Identification of key microRNAs affecting drip loss in porcine longissimus dorsi by RNA-Seq

Integration of transcriptome and machine learning to identify the potential key genes and regulatory networks affecting drip loss in pork

Low level of drip loss (DL) is an important quality characteristic of meat with high economic value. However, the key genes and regulatory networks contributing to DL in pork remain largely unknown. To accurately identify the key genes affecting DL in muscles postmortem, 12 Duroc × (Landrace × Yorkshire) pigs with extremely high (n = 6, H group) and low (n = 6, L group) DL at both 24 and 48 h postmortem were selected for transcriptome sequencing. The analysis of differentially expressed genes and weighted gene co-expression network analysis (WGCNA) were performed to find the overlapping genes using the transcriptome data, and functional enrichment and protein-protein interaction (PPI) network analysis were conducted using the overlapping genes. Moreover, we used machine learning to identify the key genes and regulatory networks related to DL based on the interactive genes of the PPI network. Finally, nine potential key genes (IRS1, ESR1, HSPA6, INSR, SPOP, MSTN, LGALS4, MYLK2, and FRMD4B) mainly associated with the MAPK signaling pathway, the insulin signaling pathway, and the calcium signaling pathway were identified, and a single-gene set enrichment analysis (GSEA) was performed to further annotate the functions of these potential key genes. The GSEA results showed that these genes are mainly related to ubiquitin-mediated proteolysis and oxidative reactions. Taken together, our results indicate that the potential key genes influencing DL are mainly related to insulin signaling mediated differences in glycolysis and ubiquitin-mediated changes in muscle structure and improve the understanding of gene expression and regulation related to DL and contribute to future molecular breeding for improving pork quality.

Deep Small RNA Sequencing Reveals Important miRNAs Related to Muscle Development and Intramuscular Fat Deposition in Longissimus dorsi Muscle From Different Goat Breeds

MicroRNAs (miRNAs) are a class of small non-coding RNAs that have been shown to play important post-transcriptional regulatory roles in the growth and development of skeletal muscle tissues. However, limited research into the effect of miRNAs on muscle development in goats has been reported. In this study, Liaoning cashmere (LC) goats and Ziwuling black (ZB) goats with significant phenotype difference in meat production performance were selected and the difference in Longissimus dorsi muscle tissue expression profile of miRNAs between the two goat breeds was then compared using small RNA sequencing. A total of 1,623 miRNAs were identified in Longissimus dorsi muscle tissues of the two goat breeds, including 410 known caprine miRNAs, 928 known species-conserved miRNAs and 285 novel miRNAs. Of these, 1,142 were co-expressed in both breeds, while 230 and 251 miRNAs were only expressed in LC and ZB goats, respectively. Compared with ZB goats, 24 up-regulated miRNAs and 135 miRNAs down-regulated were screened in LC goats. A miRNA-mRNA interaction network showed that the differentially expressed miRNAs would target important functional genes associated with muscle development and intramuscular fat deposition. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that the target genes of differentially expressed miRNAs were significantly enriched in Ras, Rap 1, FoxO, and Hippo signaling pathways. This study suggested that these differentially expressed miRNAs may be responsible for the phenotype differences in meat production performance between the two goat breeds, thereby providing an improved understanding of the roles of miRNAs in muscle tissue of goats.

Differential regulatory roles of microRNAs during intramuscular adipogenesis in Chinese Guizhou Congjiang Xiang pigs

Intramuscular fat development is regulated by a series of complicated processes, with non-coding RNA (ncRNA) such as microRNA (miRNA) having a critical role during intramuscular preadipocyte proliferation and differentiation in pigs. In the present study, the miRNA expression profiles of intramuscular preadipocytes from the longissimus dorsi muscle of Chinese Guizhou Congjiang Xiang pigs were detected by RNA-seq during various differentiation stages, namely, day 0 (D0), day 4 (D4), and day 8 (D8). A total of 67, 95, and 16 differentially expressed (DE) miRNAs were detected between D4 and D0, D8 and D0, and D8 and D4, respectively. According to gene ontology and Kyoto Encyclopedia of Genes analysis, target genes of DE miRNAs were enriched in categories and pathways related to lipid metabolic process, lipid biosynthetic process, as well as the PI3K-Akt, AMPK, and MAPK signalling pathways. Notably, miR-148a-3p was differentially expressed, with highest expressed abundance in D0, D4, and D8. Overexpression of miR-148a-3p in intramuscular preadipocytes increased cell proliferation and differentiation, and decreased apoptosis, in comparison to the knockdown of miR-148a-3p in intramuscular preadipocytes. Luciferase activity assays, quantitative polymerase-chain reaction, and western blot analysis confirmed that miR-148a-3p regulated adipogenesis by repressing PPARGC1A expression. Accordingly, the effect of miR-148a-3p mimic was attenuated by overexpression of PPARGC1A intramuscular preadipocytes. Furthermore, miR-148a-3p promoted intramuscular preadipocyte differentiation by inhibiting the AMPK/ACC/CPT1C signalling pathway. Taken together, we identified expression profiles of miRNAs in intramuscular preadipocytes and determined that miR-148a-3p acted as a promoter of adipogenesis.

