Subcutaneous and intramuscular fat transcriptomes show large differences in network organization and associations with adipose traits in pigs

Identification of potential tissue-specific biomarkers involved in pig fat deposition through integrated bioinformatics analysis and machine learning

Backfat thickness (BT) and intramuscular fat (IMF) content are closely appertained to meat production and quality in pig production. Deposition in subcutaneous adipose (SA) and IMF concerns different genes and regulatory mechanisms. And larger studies with rigorous design should be carried to explore the molecular regulation of fat deposition in different tissues. The purpose of this study is to gain a better understanding of the molecular mechanisms underlying differences in fat deposition among different tissues and identify tissue-specific genes involved in regulating fat deposition. The SA-associated datasets (GSE122349 and GSE145956) and IMF-associated datasets (GSE165613 and GSE207279) were downloaded from the Gene Expression Omnibus (GEO) as the BT and IMF group, respectively. Subsequently, the Robust Rank Aggregation (RRA) algorithm identified 27 down- and 29 up-regulated differentially expressed genes (DEGs) in the BT group. Based on bioinformatics and three machine learning algorithms, four SA deposition-related potential biomarkers, namely ACLY, FASN, ME1, and ARVCF were selected. FASN was evaluated as the most valuable biomarker for the SA mechanism. The 18 down- and 34 up-regulated DEGs in the IMF group were identified, and ACTA2 and HMGCL were screened as the IMF deposition-related candidate core genes, especially the ACTA2 may play the critical role in IMF deposition regulation. Moreover, based on the constructed ceRNA network, we postulated that the role of predicted ceRNA interaction network of XIST, NEAT1/miR-15a-5p, miR-16-5p, miR-424-5p, miR-497-5p/FASN were vital in the SA metabolism, XIST, NEAT1/miR-27a/b-3p, 181a/c-5p/ACTA2 might contribute to the regulation to IMF metabolism, which all gave suggestions in molecular mechanism for regulation of fat deposition. These findings may facilitate advancements in porcine quality at the genetic and molecular levels and assist with human obesity-associated diseases.

Mulberry Leaf Dietary Supplementation Can Improve the Lipo-Nutritional Quality of Pork and Regulate Gut Microbiota in Pigs: A Comprehensive Multi-Omics Analysis

Mulberry leaves, a common traditional Chinese medicine, represent a potential nutritional strategy to improve the fat profile, also known as the lipo-nutrition, of pork. However, the effects of mulberry leaves on pork lipo-nutrition and the microorganisms and metabolites in the porcine gut remain unclear. In this study, multi-omics analysis was employed in a Yuxi black pig animal model to explore the possible regulatory mechanism of mulberry leaves on pork quality. Sixty Yuxi black pigs were divided into two groups: the control group (n = 15) was fed a standard diet, and the experimental group (n = 45) was fed a diet supplemented with 8% mulberry leaves. Experiments were performed in three replicates (n = 15 per replicate); the two diets were ensured to be nutritionally balanced, and the feeding period was 120 days. The results showed that pigs receiving the diet supplemented with mulberry leaves had significantly reduced backfat thickness (p < 0.05) and increased intramuscular fat (IMF) content (p < 0.05) compared with pigs receiving the standard diet. Lipidomics analysis showed that mulberry leaves improved the lipid profile composition and increased the proportion of triglycerides (TGs). Interestingly, the IMF content was positively correlated with acyl C18:2 and negatively correlated with C18:1 of differential TGs. In addition, the cecal microbiological analysis showed that mulberry leaves could increase the abundance of bacteria such as UCG-005, Muribaculaceae_norank, Prevotellaceae_NK3B31_group, and Limosilactobacillus. Simultaneously, the relative levels of L-tyrosine-ethyl ester, oleic acid methyl ester, 21-deoxycortisol, N-acetyldihydrosphingosine, and mulberrin were increased. Furthermore, we found that mulberry leaf supplementation significantly increased the mRNA expression of lipoprotein lipase, fatty acid-binding protein 4, and peroxisome proliferators-activated receptor γ in muscle (p < 0.01). Mulberry leaf supplementation significantly increased the mRNA expression of diacylglycerol acyltransferase 1 (p < 0.05) while significantly decreasing the expression of acetyl CoA carboxylase in backfat (p < 0.05). Furthermore, mulberry leaf supplementation significantly upregulated the mRNA expression of hormone-sensitive triglyceride lipase and peroxisome proliferator-activated receptor α (p < 0.05) in backfat. In addition, mulberry leaf supplementation led to increased serum leptin and adiponectin (p < 0.01). Collectively, this omic profile is consistent with an increased ratio of IMF to backfat in the pig model.

