A Key Gene, PLIN1, Can Affect Porcine Intramuscular Fat Content Based on Transcriptome Analysis

Therapeutic of a white adipose tissue-specific bivalent aptamer in obesity

The white adipose tissue-specific aptamer Adipo8 can specificity bindwith mature adipocytes or tissues and inhibit adipogenesis.In this research, we exploredthe effect of Adipo8 intervention on the transcriptome in the process of adipogenesis using mRNA-level sequencing,analyzed the mechanism ofAdipo8 ininhibiting adipogenesis. The results showed that Adipo8 can inhibit lipid formation and downregulate PPARγ and C/EBPα in differentiated 3 T3-L1 cells. Transcriptome mRNA sequencing of 3 T3-L1 cells after Adipo8 interventionrevealed that Adipo8 might inhibit the biological function of adipogenesis by downregulating Acsl1 and Plin1 to inhibit fatty acid metabolism and PPAR signaling pathways.After that, using Spacer18 to connect the optimized and truncated Adipo8, we constructed a bivalent aptamer Adipo8cBand compared the affinity, biological effects, and biological stability between the aptamers in differentiated and mature 3 T3-L1 cells. At the cellular level,the affinity, biological effects, and serum stability of Adipo8cB were verified to be superior to those of Adipo8in 3 T3-L1 cells.We then investigated the biological properties of Adipo8cB as a lipid-inhibiting drug invivo, using C57BL/6J mice with diet-induced obesity. The body weight, blood sugar, lipid levels, liver function, glucose tolerance, and other related indicators in each group of mice were observed and compared after intervention with the bivalent aptamers Adipo8cB and Adipo8. Both Adipo8cB and Adipo8 effectively prevented weight gain caused by fat accumulation in micewith diet induced obesity, while also reducing blood lipid levels, improving glucose tolerance, and protecting against liver steatosis, moreover, Adipo8cB has a better effect than Adipo8.

Gene co-expression network analysis for porcine intramuscular fatty acid composition

In pigs, meat quality depends markedly on the fatty acid (FA) content and composition of the intramuscular fat, which is partly determined by the gene expression in this tissue. The aim of this work was to identify the link between muscle gene expression and its FA composition. In an (Iberian × Duroc) × Duroc backcrossed pig population, we identified modules of co-expressed genes, and correlation analyses were performed for each of them versus the phenotypes, finding four relevant modules. Two of the modules were positively correlated with saturated FAs (SFAs) and monounsaturated FAs (MUFAs), while negatively correlated with polyunsaturated FAs (PUFAs) and the omega-6/omega-3 ratio. The gene-enrichment analysis showed that these modules had over-representation of pathways related with the biosynthesis of unsaturated FAs, the Peroxisome proliferator-activated receptor signalling pathway and FA elongation. The two other relevant modules were positively correlated with PUFA and the n-6/n-3 ratio, but negatively correlated with SFA and MUFA. In this case, they had an over-representation of pathways related with fatty and amino acid degradation, and with oxidative phosphorylation. Using a graphical Gaussian model, we inferred a network of connections between the genes within each module. The first module had 52 genes with 87 connections, and the most connected genes were ADIPOQ, which is related with FA oxidation, and ELOVL6 and FABP4, both involved in FA metabolism. The second module showed 196 genes connected by 263 edges, being FN1 and MAP3K11 the most connected genes. On the other hand, the third module had 161 genes connected by 251 edges and ATG13 was the top neighbouring gene, while the fourth module had 224 genes and 655 connections, and its most connected genes were related with mitochondrial pathways. Overall, this work successfully identified relevant muscle gene networks and modules linked with FA composition, providing further insights on how the physiology of the pigs influences FA composition.

Identification of several lncRNA-mRNA pairs associated with marbling trait between Nanyang and Angus cattle

BACKGROUND

The marbling trait of cattle muscles, being a key indicator, played an important role in evaluating beef quality. Two breeds of cattle, namely a high-marbling (Angus) and a low-marbling (Nanyang) one, with their cattle muscles selected as our samples for transcriptome sequencing, were aimed to identify differentially expressed long non-coding RNAs (lncRNAs) and their targets associated with the marbling trait.

RESULTS

Transcriptome sequencing identified 487 and 283 differentially expressed mRNAs and lncRNAs respectively between the high-marbling (Angus) and low-marbling (Nanyang) cattle muscles. Twenty-seven pairs of differentially expressed lncRNAs-mRNAs, including eighteen lncRNAs and eleven target genes, were found to be involved in fat deposition and lipid metabolism. We established a positive correlation between fourteen up-regulated (NONBTAT000849.2, MSTRG.9591.1, NONBTAT031089.1, MSTRG.3720.1, NONBTAT029718.1, NONBTAT004228.2, NONBTAT007494.2, NONBTAT011094.2, NONBTAT015080.2, NONBTAT030943.1, NONBTAT021005.2, NONBTAT021004.2, NONBTAT025985.2, and NONBTAT023845.2) and four down-regulated (NONBTAT000850.2, MSTRG.22188.3, MSTRG.22188.4, and MSTRG.22188.5) lncRNAs and eleven genes related to adiponectin family protein (ADIPOQ), cytochrome P450 family (CYP4V2), 3-hydroxyacyl-CoA dehydratase family (HACD4), kinesin family (KIF5C), lipin family (LPIN2), perilipin family (PLIN1), prostaglandin family (PTGIS), solute carrier family (SLC16A7, SLC2213, and SLCO4C1), and containing a transmembrane domain protein family (VSTM1).

CONCLUSIONS

These candidate genes and lncRNAs can be regarded as being responsible for regulating the marbling trait of cattle. lncRNAs along with the variations in intramuscular fat marbling established a foundation for elucidating the genetic basis of high marbling in cattle.

Key co-expressed genes correlated with blood serum parameters of pigs fed with different fatty acid profile diets

This study investigated how gene expression is affected by dietary fatty acids (FA) by using pigs as a reliable model for studying human diseases that involve lipid metabolism. This includes changes in FA composition in the liver, blood serum parameters and overall metabolic pathways. RNA-Seq data from 32 pigs were analyzed using Weighted Gene Co-expression Network Analysis (WGCNA). Our aim was to identify changes in blood serum parameters and gene expression between diets containing 3% soybean oil (SOY3.0) and a standard pig production diet containing 1.5% soybean oil (SOY1.5). Significantly, both the SOY1.5 and SOY3.0 groups showed significant modules, with a higher number of co-expressed modules identified in the SOY3.0 group. Correlated modules and specific features were identified, including enriched terms and pathways such as the histone acetyltransferase complex, type I diabetes mellitus pathway, cholesterol metabolism, and metabolic pathways in SOY1.5, and pathways related to neurodegeneration and Alzheimer's disease in SOY3.0. The variation in co-expression observed for HDL in the groups analyzed suggests different regulatory patterns in response to the higher concentration of soybean oil. Key genes co-expressed with metabolic processes indicative of diseases such as Alzheimer's was also identified, as well as genes related to lipid transport and energy metabolism, including CCL5, PNISR, DEGS1. These findings are important for understanding the genetic and metabolic responses to dietary variation and contribute to the development of more precise nutritional strategies.

RNA-Seq Reveals Pathways Responsible for Meat Quality Characteristic Differences between Two Yunnan Indigenous Chicken Breeds and Commercial Broilers

Poultry is a source of meat that is in great demand in the world. The quality of meat is an imperative point for shoppers. To explore the genes controlling meat quality characteristics, the growth and meat quality traits and muscle transcriptome of two indigenous Yunnan chicken breeds, Wuding chickens (WDs) and Daweishan mini chickens (MCs), were compared with Cobb broilers (CBs). The growth and meat quality characteristics of these two indigenous breeds were found to differ from CB. In particular, the crude fat (CF), inosine monophosphate content, amino acid (AA), and total fatty acid (TFA) content of WDs were significantly higher than those of CBs and MCs. In addition, it was found that MC pectoralis had 420 differentially expressed genes (DEGs) relative to CBs, and WDs had 217 DEGs relative to CBs. Among them, 105 DEGs were shared. The results of 10 selected genes were also confirmed by qPCR. The differentially expressed genes were six enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) biological pathways including lysosomes, phagosomes, PPAR signaling pathways, cell adhesion molecules, cytokine-cytokine receptor interaction, and phagosome sphingolipid metabolism. Interestingly, four genes (LPL, GK, SCD, and FABP7) in the PPAR signal pathway related to fatty acid (FA) metabolism were elevated in WD muscles, which may account for higher CF, inosine monophosphate content, and AA and FA contents, key factors affecting meat quality. This work laid the foundation for improving the meat quality of Yunnan indigenous chickens, especially WD. In future molecular breeding, the genes in this study can be used as molecular screening markers and applied to the molecular breeding of chicken quality characteristics.

