Comparative transcriptome analysis reveals that PCK1 is a potential gene affecting IMF deposition in buffalo

A review of emerging technologies, nutritional practices, and management strategies to improve intramuscular fat composition in beef cattle

The flavour, tenderness and juiciness of the beef are all impacted by the composition of the intramuscular fat (IMF), which is a key determinant of beef quality. Thus, enhancing the IMF composition of beef cattle has become a major area of research. Consequently, the aim of this paper was to provide insight and synthesis into the emerging technologies, nutritional practices and management strategies to improve IMF composition in beef cattle. This review paper examined the current knowledge of management techniques and nutritional approaches relevant to cattle farming in the beef industry. It includes a thorough investigation of animal handling, weaning age, castration, breed selection, sex determination, environmental factors, grazing methods, slaughter weight and age. Additionally, it rigorously explored dietary energy levels and optimization of fatty acid profiles, as well as the use of feed additives and hormone implant techniques with their associated regulations. The paper also delved into emerging technologies that are shaping future beef production, such as genomic selection methods, genome editing techniques, epigenomic analyses, microbiome manipulation strategies, transcriptomic profiling approaches and metabolomics analyses. In conclusion, a holistic approach combining genomic, nutritional and management strategies is imperative for achieving targeted IMF content and ensuring high-quality beef production.

Fat deposition and partitioning for meat production in cattle and sheep

In markets for beef and sheep meat, an appropriate level of intramuscular fat (IMF) is highly desirable for meat-eating quality, but strategies to improve it usually lead to an undesirable excess in carcase fat, presenting a major challenge to livestock producers. To solve this problem, we need to understand the partitioning of fat among the major fat depots: IMF, subcutaneous fat (SCF) and visceral fat (VF). In most genotypes of cattle and sheep, the rate of accretion is lower for IMF than for SCF and VF, so genetic selection for a high level of IMF, or the use of an increased dietary energy supply to promote IMF deposition, will increase overall fatness and feed costs. On the other hand, feeding postnatal calves with excessive concentrates promotes IMF deposition, so a nutritional strategy is feasible. With genetic strategies, several problems arise: 1) positive genetic correlations between IMF, SCF and VF differ among genotypes in both cattle and sheep; 2) genotypes appear to have specific, characteristic rates of accretion of IMF during periods of growth and fattening; 3) most breeds of cattle and sheep naturally produce meat with relatively low levels of IMF, but IMF does vary substantially among individuals and breeds so progress is possible through accurate measurement of IMF. Therefore, an essential prerequisite for selection will be knowledge of the genetic correlations and fat accretion rates for each genotype. Currently, selection for IMF is based on existing technology that directly measures IMF in the progeny or siblings, or estimates IMF in live animals. New technology is needed to permit the simultaneous measurement of SCF and IMF in the field, thus opening up the possibility of accurate selection, particularly for fat partitioning in live animals. Specifically, there would be great value in detecting individuals with an IMF advantage at an early age so the generation interval could be shortened and genetic gain accelerated. Genetic gain would also be greatly aided if we could select for genes that control adipogenesis and lipogenesis and are also differentially expressed in the various depots.

Isolation methods, proliferation, and adipogenic differentiation of adipose-derived stem cells from different fat depots in bovines

The adipose-derived stem cells (ASCs) are a valuable resource for regenerative medicine and essential materials for research in fat deposition. However, the isolation procedure of ASCs has not been standardized and needs to be harmonized; differences in proliferation and adipogenic differentiation of ASCs obtained from different fat depots have not been well characterized. In the present study, we compared the efficiency of ASCs isolation by enzymatic treatment and explant culture methods and the proliferation ability and adipogenic differentiation potential of ASCs isolated from subcutaneous and visceral fat depots. The explant culture method was simple and with no need for expensive enzymes while the enzymatic treatment method was complex, time consuming and costly. By the explant culture method, a larger number of ASCs were isolated from subcutaneous and visceral fat depots. By contrast, fewer ASCs were obtained by the enzymatic treatment method, especially from visceral adipose. ASCs isolated by the explant culture method performed well in cell proliferation and adipogenic differentiation, though they were slightly lower than those by the enzymatic treatment method. ASCs isolated from visceral depot demonstrated higher proliferation ability and adipogenic differentiation potential. In total, the explant culture method is simpler, more efficient, and lower cost than the enzymatic treatment method for ASCs isolation; compared with visceral adipose, subcutaneous adipose is easier to isolate ASCs; however, the visceral ASCs are superior to subcutaneous ASCs in proliferation and adipogenic differentiation.

