuquan, ZHANG Jing, ZHANG Shumin. Polymorphism of HBEGF Gene and Its Association with Reproductive Traits in Songliao Black Pigs [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(6): 2370-2379.
[5]	PAN Pengcheng, LEI Zongquan, LI Xian, HU Xiangyun, QIN Qiantao, QIN Zhaoxian, GUAN Zhihui, CHEN Baojian, XIE Bingkun. Bioinformatics Analysis,Eukaryotic Expression Vector Construction and Tissue Expression of MYL2 Gene in Luchuan Pigs [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(5): 1796-1806.
[6]	LIU Hongrun, ZHU Siran, FENG Lingli, ZHANG Kun, YAN Gang, WANG Yubin, ZHANG Shuai, JIANG Shan, XU Di, LAN Ganqiu, LIANG Jing. Cloning,Bioinformatics Analysis and Tissue Expression Localization of CDO1 Gene in Large White Pigs [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(4): 1352-1363.
[7]	LI Mengyuan, LIU Mengqian, KANG Jiajia, HUANG Ying, DUAN Yong, JIA Junjing, GE Changrong, CAO Weina. Effects of Guanidinoacetic Acid on Meat Quality and Abdominal Fat Deposition in Broilers [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(4): 1385-1394.
[8]	CHANG Yitong, ZHANG Wei, PENG Yinglin, CHEN Chen. Evolutionary Analysis,Target Gene Prediction and Tissue Expression Analysis of miR-192 [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(3): 882-892.
[9]	YIN Yi, LYU Yanqiu, CHEN Xuan, CAO Lipeng, ZHANG Junzheng, JIN Yi. Effects of Capacitation on Sperm Quality and Regulation of Acrosin Inhibitor Levels by Ubiquitin in Pigs [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(1): 174-185.
[10]	CHEN Chuanhe, LIU Jiali, ZHANG Lilan, ZHAO Ying, TAO Cong. Bioinformatics Analysis of Porcine SGK Family Genes and Their Expression in Porcine Adipose Tissues and Adipocytes [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(9): 3310-3320.
[11]	YANG Man, LIU Hai, ZHANG Run, HU Ziping, NIU Naiqi, WANG Lixian, ZHANG Longchao. Association Analysis of Polymorphism of MYH3 and MYH13 Genes with Meat Quality Traits in Beijing Black Pigs [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(9): 3428-3437.
[12]	YU Peng, NIU Xiaoyu, DONG Ling, LU Mengqi, CHEN Yanhong, LI Fan, SONG Hui. Research Progress on the Role of lncRNA in Porcine Abortion-related Virus Infection [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(9): 3559-3568.
[13]	NIE Jingru, MA Li, YAN Dawei, DENG Jun, ZHANG Hao, ZHANG Bo, LIU Jinqiao, DONG Xinxing. Analysis of Differentially Expressed Genes and Regulation Pathways of Intramuscular Fat Deposition in Large Diqing Tibetan Pigs at Different Growth Stages [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(8): 2855-2868.
[14]	YU Zonggang, MA Haiming. Research Progress on Isolation and Culture of Porcine Skeletal Muscle Satellite Cells in vitro [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(8): 2931-2942.
[15]	YANG Tao, ZHANG Mingjie, XU Ran, ZHANG Han, ZHANG Mengmeng, WU Keliang. Study on Genetic Evaluation of Reproductive and Growth Traits in Pigs by BLUP Method [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(8): 2971-2981.