Effects of sex on meat quality traits, amino acid and fatty acid compositions, and plasma metabolome profiles in White King squabs

The objective of this study was to investigate the effects of sex on meat quality and the composition of amino and fatty acids in the breast muscles of White King pigeon squabs. Untargeted metabolomics was also conducted to distinguish the metabolic composition of plasma in different sexes. Compared with male squabs, female squabs had greater intramuscular fat (IMF) deposition and lower myofiber diameter and hydroxyproline content, leading to a lower shear force. Female squabs also had higher monounsaturated fatty acid and lower n-6 and n-3 polyunsaturated fatty acid proportions in the breast muscle, and had greater lipogenesis capacity via upregulation of PPARγ, FAS and LPL gene expression. Moreover, female squabs had lower inosine 5'-monophosphate, essential, free and sweet-tasting amino acid contents. Furthermore, Spearman's correlations between the differential plasma metabolites and key meat parameters were assessed, and putrescine, N-acetylglutamic acid, phophatidylcholine (18:0/P-16:0) and trimethylamine N-oxide were found to contribute to meat quality. In summary, the breast meat of male squabs may have better nutritional value than that of females, but it may inferior in terms of sensory properties, which can be attributed to the lower IMF content and higher shear force value. Our findings enhance our understanding of sex variation in squab meat quality, providing a basis for future research on pigeon breeding.

Identification of candidate regulatory genes for intramuscular fatty acid composition in pigs by transcriptome analysis

BACKGROUND

Intramuscular fat (IMF) content and its fatty acid (FA) composition are typically controlled by several genes, each with a small effect. In the current study, to pinpoint candidate genes and putative regulators involved in FA composition, we performed a multivariate integrative analysis between intramuscular FA and transcriptome profiles of porcine longissimus dorsi (LD) muscle. We also carried out a combination of network, regulatory impact factor (RIF), in silico prediction of putative target genes, and functional analyses to better support the biological relevance of our findings.

RESULTS

For this purpose, we used LD RNA-Seq and intramuscular FA composition profiles of 129 Iberian × Duroc backcrossed pigs. We identified 378 correlated variables (13 FA and 365 genes), including six FA (C20:4n-6, C18:2n-6, C20:3n-6, C18:1n-9, C18:0, and C16:1n-7) that were among the most interconnected variables in the predicted network. The detected FA-correlated genes include genes involved in lipid and/or carbohydrate metabolism or in regulation of IMF deposition (e.g., ADIPOQ, CHUK, CYCS, CYP4B1, DLD, ELOVL6, FBP1, G0S2, GCLC, HMGCR, IDH3A, LEP, LGALS12, LPIN1, PLIN1, PNPLA8, PPP1R1B, SDR16C5, SFRP5, SOD3, SNW1, and TFRC), meat quality (GALNT15, GOT1, MDH1, NEU3, PDHA1, SDHD, and UNC93A), and transport (e.g., EXOC7 and SLC44A2). Functional analysis highlighted 54 over-represented gene ontology terms, including well-known biological processes and pathways that regulate lipid and carbohydrate metabolism. RIF analysis suggested a pivotal role for six transcription factors (CARHSP1, LBX1, MAFA, PAX7, SIX5, and TADA2A) as putative regulators of gene expression and intramuscular FA composition. Based on in silico prediction, we identified putative target genes for these six regulators. Among these, TADA2A and CARHSP1 had extreme RIF scores and present novel regulators in pigs. In addition, the expression of TADA2A correlated (either positively or negatively) with C20:4n-6, C18:2n-6, C20:3n-6, C18:1n-9, and that of CARHSP1 correlated (positively) with the C16:1n-7 lipokine. We also found that these two transcription factors share target genes that are involved in lipid metabolism (e.g., GOT1, PLIN1, and TFRC).

CONCLUSIONS

This integrative analysis of muscle transcriptome and intramuscular FA profile revealed valuable information about key candidate genes and potential regulators for FA and lipid metabolism in pigs, among which some transcription factors are proposed to control gene expression and modulate FA composition differences.

A transcriptomic analysis of skeletal muscle tissues reveals promising candidate genes and pathways accountable for different daily weight gain in Hanwoo cattle

Cattle traits like average daily weight gain (ADG) greatly impact profitability. Selecting based on ADG considering genetic variability can lead to economic and genetic advancements in cattle breeding. This study aimed to unravel genetic influences on ADG variation in Hanwoo cattle at the skeletal muscle transcriptomic level. RNA sequencing was conducted on longissimus dorsi (LD), semimembranosus (SB), and psoas major (PM) muscles of 14 steers assigned to same feed, grouped by low (≤ 0.71 kg) and high (≥ 0.77 kg) ADG. At P ≤ 0.05 and log2fold > 1.5, the distinct pattern of gene expression was identified with 184, 172, and 210 differentially expressed genes in LD, SB, and PM muscles, respectively. Tissue-specific responses to ADG variation were evident, with myogenesis and differentiation associated JAK-STAT signaling pathway and prolactin signaling pathways enriched in LD and SB muscles, while adipogenesis-related PPAR signaling pathways were enriched in PM muscle. Key hub genes (AXIN2, CDKN1A, MYC, PTGS2, FZD5, SPP1) were upregulated and functionally significant in muscle growth and differentiation. Notably, DPP6, CDKN1A, and FZD5 emerged as possible candidate genes linked to ADG variation. These findings enhance our understanding of genetic factors behind ADG variation in Hanwoo cattle, illuminating skeletal muscle mechanisms influencing ADG.

Characteristics of Transcriptome and Metabolome Concerning Intramuscular Fat Content in Beijing Black Pigs

To study the characteristics of genes and metabolites related to intramuscular fat (IMF) content with less influence by breed background and individual differences, the skeletal muscle samples from 40 Beijing black pigs with either high or low IMF content were used to perform transcriptome and metabolome analyses. About 99 genes (twofold-change) were differentially expressed. Up-regulated genes in the high IMF pigs were mainly related to fat metabolism. The key genes in charge of IMF deposition are ADIPOQ, CIDEC, CYP4B1, DGAT2, LEP, OPRL1, PLIN1, SCD, and THRSP. KLHL40, TRAFD1, and HSPA6 were novel candidate genes for the IMF trait due to their high abundances. In the low IMF pigs, the differentially expressed genes involved in virus resistance were up-regulated. About 16 and 18 differential metabolites (1.5 fold-change) were obtained in the positive and negative modes, respectively. Pigs with low IMF had weaker fatty acid oxidation due to the down-regulation of various carnitines. Differentially expressed genes were more important in determining IMF deposition than differential metabolites because relatively few differential metabolites were obtained, and they were merely the products under the physiological status of diverged IMF content. This study provided valuable information for further studies on IMF deposition.

Transcriptome profile of skeletal muscle using different sources of dietary fatty acids in male pigs

Pork is of great importance in world trade and represents the largest source of fatty acids in the human diet. Lipid sources such as soybean oil (SOY), canola (CO), and fish oil (FO) are used in pig diets and influence blood parameters and the ratio of deposited fatty acids. In this study, the main objective was to evaluate changes in gene expression in porcine skeletal muscle tissue resulting from the dietary oil sources and to identify metabolic pathways and biological process networks through RNA-Seq. The addition of FO in the diet of pigs led to intramuscular lipid with a higher FA profile composition of C20:5 n-3, C22:6 n-3, and SFA (C16:0 and C18:0). Blood parameters for the FO group showed lower cholesterol and HDL content compared with CO and SOY groups. Skeletal muscle transcriptome analyses revealed 65 differentially expressed genes (DEG, FDR 10%) between CO vs SOY, and 32 DEG for CO vs FO, and 531 DEG for SOY vs FO comparison. Several genes, including AZGP1, PDE3B, APOE, PLIN1, and LIPS, were found to be down-regulated in the diet of the SOY group compared to the FO group. The enrichment analysis revealed DEG involved in lipid metabolism, metabolic diseases, and inflammation between the oil groups, with specific gene functions in each group and altered blood parameters. The results provide mechanisms to help us understand the behavior of genes according to fatty acids.