Transcriptome analysis in comparing carcass and meat quality traits of Jiaxing Black Pig and Duroc × Duroc × Berkshire × Jiaxing Black Pig crosses

This study compares two typical strains: Chinese local excellent meat quality of Jiaxing Black (JXB) Pig and quadratic crossbred pig strain Duroc × Duroc × Berkshire × Jiaxing Black (DDBJ). It was found that between the two pig strains, carcass traits and meat quality traits differed significantly. This is exemplified by the leanness and dressing out percent of DDBJ that were significantly higher than JXB pigs of the same age (P < 0.05) and the better growth rate of DDBJ pigs as to JXB pigs was shown by quantifying muscle proliferation and differentiation of longissimus dorsi muscle employing Hematoxylin and Eosin staining of longissimus dorsi muscle. Nutrients such as inosinic acid, intramuscular fat, and free amino acids in the longissimus dorsi muscle were significantly higher in JXB pigs than DDBJ pigs (p < 0.0001); saturated fatty acids were higher in JXB than in DDBJ pigs (p = 0.0097); essential amino acids and fresh taste amino acids (serine, glutamic acid, proline, glycine, alanine) of JXB pigs was higher than that of DDBJ pigs (p < 0.0001) and amino acids in longissimus dorsi muscle of JXB pigs surpasses the amino acid concentration of DDBJ pigs (p < 0.0001), thus showing the superiority of JXB in terms of meat quality. However, the content of polyunsaturated fatty acids, which is responsible for poor meat quality, was significantly higher in the longissimus dorsi muscle of DDBJ pig than JXB pigs (p < 0.0001); RNA-seq analysis of 5 biological replicates from two of the strains was performed. The screening of 164 up-regulated genes and 183 down-regulated genes found in longissimus dorsi muscle of DDBJ was done and the results identified differentially expressed genes related to muscle development, adipogenesis, amino acid metabolism, fatty acid metabolism and inosine synthesis. In conclusion, the study identified functional genes, elucidated the mechanisms associated with carcass quality traits, meat quality traits and other related traits, and provided means of genetic enhancement to improve meat quality traits and carcass traits in Chinese commercial pigs.

Parsing the microRNA genetics basis regulating skeletal muscle fiber types and meat quality traits in pigs

Muscle fibers are closely related to human diseases and livestock meat quality. However, the genetics basis of microRNAs (miRNAs) in regulating muscle fibers is not completely understood. In this study, we constructed the whole genome-wide miRNA expression profiles of porcine fast-twitch muscle [biceps femoris (Bf)] and slow-twitch muscle [soleus (Sol)], and identified hundreds of miRNAs, including four skeletal muscle-highly expressed miRNAs, ssc-miR-378, ssc-let-7f, ssc-miR-26a, and ssc-miR-27b-3p. Moreover, we identified 63 differentially expressed (DE) miRNAs between biceps femoris vs. soleus, which are the key candidate miRNAs regulating the skeletal muscle fiber types. In addition, we found that the expression of DE ssc-miR-499-5p was significantly correlated to the expression of Myoglobin (r = 0.6872, P < 0.0001) and Myosin heavy chain 7 (MYH7; r = 0.5408, P = 0.0020), and pH_45 min (r = 0.3806, P = 0.0380) and glucose content (r = -0.4382, P = 0.0154); while the expression of DE ssc-miR-499-3p was significantly correlated to the expression of Myoglobin (r = 0.5340, P = 0.0024) and pH_45 min (r = 0.4857, P = 0.0065). Taken together, our data established a sound foundation for further studies on the regulatory mechanisms of miRNAs in skeletal muscle fiber conversion and meat quality traits in livestock, and could provide a genetic explanation of the role of miRNAs in human muscular diseases.