The role of lncFABP4 in modulating adipogenic differentiation in buffalo intramuscular preadipocytes

Intramuscular fat (IMF) is a crucial determinant of meat quality and is influenced by various regulatory factors. Despite the growing recognition of the important role of long noncoding RNAs (lncRNAs) in IMF deposition, the mechanisms underlying buffalo IMF deposition remain poorly understood. In this study, we identified and characterized a lncRNA, lncFABP4, which is transcribed from the antisense strand of fatty acid-binding protein 4 (FABP4). lncFABP4 inhibited cell proliferation in buffalo intramuscular preadipocytes. Moreover, lncFABP4 significantly increased intramuscular preadipocyte differentiation, as indicated by an increase in the expression of the adipogenic markers peroxisome proliferator-activated receptor gamma (PPARG), CCAAT enhancer binding protein alpha (C/EBPα), and FABP4. Mechanistically, lncFABP4 was found to have the potential to regulate downstream gene expression by participating in protein-protein interaction pathways. These findings contribute to further understanding of the intricate mechanisms through which lncRNAs modulate intramuscular adipogenesis in buffaloes.

A long non-coding RNA lnc210 promotes adipogenic differentiation of buffalo intramuscular adipocytes

Intramuscular fat (IMF) content is one of the most significant factors influencing beef quality in terms of tenderness, flavor, and juiciness. Thus, internal factors affecting IMF deposition have received considerable attention for decades. In this study, we demonstrated a long non-coding RNA, lnc210, promoted adipogenic differentiation of buffalo intramuscular adipocytes. lnc210 was rich in adipose tissue and showed increased expression with the adipogenic differentiation of buffalo intramuscular adipocytes. lnc210 was mainly expressed in the nucleus of adipocytes. Full-length lnc210 was obtained by rapid amplification of cDNA ends technology. lnc210 overexpression promoted lipid accumulation by upregulating the mRNA expression of peroxisome proliferator-activated receptor gamma (PPARG) and CCAAT enhancer binding protein alpha (C/EBPα) in buffalo intramuscular adipocytes. These results provide a basis for an in-depth analysis of the role of lnc210 in accelerating IMF deposition in buffaloes.

Identification of core genes affecting IMF deposition in bovine

Intramuscular fat (IMF) content is an important economic factor in beef production. However, knowledge on the key factors controlling bovine IMF is limited. In this study, using weighted gene co-expression network analysis (WGCNA), nine modules were identified and the number of transcripts in these modules ranged from 36 to 3191. Two modules were found to be significantly associated with fat deposition and three genes (TCAP, MYH7, and TNNC1) were further identified by Protein-protein interaction (PPI), which may be the hub genes regulating bovine IMF deposition. In addition, considering the genetic variation, the PCK1 gene was found by functional enrichment analysis of overlapping genes, which was previously reported to be involved in IMF deposition. We noted that the core promoter region of buffalo PCK1 binds to transcription factors involved in lipid metabolism while cattle PCK1 binds transcription factors involved in muscle development. The results suggest that PCK1 participated in IMF deposition of buffalo and cattle in different ways. In summary, gene expression networks and new candidate genes associated with IMF deposition identified in this study. This would lay the foundation for further research into the molecular regulatory mechanisms underlying bovine IMF deposition.