Global analysis of the association between pig muscle fatty acid composition and gene expression using RNA-Seq

Fatty acids (FAs) play an essential role as mediators of cell signaling and signal transduction, affecting metabolic homeostasis and determining meat quality in pigs. However, FAs are transformed by the action of several genes, such as those encoding desaturases and elongases of FAs in lipogenic tissues. The aim of the current work was to identify candidate genes, biological processes, and pathways involved in the modulation of intramuscular FA profile from longissimus dorsi muscle. FA profile by gas chromatography of methyl esters and gene expression by RNA-Seq were determined in 129 Iberian × Duroc backcrossed pigs. An association analysis between the muscle transcriptome and its FA profile was performed, followed by a concordance and functional analysis. Overall, a list of well-known (e.g., PLIN1, LEP, ELOVL6, SC5D, NCOA2, ACSL1, MDH1, LPL, LGALS12, TFRC, GOT1, and FBP1) and novel (e.g., TRARG1, TANK, ENSSSCG00000011196, and ENSSSCG00000038429) candidate genes was identified, either in association with specific or several FA traits. Likewise, several of these genes belong to biological processes and pathways linked to energy, lipid, and carbohydrate metabolism, which seem determinants in the modulation of FA compositions. This study can contribute to elucidate the complex relationship between gene expression and FA profile in pig muscle.

Integrative methylome and transcriptome analysis of porcine abdominal fat indicates changes in fat metabolism and immune responses during different development

Fat is involved in synthesizing fatty acids (FAs), FA circulation, and lipid metabolism. Various genetic studies have been conducted on porcine fat but understanding the growth and specific adipose tissue is insufficient. The purpose of this study is to investigate the epigenetic difference in abdominal fat according to the growth of porcine. The samples were collected from the porcine abdominal fat of different developmental stages (10 and 26 weeks of age). Then, the samples were sequenced using MBD-seq and RNA-seq for profiling DNA methylation and RNA expression. In 26 weeks of age pigs, differentially methylated genes (DMGs) and differentially expressed genes (DEGs) were identified as 2,251 and 5,768, compared with 10 weeks of age pigs, respectively. Gene functional analysis was performed using GO and KEGG databases. In functional analysis results of DMGs and DEGs, immune responses such as chemokine signaling pathways, B cell receptor signaling pathways, and lipid metabolism terms such as PPAR signaling pathways and fatty acid degradation were identified. It is thought that there is an influence between DNA methylation and gene expression through changes in genes with similar functions. The effects of DNA methylation on gene expression were investigated using cis-regulation and trans-regulation analysis to integrate and interpret different molecular layers. In the cis-regulation analysis using 629 overlapping genes between DEGs and DMGs, immune response functions were identified, while in trans-regulation analysis through the TF-target gene network, the co-expression network of lipid metabolism-related functions was distinguished. Our research provides an understanding of the underlying mechanisms for epigenetic regulation in porcine abdominal fat with aging.

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.

The mRNA Expression Profile of Psoriatic Lesion Distinct from Non-Lesion

Purpose

Psoriasis is a chronic recurring autoimmune skin disease with a complex etiology and chronic progression; however, its molecular mechanisms remain unclear.

Patients and Methods

We performed transcriptomic analysis to profile the mRNA expression of psoriatic lesions (PL) and non-lesion (NL) tissues from psoriasis patients along with normal skin from healthy donors. RT-qPCR was used to validate the mRNA expression profiles.

Results

A total of 237 differentially expressed genes were screened and identified by RNA sequencing. GO and KEGG analysis indicated that these DEGs were enriched in the PPAR signaling pathway and intermediate filament cytoskeleton. For PPAR signaling pathway, the expression of five genes, including ADIPOQ, AQP7, PLIN1, FABP4 and LPL, were all significantly decreased in psoriatic lesions compared to normal skin by RT-qPCR. There is a clear difference between psoriatic lesions and non-lesion in the expression of ADIPOQ, AQP7 and LPL. For intermediate filament cytoskeleton, including KRT27, KRT25, KRT71, KRT86 and KRT85 were significantly decreased in the psoriasis lesions, showing agreement with the RNA-seq data.

Conclusion

This study revealed a significant difference between the mRNA expression profiles of PL, NL tissue and normal skin.

Effects of Fatty-Type and Lean-Type on Growth Performance and Lipid Droplet Metabolism in Pekin Ducks

Simple Summary

Lipid deposition in animals is closely related to lipid anabolism. In order to further explore how differences in different metabolic types regulate lipid deposition, we compared the growth performance and lipid droplet metabolism of fatty-type ducks and lean-type ducks. The results showed that fatty-type ducks showed a faster growth rate and more fat deposition in the early growth stage after feeding the same diet, and produced more lipoproteins in serum and deposited in adipose tissue. However, fewer triglycerides accumulated in the liver. We believe that this performance of fatty-type ducks is caused by the increased expression level of lipid droplet-related genes.

Abstract

The reasons for differences in lipid depositions between fatty-type (F-T) and lean-type (L-T) ducks remain unknown. The present study aimed to compare the growth performance, lipid deposition, and gene expression related to lipid droplet formation in F-T and L-T Pekin ducks. One-day-old, 140 each L-T and F-T male ducks were selected and distributed separately into 20 replicate cages. All ducks were fed commercial diets up to 35 d of age. F-T ducks had a higher average daily gain from 21 to 28 d of age. On 35-day-old, F-T ducks had higher serum levels of high- and low-density lipoprotein cholesterol, cholesterol, albumin, and hydroxybutyrate dehydrogenase activity than L-T ducks. F-T ducks had higher abdominal fat and subcutaneous fat percentages than those in L-T ducks. Liver histological examination showed that L-T ducks contained more lipid droplets in the liver, which gradually decreased with increasing age. The average adipocyte area and diameter of abdominal fat and subcutaneous fat in the F-T and L-T ducks increased with age and were higher in F-T ducks than those in L-T ducks. Furthermore, the gene expression of perilipin 1, perilipin 2, angiopoietin-like protein 4, adipose triglyceride lipase, alpha/beta-hydrolase domain-containing protein 5 (ABHD5), and serine/threonine kinase 17a in the liver, abdominal fat, and subcutaneous fat of F-T ducks was higher than that in L-T ducks, and it increased with age. Compared to L-T ducks, F-T ducks had higher expression of ABHD5 in the abdominal fat and subcutaneous fat and lower expression in the liver. Thus, F-T ducks displayed lower hepatic lipid deposition and a higher percentage of abdominal fat and subcutaneous fat, suggesting that F-T ducks had higher lipid storage capacity due to increased gene expression related to lipid droplets.

Effects of intramuscular fat on meat quality and its regulation mechanism in Tan sheep

Intramuscular fat (IMF) contributes importantly to various aspects of meat quality, and genetic regulation is an effective pathway to improve IMF deposition in sheep. In this study, we systematically explored the effect of IMF content on meat quality in Tan sheep and investigated the regulatory mechanism of flavor precursors metabolism and IMF deposition. The results revealed that IMF significantly affected meat color, total muscle fiber numbers, and muscle fiber types in Tan sheep. Widely-targeted metabolomic analysis showed that amino acids were the main differential flavor precursors between lambs with different IMF content. Importantly, the comparison of fatty acid profiles revealed that saturated fatty acids and monounsaturated fatty acids are beneficial for IMF deposition. Furthermore, integrated analysis between metabolome and transcriptome indicated that MME is a key gene resulting in the reduction of amino acids in lambs with high IMF content; and the joint analysis between fatty acid profiles and transcript profiles showed that ADIPOQ, FABP4, PLIN1, PPARGC1A, SLC2A1 accelerated IMF deposition through positive regulation of saturated fatty acids and monounsaturated fatty acids metabolism. These results revealed key changes in meat quality affected by IMF content and the corresponding genetic mechanism, which may provide a new insight for understanding the IMF differential deposition and for improving meat quality in Tan sheep.

Comparative analysis of differentially abundant proteins between high and low intramuscular fat content groups in donkeys

Intramuscular fat (IMF) is an important regulator that determines meat quality, and its content is closely related to flavor, tenderness, and juiciness. Many studies have used quantitative proteomic analysis to identify proteins associated with meat quality traits in livestock, however, the potential candidate proteins that influence IMF in donkey muscle are not fully understood. In this study, we performed quantitative proteomic analysis, with tandem-mass-tagged (TMT) labeling, with samples from the longissimus dorsi (LD) muscle of the donkey. A total of 585,555 spectra were identified from the six muscle samples used in this study. In total, 20,583 peptides were detected, including 15,279 unique peptides, and 2,540 proteins were identified. We analyzed differentially abundant proteins (DAPs) between LD muscles of donkeys with high (H) and low (L) IMF content. We identified 30 DAPs between the H and L IMF content groups, of which 17 were upregulated and 13 downregulated in the H IMF group. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analysis of these DAPs revealed many GO terms (e.g., bone morphogenetic protein (BMP) receptor binding) and pathways (e.g., Wnt signaling pathway and Hippo signaling pathway) involved in lipid metabolism and adipogenesis. The construction of protein-protein interaction networks identified 16 DAPs involved in these networks. Our data provide a basis for future investigations into candidate proteins involved in IMF deposition and potential new approaches to improve meat quality in the donkey.