Comparative transcriptome analysis of longissimus dorsi muscle reveal potential genes affecting meat trait in Chinese indigenous Xiang pig

In this study, we compared the transcriptome of longissimus dorsi muscle between Guizhou Xiang pigs (XP) and Western commercial Large White pigs (LW), which show diffirent meat quality between them. In terms of meat quality traits, the pH 45 min, color score, backfat thickness, and intramuscular fat (IMF) content were higher in Xiang pigs than in Large White pigs (P < 0.01), while the drip loss, lean meat percentage, shear force, and longissimus dorsi muscle area of Xiang pigs were lower than that of Large White pigs (P < 0.01). Nutrients such as monounsaturated fatty acid (MUFA), total amino acids (TAA), delicious amino acids (DAA) and essential amino acids (EAA) in Xiang pigs were higher than that in Large White pigs, and the proportion of polyunsaturated fatty acid (PUFA) of Xiang pigs was significantly lower than Large White pigs (P < 0.01). Transcriptome analysis identified 163 up-regulated genes and 88 genes down-regulated in Xiang pigs longissimus dorsi muscle. Combined with the correlation analysis and quantitative trait locis (QTLs) affecting meat quality, a total of 227 DEGs were screened to be significantly associated with meat quality values. Enrichment analysis indicated that numerous members of genes were gathered in muscle development, adipogenesis, amino acid metabolism, fatty acid metabolism and synthesis. Of those, 29 genes were identified to be hub genes that might be related with the meat quality of Xiang pig, such as MYOD1, ACTB, ASNS, FOXO1, ARG2, SLC2A4, PLIN2, and SCD. Thus, we screened and identified the potential functional genes for the formation of meat quality in Xiang pigs, which provides a corresponding theoretical basis for the study of the molecular regulatory mechanism of pork quality and the improvement of pork quality.

CRISPR/Cas9-meditated gene knockout in pigs proves that LGALS12 deficiency suppresses the proliferation and differentiation of porcine adipocytes

LGALS12, also known as galectin12, belongs to the galectin family with β-galactoside-binding activity. We previously reported that LGALS12 is an important regulator of adipogenesis in porcine adipocytes in vitro, but its value in pig breeding needed to be explored in vivo. In this study, we used CRISPR/Cas9 to construct porcine fetal fibroblasts (PFFs) with a 43 bp deletion in LGALS12 exon 2. Using these PFFs as donor cells, a LGALS12 knockout pig model was generated via somatic cell nuclear transfer. Primary cultures of porcine intramuscular (IM) and subcutaneous (SC) adipocytes were established using cells from LGALS12 knockout pigs and wild-type pigs. A comparison of these cells proved that LGALS12 deficiency suppresses cell proliferation via the RAS-p38MAPK pathway and promotes lipolysis via the PKA pathway in both IM and SC adipocytes. In addition, we observed AKT activation only in IM adipocytes and suppression of the Wnt/β-catenin only in SC adipocytes. Our findings suggest that LGALS12 deficiency affects the adipogenesis of IM and SC adipocytes through different mechanisms.