IMF deposition ceRNA network analysis and functional study of HIF1a in yak

The concentration of intramuscular fat (IMF) is a crucial determinant of yak meat quality. However, the molecular mechanisms that regulate IMF in yak remain largely elusive. In our study, we conducted transcriptome sequencing on the longissimus dorsi muscle tissues of yaks with varying IMF contents. We then filtered differentially expressed genes (DEGs), microRNAs (DEMs), and long non-coding RNAs (DELs) to elucidate potential regulatory pathways of adipogenesis in yaks. Overall, our research sheds light on an array of potential mRNAs and noncoding RNAs implicated in IMF deposition and elaborates on the role of HIF1α in yaks. These findings contribute valuable insights that can serve as a guide for further research into the molecular mechanisms governing IMF deposition.

miR-128-3p inhibits intramuscular adipocytes differentiation in chickens by downregulating FDPS

BACKGROUND

Intramuscular fat (IMF) content is the major indicator for evaluating chicken meat quality due to its positive correlation with tenderness, juiciness, and flavor. An increasing number of studies are focusing on the functions of microRNAs (miRNAs) in intramuscular adipocyte differentiation. However, little is known about the association of miR-128-3p with intramuscular adipocyte differentiation. Our previous RNA-seq results indicated that miR-128-3p was differentially expressed at different periods in chicken intramuscular adipocytes, revealing a possible association with intramuscular adipogenesis. The purpose of this research was to investigate the biological functions and regulatory mechanism of miR-128-3p in chicken intramuscular adipogenesis.

RESULTS

The results of a series of assays confirmed that miR-128-3p could promote the proliferation and inhibit the differentiation of intramuscular adipocytes. A total of 223 and 1,050 differentially expressed genes (DEGs) were identified in the mimic treatment group and inhibitor treatment group, respectively, compared with the control group. Functional enrichment analysis revealed that the DEGs were involved in lipid metabolism-related pathways, such as the MAPK and TGF-β signaling pathways. Furthermore, target gene prediction analysis showed that miR-128-3p can target many of the DEGs, such as FDPS, GGT5, TMEM37, and ASL2. The luciferase assay results showed that miR-128-3p targeted the 3' UTR of FDPS. The results of subsequent functional assays demonstrated that miR-128-3p acted as an inhibitor of intramuscular adipocyte differentiation by targeting FDPS.

CONCLUSION

miR-128-3p inhibits chicken intramuscular adipocyte differentiation by downregulating FDPS. Our findings provide a theoretical basis for the study of lipid metabolism and reveal a potential target for molecular breeding to improve meat quality.

Effects of HOXC8 on the Proliferation and Differentiation of Porcine Preadipocytes

Transcription factor Homeobox C8 (HOXC8) is identified as a white adipose gene as revealed by expression profile analysis in fat tissues. However, the specific role of HOXC8 in fat accumulation remains to be identified. This study was designed to reveal the effects of HOXC8 on preadipocyte proliferation and differentiation. We first make clear that the expression of HOXC8 is associated with fat contents in muscles, highlighting a role of HOXC8 in fat accumulation. Next, it is demonstrated that HOXC8 promotes the proliferation and differentiation of preadipocytes through gain- and loss-of-function assays in primary cultured porcine preadipocytes. Then, mechanisms underlying the regulation of HOXC8 on preadipocyte proliferation and differentiation are identified with RNA sequencing, and a number of differentially expressed genes (DEGs) in response to HOXC8 knockdown are identified. The top GO (Gene Ontology) terms enriched by DEGs involved in proliferation and differentiation, respectively, are identical. IL-17 signaling pathway is the common one significantly enriched by DEGs involved in preadipocyte proliferation and differentiation, respectively, indicating its importance in mediating fat accumulation regulated by HOXC8. Additionally, we find that the inhibition of proliferation is one of the main processes during preadipocyte differentiation. The results will contribue to further revealing the mechanisms underlying fat accumulation regulated by HOXC8.

