Identification and characterization of a differentially expressed protein (CAPZB) in skeletal muscle between Meishan and Large White pigs

Construction of LncRNA-Related ceRNA Networks in Longissimus Dorsi Muscle of Jinfen White Pigs at Different Developmental Stages

The development of skeletal muscle in pigs might determine the quality of pork. In recent years, long non-coding RNAs (lncRNAs) have been found to play an important role in skeletal muscle growth and development. In this study, we investigated the whole transcriptome of the longissimus dorsi muscle (LDM) of Jinfen White pigs at three developmental stages (1, 90, and 180 days) and performed a comprehensive analysis of lncRNAs, mRNAs, and micro-RNAs (miRNAs), aiming to find the key regulators and interaction networks in Jinfen White pigs. A total of 2638 differentially expressed mRNAs (DE mRNAs) and 982 differentially expressed lncRNAs (DE lncRNAs) were identified. Compared with JFW_1d, there were 497 up-regulated and 698 down-regulated DE mRNAs and 212 up-regulated and 286 down-regulated DE lncRNAs in JFW_90d, respectively. In JFW_180d, there were 613 up-regulated and 895 down-regulated DE mRNAs and 184 up-regulated and 131 down-regulated DE lncRNAs compared with JFW_1d. There were 615 up-regulated and 477 down-regulated DE mRNAs and 254 up-regulated and 355 down-regulated DE lncRNAs in JFW_180d compared with JFW_90d. Compared with mRNA, lncRNA has fewer exons, fewer ORFs, and a shorter length. We performed GO and KEGG pathway functional enrichment analysis for DE mRNAs and the potential target genes of DE lncRNAs. As a result, several pathways are involved in muscle growth and development, such as the PI3K-Akt, MAPK, hedgehog, and hippo signaling pathways. These are among the pathways through which mRNA and lncRNAs function. As part of this study, bioinformatic screening was used to identify miRNAs and DE lncRNAs that could act as ceRNAs. Finally, we constructed an lncRNA-miRNA-mRNA regulation network containing 26 mRNAs, 7 miRNAs, and 17 lncRNAs; qRT-PCR was used to verify the key genes in these networks. Among these, XLOC_022984/miR-127/ENAH and XLOC_016847/miR-486/NRF1 may function as key ceRNA networks. In this study, we obtained transcriptomic profiles from the LDM of Jinfen White pigs at three developmental stages and screened out lncRNA-miRNA-mRNA regulatory networks that may provide crucial information for the further exploration of the molecular mechanisms during skeletal muscle development.

Identification of Two Novel Single Nucleotide Polymorphisms in the Promoter Region of the Pig AMP Deaminase 1 Gene Associated with Carcass Traits

The AMP deaminase 1 (AMPD1) gene plays an important role in purine nucleotide interconversion and energy metabolism. In this study, two novel single nucleotide polymorphisms (SNPs) (g.-626 G > A and g.-566 A>G) were detected in the proximal promoter region of the AMPD1 gene. The Chinese indigenous pig breeds (Meishan and Tongcheng) had higher frequencies of the G and A alleles than Western meat-type breeds (Landrace and Large White) at the g.-626 G > A and g.-566 A>G loci. The transcriptional activity of the AMPD1 promoter carrying the haplotype H1 (A^-626G^-566) was significantly (p < 0.05) higher than that of the haplotype H2 (G^-626A^-566). In addition, pigs with the haplotype combination H1H1 had significantly (p < 0.05) higher mRNA expression levels of the AMPD1 gene than those with haplotype combinations H1H2 and H2H2 in two different skeletal muscles. Association analyses revealed that the pigs with the haplotype combination H1H1 had significantly higher lean meat percentage values but lower average backfat thickness (ABT, cm), buttock fat thickness (cm), and thorax-waist fat thickness (cm) values than the pigs with the haplotype combinations H1H2 and H2H2. These findings demonstrate that the two novel SNPs in the promoter region of the AMPD1 gene have significant associations with pig fat deposition traits.

Molecular characterization and expression patterns of emerin (EMD) gene in skeletal muscle between Meishan and Large White pigs

The emerin protein is a nuclear membrane protein and has important functions in muscle development, regeneration, and cell signal transduction. However, knowledge regarding emerin in the domestic animal is limited. In this study, we cloned and characterized the pig emerin (EMD) gene. Semi-quantitative RT-PCR analysis revealed that the EMD gene was expressed at the highest level in the heart and fat at 120d. However, the fetal skeletal muscles displayed a greater abundance of EMD mRNA than that in skeletal muscles at postnatal development stages. In addition, the expression level of EMD at 60 day was significantly higher (p<0.05) in Meishan than Large White pigs. Pig EMD protein displayed the sarcolemma and perinuclear distribution in skeletal muscle sections, and there was no distribution change of EMD in skeletal muscle sections between Large White and Meishan pigs. These studies provide useful information for further research on the functions of pig EMD gene in skeletal muscle.