Skip to main content
SpringerLink
Log in

Longissimus lumborum muscle transcriptome analysis of Laiwu and Yorkshire pigs differing in intramuscular fat content

  • Research Article
  • Published:
Genes & Genomics Aims and scope Submit manuscript

Abstract

The pig provides meat products for human consumption on a large scale. High-throughput sequencing technology provides a powerful approach for the characterization of the muscle transcriptome of pigs. Despite many studies using high-throughput technologies, the functional complexity of porcine muscle transcriptome is not fully elucidated. Therefore, the aim of this study was to gain insight into the longissimus lumborum muscle transcriptome between two pig breeds with distinct phenotypes, Laiwu pig, a Chinese indigenous pig breed, and Yorkshire pig, a Western breed. RNA-seq was applied to sample transcripts of the longissimus lumborum muscle between the two pig breeds to gain insights into whole-genome transcription profiles. For the Laiwu and Yorkshire libraries, we obtained a total of 40,498,476 and 59,072,892 high quality reads, respectively. Moreover, the resulting data set provided expression patterns for many annotated, predicted and novel pig genes. 178 significantly differentially expressed genes were identified between the Laiwu and Yorkshire pigs, with 98 up-regulated and 80 down-regulated genes in Laiwu pig compared with Yorkshire pig. Gene expression results of the RNA-seq data were validated by qRT-PCR for twelve genes. Genes that were differentially expressed were involved in lipid metabolism and were more highly expressed in Laiwu pigs. The present study provides a comprehensive view of differences in the muscle transcriptome between two pig phenotypes. These results expand our knowledge of the genes transcribed in the skeletal muscle of two breeds and provide a basis for future research of the molecular mechanisms underlying the phenotypic differences on meat quality.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • Anders S (2010) HTSeq: Analysing high-throughput sequencing data with Python. http://www-huber.embl.de/users/anders/HTSeq/doc/index.html

  • Bakhtiarizadeh MR, Moradi-Shahrbabak M, Ebrahimie E (2013) Underlying functional genomics of fat deposition in adipose tissue. Gene 521:122–128

    Article  CAS  PubMed  Google Scholar 

  • Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B 57:289–300

    Google Scholar 

  • Bonnet A, Bevilacqua C, Benne F, Bodin L, Cotinot C, Liaubet L, Sancristobal M, Sarry J, Terenina E, Martin P et al (2011) Transcriptome profiling of sheep granulosa cells and oocytes during early follicular development obtained by laser capture microdissection. BMC Genom 12:417

    Article  CAS  Google Scholar 

  • Chen C, Ai H, Ren J, Li W, Li P, Qiao R, Ouyang J, Yang M, Ma J, Huang L (2011a) A global view of porcine transcriptome in three tissues from a full-sib pair with extreme phenotypes in growth and fat deposition by paired-end RNA sequencing. BMC Genom 12:448

    Article  CAS  Google Scholar 

  • Chen W, Zeng Y, Cui J, Chen Q, Du J, Yang L, Hu Y, Song Y, Qian Y (2011b) Effects of phospholipid hydroperoxide glutathione peroxidase mRNA expression on meat quality of M. longissimus dorsi in pigs. Eur Food Res Technol 232:433–440

    Article  CAS  Google Scholar 

  • Chen Q-M, Wang H, Zeng Y-Q, Chen W (2013) Developmental changes and effect on intramuscular fat content of H-FABP and A-FABP mRNA expression in pigs. J Appl Genet 54:119–123

    Article  CAS  PubMed  Google Scholar 

  • Damon M, Wyszynska-Koko J, Vincent A, Hérault F, Lebret B (2012) Comparison of muscle transcriptome between pigs with divergent meat quality phenotypes identifies genes related to muscle metabolism and structure. PLoS ONE 7:e33763

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Freeman T, Ivens A, Baillie JK, Beraldi D, Barnett M, Dorward D, Downing A, Fairbairn L, Kapetanovic R, Raza S et al (2012) A gene expression atlas of the domestic pig. BMC Biol 10:90

    Article  PubMed  PubMed Central  Google Scholar 

  • Hamill R, Aslan O, Mullen A, O’Doherty J, McBryan J, Morris D, Sweeney T (2013) Transcriptome analysis of porcine M. semimembranosus divergent in intramuscular fat as a consequence of dietary protein restriction. BMC Genom 14:453

    Article  CAS  Google Scholar 

  • Kim JH, Lim HT, Park EW, Rodríguez C, Silio L, Varona L, Mercade A, Jeon JT, Ovilo C (2006) Polymorphisms in the promoter region of the porcine acyl-coA dehydrogenase, medium-chain (ACADM) gene have no effect on fat deposition traits in a pig Iberian × Landrace cross. Anim Genet 37:430–431

    Article  CAS  PubMed  Google Scholar 

  • Kim N-K, Park H-R, Lee H-C, Yoon D, Son E-S, Kim Y-S, Kim S-R, Kim O-H, Lee C-S (2010) Comparative studies of skeletal muscle proteome and transcriptome profilings between pig breeds. Mamm Genome 21:307–319