Integrated Comparative Transcriptome and circRNA-lncRNA-miRNA-mRNA ceRNA Regulatory Network Analyses Identify Molecular Mechanisms Associated with Intramuscular Fat Content in Beef Cattle

Intramuscular fat content (IMF), one of the most important carcass traits in beef cattle, is controlled by complex regulatory factors. At present, molecular mechanisms involved in regulating IMF and fat metabolism in beef cattle are not well understood. Our objective was to integrate comparative transcriptomic and competing endogenous RNA (ceRNA) network analyses to identify candidate messenger RNAs (mRNAs) and regulatory RNAs involved in molecular regulation of longissimus dorsi muscle (LDM) tissue for IMF and fat metabolism of 5 beef cattle breeds (Angus, Chinese Simmental, Luxi, Nanyang, and Shandong Black). In total, 34 circRNAs, 57 lncRNAs, 15 miRNAs, and 374 mRNAs were identified by integrating gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Furthermore, 7 key subnets with 16 circRNAs, 43 lncRNAs, 7 miRNAs, and 237 mRNAs were detected through clustering analyses, whereas GO enrichment analysis of identified RNAs revealed 48, 13, and 28 significantly enriched GO terms related to IMF in biological process, molecular function, and cellular component categories, respectively. The main metabolic-signaling pathways associated with IMF and fat metabolism that were enriched included metabolic, calcium, cGMP-PKG, thyroid hormone, and oxytocin signaling pathways. Moreover, MCU, CYB5R1, and BAG3 genes were common among the 10 comparative groups defined as important candidate marker genes for fat metabolism in beef cattle. Contributions of transcriptome profiles from various beef breeds and a competing endogenous RNA (ceRNA) regulatory network underlying phenotypic differences in IMF provided novel insights into molecular mechanisms associated with meat quality.

Comparative transcriptome analysis of longissimus dorsi tissues with different intramuscular fat contents from Guangling donkeys

Background

Donkey meat has low fat and high protein contents and is rich in various unsaturated fatty acids and trace elements that are beneficial to human digestion and absorption. IMF (intramuscular fat), also known as marbling, is an important indicator of the lean meat to fat ratio, which directly affects the tenderness and juiciness of the meat. At present, the underlying molecular variations affecting IMF content among donkey breeds are unclear. The Guangling donkey is an indigenous species in China. This study explored candidate regulatory genes that affect IMF content in Guangling donkeys. The IMF content of the longissimus dorsi muscle in 30 Guangling donkeys was measured. Six donkeys of similar age were selected according to age factors and divided into two groups, the high (H) and low (L) fat groups, according to their IMF content.

Results

RNA-seq technology was used to compare the muscle transcriptome between the two groups. More than 75.0% of alternative splicing (AS) events were of the skipped exon (SE) type. A total of 887 novel genes were identified; only 386 novel genes were aligned to the annotation information of various databases. Transcriptomics analysis revealed 167 differentially expressed genes (DEGs), of which 64 were upregulated and 103 were downregulated between the H and L groups. Gene ontology analysis showed that the DEGs were enriched in multiple biological processes and pathways that are related to adipocyte differentiation, lipid synthesis, and neutral lipid metabolism. KEGG pathway analysis suggested that arachidonic acid metabolism, the HIF-1 signalling pathway, fructose and mannose metabolism, glycerophospholipid metabolism, and the AMPK signalling pathway were involved in lipid deposition. In addition, a gene–gene interaction network was constructed that revealed that the DEGs, including SCD, LEPR, CIDEA, DLK1, DGAT2, ITGAL, HMOX1, WNT10B, and DGKA, had significant roles in adipocyte differentiation and adipogenesis. The selected DEGs were further validated by qRT–PCR.

Conclusion

This study improves the in-depth understanding of gene regulation and protein expression regarding IMF deposition and lays a basis for subsequent molecular breeding studies in Guangling donkeys.

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.