Omics-based construction of regulatory variants can be applied to help decipher pig liver-related traits

Genetic variants can influence complex traits by altering gene expression through changes to regulatory elements. However, the genetic variants that affect the activity of regulatory elements in pigs are largely unknown, and the extent to which these variants influence gene expression and contribute to the understanding of complex phenotypes remains unclear. Here, we annotate 90,991 high-quality regulatory elements using acetylation of histone H3 on lysine 27 (H3K27ac) ChIP-seq of 292 pig livers. Combined with genome resequencing and RNA-seq data, we identify 28,425 H3K27ac quantitative trait loci (acQTLs) and 12,250 expression quantitative trait loci (eQTLs). Through the allelic imbalance analysis, we validate two causative acQTL variants in independent datasets. We observe substantial sharing of genetic controls between gene expression and H3K27ac, particularly within promoters. We infer that 46% of H3K27ac exhibit a concomitant rather than causative relationship with gene expression. By integrating GWAS, eQTLs, acQTLs, and transcription factor binding prediction, we further demonstrate their application, through metabolites dulcitol, phosphatidylcholine (PC) (16:0/16:0) and published phenotypes, in identifying likely causal variants and genes, and discovering sub-threshold GWAS loci. We provide insight into the relationship between regulatory elements and gene expression, and the genetic foundation for dissecting the molecular mechanism of phenotypes.

Melatonin decreases GSDME mediated mesothelial cell pyroptosis and prevents peritoneal fibrosis and ultrafiltration failure

Peritoneal fibrosis together with increased capillaries is the primary cause of peritoneal dialysis failure. Mesothelial cell loss is an initiating event for peritoneal fibrosis. We find that the elevated glucose concentrations in peritoneal dialysate drive mesothelial cell pyroptosis in a manner dependent on caspase-3 and Gasdermin E, driving downstream inflammatory responses, including the activation of macrophages. Moreover, pyroptosis is associated with elevated vascular endothelial growth factor A and C, two key factors in vascular angiogenesis and lymphatic vessel formation. GSDME deficiency mice are protected from high glucose induced peritoneal fibrosis and ultrafiltration failure. Application of melatonin abrogates mesothelial cell pyroptosis through a MT1R-mediated action, and successfully reduces peritoneal fibrosis and angiogenesis in an animal model while preserving dialysis efficacy. Mechanistically, melatonin treatment maintains mitochondrial integrity in mesothelial cells, meanwhile activating mTOR signaling through an increase in the glycolysis product dihydroxyacetone phosphate. These effects together with quenching free radicals by melatonin help mesothelial cells maintain a relatively stable internal environment in the face of high-glucose stress. Thus, Melatonin treatment holds some promise in preserving mesothelium integrity and in decreasing angiogenesis to protect peritoneum function in patients undergoing peritoneal dialysis.

Effects of weaning on intestinal longitudinal muscle-myenteric plexus function in piglets

Weaning piglets usually suffer from severe diarrhea (commonly known as postweaning diarrhea, PWD) along with intestinal motility disorder. Intestinal peristalsis is mainly regulated by the longitudinal muscle-myenteric plexus (LM-MP). To understand the relationship between intestinal LM-MP function and the development of PWD, we compared the intestinal electrical activity, and the transcriptional profile of the LM-MP between 21-day-old piglets (just weaned, n=7) and 24-day-old piglets (suffered the most severe weaning stress, n=7). The results showed that 24-day-old piglets exhibited different degrees of diarrhea. A significant increase in the slow-wave frequency in the ileum and colon was observed in 24-day-old piglets, while c-kit expression in the intestinal LM-MPs was significantly decreased, indicating that PWD caused by elevated slow-wave frequency may be associated with loss of c-kit. The real-time quantitative PCR (RT-qPCR) and enzyme-linked immunosorbent assay (ELISA) showed that intestinal LM-MPs in 24-day-old piglets may undergo inflammation and oxidative stress. Significant increases in 8-hydroxy-2'-deoxyguanosine and decreases in thioredoxin suggest that weaning may lead to DNA damage in the LM-MP of 24-day-old piglets. In addition, activating transcription factor 3 was significantly upregulated, indicating nerve damage in the LM-MP of 24-day-old piglets. The transcriptomic results showed that most of the differentially expressed genes in the ileal LM-MP after weaning were downregulated and closely related to the cell cycle process. Subsequent RT-qPCR analysis showed that the relative expression of p21 was upregulated, while the expression of cyclin A2, cyclin B1, and proliferating cell nuclear antigen was downregulated in the ileal and colonic LM-MP of 24-day-old piglets, suggesting that weaning may inhibit cell proliferation and cause G1/S cell cycle arrest in ileal and colonic LM-MP. In conclusion, weaning may lead to cell cycle arrest by causing DNA damage in the LM-MP, impairing intestinal motility regulation, and ultimately leading to diarrhea in piglets.

