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

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.

Integrative metabolomic and transcriptomic analysis reveals difference in glucose and lipid metabolism in the longissimus muscle of Luchuan and Duroc pigs

“…We identified 3638 DEGs based on our RNA-seq data, which account for 15.9% of all annotated genes in the reference genome. The number of DEGs is substantially larger than observed in some of the other transcriptome studies between various pig breeds ( Song et al, 2019 ; Zhang et al, 2021 ), but the proportion of upregulated genes and downregulated genes in our research is roughly the same as in these studies. A stronger correlation in gene expression is observed between individuals within the same breed compared to individuals from both breeds, which coincides with our observation in the metabolic profile that the Luchuan and Duroc pigs are very diverse.…”

Characterization of Growth Secondary Hair in Min Pig Activated by Follicle Stem Cell Stimulated by Wnt and BMP Signaling Pathway

“…Furthermore, the Q30, Q20, GC content, and sequence duplication levels of the efficient data were calculated. The pig genome sequence (Sus10.2) and annotation files were downloaded from the Ensemble database [ 20 ]. After quality control analysis of the original sequencing dataset, the RNA-seq sequences were compared with the pig genome using TOPHAT and TAIR10 annotations as references [ 21 , 22 ].…”

Transcriptome Analysis Reveals the Age-Related Developmental Dynamics Pattern of the Longissimus Dorsi Muscle in Ningxiang Pigs

“…In recent years, an increasing number of researchers have aimed to explore and elucidate the molecular mechanisms involved in the development of the Longissimus Dorsi muscle [7,8].…”