FATP1 Exerts Variable Effects on Adipogenic Differentiation and Proliferation in Cells Derived From Muscle and Adipose Tissue

In livestock, intramuscular adipose tissue is highly valued whereas adipose tissue in other depots is considered as waste. Thus, genetic factors that favor fat deposition in intramuscular compartments over that in other adipose depots are highly desirable in meat-producing animals. Fatty acid transport 1 (FATP1) has been demonstrated to promote cellular fatty acid uptake and metabolism; however, whether it also influences cellular lipid accumulation remains unclear. In the present study, we investigated the effects of FATP1 on the differentiation and proliferation of adipocytes in five types of cells derived from muscle and adipose tissue and estimated the effects of FATP1 on intramuscular fat (IMF) deposition. We showed that FATP1 is mainly expressed in heart and muscle tissue in buffaloes as well as cells undergoing adipogenic differentiation. Importantly, we found that FATP1 promoted the adipogenic differentiation of muscle-derived cells (buffalo myocytes and intramuscular preadipocytes and mouse C2C12 cells) but did not affect, or even inhibited, that of adipose-derived cells (buffalo subcutaneous preadipocytes and mouse 3T3-L1 cells, respectively). Correspondingly, our results further indicated that FATP1 promotes IMF deposition in mice in vivo. Meanwhile, FATP1 was found to enhance the proliferative activity of all the assessed cells, except murine 3T3-L1 cells. These results provide new insights into the potential effects of FATP1 on IMF deposition, especially regarding its positive effects on meat quality in buffaloes and other livestock.

Weighted Gene Co-expression Network Analysis Revealed That CircMARK3 Is a Potential CircRNA Affects Fat Deposition in Buffalo

Background

Buffalo meat is increasingly widely accepted for consumption as it shares several quality attributes with cattle meat (beef). Hence, there is a huge opportunity for growth in the buffalo meat industry. However, buffalo meat has relatively low intramuscular fat (IMF) content, affecting its flavor, tenderness and juiciness. As there is a dearth of information on factors that control fat deposition, this study was undertaken to provide new candidate factor associated with buffalo fat deposition. Circular RNA (circRNA) is a novel class of non-coding RNA with a closed-loop structure, and play an important role in fat deposition.

Methods

In this study, weighted gene co-expression network analysis (WGCNA) was used to construct a circRNA co-expression network and revealed a candidate circRNA that may affect the IMF deposition of buffalo as determined by RT-qPCR, semiquantitative PCR and gain-of-function experiments.

Results

Herein, WGCNA determined that one module (turquoise module) is significantly associated with the growth and development stages of buffalo. Further analysis revealed a total of 191 overlapping circRNAs among differentially expressed (DE) circRNAs and the co-expression module. A candidate circRNA was found, 21:6969877|69753491 (circRNA_ID), with a reported involvement in lipid metabolism. This circRNA is stably expressed and originates from the MARK3 gene, hence the name circMARK3. circMARK3 is highly expressed in adipose tissue and mature adipocytes and is located in the cytoplasm. Gain-of-function experiments demonstrated that circMARK3 promoted adipogenic differentiation of buffalo adipocytes and 3T3-L1 cells by up-regulating the expression levels of adipogenic marker genes PPARG, C/EBPα and FABP4.

Conclusion

These results indicate that circMARK3 is a potential factor that promotes fat deposition by regulating adipocyte differentiation and adipogenesis in buffalo.

Characterization of novel lncRNA muscle expression profiles associated with meat quality in beef cattle