Mechanism of iron on the intestinal epithelium development in suckling piglets

This study aimed to investigate the mechanism of iron on intestinal epithelium development of suckling piglets. Compared with newborn piglets, 7-day-old and 21-day-old piglets showed changes in the morphology of the jejunum, increased proliferation, differentiated epithelial cells, and expanded enteroids. Intestinal epithelium maturation markers and iron metabolism genes were significantly changed. These results suggest that lactation is a critical stage in intestinal epithelial development, accompanied by changes in iron metabolism. In addition, deferoxamine (DFO) treatment inhibited the activity of intestinal organoids at passage 4 (P4) of 0-day-old piglets, but no significant difference was observed in epithelial maturation markers at passage 1 (P1) and P4, and only argininosuccinate synthetase 1 (Ass1) and β-galactosidase (Gleb) were up-regulated at passage 7 (P7). These results in vitro show that iron deficiency may not directly affect intestinal epithelium development through intestinal stem cells (ISCs). The iron supplementation significantly down-regulated the mRNA expression of interleukin-22 receptor subunit alpha-2 (IL-22RA2) in the jejunum of piglets. Furthermore, the mRNA expression of IL-22 in 7-day-old piglets was significantly higher than that in 0-day-old piglets. Adult epithelial markers were significantly up-regulated in organoids treated with recombinant murine cytokine IL-22. Thus, IL-22 may play a key role in iron-affecting intestinal epithelium development.

Selenium deficiency-induced multiple tissue damage with dysregulation of immune and redox homeostasis in broiler chicks under heat stress

Broiler chicks are fast-growing and susceptible to dietary selenium (Se) deficiency. This study sought to reveal the underlying mechanisms of how Se deficiency induces key organ dysfunctions in broilers. Day-old male chicks (n=6 cages/diet, 6 chicks/cage) were fed with a Se-deficient diet (Se-Def, 0.047 mg Se/kg) or the Se-Def+0.3 mg Se/kg (Control, 0.345 mg Se/kg) for 6 weeks. The serum, liver, pancreas, spleen, heart, and pectoral muscle of the broilers were collected at week 6 to assay for Se concentration, histopathology, serum metabolome, and tissue transcriptome. Compared with the Control group, Se deficiency induced growth retardation and histopathological lesions and reduced Se concentration in the five organs. Integrated transcriptomics and metabolomics analysis revealed that dysregulation of immune and redox homeostasis related biological processes and pathways contributed to Se deficiency-induced multiple tissue damage in the broilers. Meanwhile, four metabolites in the serum, daidzein, epinephrine, L-aspartic acid and 5-hydroxyindoleacetic acid, interacted with differentially expressed genes with antioxidative effects and immunity among all the five organs, which contributed to the metabolic diseases induced by Se deficiency. Overall, this study systematically elucidated the underlying molecular mechanisms in the pathogenesis of Se deficiency-related diseases, which provides a better understanding of the significance of Se-mediated heath in animals.

