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Identification of differentially expressed genes in longissimus dorsi muscle between Wei and Yorkshire pigs using RNA sequencing

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Abstract

Intramuscular fat (IMF) content is an important trait closely related to meat quality, which is highly variable among pig breeds from diverse genetic backgrounds. High-throughput sequencing has become a powerful technique for analyzing the whole transcription profiles of organisms. In order to elucidate the molecular mechanism underlying porcine meat quality, we adopted RNA sequencing to detect transcriptome in the longissimus dorsi muscle of Wei pigs (a Chinese indigenous breed) and Yorkshire pigs (a Western lean-type breed) with different IMF content. For the Wei and Yorkshire pig libraries, over 57 and 64 million clean reads were generated by transcriptome sequencing, respectively. A total of 717 differentially expressed genes (DEGs) were identified in our study (false discovery rate < 0.05 and fold change > 2), with 323 up-regulated and 394 down-regulated genes in Wei pigs compared with Yorkshire pigs. Gene Ontology analysis showed that DEGs significantly related to skeletal muscle cell differentiation, phospholipid catabolic process, and extracellular matrix structural constituent. Pathway analysis revealed that DEGs were involved in fatty acid metabolism, steroid biosynthesis, glycerophospholipid metabolism, and protein digestion and absorption. Quantitative real time PCR confirmed the differential expression of 11 selected DEGs in both pig breeds. The results provide useful information to investigate the transcriptional profiling in skeletal muscle of different pig breeds with divergent phenotypes, and several DEGs can be taken as functional candidate genes related to lipid metabolism (ACSL1, FABP3, UCP3 and PDK4) and skeletal muscle development (ASB2, MSTN, ANKRD1 and ANKRD2).

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Acknowledgements

This work was supported by the Provincial Natural Science Research Project of Anhui Colleges (KJ2016A180 and KJ2017ZD43), the Anhui Provincial Science and Technology Major Special Project (16030701066), the Anhui Provincial Science and Technology Plan Project (1704a07020093), and Open Fund of Anhui Province Key Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding (AKLGRCB2017012).

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Authors and Affiliations

  1. College of Animal Science, Anhui Science and Technology University, Fengyang, 233100, Anhui, People’s Republic of China

    Jingen Xu, Erhui Jin, Youfang Gu & Shenghe Li

  2. Anhui Province Key Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, Hefei, 230036, Anhui, People’s Republic of China

    Jingen Xu

  3. Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, Anhui, People’s Republic of China

    Chonglong Wang & Qinggang Li

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  1. Jingen Xu
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Correspondence to Shenghe Li or Qinggang Li.

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Jingen Xu, Chonglong Wang, Erhui Jin, Youfang Gu, Shenghe Li and Qinggang Li declare that they have no conflict of interest.

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This work was approved by the Animal Welfare and Use Committee of Anhui Science and Technology University.

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Xu, J., Wang, C., Jin, E. et al. Identification of differentially expressed genes in longissimus dorsi muscle between Wei and Yorkshire pigs using RNA sequencing. Genes Genom 40, 413–421 (2018). https://doi.org/10.1007/s13258-017-0643-3

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  • DOI: https://doi.org/10.1007/s13258-017-0643-3

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