The aim of this study was to identify novel lncRNA differentially expressed (DE) between divergent animals for beef tenderness and marbling traits in Nellore cattle. Longissimus thoracis muscle samples from the 20 most extreme bulls (of 80 bulls set) for tenderness, tender (n = 10) and tough (n = 10) groups, and marbling trait, high (n = 10) and low (n = 10) groups were used to perform transcriptomic analysis using RNA‐Sequencing. For tenderness, 29 lncRNA were DE (p‐value ≤ 0.01) in tough beef animals in relation to tender beef animals. We observed that genic lncRNAs, for example, lncRNA_595.1, were overlapping exonic part of the PICK gene, while lncRNA_3097.2 and lncRNA_3129.5 overlapped intronic part of the genes GADL1 and PSMD6. The lncRNA associated with PICK1, GADL1, and PMD6 genes were enriched in the pathways associated with the ionotropic glutamate receptor, gamma‐aminobutyric acid synthesis, and the ubiquitin–proteasome pathway. For marbling, 50 lncRNA were DE (p‐value ≤ 0.01) in high marbling group compared with low marbling animals. The genic lncRNAs, such as lncRNA_3191.1, were overlapped exonic part of the ITGAL gene, and the lncRNA_512.1, lncRNA_3721.1, and lncRNA_41.4 overlapped intronic parts of the KRAS and MASP1 genes. The KRAS and ITGAL genes were enriched in pathways associated with integrin signaling, which is involved in intracellular signals in response to the extracellular matrix, including cell form, mobility, and mediates progression through the cell cycle. In addition, the lincRNAs identified to marbling trait were associated with several genes related to calcium binding, muscle hypertrophy, skeletal muscle, lipase, and oxidative stress response pathways that seem to play a role important in the physiological processes related to meat quality. These findings bring new insights to better understand the biology mechanisms involved in the gene regulation of these traits, which will be valuable for a further investigation of the interactions between lncRNA and mRNAs, and of how these interactions may affect meat quality traits.

Identification and Functional Verification Reveals that miR-195 Inhibiting THRSP to Affect Fat Deposition in Xinyang Buffalo

The buffalo population is extensive in China, but its meat quality is relatively inferior. Therefore, improving meat quality should be one of the breeding goals. microRNAs (miRNAs) play an essential regulatory role in the post-transcriptional expression of genes. Some studies have reported their function regulating genes related to fat deposition and adipocyte differentiation in cattle, but there is limited reports in buffalo. We performed small RNA transcriptome sequencing of Xinyang buffalo adipose tissue between calves and adults in this study. As a result, 282 mature miRNAs were significantly differentially expressed, and co-expression analysis showed that 454 miRNAs were significantly associated with developmental stages. Target gene identification, GO (gene ontology) annotation, and KEGG analysis of miRNAs showed that miR-195, miR-192, and miR-24-3p could target key genes for lipogenesis and thus regulate adipose deposition and differentiation. Among them, miR-195 was significantly upregulated in adipose tissue and induced adipocytes of adult buffaloes, and its overexpression significantly inhibited lipid accumulation in primary adipocytes. Dual-luciferase reporter gene analysis showed that miR-195 reduced the expression of thyroid hormone response protein (THRSP) by targeting its 3′ untranslated terminal region, suggesting that miR-195 may inhibit lipid accumulation in adipocytes by regulating THRSP. The results confirmed the reliability of predictive screening of miRNAs and provided theoretical support for buffalo fattening.

Perspectives on scaling production of adipose tissue for food applications

With rising global demand for food proteins and significant environmental impact associated with conventional animal agriculture, it is important to develop sustainable alternatives to supplement existing meat production. Since fat is an important contributor to meat flavor, recapitulating this component in meat alternatives such as plant based and cell cultured meats is important. Here, we discuss the topic of cell cultured or tissue engineered fat, growing adipocytes in vitro that could imbue meat alternatives with the complex flavor and aromas of animal meat. We outline potential paths for the large scale production of in vitro cultured fat, including adipogenic precursors during cell proliferation, methods to adipogenically differentiate cells at scale, as well as strategies for converting differentiated adipocytes into 3D cultured fat tissues. We showcase the maturation of knowledge and technology behind cell sourcing and scaled proliferation, while also highlighting that adipogenic differentiation and 3D adipose tissue formation at scale need further research. We also provide some potential solutions for achieving adipose cell differentiation and tissue formation at scale based on contemporary research and the state of the field.

TMT-based quantitative proteomics analysis reveals the key proteins related with the differentiation process of goat intramuscular adipocytes

Background

Intramuscular adipocytes differentiation is a complex process, which is regulated by various transcription factor, protein factor regulators and signal transduction pathways. However, the proteins and signal pathways that regulates goat intramuscular adipocytes differentiation remains unclear.

