Identification of candidate genes of growth traits in pigs using RNA-sequencing

Abstract

The aim of this research was to screen candidate genes affecting growth traits in pigs by studying the difference expression genes (DEGs) between the longissimus dorsi of Large White (LW) and Mashen (MS) pigs. RNA-sequencing (RNA-seq) technology was applied to analyse the transcriptomes from six longissimus dorsi in two pig breeds (LW and MS). Based on sequencing, the DEGs were screened, and functional annotation and enrichment analysis were performed. The results showed that 697 different significant genes were obtained (p < 0.05, FDR <0.05 and |FC| ≥ 2). The results of Gene Ontology (GO) functional annotation showed that DEGs were mainly related to the growth and development of skeletal muscle, the formation of organelles and the function of protein binding. DEGs were mainly involved in the pathways of Phagosome, Viral myocarditis, Antigen processing and presentation, Allograft rejection, Graft-versus-host disease, Cardiac muscle contraction by Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Combined with other livestock genomics studies, SFRP2, KDM6A, OGT may be candidate genes involved in pig growth traits. The results provided a theoretical basis for the improvement of pig growth traits and the study of candidate genes.

Highlights

• In this study, three candidate genes (SFRP2, KDM6A, OGT) which affecting growth traits were screened.

• The experimental animals selected in this study were the local breed Mashen pig and the Western commercial breed Large White pig with obvious growth traits difference.

• In this study, RNA-Seq technology was applied to analysis the transcriptomes of pig muscle.

KEYWORDS:

• Pig
• longissimus dorsi
• growth trait
• differentially expressed gene
• RNA-seq

Ethical approval

The methods were performed in accordance with the Good Experimental Practices adopted by the College of Animal Science and Veterinary Medicine, Shanxi Agricultural University (Taigu, P.R. China), and the experimental protocols were approved by it.

Acknowledgements

The authors thank Editage (www.editage.cn) for its linguistic assistance during the preparation of this manuscript. They also thank the staff of the Datong pig farm.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work was supported by the Program for Sanjin Scholar, the Fund for Shanxi 1331 Project and the Foundation of Science and Technology Innovation Team of Shanxi Province [grants No. 201705D131028-19].