Analysis of porcine adipose tissue transcriptome reveals differences in de novo fatty acid synthesis in pigs with divergent muscle fatty acid composition

Corominas, Jordi; Ramayo-Caldas, Yuliaxis; Puig-Oliveras, Anna; Estellé, Jordi; Castelló, Anna; Alves, E.; Pena, Ramona N.; Ballester, María; Folch, Josep María

doi:10.1186/1471-2164-14-843

Cited by 86 publications

(85 citation statements)

References 72 publications

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“…Some of the 52 genes, for example ACACA , ANKRD23 , GM2A , KIT, MOGAT2, MTTP, FASN, SGMS1, SLC27A6 and RETSAT , which we have highlighted here, have been previously described in the context of fat-related characteristics in pigs [50–54]. Of these genes, FASN , a gene encoding a fatty acid synthase, has been shown to be associated with a cis -11-Eicosenoic acid (C20:1) percentage QTL in a Guadyerbas × Landrace cross, although none of the identified SNPs had any putative effect on the protein structure [50].…”

Section: Discussionmentioning

confidence: 99%

Genome sequencing and analysis of Mangalica, a fatty local pig of Hungary

et al. 2014

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BackgroundMangalicas are fatty type local/rare pig breeds with an increasing presence in the niche pork market in Hungary and in other countries. To explore their genetic resources, we have analysed data from next-generation sequencing of an individual male from each of three Mangalica breeds along with a local male Duroc pig. Structural variations, such as SNPs, INDELs and CNVs, were identified and particular genes with SNP variations were analysed with special emphasis on functions related to fat metabolism in pigs.ResultsMore than 60 Gb of sequence data were generated for each of the sequenced individuals, resulting in 11× to 19× autosomal median coverage. After stringent filtering, around six million SNPs, of which approximately 10% are novel compared to the dbSNP138 database, were identified in each animal. Several hundred thousands of INDELs and about 1,000 CNV gains were also identified. The functional annotation of genes with exonic, non-synonymous SNPs, which are common in all three Mangalicas but are absent in either the reference genome or the sequenced Duroc of this study, highlighted 52 genes in lipid metabolism processes. Further analysis revealed that 41 of these genes are associated with lipid metabolic or regulatory pathways, 49 are in fat-metabolism and fatness-phenotype QTLs and, with the exception of ACACA, ANKRD23, GM2A, KIT, MOGAT2, MTTP, FASN, SGMS1, SLC27A6 and RETSAT, have not previously been associated with fat-related phenotypes.ConclusionsGenome analysis of Mangalica breeds revealed that local/rare breeds could be a rich source of sequence variations not present in cosmopolitan/industrial breeds. The identified Mangalica variations may, therefore, be a very useful resource for future studies of agronomically important traits in pigs.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-761) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Genome sequencing and analysis of Mangalica, a fatty local pig of Hungary

et al. 2014

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“…Many researchers have used genome-wide RNA seq to study gene expression in pig intramuscular adipose tissue [50,51]. In light of their works, we compared the expression profile of genes and lncRNAs in intramuscular adipose tissue between LW and LY pigs by RNA-seq technology and comprehensively investigated intramuscular fat deposition and metabolism.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Analysis of mRNAs and lncRNAs of Intramuscular Fat Related to Lipid Metabolism in Two Pig Breeds

