Transcriptome analysis of differential gene expression in the longissimus dorsi muscle from Debao and landrace pigs based on RNA-sequencing.

Shang-Qiao Song,Cui-Cui Sun,Zong-Qiang Li,Xin Li,Chao-Long Zhang,Wei-Wei Ma,Su-Xian Zeng,Rui-Min Wang,Jin Yan

doi:10.1042/bsr20192144

Shang-Qiao Song, Cui-Cui Sun + Show 7 more

Open Access

https://doi.org/10.1042/bsr20192144

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Abstract

RNA-seq analysis was used to identify differentially expressed genes (DEGs) at the genetic level in the longissimus dorsi muscle from two pigs to investigate the genetic mechanisms underlying the difference in meat quality between Debao pigs and Landrace pigs. Then, these DEGs underwent functional annotation, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and protein–protein interaction (PPI) analyses. Finally, the expression levels of specific DEGs were assessed using qRT-PCR. The reference genome showed gene dosage detection of all samples which showed that the total reference genome comprised 22342 coding genes, including 14743 known and 190 unknown genes. For detection of the Debao pig genome, we obtained 14168 genes, including 13994 known and 174 unknown genes. For detection of the Landrace pig genome, we obtained 14404 genes, including 14223 known and 181 unknown genes. GO analysis and KEGG signaling pathway analysis show that DEGs are significantly related to metabolic regulation, amino acid metabolism, muscular tissue, muscle structure development etc. We identified key genes in these processes, such as FOS, EGR2, and IL6, by PPI network analysis. qRT-PCR confirmed the differential expression of six selected DEGs in both pig breeds. In conclusion, the present study revealed key genes and related signaling pathways that influence the difference in pork quality between these breeds and could provide a theoretical basis for improving pork quality in future genetic thremmatology.

Highlights

Pigs are an important source of meat production worldwide [1,2]
Debao black pig (DB) pig sample clean reads contained 0.56% of the linker sequence, the number of unknown base reads was 0.00% of the total number of reads, the number of low-quality reads accounted for 1.77% of the total number of reads, and the data obtained by removing the impurities from the original sequence data accounted for 97.67% of the total number of reads
Genomic study of the two longissimus dorsi muscle samples showed that the key genes and influencing factors causing the difference in phenotype between the two pigs could provide a basis for future genetic breeding to meet social needs [32]

Summary

Introduction

Pigs are an important source of meat production worldwide [1,2]. Meat quality has many influencing factors, such as breed and post slaughter handling. Between these influential factors, breed is more important [4–6]. More indigenous pig breeds exist in China than in any other country worldwide [7,8]. In China, 118 indigenous pig breeds are listed on the World Watch List for Domestic Animal Diversity [9]. Western commercial pig breeds, over the past several decades, have been artificially selected consistently by breeders and farmers for higher muscle percentage and lower carcass fatness [10], and considerable progress has been made regarding these characteristics. Large White pigs (LW) and Yorkshire pigs have faster growth characteristics and a higher muscle percentage compared with other pigs [11–13]

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