Comprehensive Analysis of Differentially Expressed mRNAs, lncRNAs and circRNAs Related to Intramuscular Fat Deposition in Laiwu Pigs

Long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) are important classes of small noncoding RNAs that can regulate numerous biological processes. To understand the role of message RNA (mRNAs, lncRNAs and circRNAs) in the regulation of intramuscular fat (IMF) deposition, in this study the expression profiles of longissimus dorsi (LD) muscle from six Laiwu pigs (three with extremely high and three with extremely low IMF content) were sequenced based on rRNA-depleted library construction. In total, 323 differentially expressed protein-coding genes (DEGs), 180 lncRNAs (DELs) and 105 circRNAs (DECs) were detected between the high IMF and low IMF groups. Functional analysis indicated that most DEGs, and some target genes of DELs, were enriched into GO terms and pathways related to adipogenesis, suggesting their important roles in regulating IMF deposition. In addition, 12 DELs were observed to exhibit a positive relationship with stearoyl-CoA desaturase (SCD), phosphoenolpyruvate carboxykinase 1 (PCK1), and adiponectin (ADIPOQ), suggesting they are highly likely to be the target genes of DELs. Finally, we constructed a source gene-circRNA-miRNA connective network, and some of miRNA of the network have been reported to affect lipid metabolism or adipogenesis. Overall, this work provides a valuable resource for further research and helps to understand the potential functions of lncRNAs and circRNAs in IMF deposition.

The effect of the PLIN1 gene on the metabolism and mitochondria of porcine skeletal muscle satellite cells

BACKGROUND

Perilipin 1 (PLIN1) is a lipid droplet scaffolding protein that plays a regulatory role in fat decomposition and mitochondrial function.

OBJECTIVE

In this study, the effects of PLIN1 gene knockout (PLIN1-KO) and PLIN1 gene overexpression (PLIN1-EX) on cell metabolism and mitochondrial function in porcine skeletal muscle satellite cells were assessed.

METHODS

Porcine skeletal muscle satellite cells were used as the control group (NC). The expression of mitochondrial function-related proteins was detected by western blot. Apoptosis, cell cycle, mitochondrial function-related indices, mitochondrial structure, and morphology were measured by flow cytometry.

RESULTS

Our results demonstrated that stable expression of the PLIN1 gene in skeletal muscle satellite cells is critical to maintaining cell metabolism and mitochondrial function. After knockout and overexpression of the PLIN1 gene, the anti-apoptotic ability of cells was enhanced, and the metabolic activity of the cells was accelerated, but at the cost of mitochondrial structural damage, reduction in the number of mitochondria, and decreased mitochondrial function.

CONCLUSION

This study explored the effect of the PLIN1 gene on the mitochondria and metabolism of porcine skeletal muscle satellite cells and provided a theoretical basis for the subsequent study of the effects of PLIN1 on muscle tissue development and meat quality.

Circular RNA Profiling Identifies Novel circPPARA that Promotes Intramuscular Fat Deposition in Pigs

Intramuscular fat (IMF) content plays an important role in pork quality. Circular RNAs (circRNAs) implicate various biological processes; however, the regulatory mechanisms and functions of circRNAs in porcine IMF remains elusive. Hence, the study assessed the circRNA expression profiling in the longissimus dorsi muscle of pigs with high (H) and low (L) IMF content to unravel their regulatory functions in improving meat quality. The RNA sequencing analysis identified 29,732 circRNAs from six sampled pigs, most of which were exon-derived. In the muscle, 336 were differentially expressed (DE) between the H and L IMF groups; 196 circRNAs were upregulated, and 140 were downregulated. Subsequent qRT-PCR validation of 10 DE circRNAs revealed expression patterns consistent with the RNA-seq data. Gene ontology and KEGG enrichment analysis revealed that most significantly enriched DE circRNAs' host genes were linked to lipid metabolism and adipogenesis processes. The circRNA-miRNA regulatory network analysis found several circRNAs targeting miRNAs associated with adipogenesis. Finally, a novel circRNA, circPPARA, was identified with the expression positively correlated with the IMF content. Detailed analysis revealed that circPPARA was formed via head-to-tail splicing and was more stable than the linear PPARA, predominantly located in the cytoplasm. Functional studies using overexpression and siRNA constructs demonstrated that circPPARA promotes differentiation and hinders the proliferation of porcine intramuscular preadipocytes. Moreover, the dual-luciferase assay revealed that circPPARA adsorbed miR-429 and miR-200b, thereby promoting intramuscular adipogenesis in pigs. Our results identified a candidate circRNA, circPPARA, that affects porcine IMF content. The study provides knowledge of the regulatory functions of circRNAs in intramuscular adipogenesis and abundant resource for future research on circRNAs in pigs.

Differential Proteomic Identification and Bioinformatics Analysis of Femoral Neck in Elderly Female Patients with Hyperuricaemia

Background::

Serum uric acid (UA) is positively correlated with bone mineral density (BMD). However, the mechanism by which serum UA affects BMD remains unclear.

Objective::

The aim was carried out to search for the functional proteins related to serum UA and femoral neck BMD to better understand the pathophysiological mechanism of osteoporosis.

Materials and methods::

In this study, patients in the UA group (hyperuricaemia combined with femoral neck fracture) and the control group (normal uricaemia combined with femoral neck fracture) were selected according to the inclusion criteria. Total protein was extracted from the femoral neck of each patient. Fluorescence differential gel electrophoresis was used to separate the total proteins, and the differentially expressed protein spots were detected by image analysis. After enzyme digestion, peptide mass fingerprinting and database searches were performed to identify the differentially expressed proteins. DAVID software and Kyoto Encyclopedia of Genes and Genomes (KEGG) data were used for enrichment analysis of the screened differential proteins.

Results::

After mass spectrometry and database searching, 66 differentially expressed protein spots were identified between the UA group and the control group. Most differentially expressed proteins functioned in cytoskeleton formation, energy metabolism, or signal transduction. They were mainly involved in 50 biological processes, including peroxisome proliferator-activated receptor (PPAR) signalling and fatty acid metabolism. PPARγ and PLIN1 were subject to Western blotting analysis detection; results were consistent with the Label-Free result.

Conclusion::

Based on an analysis of the biological information, these proteins may be associated with the incidence and progression of the femoral neck bone tissues of hyperuricaemia patients.

Epididymal mRNA and miRNA transcriptome analyses reveal important genes and miRNAs related to sperm motility in roosters

Sperm motility is a crucial trait in chicken production, and the epididymis is an essential organ in the reproductive system. Currently, the molecular mechanisms underlying sperm motility in the epididymis are unclear. In this study, 8 cDNA libraries and eight miRNA libraries were constructed from roosters (4 chickens per group) with diverse sperm motility. After a comparative analysis of epididymal transcriptomes, we detected 84 differentially expressed genes (DEGs) using the edgeR package. Integrated interpretation of DEGs indicated that MMP9, SLN, WT1, PLIN1, and LRRIQ1 are the most promising candidate genes affecting sperm motility in the epididymis of roosters. MiR-146a, mir-135b, and mir-205 could play important regulatory roles in sperm maturation, capacitation, and motility. Additionally, a comprehensive analysis of the mRNA and miRNAs transcriptomes in silico identified a promising gene-miRNA pair miR-135b-HPS5, which may be a vital regulator of sperm motility in the epididymis. Our findings provide novel integrated information of miRNAs and genes that shed light on the regulatory mechanisms of fertility in roosters.

Genome-wide association study reveals a quantitative trait locus and two candidate genes on Sus scrofa chromosome 5 affecting intramuscular fat content in Suhuai pigs

Intramuscular fat content (IFC) is an essential quantitative trait of meat, affecting multiple meat quality indicators. A certain amount of IFC could not only improve the sensory score of pork but also increase the flavour, tenderness, juiciness and shelf-life. To dissect the genetic determinants of IFC, two methods, including genome-wide efficient mixed-model analysis (GEMMA) and linkage disequilibrium adjusted kinships (LDAKs), were used to carry out genome-wide association studies for IFC in Suhuai pig population. A total of 14 and 18 significant single nucleotide polymorphisms (SNPs) were identified by GEMMA and LDAK, respectively. The results of these two methods were highly consistent and all 14 significant SNPs in GEMMA were detected by LDAK. Seven of the 18 SNPs reached the genome-wide significance level (P < 9.85E-07) while 11 cases reached the suggestive significance level (P < 1.77E-05). These significant SNPs were mainly distributed on Sus scrofa chromosome (SSC) 5, 3, and 7. Moreover, one locus resides in a 2.27 Mb (71.37-73.64 Mb) region on SSC5 harbouring 13 significant SNPs associated with IFC, and the lead SNP (rs81302978) also locates in this region. Linkage disequilibrium (LD) analysis showed that there were four pairs of complete LD (r² = 1) among these 13 SNPs, and the remaining 9 SNPs with incomplete LD (r² ≠ 1) were selected for subsequent analyses of IFC. Association analyses showed that 7 out of 9 SNPs were significantly associated with IFC (P < 0.05) in 330 Suhuai pigs, and the other 2 SNPs tended to reach a significant association level with IFC (P < 0.1). The phenotypic variance explained (PVE) range of these 9 SNPs was 0.92-3.55%. Meanwhile, the lead SNP was also significantly associated (rs81302978) with IFC (P < 0.05) in 378 commercial hybrid pigs (Pietrain × Duroc) × (Landrace × Yorkshire) (PDLY), and the PVE was 1.38%. Besides, two lipid metabolism-relevant candidate genes, the leucine rich repeat kinase 2 (LRRK2) and PDZ domain containing ring finger 4 (PDZRN4) were identified in the 2.27 Mb region on SSC5. In conclusion, our results may provide a set of markers useful for genetic improvement of IFC in pigs and will advance the genome selection process of IFC on pig breeding programmes.