Multi-Omics Reveals the Effect of Crossbreeding on Some Precursors of Flavor and Nutritional Quality of Pork

Over the last several decades, China has continuously introduced Duroc boars and used them as breeding boars. Although this crossbreeding method has increased pork production, it has affected pork quality. Nowadays, one of the primary goals of industrial breeding and production systems is to enhance the quality of meat. This research analyzed the molecular mechanisms that control the quality of pork and may be used as a guide for future efforts to enhance meat quality. The genetic mechanisms of cross-breeding for meat quality improvement were investigated by combining transcriptome and metabolome analysis, using Chinese native Jiaxing black (JXB) pigs and crossbred Duroc × Duroc × Berkshire × JXB (DDBJ) pigs. In the longissimus Dorsi muscle, the content of inosine monophosphate, polyunsaturated fatty acid, and amino acids were considerably higher in JXB pigs in contrast with that of DDBJ pigs, whereas DDBJ pigs have remarkably greater levels of polyunsaturated fatty acids than JXB pigs. Differentially expressed genes (DEGs) and differential metabolites were identified using transcriptomic and metabolomic KEGG enrichment analyses. Differential metabolites mainly include amino acids, fatty acids, and phospholipids. In addition, several DEGs that may explain differences in meat quality between the two pig types were found, including genes associated with the metabolism of lipids (e.g., DGKA, LIPG, and LPINI), fatty acid (e.g., ELOVL5, ELOVL4, and ACAT2), and amino acid (e.g., SLC7A2, SLC7A4). Combined with the DEGS-enriched signaling pathways, the regulatory mechanisms related to amino acids, fatty acids, and phospholipids were mapped. The abundant metabolic pathways and DEGs may provide insight into the specific molecular mechanism that regulates meat quality. Optimizing the composition of fatty acids, phospholipids, amino acids, and other compounds in pork is conducive to improving meat quality. Overall, these findings will provide useful information and further groundwork for enhancing the meat quality that may be achieved via hybrid breeding.

Profiling of N6-methyladenosine methylation in porcine longissimus dorsi muscle and unravelling the hub gene ADIPOQ promotes adipogenesis in an m6A-YTHDF1-dependent manner

BACKGROUND

Intramuscular fat (IMF) content is a critical indicator of pork quality, and abnormal IMF is also relevant to human disease as well as aging. Although N6-methyladenosine (m⁶A) RNA modification was recently found to regulate adipogenesis in porcine intramuscular fat, however, the underlying molecular mechanisms was still unclear.

RESULTS

In this work, we collected 20 longissimus dorsi muscle samples with high (average 3.95%) or low IMF content (average 1.22%) from a unique heterogenous swine population for m⁶A sequencing (m⁶A-seq). We discovered 70 genes show both differential RNA expression and m⁶A modification from high and low IMF group, including ADIPOQ and SFRP1, two hub genes inferred through gene co-expression analysis. Particularly, we observed ADIPOQ, which contains three m⁶A modification sites within 3' untranslated and protein coding region, could promote porcine intramuscular preadipocyte differentiation in an m⁶A-dependent manner. Furthermore, we found the YT521‑B homology domain family protein 1 (YTHDF1) could target and promote ADIPOQ mRNA translation.

CONCLUSIONS

Our study provided a comprehensive profiling of m⁶A methylation in porcine longissimus dorsi muscle and characterized the involvement of m⁶A epigenetic modification in the regulation of ADIPOQ mRNA on IMF deposition through an m⁶A-YTHDF1-dependent manner.