    Article  CAS  PubMed  Google Scholar 

  • Lan J, Lei M-G, Zhang Y-B, Wang J-H, Feng X-T, Xu D-Q, Gui J-F, Xiong Y-Z (2009) Characterization of the porcine differentially expressed PDK4 gene and association with meat quality. Mol Biol Rep 36:2003–2010

    Article  CAS  PubMed  Google Scholar 

  • Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Meth 9:357–359

    Article  CAS  Google Scholar 

  • Li M, Wu H, Luo Z, Xia Y, Guan J, Wang T, Gu Y, Chen L, Zhang K, Ma J et al (2012) An atlas of DNA methylomes in porcine adipose and muscle tissues. Nat Commun 3:850

    Article  PubMed  PubMed Central  Google Scholar 

  • Mao X, Cai T, Olyarchuk JG, Wei L (2005) Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. Bioinformatics 21:3787–3793

    Article  CAS  PubMed  Google Scholar 

  • Martin JA, Wang Z (2011) Next-generation transcriptome assembly. Nat Rev Genet 12:671–682

    Article  CAS  PubMed  Google Scholar 

  • Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-SEq. Nat Meth 5:621–628

    Article  CAS  Google Scholar 

  • Nie Q, Fang M, Jia X, Zhang W, Zhou X, He X, Zhang X (2011) Analysis of muscle and ovary transcriptome of Sus scrofa: assembly, annotation and marker discovery. DNA Res 18:343–351

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nowacka-Woszuk J, Szczerbal I, Fijak-Nowak H, Switonski M (2008) Chromosomal localization of 13 candidate genes for human obesity in the pig genome. J Appl Genet 49:373–377

    Article  PubMed  Google Scholar 

  • Óvilo C, Benítez R, Fernández A, Núñez Y, Ayuso M, Fernández AI, Rodríguez C, Isabel B, Rey AI, López-Bote C et al (2014) Longissimus dorsi transcriptome analysis of purebred and crossbred Iberian pigs differing in muscle characteristics. BMC Genom 15:413

    Article  Google Scholar 

  • Ozsolak F, Milos PM (2011) RNA sequencing: advances, challenges and opportunities. Nat Rev Genet 12:87–98

    Article  CAS  PubMed  Google Scholar 

  • Ropka-Molik K, Żukowski K, Eckert R, Piórkowska K, Oczkowicz M, Gurgul A, Szmatoła T (2015) Whole transcriptome analysis of the porcine muscle tissue of breeds differing in muscularity and meat quality traits. Livest Sci 182:93–100

    Article  Google Scholar 

  • SanCristobal M, Rohart F, Lascor C, Bouffaud M, Trouilh L, Martin PG, Lippi Y, Tribout T, Faraut T, Mercat MJ et al (2015) Exploring transcriptomic diversity in muscle revealed that cellular signaling pathways mainly differentiate five Western porcine breeds. BMC Genom 16:1055

    Article  Google Scholar 

  • Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-SEq. Bioinformatics 25:1105–1111

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotech 28:511–515

    Article  CAS  Google Scholar 

  • Walters E, Wolf E, Whyte J, Mao J, Renner S, Nagashima H, Kobayashi E, Zhao J, Wells K, Critser J et al (2012) Completion of the swine genome will simplify the production of swine as a large animal biomedical model. BMC Med Genom 5:55

    Article  CAS  Google Scholar 

  • Wang L, Feng Z, Wang X, Wang X, Zhang X (2010) DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics 26:136–138

    Article  PubMed  Google Scholar 

  • Young M, Wakefield M, Smyth G, Oshlack A (2010) Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol 11:R14

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhao Y, Li J, Liu H, Xi Y, Xue M, Liu W, Zhuang Z, Lei M (2015) Dynamic transcriptome profiles of skeletal muscle tissue across 11 developmental stages for both Tongcheng and Yorkshire pigs. BMC Genom 16:377

    Article  Google Scholar 

Download references

Acknowledgements

This study was supported by the National Animal Breed Resource Preservation Project of China (2130135), the National Project for Breeding Transgenic Pigs of China (2013ZX08006-002), Shandong Province Modern Pig Technology and Industry System Project (SDAIT-08-02) and Shandong Province Agricultural Animal Breeding Project of China (2013LZ02-015, 2014LZ03-016).

Author information

Authors and Affiliations

  1. Laboratory for Animal Genetics and Breeding, College of Animal Science and Technology, Shandong Agricultural University, Tai’an, 271018, Shandong, People’s Republic of China

    Wei Chen, Guo-feng Fang, Shou-dong Wang, Hui Wang & Yong-qing Zeng

Authors
  1. Wei Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Guo-feng Fang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Shou-dong Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Hui Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Yong-qing Zeng
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Hui Wang or Yong-qing Zeng.

Ethics declarations

Conflict of interest

Wei Chen, Guo-Feng Fang, Shou-Dong Wang, Hui Wang andYong-Qing Zeng declares that they have no conflict of interest.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Chen, W., Fang, Gf., Wang, Sd. et al. Longissimus lumborum muscle transcriptome analysis of Laiwu and Yorkshire pigs differing in intramuscular fat content. Genes Genom 39, 759–766 (2017). https://doi.org/10.1007/s13258-017-0540-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s13258-017-0540-9

Keywords

Search

Navigation