Distinct Roles of Perilipins in the Intramuscular Deposition of Lipids in Glutamine-Supplemented, Low-, and Normal-Birth-Weight Piglets

Piglets with low birth weight (LBW) usually have reduced muscle mass and increased lipid deposition compared with their normal-birth-weight (NBW) littermates. Supplementation of piglets with amino acids during the first days of life may improve muscle growth and simultaneously alter the intramuscular lipid deposition. The aim of the current study was to investigate the influence of glutamine (Gln) supplementation during the early suckling period on lipid deposition in the longissimus muscle (MLD) and the role of different perilipin (PLIN) family members in this process. Four groups were generated consisting of 72 male LBW piglets and 72 NBW littermates. Piglets were supplemented with either 1 g Gln/kg body weight or an isonitrogenous amount of alanine (Ala) between days post natum (dpn) 1 and 12. Twelve piglets per group were slaughtered at 5, 12, and 26 dpn, and muscle tissue was collected. Perilipins were localized by immunohistochemistry in muscle sections. The mRNA and protein abundances of PLIN family members and related lipases were quantified by quantitative RT-PCR (qPCR) and western blots, respectively. While PLIN1 was localized around lipid droplets in mature and developing adipocytes, PLIN2 was localized at intramyocellular lipid droplets, PLIN3 and 4 at cell membranes of muscle fibers and adipocytes, and PLIN5 in the cytoplasm of undefined cells. The western blot results indicated higher protein abundances of PLIN2, 3, 4, and 5 in LBW piglets (p < 0.05) at 5 dpn compared with their NBW littermates independent of supplementation, while not directly reflecting the mRNA expression levels. The mRNA abundance of PLIN2 was lower while PLIN4 was higher in piglets at 26 dpn in comparison with piglets at 5 dpn (p < 0.01). Relative mRNA expression of LPL and CGI-58 was lowest in piglets at 5 dpn (p < 0.001). However, ATGL mRNA was not influenced by birth weight or supplementation, but the Spearman correlation coefficient analysis revealed close correlations with PLIN2, 4, and 5 mRNA at 5 and 26 dpn (r > 0.5, p < 0.001). The results indicated the importance of birth weight and age for intramuscular lipid deposition and different roles of PLIN family members in this process, but no clear modulating effect of Gln supplementation.

Proteomic and lipidomic analyses reveal saturated fatty acids, phosphatidylinositol, phosphatidylserine, and associated proteins contributing to intramuscular fat deposition

Intramuscular fat (IMF) content is an important factor in porcine meat quality. Previous studies have screened multiple candidate genes related to IMF deposition, but the lipids that affect IMF deposition and their lipid-protein network remain unknown. In this study, we performed proteomic and lipidomic analyses of the longissimus dorsi (LD) muscle from high-IMF (IMFH) and low-IMF (IMF-L) groups of Xidu black pigs. Eighty-eight proteins and 143 lipids were differentially abundant between the groups. The differentially abundant proteins were found to be involved in cholesterol metabolism, the PPAR signaling pathway, and ferroptosis. The triacylglycerols (TAGs) upregulated in the IMF-H group were mainly shown to be synthesized by saturated fatty acids (SFAs), while the downregulated TAGs were mainly synthesized by polyunsaturated fatty acids (PUFAs). All differentially abundant phosphatidylinositols (PIs) and phosphatidylserines (PSs) were found to be upregulated in the IMF-H group. A correlation analysis of the proteomic and lipidomic revealed candidate proteins (APOA4, VDAC3, PRNP, CTSB, GSPT1) related to TAG, PI, and PS lipids. These results revealed differences in proteins and lipids between the IMF-H and IMF-L groups, which represent new candidate proteins and lipids that should be investigated to determine the molecular mechanisms controlling IMF deposition in pigs. SIGNIFICANCE: Intramuscular fat (IMF) is a key factor affecting meat quality, and meat with a higher IMF content can have a better flavor. In this study, proteomic results show that the ferroptosis pathway, including the PRNP, VDAC3 and CP proteins, affects IMF deposition. Lipid composition is the key factor affecting IMF deposition, but there are few reports on this. In this study, through lipidomic analysis, we suggest that saturated fatty acid (SFA), phosphatidylinositol (PI), and phosphatidylserine (PS) may contribute to IMF deposition. A correlation analysis reveals the potential regulatory network between lipids and proteins. This study clarifies the difference in protein and lipid compositions in longissimus dorsi (LD) muscle with high and low IMF contents. This information suggests that it would be beneficial to increase the intramuscular fat content of pork not only from a genetic perspective but also from a nutritional perspective.

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

Subcutaneous fat (SCF) and intramuscular fat (IMF) deposition is relevant to health in humans, as well as meat production and quality in pigs. In this study, we generated RNA sequence data for 122 SCF, 120 IMF, and 87 longissimus dorsi muscle (LDM) samples using 155 F₆ pigs from a specially designed heterogeneous population generated by intercrossing four highly selected European commercial breeds and four indigenous Chinese pig breeds. The phenotypes including waist back fat thickness and intramuscular fat content were also measured in the 155 F₆ pigs. We found that the genes in SCF and IMF differed largely in both expression levels and network connectivity, and highlighted network modules that exhibited strongest gain of connectivity in SCF and IMF, containing genes that were associated with the immune process and DNA double-strand repair, respectively. We identified 215 SCF genes related to kinase inhibitor activity, mitochondrial fission, and angiogenesis, and 90 IMF genes related to lipolysis and fat cell differentiation, displayed a tissue-specific association with back fat thickness and IMF content, respectively. We found that cis-expression QTL for trait-associated genes in the two adipose tissues tended to have tissue-dependent predictability for the two adipose traits. Alternative splicing of genes was also found to be associated with SCF or IMF deposition, but the association was much less extensive than that based on expression levels. This study provides a better understanding of SCF and IMF gene transcription and network organization and identified critical genes and network modules that displayed tissue-specific associations with subcutaneous and intramuscular fat deposition. These features are helpful for designing breeding programs to genetically improve the two adipose traits in a balanced way.

Identification of Candidate Circular RNAs Underlying Intramuscular Fat Content in the Donkey

Intramuscular fat (IMF) content is a crucial indicator of meat quality. Circular RNAs (circRNAs) are a large class of endogenous RNAs that are involved in many physiological processes. However, the expression and function of circRNA in IMF in the donkey remains unresolved. Here we performed an expression profiling of circRNAs in the donkey longissimus dorsi muscle and identified 12,727 candidate circRNAs. Among these, 70% were derived from the exons of protein genes. Furthermore, a total of 127 differentially expressed (DE) circRNAs were identified in high (H) and low (L) IMF content groups, including 63 upregulated and 64 downregulated circRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the host genes of the DE circRNAs showed that the host genes were enriched in lipid metabolism related GO terms (e.g., fatty acid beta-oxidation using acyl-CoA dehydrogenase and MLL3/4 complex), and signaling pathways (e.g., TGF-beta and lysine degradation signaling pathway). Further analyses indicated that 127 DE circRNAs were predicted to potentially interact with miRNAs, leading to the construction of circRNA-miRNA regulatory network. Multiple circRNAs can potentially function as sponges of miRNAs that regulate the differentiation of adipocytes. Our results provide valuable expression profile information for circRNA in the donkey and new insight into the regulatory mechanisms of circRNAs in the regulation of IMF content.

Muscle Transcriptome Analysis Reveals Potential Candidate Genes and Pathways Affecting Intramuscular Fat Content in Pigs

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, |log2(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 protein-protein 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.