Caveolae-associated protein 3 promotes adipogenic differentiation of porcine preadipocytes by promoting extracellular signal-regulated kinase phosphorylation

Fat deposition is one of the key factors affecting the economic development of pig husbandry. The aim of this study was to investigate the expression characteristics of caveolae-associated protein 3 (CAVIN3) and to elucidate its effect and mechanism on adipogenic differentiation of porcine preadipocytes. Cell transfection, quantitative reverse transcription polymerase chain reaction (qRT-PCR), western blot, and oil red O staining were used to detect the effect of CAVIN3 on the differentiation of porcine preadipocytes. The results showed that CAVIN3 was expressed in various tissues, with higher expression in adipose tissue, differentially expressed during cell adipogenic differentiation, and mainly distributed in the cytoplasm. Functional studies showed that, after CAVIN3 interference in preadipocytes, the expression of adipogenic factors and the content of lipid droplets were significantly decreased (p < 0.05). The results were reversed after CAVIN3 was overexpressed. The mechanism research showed that LY3214996 inhibited the extracellular signal-regulated kinase (ERK) phosphorylation and further inhibited lipogenic factors expression. Overexpression of CAVIN3 attenuates the inhibitory effect of LY3214996 on ERK phosphorylation and attenuates its inhibitory effect on adipogenic differentiation. Therefore, this study demonstrated that CAVIN3 promotes the differentiation of porcine preadipocytes by promoting ERK phosphorylation. The present study can lay a theoretical foundation for further studying the molecular mechanism of porcine fat deposition.

Profiles of muscular amino acids, fatty acids, and metabolites in Shaziling pigs of different ages and relation to meat quality

Pork meat is closely related to physicochemical alterations during growth and development, resulting in differences in nutritional value and meat flavor. This study aimed to evaluate the composition of amino acids, fatty acids, and metabolic profiles in the longissimus thoracis muscle (LM) of Shaziling pigs aged 30, 90, 150, 210, and 300 days. The results showed that the predominant fatty acids identified in the LM of Shaziling pigs were C16:0, C16:1, C18:0, C18:1n9c, and C18:2n6c. An opposite correlation was observed for C18:2n6c and n6/n3 polyunsaturated fatty acids (P<0.05). Alanine, aspartate, glutamate, D-glutamine, and D-glutamate metabolism were the main metabolic pathways for the Shaziling pig meat flavor (P<0.05). Moreover, the correlation coefficients revealed that the contents of anserine, C16:0, C16:1, and C18:1n9c were positively correlated with intramuscular fat and/or pH_24h and were negatively correlated with the values of L* (lightness) and b* (yellowness) (P<0.05). In conclusion, age greatly affected the meat quality of Shaziling pigs, and the contents of muscular anserine, C16:0, C16:1, and C18:1n9c might be promising indicators for better meat quality.

Identification of Candidate Genes and Regulatory Competitive Endogenous RNA (ceRNA) Networks Underlying Intramuscular Fat Content in Yorkshire Pigs with Extreme Fat Deposition Phenotypes

Intramuscular fat (IMF) content is vital for pork quality, serving an important role in economic performance in pig industry. Non-coding RNAs, with mRNAs, are involved in IMF deposition; however, their functions and regulatory mechanisms in porcine IMF remain elusive. This study assessed the whole transcriptome expression profiles of the Longissimus dorsi muscle of pigs with high (H) and low (L) IMF content to identify genes implicated in porcine IMF adipogenesis and their regulatory functions. Hundreds of differentially expressed RNAs were found to be involved in fatty acid metabolic processes, lipid metabolism, and fat cell differentiation. Furthermore, combing co-differential expression analyses, we constructed competing endogenous RNAs (ceRNA) regulatory networks, showing crosstalk among 30 lncRNAs and 61 mRNAs through 20 miRNAs, five circRNAs and 11 mRNAs through four miRNAs, and potential IMF deposition-related ceRNA subnetworks. Functional lncRNAs and circRNAs (such as MSTRG.12440.1, ENSSSCT00000066779, novel_circ_011355, novel_circ_011355) were found to act as ceRNAs of important lipid metabolism-related mRNAs (LEP, IP6K1, FFAR4, CEBPA, etc.) by sponging functional miRNAs (such as ssc-miR-196a, ssc-miR-200b, ssc-miR10391, miR486-y). These findings provide potential regulators and molecular regulatory networks that can be utilized for research on IMF traits in pigs, which would aid in marker-assisted selection to improve pork quality.