The Effect of Dietary Lycopene Supplementation on Drip Loss during Storage of Lamb Meat by iTRAQ Analysis

This study was designed to investigate the impact of dietary lycopene (antioxidant extracted from tomato) supplementation on postmortem antioxidant capacity, drip loss and protein expression profiles of lamb meat during storage. Thirty male Hu lambs were randomly divided into three treatment groups and housed in individual pens and received 0, 200 or 400 mg·kg-1 lycopene in their diet, respectively. All lambs were slaughtered after 3 months of fattening, and the longissimus thoracis (LT) muscle was collected for analyses. The results indicated that drip loss of LT muscle increased with storage days (P < 0.05). After storage for 7 days, significantly lower drip loss of meat was found in fed the lycopene-supplemented diet (P < 0.05). Dietary lycopene supplementation increased the activity of antioxidant enzymes (total antioxidant capacity (T-AOC), superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), catalase (CAT)) (P < 0.05) and decreased the thiobarbituric acid reactive substance (TBARS) and carbonyl contents (P < 0.05). During the storage period (days 0, 5 and 7), a number of differentially abundant proteins (DAPs), including oxidases, metabolic enzymes, calcium channels and structural proteins, were identified based on iTRAQ data, with roles predominantly in carbon metabolism, oxidative phosphorylation, cardiac muscle contraction and proteasome pathways, and which contribute to decreased drip loss of lamb meat during storage. It can be concluded that dietary lycopene supplementation increased antioxidant capacity after slaughter, and the decreased drip loss during postmortem storage might occur by changing the expression of proteins related to enzyme activity and cellular structure in lamb muscle.

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

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.

Identification of key microRNAs affecting melanogenesis of breast muscle in Muchuan black-boned chickens by RNA sequencing

1. Melanin content is considered an important indicator of meat quality in black-boned chickens, which have a high market value. To understand the complex physiological processes underlying muscle melanogenesis in this chicken, differentially expressed miRNAs (DEMs) were detected between black muscle (BM) and white muscle (WM) of chickens using high-throughput sequencing technology. Six small RNA libraries were constructed, and more than 16.75 million clean reads were obtained for each library. 2. A total of 582 known miRNAs and 65 novel miRNAs were identified from the six chicken sequence libraries. A total of 19 DEMs were identified between the two groups, of which nine were upregulated and 10 were downregulated. Furthermore, the DEMs were predicted to target 572 genes. 3. Certain DEMs (such as miR-204, miR-133b, and miR-12 229-3p) and their target genes may play an important role in muscle melanogenesis of chickens. These findings provide a foundation for clarifying the miRNA regulatory mechanisms involved in muscle pigmentation in avian species.

Comprehensive Analysis of Differentially Expressed mRNA, lncRNA and circRNA and Their ceRNA Networks in the Longissimus Dorsi Muscle of Two Different Pig Breeds

Circular RNA (circRNA) and long non-coding RNA (lncRNA) are known to participate in adipogenesis and myogenic differentiation, but their impact on porcine muscle traits is not well understood. We compared their expressional profiles in the longissimus dorsi muscle of Chinese Huainan pigs (HN, the fat type) and Western commercial Duroc×(Landrace×Yorkshire) (DLY, the thin type) pigs, and 854 mRNAs, 233 lncRNAs, and 66 circRNAs (p < 0.05 and ｜log₂FoldChange｜>1) were found to be differentially expressed. The differentially expressed mRNA and circRNA parental genes were enriched in the Wnt signaling pathway (adipogenesis), the transition between fast and slow fibers (myogenic differentiation), and alanine, aspartate and glutamate metabolism (pork flavor). The potential lncRNAs/circRNAs-miRNAs-mRNAs regulatory networks shared MYOD1, PPARD, miR-423-5p and miR-874, which were associated with skeletal muscle muscular proliferation, differentiation/regeneration and adipogenesis. Taken together, these differentially expressed non-coding RNAs may be involved in the molecular basis of muscle traits, acting as the competing endogenous RNA (ceRNA) for miRNAs.