Huang

Zhang

et al. 2018

Cell Physiol Biochem

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Background/Aims: Long non-coding RNAs (lncRNAs) can regulate adipogenesis and lipid accumulation. Intramuscular fat deposition appears to vary in different pig breeds, and the regulation mechanism has not yet been fully elucidated at molecular level. Moreover, little is known about the function and profile of lncRNAs in intramuscular fat deposition and metabolism in pig. The aim of this study was thus to explore the regulatory functions of lncRNAs in intramuscular fat deposition. Methods: In this study, Laiwu (LW) pig and Large White (LY) pig with significant difference in fat deposition were selected for use. RNA-seq technology and bioinformatics methods were used to comparatively analyze the gene expression profiles of intramuscular fat between LW and LY pigs to identify key mRNAs and lncRNAs associated with lipid metabolism and adipogenesis. Real-time fluorescence-based quantitative PCR was applied to verify the expression level of the differentially expressed mRNAs and lncRNAs. Results: A total of 513 mRNAs and 55 lncRNAs were differentially expressed between two pig breeds. By co-expression network construction as well as cis- and trans-regulated target gene analysis, 31 key lncRNAs were identified. Gene Ontology and KEGG pathway analyses revealed that differentially expressed genes and lncRNAs were mainly involved in the biological processes and pathways related to adipogenesis and lipid metabolism. Conclusion: XLOC_046142, XLOC_004398 and XLOC_015408 may target MAPKAPK2, NR1D2 and AKR1C4, respectively, and play critical regulatory roles in intramuscular adipogenesis and lipid accumulation in pig. XLOC_064871 and XLOC_011001 may play a role in lipid metabolism-related disease via regulating TRIB3 and BRCA1. This study provides a valuable resource for lncRNA study and improves our understanding of the biological roles of lipid metabolism- related genes and molecular mechanism of intramuscular fat metabolism and deposition.

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“…During the last decade, pig transcriptomic data have been obtained initially by expressed sequence tag sequencing (Mikawa et al 2004;Uenishi et al 2004Uenishi et al , 2007Chen et al 2006;Gorodkin et al 2007) and microarrays (Hornshøj et al 2007;Ferraz et al 2008;Moon et al 2009), which allowed the comparison of gene expression levels in several pig tissues. More recently, the RNA-seq approach was used to compare the transcription profile of different pig fat tissues or different pig breeds (Chen et al 2011;Li et al 2012;Corominas et al 2013;Jiang et al 2013;Zhou et al 2013;Sodhi et al, 2014;Toedebusch et al 2014;Wang et al 2014). The differentially expressed genes (DEGs) reported in these studies are useful for investigating the metabolic pathways activated by or associated with increased fat deposition in pig.…”

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confidence: 99%

Transcriptional profiling of subcutaneous adipose tissue in Italian Large White pigs divergent for backfat thickness

Zambonelli¹,

Gaffo

Zappaterra³

et al. 2016

Animal Genetics

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Fat deposition is a widely studied trait in pigs because of its implications with animal growth efficiency, technological and nutritional characteristics of meat products, but the global framework of the biological and molecular processes regulating fat deposition in pigs is still incomplete. This study describes the backfat tissue transcription profile in Italian Large White pigs and reports genes differentially expressed between fat and lean animals according to RNA-seq data. The backfat transcription profile was characterised by the expression of 23 483 genes, of which 54.1% were represented by known genes. Of 63 418 expressed transcripts, about 80% were non-previously annotated isoforms. By comparing the expression level of fat vs. lean pigs, we detected 86 robust differentially expressed transcripts, 72 more highly expressed (e.g. ACP5, BCL2A1, CCR1, CD163, CD1A, EGR2, ENPP1, GPNMB, INHBB, LYZ, MSR1, OLR1, PIK3AP1, PLIN2, SPP1, SLC11A1, STC1) and 14 lower expressed (e.g. ADSSL1, CDO1, DNAJB1, HSPA1A, HSPA1B, HSPA2, HSPB8, IGFBP5, OLFML3) in fat pigs. The main functional categories enriched in differentially expressed genes were immune system process, response to stimulus, cell activation and skeletal system development, for the overexpressed genes, and unfolded protein binding and stress response, for the underexpressed genes, which included five heat shock proteins. Adipose tissue alterations and impaired stress response are linked to inflammation and, in turn, to adipose tissue secretory activity, similar to what is observed in human obesity. Our results provide the opportunity to identify biomarkers of carcass fat traits to improve the pig production chain and to identify genetic factors that regulate the observed differential expression.

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Analysis of porcine adipose tissue transcriptome reveals differences in de novo fatty acid synthesis in pigs with divergent muscle fatty acid composition

Cited by 86 publications

References 72 publications

Genome sequencing and analysis of Mangalica, a fatty local pig of Hungary

Genome sequencing and analysis of Mangalica, a fatty local pig of Hungary

Genome-Wide Analysis of mRNAs and lncRNAs of Intramuscular Fat Related to Lipid Metabolism in Two Pig Breeds

Transcriptional profiling of subcutaneous adipose tissue in Italian Large White pigs divergent for backfat thickness

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