Genome-Wide Expression Profiling and Networking Reveals an Imperative Role of IMF-Associated Novel CircRNAs as ceRNA in Pigs

Intramuscular fat (IMF) deposition is a biological process that has a strong impact on the nutritional and sensorial properties of meat, with relevant consequences on human health. Pork loins determine the effects of marbling on the sensory attributes and meat quality properties, which differ among various pig breeds. This study explores the crosstalk of non-coding RNAs with mRNAs and analyzes the potential pathogenic role of IMF-associated competing endogenous RNA (ceRNA) in IMF tissues, which offer a framework for the functional validation of key/potential genes. A high-throughput whole-genome transcriptome analysis of IMF tissues from longissimus dorsi muscles of Large White (D_JN) and Laiwu (L_JN) pigs resulted in the identification of 283 differentially expressed circRNAs (DECs), including two key circRNAs (circRNA-23437, circRNA-08840) with potential binding sites for multiple miRNAs regulating the whole network. The potential ceRNA mechanism identified the DEC target miRNAs-mRNAs involved in lipid metabolism, fat deposition, meat quality, and metabolic syndrome via the circRNA-miRNA-mRNA network, concluding that ssc-mir-370 is the most important target miRNA shared by both key circRNAs. TGM2, SLC5A6, ECI1, FASN, PER1, SLC25A34, SOD1, and COL5A3 were identified as hub genes through an intensive protein-protein interaction (PPI) network analysis of target genes acquired from the ceRNA regulatory network. Functional enrichments, pathway examinations, and qRT-PCR analyses infer their implications in fat/cholesterol metabolism, insulin secretion, and fatty acid biosynthesis. Here, circRNAs and miRNA sequencing accompanied by computational techniques were performed to analyze their expressions in IMF tissues from the longissimus dorsi muscles of two pig breeds. Their target gene evolutionary trajectories, expression profiling, functional enrichments, subcellular localizations, and structural advances with high-throughput protein modeling, following genomic organizations, will provide new insights into the underlying molecular mechanisms of adipocyte differentiation and IMF deposition and a much-needed qualitative framework for future research to improve meat quality and its role as a biomarker to treat lipid metabolic syndromes.

Mapping and analysis of a spatiotemporal H3K27ac and gene expression spectrum in pigs

The limited knowledge of genomic noncoding and regulatory regions has restricted our ability to decipher the genetic mechanisms underlying complex traits in pigs. In this study, we characterized the spatiotemporal landscape of putative enhancers and promoters and their target genes by combining H3K27ac-targeted ChIP-Seq and RNA-Seq in fetal (prenatal days 74-75) and adult (postnatal days 132-150) tissues (brain, liver, heart, muscle and small intestine) sampled from Asian aboriginal Bama Xiang and European highly selected Large White pigs of both sexes. We identified 101,290 H3K27ac peaks, marking 18,521 promoters and 82,769 enhancers, including peaks that were active across all tissues and developmental stages (which could indicate safe harbor locus for exogenous gene insertion) and tissue- and developmental stage-specific peaks (which regulate gene pathways matching tissue- and developmental stage-specific physiological functions). We found that H3K27ac and DNA methylation in the promoter region of the XIST gene may be involved in X chromosome inactivation and demonstrated the utility of the present resource for revealing the regulatory patterns of known causal genes and prioritizing candidate causal variants for complex traits in pigs. In addition, we identified an average of 1,124 super-enhancers per sample and found that they were more likely to show tissue-specific activity than ordinary peaks. We have developed a web browser to improve the accessibility of the results ( http://segtp.jxau.edu.cn/pencode/?genome=susScr11 ).

