Comparative transcriptomic analysis by RNA-seq to discern differential expression of genes in liver and muscle tissues of adult Berkshire and Jeju Native Pig

Sodhi, Simrinder Singh; Song, Ki-Duk; Ghosh, Mrinmoy; Sharma, Neelesh; Lee, Sung‐Jin; Kim, Jeong Hyun; Kim, Nameun; Mongre, Raj Kumar; Adhikari, Pradeep; Kim, Jin Young; Hong, Sang Pyo; Oh, Sung Jong

doi:10.1016/j.gene.2014.06.005

Cited by 27 publications

(21 citation statements)

References 63 publications

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“…Our results agree with recent studies showing that several immune system and anti-inflammatory processes are activated and play a critical role in the response to fat accumulation in porcine backfat tissue (Sodhi et al 2014) and in visceral fat tissue (Toedebusch et al 2014;Wang et al 2014). Wang et al (2014) and Zhou et al (2013) used three female Landrace pigs to identify DEGs between subcutaneous, visceral and intramuscular fat, indicating that visceral and intramuscular adipose tissues are associated mainly with inflammatory features of the tissue and immune response.…”

Section: Pig Backfat Deposition and Impaired Stress Response May Actisupporting

confidence: 92%

“…In the present study, we applied stringent cleaning and filtering procedures of the sequencing data and, on average, 90 million reads per sample were mapped, obtaining a higher sequencing depth compared to previous studies (Chen et al 2011;Jiang et al 2013;Sodhi et al 2014;Wang et al 2014).…”

Section: Transcriptome Data Highlight the Adipose Tissue Complexitymentioning

confidence: 99%

“…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%

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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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Section: Pig Backfat Deposition and Impaired Stress Response May Actisupporting

confidence: 92%

Section: Transcriptome Data Highlight the Adipose Tissue Complexitymentioning

confidence: 99%

mentioning

confidence: 99%

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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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“…In this study, about 50% of genes annotated in the sheep genome were covered by more than 80% of the sequenced reads, demonstrating that RNA-Seq was more sensitive in finding transcripts, even for genes with low expression patterns, which is in agreement with Wang et al (2009). Although several recent studies have identified DEGs in the liver tissue of pigs (Gunawan et al, 2013a,b;Sodhi et al, 2014), cows (Graugnard et al, 2013), rats (Tran and Huang, 2014;Wang et al, 2014) and fish (Yang et al, 2012;Lau et al, 2014;Magnanou et al, 2014) when using next-generation sequencing platforms, very few studies have clarified transcriptomic analyses regarding the liver tissue of sheep. In this study, seven genes were found to be differentially expressed (three were upregulated and four downregulated) in a DEG analysis comparing the liver tissues of the LCL and MCL libraries.…”

Section: Discussionsupporting

confidence: 70%

“…In addition, data from RNA-Seq can help identify new transcripts (Hansey et al, 2012), single nucleotide polymorphisms (Esteve-Codina et al, 2011), alternative splicing events (Xiong et al, 2012), and other information. Several recent studies have used this type of next-generation sequencing platform in the liver tissue of pigs (Gunawan et al, 2013a,b;Sodhi et al, 2014), cows (Graugnard et al, 2013), rats (Tran and Huang, 2014;Wang et al, 2014), and fish (Yang et al, 2012;Lau et al, 2014;Magnanou et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

Comparative analysis of the liver tissue transcriptomes of Mongolian and Lanzhou fat-tailed sheep

Xu¹,

Zhao²,

Yuan³

et al. 2016

Genet. Mol. Res.

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ABSTRACT. Research on gene regulation has been made possible with the help of RNA sequencing applications such as RNA-Seq technology for high-throughput sequencing platforms. Recent studies have explored the transcriptomes from different tissues of domestic animals using RNA-Seq technology, but little research has been done to study the transcriptomes of breeds of sheep having different adipose tissue deposition mechanisms, such as Mongolian and Lanzhou fattailed sheep. In this study, Mongolian and Lanzhou fat-tailed sheep were selected as experimental breeds, and six libraries (three libraries per breed) were constructed. A total of 286 Mb of high-quality reads was obtained, and three-quarters of the reads were mapped to the reference genome per library. In addition, there were 16,257, 16,186, 16,254, 16,827, 16,437, and 15,761 known reference genes in the six constructed libraries (LCL1, LCL2, LCL3, MCL1, MCL2, and MCL3, respectively). Seven genes were differentially expressed: four were upregulated and three were downregulated in liver tissue between the MCL and LCL groups; 65,303, 65,442, 63,426, 76,267, 69,853, and 57,439 potential cSNPs were detected in the six libraries, respectively, with the G/R substitution occurring most commonly. There were 24,239, 22,283, 22,457, 26,635, 27,093, and 18,700 alternate splicing (AS) events in the six libraries. Intron retention was the most common AS event, followed by alternative 3' splice sites. These results indicate that there are many differences in the liver transcriptomes of Mongolian and Lanzhou fat-tailed sheep breeds. Such results may provide fundamental information for further research on defining the sheep genome.

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Retracted: Myogenic regulatory factors are key players in determining muscle mass and meat quality in Jeju native and Berkshire pigs

Kim

Min

et al. 2020

Veterinary Medicine & Sci

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Comparative transcriptomic analysis by RNA-seq to discern differential expression of genes in liver and muscle tissues of adult Berkshire and Jeju Native Pig

Cited by 27 publications

References 63 publications

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

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

Comparative analysis of the liver tissue transcriptomes of Mongolian and Lanzhou fat-tailed sheep

Retracted: Myogenic regulatory factors are key players in determining muscle mass and meat quality in Jeju native and Berkshire pigs

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