Result

In this study, based on nanoscale liquid chromatography mass spectrometry analysis (LC-MS/MS), the tandem mass tag (TMT) labeling analysis was used to investigate the differentially abundant proteins (DAPs) related with the differentiation process of goat intramuscular adipocytes. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes enrichment and protein-protein interaction network analyses were performed for the characterization of the identified DAPs. The candidate proteins were verified by parallel reaction monitoring analysis. As a result, a total of 123 proteins, 70 upregulation proteins and 53 downregulation proteins, were identified as DAPs which may be related with the differentiation process of goat intramuscular adipocytes. Furthermore, the cholesterol metabolism pathway, glucagon signaling pathway and glycolysis / gluconeogenesis pathway were noticed that may be the important signal pathways for goat Intramuscular adipocytes differentiation.

Conclusions

By proteomic comparison between goat intramuscular preadipocytes (P_IMA) and intramuscular adipocytes (IMA), we identified a series protein that might play important role in the goat intramuscular fat differentiation, such as SRSF10, CSRP3, APOH, PPP3R1, CRTC2, FOS, SERPINE1 and AIF1L, could serve as candidates for further elucidate the molecular mechanism of IMF differentiation in goats.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07730-y.

lncSAMM50 Enhances Adipogenic Differentiation of Buffalo Adipocytes With No Effect on Its Host Gene

Fat deposition is one of the most important traits that are mediated by a set of complex regulatory factors in meat animals. Several researches have revealed the significant role of long non-coding RNAs (lncRNAs) in fat deposition while the precise regulatory mechanism is still largely elusive. In this study, we investigated the lncRNA profiles of adipose and muscle tissues in buffalo by using the Illumina HiSeq 3000 platform. In total, 43,809 lncRNAs were finally identified based on the computer algorithm. A comparison analysis revealed 241 lncRNAs that are differentially expressed (DE) in adipose and muscle tissues. We focused on lncSAMM50, a DE lncRNA that has a high expression in adipose tissue. Sequence alignment showed that lncSAMM50 is transcribed from the antisense strand of the upstream region of sorting and assembly machinery component 50 homolog (SAMM50), a gene involved in the function of mitochondrion and is subsequently demonstrated to inhibit the adipogenic differentiation of 3T3-L1 adipocyte cells in this study. lncSAMM50 is highly expressed in adipose tissue and upregulated in the mature adipocytes and mainly exists in the nucleus. Gain-of-function experiments demonstrated that lncSAMM50 promotes the adipogenic differentiation by upregulating adipogenic markers but with no effect on its host gene SAMM50 in buffalo adipocytes. These results indicate that lncSAMM50 enhances fat deposition in buffalo and provide a new factor for the regulatory network of adipogenesis.

Adipose Tissue Gene Expression of Entire Male, Immunocastrated and Surgically Castrated Pigs

Differences in adipose tissue deposition and properties between pig male sex categories, i.e., entire males (EM), immunocastrates (IC) and surgical castrates (SC) are relatively well-characterized, whereas the underlying molecular mechanisms are still not fully understood. To gain knowledge about the genetic regulation of the differences in adipose tissue deposition, two different approaches were used: RNA-sequencing and candidate gene expression by quantitative PCR. A total of 83 differentially expressed genes were identified between EM and IC, 15 between IC and SC and 48 between EM and SC by RNA-sequencing of the subcutaneous adipose tissue. Comparing EM with IC or SC, upregulated genes related to extracellular matrix dynamics and adipogenesis, and downregulated genes involved in the control of lipid and carbohydrate metabolism were detected. Differential gene expression generally indicated high similarity between IC and SC as opposed to EM, except for several heat shock protein genes that were upregulated in EM and IC compared with SC. The candidate gene expression approach showed that genes involved in lipogenesis were downregulated in EM compared with IC pigs, further confirming RNA-sequencing results.