Transcriptome Profiling Associated with Carcass Quality of Loin Muscles in Crossbred Pigs

Carcass quality traits, such as lean depth and loin depth, are of extreme economic importance for the swine industry. This study aimed to identify the gene expression pattern related to carcass quality in crossbred pigs ((Landrace × Yorkshire) × Duroc). In total, 20 crossbred pigs were used in this study and they were divided into two groups (class I grade, n = 10; class II grade, n = 10) based on the carcass grades. Total RNA samples extracted from the loin muscles of both groups were submitted for RNA-seq. The quality assessment of the sequencing reads resulted in 25,458 unigenes and found 12,795 candidate coding unigenes with homology to other species after annotation. Differentially expressed gene (DEG) analysis of the two groups revealed 282 up-regulated and 189 down-regulated genes (p ≤ 0.01), linked to tissue development, striated muscle tissue development, tissue morphogenesis, and lipid metabolic process gene ontology (GO) terms. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis highlighted genes related to the calcium signaling pathway, melanogenesis, the sphingolipid signaling pathway, the apelin signaling pathway, and the mTOR signaling pathway. We constructed an expressed gene profile, which may serve as a resource for genomic studies focused on uncovering the molecular mechanisms underlying carcass quality in crossbred pigs.

Polymorphism of the PLIN1 gene and its association with body measures and ultrasound carcass traits in Qinchuan beef cattle

The PLIN1 gene produces a phosphorylated protein wrapped in lipid droplets in adipocytes. This phosphorylation assists the mobilization of fat into adipose tissue. The purpose of the experiment was to study the polymorphism of the PLIN1 gene and its relationship with the body and carcass characteristics of Qinchuan cattle to find molecular genetic markers that can be used for breeding. The expression level of the PLIN1 gene was determined in various tissues by qRT-PCR. The results showed that the highest level of PLN1 expression was found in subcutaneous fat, followed by the heart and longissimus muscle, and the lowest level was found in the kidney. Five SNP loci of the PLIN1 gene were identified in 510 Qinchuan cattle, including g.3580T>C (SNP1), g.3898G>A (SNP2), g.8333G>A (SNP3), g.10517T>C (SNP4), and g.10538G>T (SNP5). The results show that SNP1, SNP2, SNP3, and SNP4 were moderately polymorphic (0.25 < PIC < 0.5), while SNP5 was minimally polymorphic (PIC < 0.25). SNP2, SNP3, and SNP5 were within Hardy-Weinberg equilibrium (P > 0.05), but SNP1 and SNP4 were not (P < 0.05). Correlation analysis showed that the five SNPs of the PLIN1 gene were correlated with back-fat depth, intramuscular fat, and chest depth of Qinchuan cattle. The double haplotype H2H4 in Qinchuan beef was associated with body and carcass traits. We conclude that variants mapped within PLIN1 can be used in marker-assisted selection for carcass quality and body traits in breed improvement programs for Qinchuan cattle.

Muscle transcriptome analysis identifies genes involved in ciliogenesis and the molecular cascade associated with intramuscular fat content in Large White heavy pigs

Intramuscular fat content (IMF) is a complex trait influencing the technological and sensorial features of meat products and determining pork quality. Thus, we aimed at analyzing through RNA-sequencing the Semimembranosus muscle transcriptome of Italian Large White pigs to study the gene networks associated with IMF deposition. Two groups of samples were used; each one was composed of six unrelated pigs with extreme and divergent IMF content (0.67 ± 0.09% in low IMF vs. 6.81 ± 1.17% in high IMF groups) that were chosen from 950 purebred individuals. Paired-end RNA sequences were aligned to Sus scrofa genome assembly 11.1 and gene counts were analyzed using WGCNA and DeSeq2 packages in R environment. Interestingly, among the 58 differentially expressed genes (DEGs), several were related to primary cilia organelles (such as Lebercilin 5 gene), in addition to the genes involved in the regulation of cell differentiation, in the control of RNA-processing, and G-protein and ERK signaling pathways. Together with cilia-related genes, we also found in high IMF pigs an over-expression of the Fibroblast Growth Factor 2 (FGF2) gene, which in other animal species was found to be a regulator of ciliogenesis. Four WGCNA gene modules resulted significantly associated with IMF deposition: grey60 (P = 0.003), darkturquoise (P = 0.022), skyblue1 (P = 0.022), and lavenderblush3 (P = 0.030). The genes in the significant modules confirmed the results obtained for the DEGs, and the analysis with “cytoHubba” indicated genes controlling RNA splicing and cell differentiation as hub genes. Among the complex molecular processes affecting muscle fat depots, genes involved in primary cilia may have an important role, and the transcriptional reprogramming observed in high IMF pigs may be related to an FGF-related molecular cascade and to ciliogenesis, which in the literature have been associated with fibro-adipogenic precursor differentiation.

Transcriptomic comparison of liver tissue between Anqing six-end-white pigs and Yorkshire pigs based on RNA sequencing

Chinese indigenous pig and Western commercial pig breeds show different patterns of lipid metabolism, fat deposition, and fatty acid composition; for these reasons, they have become vitally important models of energy metabolism and obesity in humans. To compare the mechanisms underlying lipid metabolism between Yorkshire pigs (lean type) and Anqing six-end-white pigs (obese type), the liver transcriptomes of six castrated boars with a body weight of approximately 100 kg (three Yorkshire and three Anqing) were analyzed by RNA-seq. The total number of reads produced for each liver sample ranged from 47.05 to 62.6 million. Among 362 differentially expressed genes, 142 were up-regulated and 220 were down-regulated in Anqing six-end-white pigs. Based on these data, 79 GO terms were significantly enriched. The top 10 (the 10 with lowest corrected P-value) significantly enriched GO terms were identified, including lipid metabolic process and carboxylic acid metabolic process. Pathway analysis revealed three significantly enriched KEGG pathways including PPAR signaling pathway, steroid hormone biosynthesis, and retinol metabolism. Based on protein–protein interaction networks, multiple genes responsible for lipid metabolism were identified, such as PCK1, PPARA, and CYP7A1, and these were considered promising candidate genes that could affect porcine liver lipid metabolism and fat deposition. Our results provide abundant transcriptomic information that will be useful for animal breeding and biomedical research.

Impact of genotype, body weight and sex on the prenatal muscle transcriptome of Iberian pigs

Growth is dependent on genotype and diet, even at early developmental stages. In this study, we investigated the effects of genotype, sex, and body weight on the fetal muscle transcriptome of purebred Iberian and crossbred Iberian x Large White pigs sharing the same uterine environment. RNA sequencing was performed on 16 purebred and crossbred fetuses with high body weight (340±14g and 415±14g, respectively) and 16 with low body weight (246±14g and 311±14g, respectively), on gestational day 77. Genotype had the greatest effect on gene expression, with 645 genes identified as differentially expressed (DE) between purebred and crossbred animals. Functional analysis showed differential regulation of pathways involved in energy and lipid metabolism, muscle development, and tissue disorders. In purebred animals, fetal body weight was associated with 35 DE genes involved in development, lipid metabolism and adipogenesis. In crossbred animals, fetal body weight was associated with 60 DE genes involved in muscle development, viability, and immunity. Interestingly, the results suggested an interaction genotype*weight for some DE genes. Fetal sex had only a modest effect on gene expression. This study allowed the identification of genes, metabolic pathways, biological functions and regulators related to fetal genotype, weight and sex, in animals sharing the same uterine environment. Our findings contribute to a better understanding of the molecular events that influence prenatal muscle development and highlight the complex interactions affecting transcriptional regulation during development.

Effect of Divergent Selection for Intramuscular Fat Content on Muscle Lipid Metabolism in Chickens

Simple Summary

Intramuscular fat is an important factor affecting meat quality and consumer acceptance. Appropriate increases in the intramuscular fat content contribute to the improvement of meat quality, and genetic selection is an effective method to increase the intramuscular fat content in chickens. In this study, chicken lines divergently selected for their intramuscular fat content were used to investigate the mechanisms behind differential intramuscular fat deposition. These results found in this study may contribute to the improvement of meat quality in chickens.

Abstract

Intramuscular fat (IMF)—an important factor affecting meat quality—can be appropriately increased by genetic selection. Chicken lines divergently selected for IMF content were used in this study to investigate the mechanisms behind differential IMF deposition. Sixty 15th generation chickens were genotyped using the IASCHICK 55K single nucleotide polymorphism (SNP) chip. After quality control, 59 chickens and 36,893 SNPs were available for subsequent analysis. Population structure assessment indicated that the lines were genetically differentiated. Based on the top 1% paired fixation index values, three pathways were significantly (p < 0.05) enriched, and nine genes were considered candidate genes for differential IMF deposition. Differences between the lines in the expressions of representative genes involved in the above pathways were detected in 16th generation chickens. This study suggests that genetic selection for increased IMF in the pectoralis major muscle may enhance fatty acid synthesis, transport, and esterification, and reduce triglyceride hydrolysis. The peroxisome proliferator-activated receptor (PPAR) signaling pathway, glycerolipid metabolism, and fatty acid degradation pathway may have contributed to the differences in IMF deposition between the lines. These results contribute to the understanding of the genetic mechanisms behind IMF deposition, and the improvement of chicken meat quality.