RNA Sequencing of the Pituitary Gland and Association Analyses Reveal PRKG2 as a Candidate Gene for Growth and Carcass Traits in Chinese Ningdu Yellow Chickens

Growth and carcass traits are of great economic importance to the chicken industry. The candidate genes and mutations associated with growth and carcass traits can be utilized to improve chicken growth. Therefore, the identification of these genes and mutations is greatly importance. In this study, a total of 17 traits related to growth and carcass were measured in 399 Chinese Ningdu yellow chickens. RNA sequencing (RNA-seq) was performed to detect candidate genes using 12 pituitary gland samples (six per group), which exhibited extreme growth and carcass phenotypes: either a high live weight and carcass weight (H group) or a low live weight and carcass weight (L group). A differential expression analysis, utilizing RNA-seq, between the H and L groups identified 428 differentially expressed genes (DEGs), including 110 up-regulated genes and 318 down-regulated genes. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of the identified genes showed a significant enrichment of 158 GO terms and two KEGG pathways, including response to stimulus and neuroactive ligand-receptor interaction, respectively. Furthermore, RNA-seq data, qRT–PCR, and quantitative trait transcript (QTT) analysis results suggest that the PRKG2 gene is an important candidate gene for growth and carcass traits of Chinese Ningdu yellow chickens. More specifically, association analyses of a single nucleotide polymorphism (SNP) in PRKG2 and growth and carcass traits showed that the SNP rs16400745 was significantly associated with 12 growth and carcass traits (P < 0.05), such as carcass weight (P = 9.68E-06), eviscerated weight (P = 3.04E-05), and semi-eviscerated weight (P = 2.14E-04). Collectively, these results provide novel insights into the genetic basis of growth in Chinese Ningdu yellow chickens and the SNP rs16400745 reported here could be incorporated into the selection programs involving this breed.

Integrating genomics and transcriptomics to identify candidate genes for subcutaneous fat deposition in beef cattle

Fat deposition is a complex economic trait regulated by polygenic genetic basis and environmental factors. Therefore, integrating multi-omics data to uncover its internal regulatory mechanism has attracted extensive attention. Here, we performed genomics and transcriptomics analysis to detect candidates affecting subcutaneous fat (SCF) deposition in beef cattle. The association of 770K SNPs with the backfat thickness captured nine significant SNPs within or near 11 genes. Additionally, 13 overlapping genes regarding fat deposition were determined via the analysis of differentially expressed genes and weighted gene co-expression network analysis (WGCNA). We then calculated the correlations of these genes with BFT and constructed their interaction network. Finally, seven biomarkers including ACACA, SCD, FASN, ACOX1, ELOVL5, HACD2, and HSD17B12 were screened. Notably, ACACA, identified by the integration of genomics and transcriptomics, was more likely to exert profound effects on SCF deposition. These findings provided novel insights into the regulation mechanism underlying bovine fat accumulation.

Identification of candidate genes that specifically regulate subcutaneous and intramuscular fat deposition using transcriptomic and proteomic profiles in Dingyuan pigs

Subcutaneous fat and intramuscular fat (IMF) deposition are closely related to meat production and pork quality. Dingyuan pig, as a native pig breed in China, low selection leads to obvious genetic and phenotypic differences in the population. Individuals with extreme fat content in the population are ideal models for studying the mechanism of fat deposition. In this study, we used RNA-Seq and tandem mass tags-based (TMT) proteomics to analyze the key pathways and genes that specifically regulate subcutaneous fat and IMF deposition in Dingyuan pigs. We identified 191 differentially expressed genes (DEGs) and 61 differentially abundant proteins (DAPs) in the high and low back fat thickness (HBF, LBF) groups, 85 DEGs and 12 DAPs were obtained in the high and low intramuscular fat (HIMF, LIMF) groups. The functional analysis showed that the DEGs and DAPs in the backfat groups were mainly involved in carbohydrates, amino acids, and fatty acids metabolism, whereas the IMF groups were involved in the insulin pathway, longevity, and some disease-related pathways. We found 40 candidate genes that might tissue-specifically lipids deposition for subcutaneous and intramuscular fat. Our research provides theoretical reference materials for the improvement of fat deposition traits of local pig breeds in my country.