Intramuscular fat (IMF) content plays an essential role in meat quality. For identifying potential candidate genes and pathways regulating IMF content, the IMF content and the longissimus dorsi transcriptomes of 28 purebred Duroc pigs were measured. As a result, the transcriptome analysis of four high-and four low-IMF individuals revealed a total of 309 differentially expressed genes (DEGs) using edgeR and DESeq2 (p < 0.05, |log 2 (fold change)| ≥ 1). Functional enrichment analysis of the DEGs revealed 19 hub genes significantly enriched in the Gene Ontology (GO) terms and pathways (q < 0.05) related to lipid metabolism and fat cell differentiation. The weighted gene coexpression network analysis (WGCNA) of the 28 pigs identified the most relevant module with 43 hub genes. The combined results of DEGs, WGCNA, and proteinprotein interactions revealed ADIPOQ, PPARG, LIPE, CIDEC, PLIN1, CIDEA, and FABP4 to be potential candidate genes affecting IMF. Furthermore, the regulation of lipolysis in adipocytes and the peroxisome proliferator-activated receptor (PPAR) signaling pathway were significantly enriched for both the DEGs and genes in the most relevant module. Some DEGs and pathways detected in our study play essential roles and are potential candidate genes and pathways that affect IMF content in pigs. This study provides crucial information for understanding the molecular mechanism of IMF content and would be helpful in improving pork quality.

BackgroundDrip loss is a key aspect of meat quality. Transcriptome profiles of muscle with divergent drip loss would offer important insight into the genetic factors responsible for the trait. In this study, drip loss and other meat quality traits of 28 purebred Duroc pigs were measured, muscles of these individuals were RNA sequenced, and eight individuals with extremely low and high drip loss were selected for analyzing their transcriptome differences and identifying potential candidate genes affecting drip loss.ResultsAs a result, 363 differentially expressed (DE) genes were detected in the comparative gene expression analysis, of which 239 were up-regulated and 124 were down-regulated in the low drip loss group. The DE genes were further filtered by correlation analysis between their expression and drip loss values in the 28 Duroc pigs measured and comparison of them with QTLs affecting drip loss. Consequently, of the 363 DE genes, 100 were identified as critical DE genes for drip loss. Functional analysis of these critical DE genes revealed some GO terms (extracellular matrix, cell adhesion mediated by integrin, heterotypic cell-cell adhesion), pathway (ECM-receptor interaction), and new potential candidate genes (TNC, ITGA5, ITGA11, THBS3 and CD44) which played an important role in regulating the variation of drip loss, and deserved to carry further studies to unravel their specific mechanism on drip loss.ConclusionsOur study revealed some GO terms, pathways and potential candidate genes affecting drip loss. It provides crucial information to understand the molecular mechanism of drip loss, and would be of help for improving meat quality of pigs.

In pigs, successful embryo implantation is an important guarantee for producing litter size, and early embryonic loss occurring on day 12–30 of gestation critically affects the potential litter size. The implantation process is regulated by the expression of numerous genes, so comprehensive analysis of the endometrium is necessary. In this study, RNA sequencing (RNA-Seq) technology is used to analyze endometrial tissues during early pregnancy. We investigated the changes of gene expression between three stages (day 12, 18, and 25) by multiple comparisons. There were 1557, 8951, and 2345 differentially expressed genes (DEGs) revealed between the different periods of implantation. We selected several genes for validation by the use of quantitative real-time RT-PCR. Bioinformatic analysis of differentially expressed genes in the endometrium revealed a number of biological processes and pathways potentially involved in embryo implantation in the pig, most noticeably cell proliferation, regulation of immune response, interaction of cytokine-cytokine receptors, and cell adhesion. These results showed that specific gene expression patterns reflect the different functions of the endometrium in three stages (maternal recognition, conceptus attachment, and embryo implantation). This study identified comprehensive transcriptomic profile in the porcine endometrium and thus could be a foundation for targeted studies of genes and pathways potentially involved in abnormal endometrial receptivity and embryo loss in early pregnancy.

Integrin are adhesion molecules involved in uterine-conceptus interactions during the perimplantation period. In this study, the expression of alphaV and beta3 integrin subunits in endometrium during implantation in pigs was investigated. The immunohistochemical location was performed on paraformaldehyde-fixed, paraffin-embedded tissue sections, and the mRNA expression of alphaV was detected in endometrium. In addition, serum levels of estradiol, progesterone, follicle-stimulating hormone, and luteinizing hormone were measured on Days 0, 12, 18, and 25 of pregnancy. The results indicate that endometrium expressed integrin alphaV and beta3 in all stages examined. The most intensive staining for integrin alphaV and beta3 was observed in endometrial stroma in porcine pregnancy on Day 18. The mRNA of alphaV integrin strongly expressed on Day 18, and moderately expressed on Days 12 and 25. The correlation between serum hormone level and the mRNA expression of alphaV integrin was not significant. The expression patterns of integrin alphaV and beta3 during implantation provide insights into the important physiological function of alphaVbeta3 integrin in pig, and the strong expression of integrin alphaV and beta3 in mid-implantation may indicate its crucial role in successful implantation and embryo survival.