Unraveling the action mechanism of polygonum cuspidatum by a network pharmacology approach

As a popular Chinese herbal medicine (CHM), polygonum cuspidatum is widely used to treat various diseases in China. However, its biological function and action mechanism have yet to be systematically explored. In the present study, we first identified 14 potential active ingredients of polygonum cuspidatum using the TCMSP server and then conducted an in silico target prediction for these ingredients using PharmMapper. The subsequent KEGG pathway enrichment analysis of the 57 identified potential targets revealed that they were closely associated with cancer and gynecological disorders. Furthermore, a protein-protein interaction network of these targets was constructed using STRING and Cytoscape, through which 11 core targets were excavated according to degree, a key topological parameter. Meanwhile, we developed a novel formula, in which the "R value" is determined by average shortest path length and closeness centrality, two other key topological parameters, to evaluate the reliability of these predicted core targets. Intriguingly, among the top 10 core targets excavated using this new formula, 7 overlapped with the former 11 core targets, showing a good consistency in these core targets between the different prediction algorithms. Next, 7 ingredients were identified/validated from the crude extract of polygonum cuspidatum using UPLC-MS/MS. Noteworthy, 6 potential targets predicted for these 7 ingredients overlapped with the 7 core targets excavated from the previous in silico analyses. Further molecular docking and druggability analyses suggested that polydatin may play a pivotal role in manifesting the therapeutic effects of polygonum cuspidatum. Finally, we carried out a series of cell functional assays, which validated the anti-proliferative effects of polygonum cuspidatum on gynecological cancer cells, thus demonstrating our network pharmacology approach is reliable and powerful enough to guide the CHM mechanism study.

Transcriptional insights into key genes and pathways controlling muscle lipid metabolism in broiler chickens

Background

Intramuscular fat (IMF) is one of the most important factors positively associated with meat quality. Triglycerides (TGs), as the main component of IMF, play an essential role in muscle lipid metabolism. This transcriptome analysis of pectoralis muscle tissue aimed to identify functional genes and biological pathways likely contributing to the extreme differences in the TG content of broiler chickens.

Results

The study included Jingxing-Huang broilers that were significantly different in TG content (5.81 mg/g and 2.26 mg/g, p < 0.01) and deposition of cholesterol also showed the same trend. This RNA sequencing analysis was performed on pectoralis muscle samples from the higher TG content group (HTG) and the lower TG content group (LTG) chickens. A total of 1200 differentially expressed genes (DEGs) were identified between two groups, of which 59 DEGs were related to TG and steroid metabolism. The HTG chickens overexpressed numerous genes related to adipogenesis and lipogenesis in pectoralis muscle tissue, including the key genes ADIPOQ, CD36, FABP4, FABP5, LPL, SCD, PLIN1, CIDEC and PPARG, as well as genes related to steroid biosynthesis (DHCR24, LSS, MSMO1, NSDHL and CH25H). Additionally, key pathways related to lipid storage and metabolism (the steroid biosynthesis and peroxisome proliferator activated receptor (PPAR) signaling pathway) may be the key pathways regulating differential lipid deposition between HTG group and LTG group.

Conclusions

This study showed that increased TG deposition accompanying an increase in steroid synthesis in pectoralis muscle tissue. Our findings of changes in gene expression of steroid biosynthesis and PPAR signaling pathway in HTG and LTG chickens provide insight into genetic mechanisms involved in different lipid deposition patterns in pectoralis muscle tissue.

Transcript profile of skeletal muscle lipid metabolism genes affected by diet in a piglet model of low birth weight

Dysregulated skeletal muscle metabolism (DSMM) is associated with increased inter- and intramuscular fat deposition in low birth weight (L) individuals. The mechanisms behind DSMM in L individuals are not completely understood but decreased muscle mass and shifts in lipid and carbohydrate utilisation may contribute. Previously, we observed lower fat oxidation in a porcine model of low birth weight. To elucidate the biological activities underpinning this difference microfluidic arrays were used to assess mRNA associated with lipid metabolism in longissimus dorsi (LD) and semitendinosus (ST) skeletal muscle samples from thirty-six female L and normal birth weight (N) pigs. Plasma samples were collected from a sub-population to measure metabolite concentrations. Following overnight fasting, skeletal muscle and plasma samples were collected and the association with birth weight, diet and age was assessed. Reduced dietary fat was associated with decreased LD intermuscular fat deposition and beta-oxidation associated mRNA, in both birth weight groups. Lipid uptake and intramuscular fat deposition associated mRNA was reduced in only L pigs. Abundance of ST mRNA associated with lipolysis, lipid synthesis and transport increased in both birth weight groups. Lipid uptake associated mRNA reduced in only L pigs. These changes were associated with decreased plasma L glucose and N triacylglycerol. Post-dietary fat reduction, LD mRNA associated with lipid synthesis and inter- and intramuscular fat deposition increased in L, whilst beta-oxidation associated mRNA remains elevated for longer in N. In the ST, mRNA associated with lipolysis and intramuscular fat deposition increased in both birth weight groups, however this increase was more significant in L pigs and associated with reduced beta-oxidation. Analysis of muscle lipid metabolism associated mRNA revealed that profile shifts are a consequence of birth weight. Whilst, many of the adaptions to diet and age appear to be similar in birth weight groups, the magnitude of response and individual changes underpin the previously observed lower fat oxidation in L pigs.

Association of Twelve Candidate Gene Polymorphisms with the Intramuscular Fat Content and Average Backfat Thickness of Chinese Suhuai Pigs

Simple Summary

Appropriate intramuscular fat content (IFC) is the goal of consumers and the direction that breeders must pursue. However, it is difficult to improve the IFC but not average backfat thickness (ABT) by traditional breeding methods, and pigs must be slaughtered to accurately measure IFC. Marker-assisted selection (MAS) provides an economic and efficient method to improve the IFC in pigs. Our research indicated that the FABP3 (rs1110770079) single nucleotide polymorphism (SNP) could be a candidate gene associated with IFC (but not ABT), and IFC could be improved by selecting the individuals with a favorable genotype (GG) of FABP3 (rs1110770079) SNP for pig breeding.

Abstract

The present study aimed to identify the molecular markers for genes that influence intramuscular fat content (IFC), but not average backfat thickness (ABT). A total of 330 Suhuai pigs were slaughtered, and measurements of IFC and ABT were obtained. Phenotypic and genetic correlations between IFC and ABT were calculated. Thirteen single nucleotide polymorphisms (SNPs) among 12 candidate genes for IFC were analyzed, including FABP3, LIPE, IGF1, IGF2, LEP, LEPR, MC4R, PHKG1, RETN, RYR1, SCD, and UBE3C. Associations of the evaluated SNPs with IFCIFC and ABT were performed. Our results showed that the means of IFC and ABT were 1.99 ± 0.03 % and 26.68 ± 0.28 mm, respectively. The coefficients of variation (CVs) of IFC and ABT were 31.21% and 19.36%, respectively. The phenotypic and genetic correlations between IFC and ABT were moderate. Only the FABP3 (rs1110770079) was associated with IFC (p < 0.05) but not with ABT. Besides, there was a tendency for associations of RYR1 (rs344435545) and SCD (rs80912566) with IFC (p < 0.1). Our results indicated that the FABP3 (rs1110770079) SNP could be used as a marker to improve IFC without changing ABT in the Suhuai pig breeding system.

Identification and Analysis of lncRNAs by Whole-Transcriptome Sequencing in Porcine Preadipocytes Induced by BMP2

Bone morphogenetic protein 2 (BMP2) can mediate the signaling of R-Smads and regulate different biological functions, including adipocyte differentiation. Long noncoding RNAs (lncRNAs) can be involved in many important biological processes, including fat metabolism, as miRNA sponges. This study aimed to investigate the molecular mechanism of fat deposition and to provide useful information for the prevention and treatment of lipid-related diseases. lncRNA sequencing was performed to compare and analyze, for the first time, the expression of lncRNAs in BMP2-induced and non-BMP2-induced preadipocytes from Junmu1 pigs. In addition, functional annotation and enrichment analysis of differentially expressed lncRNA target genes were carried out. lncRNAs and mRNAs were compared and analyzed. lncRNAs were identified that may regulate adipogenesis and lipid metabolism. The results give a theoretical basis for further studies on fat deposition mechanisms and provide potential therapeutic targets for metabolic diseases.

Comparison of liver transcriptome from high- and low-intramuscular fat Chaohu ducks provided additional candidate genes for lipid selection

The meat quality of ducks is closely related to the intramuscular fat (IMF) content. This study explored the candidate regulatory genes of IMF formation and lipid deposition in Chaohu ducks. The IMF of breast muscle in 100 ducks was determined and statistically analysed by normal distribution test. Duck liver samples with high IMF (CH, n = 3) and low IMF (CL, n = 3) were selected for transcriptome analysis by RNA sequencing (RNA-Seq). The IMF was in accordance with normal distribution (T = 0.001, P = 0.999). The IMF from two tails of the normal distribution was significantly different with 2.9983% ± 0.3296% in the CH group and 1.1960% ± 0.1481% in the CL group (P < 0.0001). RNA-Seq revealed 147 differentially expressed genes, including 78 up-regulated and 69 down-regulated genes in both groups. Validation by qRT-PCR was in agreement with RNA-Seq (R ² = 0.838). Gene ontology analysis revealed that organophosphate catabolism, oxidation-reduction process, cellular lipid catabolism, lipid transport, lipid localisation, lipid biosynthesis and cellular lipid catabolism were involved in lipid metabolism. Meanwhile, Kyoto Encyclopedia of Genes and Genomes pathway analysis suggested that steroid hormone biosynthesis, ovarian steroidogenesis, alpha-linolenic acid metabolism, glycosylphosphatidylinositol anchor biosynthesis and linoleic acid metabolism were involved in lipid deposition, wherein the genes COMT, NT5E, PDE4D, PLA2G4F, A-FABP, ADRA2A, HSD17B2, PPP1R3C, PPP1R3B and NR0B2 were involved in lipid deposition. This study provided insights into the molecular mechanism for regulating lipid metabolism and identified candidate genes for selecting markers to control IMF formation in Chaohu ducks.

Data Mining and Validation of AMPK Pathway as a Novel Candidate Role Affecting Intramuscular Fat Content in Pigs

Simple Summary

Intramuscular fat (IMF) is increasingly being recognized as a key meat trait in the modern pork industry. The aims of this research were to identify potential signaling pathways associated with IMF content in the longissimus dorsi (LD) muscle of different pig breeds and investigate the gene expression levels in the screened signaling pathways. Our results indicated that the AMPK signaling pathway may be related to IMF deposition in the LD muscle of pigs. The results of qRT-PCR analysis showed that the expression of ten key hub genes (AMPK, ADIPOR1, ADIPOR2, LKB1, CAMKKβ, CPT1A, CPT1B, PGC-1α, CD36, and ACC1) differed between the LD muscle of Min and Large White pigs. The protein expression levels of AMPK, LKB1, CaMKK2, CPT1A, and ACC1 were similar to the genes expression patterns in the LD muscle of Large White pigs. The results of this study provide novel insights into the regulatory function of the AMPK signaling pathway in relation to the IMF content in the LD muscle of different pigs.

Abstract

Intramuscular fat (IMF) is an important economic trait for pork quality and a complex quantitative trait regulated by multiple genes. The objective of this work was to investigate the novel transcriptional effects of a multigene pathway on IMF deposition in the longissimus dorsi (LD) muscles of pigs. Potential signaling pathways were screened by mining data from three gene expression profiles in the Gene Expression Omnibus (GEO) database. We designed quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) arrays for the candidate signaling pathways to verify the results in the LD muscles of two pig breeds with different IMF contents (Large White and Min). Western blot analysis was used to detect the expression levels of several candidate proteins. Our results showed that the AMPK signaling pathway was screened via bioinformatics analysis. Ten key hub genes of this signaling pathway (AMPK, ADIPOR1, ADIPOR2, LKB1, CAMKKβ, CPT1A, CPT1B, PGC-1α, CD36, and ACC1) were differentially expressed between the Large White and Min pigs. Western blot analysis further confirmed that LKB1/CaMKK2-AMPK-ACC1-CPT1A axis dominates the activity of AMPK signaling pathway. Statistical analyses revealed that AMPK signaling pathway activity clearly varied among the two pig breeds. Based on these results, we concluded that the activation of the AMPK signaling pathway plays a positive role in reducing IMF deposition in pigs.

Identification of Candidate Genes and Regulatory Factors Underlying Intramuscular Fat Content Through Longissimus Dorsi Transcriptome Analyses in Heavy Iberian Pigs

One of the most important determinants of meat quality is the intramuscular fat (IMF) content. The development of high-throughput techniques as RNA-seq allows identifying gene pathways and networks with a differential expression (DE) between groups of animals divergent for a particular trait. The Iberian pig is characterized by having an excellent meat quality and a high content of intramuscular fat. The objectives of the present study were to analyze the longissimus dorsi transcriptome of purebred Iberian pigs divergent for their IMF breeding value to identify differential expressed genes and regulatory factors affecting gene expression. RNA-seq allowed identifying ∼10,000 of the 25,878 annotated genes in the analyzed samples. In addition to this, 42.46% of the identified transcripts corresponded to newly predicted isoforms. Differential expression analyses revealed a total of 221 DE annotated genes and 116 DE new isoforms. Functional analyses identified an enrichment of overexpressed genes involved in lipid metabolism (FASN, SCD, ELOVL6, DGAT2, PLIN1, CIDEC, and ADIPOQ) in animals with a higher content of IMF and an enrichment of overexpressed genes related with myogenesis and adipogenesis (EGR1, EGR2, EGR3, JUNB, FOSB, and SEMA4D) in the animals with a lower content of IMF. In addition to this, potential regulatory elements of these DE genes were identified. Co-expression networks analyses revealed six long non-coding RNAs (lncRNAs) (ALDBSSCG0000002079, ALDBSSCG0000002093, ALDBSSCG0000003455, ALDBSSCG0000004244, ALDBSSCG0000005525, and ALDBSSCG0000006849) co-expressed with SEMA4D and FOSB genes and one (ALDBSSCG0000004790) with SCD, ELOVL6, DGAT2, PLIN1, and CIDEC. Analyses of the regulatory impact factors (RIFs) revealed 301 transcriptionally regulatory factors involved in expression differences, with five of them involved in adipogenesis (ARID5B, CREB1, VDR, ATF6, and SP1) and other three taking part of myogenesis and development of skeletal muscle (ATF3, KLF11, and MYF6). The results obtained provide relevant insights about the genetic mechanisms underlying IMF content in purebred Iberian pigs and a set of candidate genes and regulatory factors for further identification of polymorphisms susceptible of being incorporated in a selection program.

RNA-seq of muscle from pigs divergent in feed efficiency and product quality identifies differences in immune response, growth, and macronutrient and connective tissue metabolism

BACKGROUND

Feed efficiency (FE) is an indicator of efficiency in converting energy and nutrients from feed into a tissue that is of major environmental and economic significance. The molecular mechanisms contributing to differences in FE are not fully elucidated, therefore the objective of this study was to profile the porcine Longissimus thoracis et lumborum (LTL) muscle transcriptome, examine the product quality from pigs divergent in FE and investigate the functional networks underpinning the potential relationship between product quality and FE.

RESULTS

RNA-Seq (n = 16) and product quality (n = 40) analysis were carried out in the LTL of pigs differing in FE status. A total of 272 annotated genes were differentially expressed with a P < 0.01. Functional annotation revealed a number of biological events related to immune response, growth, carbohydrate & lipid metabolism and connective tissue indicating that these might be the key mechanisms governing differences in FE. Five most significant bio-functions altered in FE groups were 'haematological system development & function', 'lymphoid tissue structure & development', 'tissue morphology', 'cellular movement' and 'immune cell trafficking'. Top significant canonical pathways represented among the differentially expressed genes included 'IL-8 signalling', 'leukocyte extravasation signalling, 'sphingosine-1-phosphate signalling', 'PKCθ signalling in T lymphocytes' and 'fMLP signalling in neutrophils'. A minor impairment in the quality of meat, in relation to texture and water-holding capacity, produced by high-FE pigs was observed. High-FE pigs also had reduced intramuscular fat content and improved nutritional profile in terms of fatty acid composition.

CONCLUSIONS

Ontology analysis revealed enhanced activity of adaptive immunity and phagocytes in high-FE pigs suggesting more efficient conserving of resources, which can be utilised for other important biological processes. Shifts in carbohydrate conversion into glucose in FE-divergent muscle may underpin the divergent evolution of pH profile in meat from the FE-groups. Moreover, altered amino acid metabolism and increased mobilisation & flux of calcium may influence growth in FE-divergent muscle. Furthermore, decreased degradation of fibroblasts in FE-divergent muscle could impact on collagen turnover and alter tenderness of meat, whilst enhanced lipid degradation in high-FE pigs may potentially underlie a more efficient fat metabolism in these animals.